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1.
Food Microbiol ; 121: 104531, 2024 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-38637091

RESUMO

The present study aimed to assess the occurrence and counts of Staphylococcus aureus in Brazilian artisanal cheeses (BAC) produced in five regions of Brazil: Coalho and Manteiga (Northeast region); Colonial and Serrano (South); Caipira (Central-West); Marajó (North); and Minas Artisanal cheeses, from Araxá, Campos das Vertentes, Cerrado, Serro and Canastra microregions (Southeast). The resistance to chlorine-based sanitizers, ability to attach to stainless steel surfaces, and antibiogram profile of a large set of S. aureus strains (n = 585) were assessed. Further, a total of 42 isolates were evaluated for the presence of enterotoxigenic genes (sea, seb, sec, sed, see, seg, sei, sej, and ser) and submitted to typing using pulsed-field gel electrophoresis (PFGE). BAC presented high counts of S. aureus (3.4-6.4 log CFU/g), varying from 25 to 62.5%. From the S. aureus strains (n = 585) assessed, 16% could resist 200 ppm of sodium hypochlorite, whereas 87.6% produced strong ability to attach to stainless steel surfaces, corroborating with S. aureus ability to persist and spread in the environment. Furthermore, the relatively high frequency (80.5%) of multidrug-resistant S. aureus and the presence of enterotoxin genes in 92.6% of the strains is of utmost attention. It reveals the lurking threat of SFP that can survive when conditions are favorable. The presence of enterotoxigenic and antimicrobial-resistant strains of S. aureus in cheese constitutes a potential risk to public health. This result calls for better control of cheese contamination sources, and taking hygienic measures is necessary for food safety. More attention should be paid to animal welfare and hygiene practices in some dairy farms during manufacturing to enhance the microbiological quality of traditional cheese products.


Assuntos
Queijo , Staphylococcus aureus Resistente à Meticilina , Infecções Estafilocócicas , Animais , Staphylococcus aureus/genética , Queijo/microbiologia , Brasil , Microbiologia de Alimentos , Aço Inoxidável/análise , Enterotoxinas/genética , Leite/microbiologia
2.
BMC Genomics ; 21(1): 757, 2020 Nov 02.
Artigo em Inglês | MEDLINE | ID: mdl-33138770

RESUMO

BACKGROUND: Unveiling fungal genome structure and function reveals the potential biotechnological use of fungi. Trichoderma harzianum is a powerful CAZyme-producing fungus. We studied the genomic regions in T. harzianum IOC3844 containing CAZyme genes, transcription factors and transporters. RESULTS: We used bioinformatics tools to mine the T. harzianum genome for potential genomics, transcriptomics, and exoproteomics data and coexpression networks. The DNA was sequenced by PacBio SMRT technology for multiomics data analysis and integration. In total, 1676 genes were annotated in the genomic regions analyzed; 222 were identified as CAZymes in T. harzianum IOC3844. When comparing transcriptome data under cellulose or glucose conditions, 114 genes were differentially expressed in cellulose, with 51 being CAZymes. CLR2, a transcription factor physically and phylogenetically conserved in Trichoderma spp., was differentially expressed under cellulose conditions. The genes induced/repressed under cellulose conditions included those important for plant biomass degradation, including CIP2 of the CE15 family and a copper-dependent LPMO of the AA9 family. CONCLUSIONS: Our results provide new insights into the relationship between genomic organization and hydrolytic enzyme expression and regulation in T. harzianum IOC3844. Our results can improve plant biomass degradation, which is fundamental for developing more efficient strains and/or enzymatic cocktails to produce hydrolytic enzymes.


Assuntos
Trichoderma , Metabolismo dos Carboidratos , Celulose/metabolismo , Genômica , Hypocreales , Trichoderma/genética , Trichoderma/metabolismo
3.
RNA Biol ; 16(11): 1643-1657, 2019 11.
Artigo em Inglês | MEDLINE | ID: mdl-31390935

RESUMO

Noncoding RNA (ncRNA) modulation of gene expression has now been ubiquitously observed across all domains of life. An increasingly apparent role of ncRNAs is to coordinate changes in gene expressions in response to environmental stress. Salmonella enterica, a common food-born pathogen, is known for its striking ability to survive, adapt, and thrive in various unfavourable environments which makes it a particularly difficult pathogen to eliminate as well as an interesting model in which to study ncRNA contributions to cellular stress response. Mounting evidence now suggests that small RNAs (sRNAs) represent key regulators of Salmonella stress adaptation. Approximately 50-500 nucleotides in length, sRNAs regulate gene expression through complementary base pairing with molecular targets and have recently been suggested to outnumber protein-coding genes in bacteria. In this work, we employ small RNA transcriptome sequencing to characterize changes in the sRNA profiles of Salmonella in response to desiccation. In all, we identify 102 previously annotated sRNAs significantly differentially expressed during desiccation; and excitingly, 71 novel sRNAs likewise differentially expressed. Small transcript northern blotting and qRT-PCRs confirm the identities and expressions of several of our novel sRNAs, and computational analyses indicate the majority are highly conserved and structurally related to characterized sRNAs. Predicted sRNA targets include several proteins necessary for desiccation survival and this, in part, suggests a role for desiccation-regulated sRNAs in this stress response. Furthermore, we find individual knock-outs of two of the novel sRNAs identified herein, either sRNA1320429 or sRNA3981754, significantly impairs the ability of Salmonella to survive desiccation, confirming their involvements (and suggesting the potential involvements of other sRNAs we identify in this work) in the Salmonella response to desiccation.


Assuntos
Perfilação da Expressão Gênica/métodos , Pequeno RNA não Traduzido/genética , Salmonella typhimurium/fisiologia , Dessecação , Regulação Bacteriana da Expressão Gênica , Anotação de Sequência Molecular , RNA Bacteriano/genética , Salmonella typhimurium/genética , Análise de Sequência de RNA , Estresse Fisiológico
4.
Food Microbiol ; 82: 426-435, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31027802

RESUMO

Salmonella enterica serotypes have been reported as the agent of various outbreaks occurred after the consumption of low water activity (aw) foods. When the pathogen encounters harsh conditions, several regulatory networks are activated through dynamic differential gene expression that lead to cell survival for prolonged periods. In this work, the transcriptome of S. enterica serovar Typhimurium using RNA-Seq, after cells' inoculation in four distinct types of low aw foods (milk chocolate, powdered milk, black pepper, and dried pet food), following storage at 25 °C per 24 and 72 h was studied. The findings of this study suggest that gene regulation is influenced by the food composition mainly in the first 24 h post-inoculum, proceeded by the induction of similar genes shared among all samples. It was possible to evaluate the differences on each type of food matrix regarding the bacteria adaptation, as well as the similarities provoked by low aw. The results reveal genes that may play key roles in response to desiccation in Salmonella, as well as the pathways in which they are involved.


Assuntos
Adaptação Fisiológica/genética , Proteínas de Bactérias/genética , Microbiologia de Alimentos , Salmonella typhimurium/genética , Água/análise , Proteínas de Bactérias/metabolismo , Análise por Conglomerados , Dessecação , Análise de Alimentos , Perfilação da Expressão Gênica , Regulação Bacteriana da Expressão Gênica , Salmonella typhimurium/fisiologia
5.
Microb Pathog ; 59-60: 1-6, 2013.
Artigo em Inglês | MEDLINE | ID: mdl-23474016

RESUMO

The 5'-nucleotidases constitute a ubiquitous family of enzymes that catalyze either the hydrolysis or the transfer of esterified phosphate at the 5' position of nucleoside monophosphates. These enzymes are responsible for the regulation of nucleotide and nucleoside levels in the cell and can interfere with the phosphorylation-dependent activation of nucleoside analogs used in therapies targeting solid tumors and viral infections. In the present study, we report the initial biochemical and functional characterization of a 5'-nucleotidase from Xylella fastidiosa that is related to the human cytosolic 5'-nucleotidase I. X. fastidiosa is a plant pathogenic bacterium that is responsible for numerous economically important crop diseases. Biochemical assays confirmed the phosphatase activity of the recombinant purified enzyme and revealed metal ion dependence for full enzyme activity. In addition, we investigated the involvement of Xf5'-Nt in the formation of X. fastidiosa biofilms, which are structures that occlude the xylem vessels of susceptible plants and are strictly associated with bacterial pathogenesis. Using polyclonal antibodies against Xf5'-Nt, we observed an overexpression of Xf5'-Nt during the initial phases of X. fastidiosa biofilm formation that was not observed during X. fastidiosa planktonic growth. Our results demonstrate that the de/phosphorylation network catalyzed by 5'-nucleotidases may play an important role in bacterial biofilm formation, thereby contributing novel insights into bacterial nucleotide metabolism and pathogenicity.


Assuntos
5'-Nucleotidase/metabolismo , Xylella/enzimologia , 5'-Nucleotidase/genética , 5'-Nucleotidase/isolamento & purificação , Biofilmes/crescimento & desenvolvimento , Coenzimas/metabolismo , Perfilação da Expressão Gênica , Metais/metabolismo , Monoéster Fosfórico Hidrolases/genética , Monoéster Fosfórico Hidrolases/isolamento & purificação , Monoéster Fosfórico Hidrolases/metabolismo , Proteínas Recombinantes/genética , Proteínas Recombinantes/isolamento & purificação , Proteínas Recombinantes/metabolismo , Xylella/fisiologia
6.
Protein Expr Purif ; 91(2): 175-83, 2013 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-23973866

RESUMO

A novel epoxide hydrolase from Aspergillus brasiliensis CCT1435 (AbEH) was cloned and overexpressed in Escherichia coli cells with a 6xHis-tag and purified by nickel affinity chromatography. Gel filtration analysis and circular dichroism measurements indicated that this novel AbEH is a homodimer in aqueous solution and contains the typical secondary structure of an α/ß hydrolase fold. The activity of AbEH was initially assessed using the fluorogenic probe O-(3,4-epoxybutyl) umbelliferone and was active in a broad range of pH (6-9) and temperature (25-45°C); showing optimum performance at pH 6.0 and 30°C. The Michaelis constant (KM) and maximum rate (Vmax) values were 495µM and 0.24µM/s, respectively. Racemic styrene oxide (SO) was used as a substrate to assess the AbEH activity and enantioselectivity, and 66% of the SO was hydrolyzed after only 5min of reaction, with the remaining (S)-SO ee exceeding 99% in a typical kinetic resolution behavior. The AbEH-catalyzed hydrolysis of SO was also evaluated in a biphasic system of water:isooctane; (R)-diol in 84% ee and unreacted (S)-SO in 36% ee were produced, with 43% conversion in 24h, indicating a discrete enantioconvergent behavior for AbEH. This novel epoxide hydrolase has biotechnological potential for the preparation of enantiopure epoxides or vicinal diols.


Assuntos
Aspergillus/enzimologia , Epóxido Hidrolases/química , Proteínas Fúngicas/química , Proteínas Recombinantes de Fusão/química , Sequência de Aminoácidos , Aspergillus/genética , Cromatografia de Afinidade , Dicroísmo Circular , Epóxido Hidrolases/genética , Epóxido Hidrolases/isolamento & purificação , Epóxido Hidrolases/metabolismo , Compostos de Epóxi/química , Escherichia coli/genética , Proteínas Fúngicas/genética , Proteínas Fúngicas/isolamento & purificação , Proteínas Fúngicas/metabolismo , Histidina/genética , Hidrólise , Dados de Sequência Molecular , Oligopeptídeos/genética , Proteínas Recombinantes de Fusão/genética , Proteínas Recombinantes de Fusão/isolamento & purificação , Proteínas Recombinantes de Fusão/metabolismo , Alinhamento de Sequência , Estereoisomerismo
7.
MicroPubl Biol ; 20232023.
Artigo em Inglês | MEDLINE | ID: mdl-37151214

RESUMO

Small RNAs (sRNAs) are short noncoding RNAs of ~50-200 nucleotides believed to primarily function in regulating crucial activities in bacteria during periods of cellular stress. This study examined the relevance of specific sRNAs on biofilm formation in nutrient starved Salmonella enterica serovar Typhimurium. Eight unique sRNAs were selected for deletion primarily based on their genomic location and/or putative targets. Quantitative and qualitative analyses confirm one of these, sRNA1186573, is required for efficient biofilm formation in S. enterica further highlighting the significance of sRNAs during Salmonella stress response.

8.
Protein Expr Purif ; 82(2): 284-9, 2012 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-22306742

RESUMO

Xylella fastidiosa is a Gram-negative xylem-limited plant pathogenic bacterium responsible for several economically important crop diseases. Here, we present a novel and efficient protein refolding protocol for the solubilization and purification of recombinant X. fastidiosa peptidoglycan-associated lipoprotein (XfPal). Pal is an outer membrane protein that plays important roles in maintaining the integrity of the cell envelope and in bacterial pathogenicity. Because Pal has a highly hydrophobic N-terminal domain, the heterologous expression studies necessary for structural and functional protein characterization are laborious once the recombinant protein is present in inclusion bodies. Our protocol based on the denaturation of the XfPal-enriched inclusion bodies with 8M urea followed by buffer-exchange steps via dialysis proved effective for the solubilization and subsequent purification of XfPal, allowing us to obtain a large amount of relatively pure and folded protein. In addition, XfPal was biochemically and functionally characterized. The method for purification reported herein is valuable for further research on the three-dimensional structure and function of Pal and other outer membrane proteins and can contribute to a better understanding of the role of these proteins in bacterial pathogenicity, especially with regard to the plant pathogen X. fastidiosa.


Assuntos
Proteínas de Bactérias/química , Escherichia coli , Lipoproteínas/química , Peptidoglicano/química , Redobramento de Proteína , Xylella , Sequência de Aminoácidos , Proteínas de Bactérias/biossíntese , Proteínas de Bactérias/isolamento & purificação , Cromatografia em Gel , Lipoproteínas/biossíntese , Lipoproteínas/isolamento & purificação , Dados de Sequência Molecular , Peptidoglicano/biossíntese , Peptidoglicano/isolamento & purificação , Ligação Proteica , Estrutura Quaternária de Proteína , Estrutura Secundária de Proteína , Homologia de Sequência de Aminoácidos , Solubilidade
9.
Int J Food Microbiol ; 372: 109695, 2022 Jul 02.
Artigo em Inglês | MEDLINE | ID: mdl-35509145

RESUMO

This study aimed to determine Salmonella enterica occurrence along the soybean meal production chain (raw material, in-processing samples, final products, and in the environment of five processing plants), characterize the isolates, and assess the survival of Salmonella Senftenberg 775W in soybeans stored under different temperature conditions. Among 713 samples analyzed, 12.9% (n = 92) were positive for Salmonella enterica. Dust collected inside and outside processing plants (n = 148) comprised the samples with the highest positivity for Salmonella enterica, 47.3%. The occurrence of Salmonella enterica varied among the different processing plants. Twenty-nine (n = 29) Salmonella serotypes were isolated, with S. Mbandaka as the most frequent serotype, whereas S. Typhimurium was mainly linked to final product samples (soybean meal). S. Senftenberg 775W did not survive for a long time in soybean stored at 20-37 °C, but at 20 °C, cells were viable for more than 60 days. This study suggests that soybean meal may harbor Salmonella serotypes related to foodborne disease outbreaks in humans and can be responsible for Salmonella introduction into livestock and, consequently, in foods of animal origin. This study provides crucial data on contamination pathways of Salmonella in the soybean production chain, contributing to the understanding of Salmonella epidemiology which is strategic for the development of preventive and control measures to reduce the burden of salmonellosis linked to products of animal origin.


Assuntos
Intoxicação Alimentar por Salmonella , Infecções por Salmonella , Salmonella enterica , Animais , Gado , Glycine max
10.
Antibiotics (Basel) ; 10(3)2021 Mar 16.
Artigo em Inglês | MEDLINE | ID: mdl-33809610

RESUMO

An increasingly apparent role of noncoding RNA (ncRNAs) is to coordinate gene expression during environmental stress. A mounting body of evidence implicates small RNAs (sRNAs) as key drivers of Salmonella stress survival. Generally thought to be 50-500 nucleotides in length and to occur in intergenic regions, sRNAs typically regulate protein expression through base pairing with mRNA targets. In this work, through employing a refined definition of sRNAs allowing for shorter sequences and sRNA loci to overlap with annotated protein-coding gene loci, we have identified 475 previously unannotated sRNAs that are significantly differentially expressed during carbon starvation (C-starvation). Northern blotting and quantitative RT-PCRs confirm the expressions and identities of several of these novel sRNAs, and our computational analyses find the majority to be highly conserved and structurally related to known sRNAs. Importantly, we show that deletion of one of the sRNAs dynamically expressed during C-starvation, sRNA4130247, significantly impairs the Salmonella C-starvation response (CSR), confirming its involvement in the Salmonella CSR. In conclusion, the work presented here provides the first-ever characterization of intragenic sRNAs in Salmonella, experimentally confirms that sRNAs dynamically expressed during the CSR are directly involved in stress survival, and more than doubles the Salmonella enterica sRNAs described to date.

11.
Adv Food Nutr Res ; 85: 131-175, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-29860973

RESUMO

Unit operations modify material properties aiming to produce uniform and high-quality food products with greater acceptance by the increasingly demanding consumers or with longer shelf life and better possibilities of storage and transport. Microorganisms, including bacteria, molds, viruses, and parasites, may have different susceptibilities to unit operations employed during food processing. On-farm (cleaning, selection and classification, cooling, storage, and transport) and on-factory unit operations (heating, refrigeration/freezing, dehydration, modification of atmosphere, irradiation, and physical, chemical, and microbial-based operations) are commonly employed throughout food production chain. The intensity and combination of unit operations along with food composition, packaging, and storage conditions will influence on the dominance of specific microorganisms, which can be pathogenic or responsible for spoilage. Thus, in the context of food safety objective (FSO), the knowledge and the quantification of the effects caused by each step of processing can enable to control and ensure the quality and safety of manufactured products.


Assuntos
Microbiologia de Alimentos , Conservação de Alimentos , Inocuidade dos Alimentos , Animais , Fazendas , Embalagem de Alimentos , Humanos
12.
Processes (Basel) ; 6(5)2018 May.
Artigo em Inglês | MEDLINE | ID: mdl-30197877

RESUMO

RNA editing by RNA specific adenosine deaminase acting on RNA (ADAR) is increasingly being found to alter microRNA (miRNA) regulation. Editing of miRNA transcripts can affect their processing, as well as which messenger RNAs (mRNAs) they target. Further, editing of target mRNAs can also affect their complementarity to miRNAs. Notably, ADAR editing is often increased in malignancy with the effect of these RNA changes being largely unclear. In addition, numerous reports have now identified an array of miRNAs that directly contribute to various malignancies although the majority of their targets remain largely undefined. Here we propose that modulating the targets of miRNAs via mRNA editing is a frequent occurrence in cancer and an underappreciated participant in pathology. In order to more accurately characterize the relationship between these two regulatory processes, this study examined RNA editing events within mRNA sequences of two breast cancer cell lines (MCF-7 and MDA-MB-231) and determined whether or not these edits could modulate miRNA associations. Computational analyses of RNA-Seq data from these two cell lines identified over 50,000 recurrent editing sites within human mRNAs, and many of these were located in 3' untranslated regions (UTRs). When these locations were screened against the list of currently-annotated miRNAs we discovered that editing caused a subset (~9%) to have significant alterations to mRNA complementarity. One miRNA in particular, miR-140-3p, is known to be misexpressed in many breast cancers, and we found that mRNA editing allowed this miRNA to directly target the apoptosis inducing gene DFFA in MCF-7, but not in MDA-MB-231 cells. As these two cell lines are known to have distinct characteristics in terms of morphology, invasiveness and physiological responses, we hypothesized that the differential RNA editing of DFFA in these two cell lines could contribute to their phenotypic differences. Indeed, we confirmed through western blotting that inhibiting miR-140-3p increases expression of the DFFA protein product in MCF-7, but not MDA-MB-231, and further that inhibition of miR-140-3p also increases cellular growth in MCF-7, but not MDA-MB-231. Broadly, these results suggest that the creation of miRNA targets may be an underappreciated function of ADAR and may help further elucidate the role of RNA editing in tumor pathogenicity.

13.
NPJ Breast Cancer ; 3: 25, 2017.
Artigo em Inglês | MEDLINE | ID: mdl-28702505

RESUMO

Genetic searches for tumor suppressors have recently linked small nucleolar RNA misregulations with tumorigenesis. In addition to their classically defined functions, several small nucleolar RNAs are now known to be processed into short microRNA-like fragments called small nucleolar RNA-derived RNAs. To determine if any small nucleolar RNA-derived RNAs contribute to breast malignancy, we recently performed a RNA-seq-based comparison of the small nucleolar RNA-derived RNAs of two breast cancer cell lines (MCF-7 and MDA-MB-231) and identified small nucleolar RNA-derived RNAs derived from 13 small nucleolar RNAs overexpressed in MDA-MB-231s. Importantly, we find that inhibiting the most differentially expressed of these small nucleolar RNA-derived RNAs (sdRNA-93) in MDA-MB-231 cells results primarily in a loss of invasiveness, whereas increased sdRNA-93 expression in either cell line conversely results in strikingly enhanced invasion. Excitingly, we recently determined sdRNA-93 expressions in small RNA-seq data corresponding to 116 patient tumors and normal breast controls, and while we find little sdRNA-93 expression in any of the controls and only sporadic expression in most subtypes, we find robust expression of sdRNA-93 in 92.8% of Luminal B Her2+tumors. Of note, our analyses also indicate that at least one of sdRNA-93's endogenous roles is to regulate the expression of Pipox, a sarcosine metabolism-related protein whose expression significantly correlates with distinct molecular subtypes of breast cancer. We find sdRNA-93 can regulate the Pipox 3'UTR via standard reporter assays and that manipulating endogenous sdRNA-93 levels inversely correlates with altered Pipox expression. In summary, our results strongly indicate that sdRNA-93 expression actively contributes to the malignant phenotype of breast cancer through participating in microRNA-like regulation.

14.
Biotechnol Biofuels ; 9: 71, 2016.
Artigo em Inglês | MEDLINE | ID: mdl-27006690

RESUMO

BACKGROUND: The conversion of biomass-derived sugars via enzymatic hydrolysis for biofuel production is a challenge. Therefore, the search for microorganisms and key enzymes that increase the efficiency of the saccharification of cellulosic substrates remains an important and high-priority area of study. Trichoderma harzianum is an important fungus known for producing high levels of cellulolytic enzymes that can be used for cellulosic ethanol production. In this context, ß-glucosidases, which act synergistically with cellobiohydrolases and endo-ß-1,4-glucanases in the saccharification process, are potential biocatalysts for the conversion of plant biomass to free glucose residues. RESULTS: In the present study, we used RNA-Seq and genomic data to identify the major ß-glucosidase expressed by T. harzianum under biomass degradation conditions. We mapped and quantified the expression of all of the ß-glucosidases from glycoside hydrolase families 1 and 3, and we identified the enzyme with the highest expression under these conditions. The target gene was cloned and heterologously expressed in Escherichia coli, and the recombinant protein (rThBgl) was purified with high yields. rThBgl was characterized using a comprehensive set of biochemical, spectroscopic, and hydrodynamic techniques. Finally, we determined the crystallographic structure of the recombinant protein at a resolution of 2.6 Å. CONCLUSIONS: Using a rational approach, we investigated the biochemical characteristics and determined the three-dimensional protein structure of a ß-glucosidase that is highly expressed by T. harzianum under biomass degradation conditions. The methodology described in this manuscript will be useful for the bio-prospection of key enzymes, including cellulases and other accessory enzymes, for the development and/or improvement of enzymatic cocktails designed to produce ethanol from plant biomass.

15.
Front Microbiol ; 7: 2030, 2016.
Artigo em Inglês | MEDLINE | ID: mdl-28066356

RESUMO

The Xylella fastidiosa subsp pauca strain 9a5c is a Gram-negative, xylem-limited bacterium that is able to form a biofilm and affects citrus crops in Brazil. Some genes are considered to be involved in biofilm formation, but the specific mechanisms involved in this process remain unknown. This limited understanding of how some bacteria form biofilms is a major barrier to our comprehension of the progression of diseases caused by biofilm-producing bacteria. Several investigations have shown that the toxin-antitoxin (TA) operon is related to biofilm formation. This operon is composed of a toxin with RNAse activity and its cognate antitoxin. Previous reports have indicated that the antitoxin is able to inhibit toxin activity and modulate the expression of the operon as well as other target genes involved in oxidative stress and mobility. In this study, we characterize a toxin-antitoxin system consisting of XfMqsR and XfYgiT, respectively, from X. fastidiosa subsp. pauca strain 9a5c. These proteins display a high similarity to their homologs in X. fastidiosa strain Temecula and a predicted tridimensional structure that is similar to MqsR-YgiT from Escherichia coli. The characterization was performed using in vitro assays such as analytical ultracentrifugation (AUC), size exclusion chromatography, isothermal titration calorimetry, and Western blotting. Using a fluorometric assay to detect RNAses, we demonstrated that XfMqsR is thermostable and can degrade RNA. XfMqsR is inhibited by XfYgiT, which interacts with its own promoter. XfYgiT is known to be localized in the intracellular compartment; however, we provide strong evidence that X. fastidiosa secretes wild-type XfYgiT into the extracellular environment via outer membrane vesicles, as confirmed by Western blotting and specific immunofluorescence labeling visualized by fluorescence microscopy. Taken together, our results characterize the TA system from X. fastidiosa strain 9a5c, and we also discuss the possible influence of wild-type XfYgiT in the cell.

16.
PLoS One ; 10(4): e0122122, 2015.
Artigo em Inglês | MEDLINE | ID: mdl-25836973

RESUMO

Trichoderma harzianum IOC-3844 secretes high levels of cellulolytic-active enzymes and is therefore a promising strain for use in biotechnological applications in second-generation bioethanol production. However, the T. harzianum biomass degradation mechanism has not been well explored at the genetic level. The present work investigates six genomic regions (~150 kbp each) in this fungus that are enriched with genes related to biomass conversion. A BAC library consisting of 5,760 clones was constructed, with an average insert length of 90 kbp. The assembled BAC sequences revealed 232 predicted genes, 31.5% of which were related to catabolic pathways, including those involved in biomass degradation. An expression profile analysis based on RNA-Seq data demonstrated that putative regulatory elements, such as membrane transport proteins and transcription factors, are located in the same genomic regions as genes related to carbohydrate metabolism and exhibit similar expression profiles. Thus, we demonstrate a rapid and efficient tool that focuses on specific genomic regions by combining a BAC library with transcriptomic data. This is the first BAC-based structural genomic study of the cellulolytic fungus T. harzianum, and its findings provide new perspectives regarding the use of this species in biomass degradation processes.


Assuntos
Trichoderma/genética , Trichoderma/metabolismo , Biodegradação Ambiental , Biocombustíveis , Biomassa , Biotecnologia , Celulase/genética , Celulase/metabolismo , Cromossomos Artificiais Bacterianos/genética , Etanol/metabolismo , Proteínas Fúngicas/genética , Proteínas Fúngicas/metabolismo , Perfilação da Expressão Gênica , Genoma Fúngico , Hidrólise
17.
PLoS One ; 10(12): e0145765, 2015.
Artigo em Inglês | MEDLINE | ID: mdl-26694028

RESUMO

Xylella fastidiosa strain 9a5c is a gram-negative phytopathogen that is the causal agent of citrus variegated chlorosis (CVC), a disease that is responsible for economic losses in Brazilian agriculture. The most well-known mechanism of pathogenicity for this bacterial pathogen is xylem vessel occlusion, which results from bacterial movement and the formation of biofilms. The molecular mechanisms underlying the virulence caused by biofilm formation are unknown. Here, we provide evidence showing that virulence-associated protein D in X. fastidiosa (Xf-VapD) is a thermostable protein with ribonuclease activity. Moreover, protein expression analyses in two X. fastidiosa strains, including virulent (Xf9a5c) and nonpathogenic (XfJ1a12) strains, showed that Xf-VapD was expressed during all phases of development in both strains and that increased expression was observed in Xf9a5c during biofilm growth. This study is an important step toward characterizing and improving our understanding of the biological significance of Xf-VapD and its potential functions in the CVC pathosystem.


Assuntos
Proteínas de Bactérias/química , Temperatura Alta , Glicoproteínas de Membrana/química , Ribonucleases/química , Xylella/enzimologia , Proteínas de Bactérias/genética , Estabilidade Enzimática , Glicoproteínas de Membrana/genética , Ribonucleases/genética , Xylella/genética , Xylella/patogenicidade
18.
PLoS One ; 9(2): e88689, 2014.
Artigo em Inglês | MEDLINE | ID: mdl-24558413

RESUMO

Profiling the transcriptome that underlies biomass degradation by the fungus Trichoderma harzianum allows the identification of gene sequences with potential application in enzymatic hydrolysis processing. In the present study, the transcriptome of T. harzianum IOC-3844 was analyzed using RNA-seq technology. The sequencing generated 14.7 Gbp for downstream analyses. De novo assembly resulted in 32,396 contigs, which were submitted for identification and classified according to their identities. This analysis allowed us to define a principal set of T. harzianum genes that are involved in the degradation of cellulose and hemicellulose and the accessory genes that are involved in the depolymerization of biomass. An additional analysis of expression levels identified a set of carbohydrate-active enzymes that are upregulated under different conditions. The present study provides valuable information for future studies on biomass degradation and contributes to a better understanding of the role of the genes that are involved in this process.


Assuntos
Celulose/metabolismo , Perfilação da Expressão Gênica , Saccharum/química , Trichoderma/genética , Trichoderma/metabolismo , Celulase/genética , Celulase/metabolismo , Bases de Dados Genéticas , Genes Fúngicos/genética , Anotação de Sequência Molecular , Análise de Sequência de RNA , Trichoderma/enzimologia
19.
FEBS J ; 279(20): 3828-43, 2012 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-22889056

RESUMO

Xylella fastidiosa is a Gram-negative bacterium that grows as a biofilm inside the xylem vessels of susceptible plants and causes several economically relevant crop diseases. In the present study, we report the functional and low-resolution structural characterization of the X. fastidiosa disulfide isomerase DsbC (XfDsbC). DsbC is part of the disulfide bond reduction/isomerization pathway in the bacterial periplasm and plays an important role in oxidative protein folding. In the present study, we demonstrate the presence of XfDsbC during different stages of X. fastidiosa biofilm development. XfDsbC was not detected during X. fastidiosa planktonic growth; however, after administering a sublethal copper shock, we observed an overexpression of XfDsbC that also occurred during planktonic growth. These results suggest that X. fastidiosa can use XfDsbC in vivo under oxidative stress conditions similar to those induced by copper. In addition, using dynamic light scattering and small-angle X-ray scattering, we observed that the oligomeric state of XfDsbC in vitro may be dependent on the redox environment. Under reducing conditions, XfDsbC is present as a dimer, whereas a putative tetrameric form was observed under nonreducing conditions. Taken together, our findings demonstrate the overexpression of XfDsbC during biofilm formation and provide the first structural model of a bacterial disulfide isomerase in solution.


Assuntos
Proteínas de Bactérias/química , Isomerases de Dissulfetos de Proteínas/química , Multimerização Proteica , Xylella/enzimologia , Sequência de Aminoácidos , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Biofilmes/efeitos dos fármacos , Biofilmes/crescimento & desenvolvimento , Cobre/farmacologia , Escherichia coli/enzimologia , Escherichia coli/genética , Escherichia coli/crescimento & desenvolvimento , Teste de Complementação Genética , Modelos Moleculares , Dados de Sequência Molecular , Mutação , Oxirredução , Doenças das Plantas/microbiologia , Isomerases de Dissulfetos de Proteínas/genética , Isomerases de Dissulfetos de Proteínas/metabolismo , Estrutura Quaternária de Proteína , Espalhamento a Baixo Ângulo , Homologia de Sequência de Aminoácidos , Difração de Raios X , Xylella/genética , Xylella/fisiologia
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