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1.
Food Res Int ; 147: 110541, 2021 09.
Artigo em Inglês | MEDLINE | ID: mdl-34399518

RESUMO

The genus Cronobacter is an opportunistic food-borne pathogen which is able to adapt to diverse environments and shows considerable genetic diversity. Genomic analysis can be used to reveal the variation across the genus with respect to virulence, drug resistance and factors involved in horizontal gene transfer mechanisms, such as integrons, conjugative plasmids, and recombinases. In this study, whole-genome comparative analysis of 27 Cronobacter genomes (12 existing and 15 newly assembled genomes) was performed. A total of 110,010 protein-coding genes were grouped into 11,262 clusters, including 2637 core genes, 4814 strain-specific genes and 3811 dispensable genes. Clusters of Orthologous Groups (COG) analysis indicated that 97.35% of the core genes were for substrate transport and metabolism, and the antibiotic resistance genetic determinants were classified into 136 antibiotic resistance ontologies (AROs). A total of 80 genomic islands (GIs) were identified which contained several type VI secretion system gene clusters, and these were likely to have been acquired by horizontal gene transfer. This study has generated a comprehensive characterization of the genus Cronobacter, leading to a better understanding of the mechanisms and ecological functions among the genome features, speciation, and environmental adaptation strategies.


Assuntos
Cronobacter , Cronobacter/genética , Genoma Bacteriano/genética , Genômica , Especificidade da Espécie , Virulência
2.
Nat Commun ; 12(1): 4702, 2021 08 04.
Artigo em Inglês | MEDLINE | ID: mdl-34349104

RESUMO

Mycobacterium tuberculosis can adapt to changing environments by non-heritable mechanisms. Frame-shifting insertions and deletions (indels) may also participate in adaptation through gene disruption, which could be reversed by secondary introduction of a frame-restoring indel. We present ScarTrek, a program that scans genomic data for indels, including those that together disrupt and restore a gene's reading frame, producing "frame-shift scars" suggestive of reversible gene inactivation. We use ScarTrek to analyze 5977 clinical M. tuberculosis isolates. We show that indel frequency inversely correlates with genomic linguistic complexity and varies with gene-position and gene-essentiality. Using ScarTrek, we detect 74 unique frame-shift scars in 48 genes, with a 3.74% population-level incidence of unique scar events. We find multiple scars in the ESX-1 gene cluster. Six scars show evidence of convergent evolution while the rest shared a common ancestor. Our results suggest that sequential indels are a mechanism for reversible gene silencing and adaptation in M. tuberculosis.


Assuntos
Adaptação Fisiológica/genética , Inativação Gênica , Mycobacterium tuberculosis/genética , Fases de Leitura/genética , Evolução Molecular , Genes Bacterianos/genética , Genoma Bacteriano/genética , Humanos , Mutação INDEL , Mycobacterium tuberculosis/isolamento & purificação , Tuberculose/microbiologia
3.
Epidemiol Infect ; 149: e164, 2021 06 28.
Artigo em Inglês | MEDLINE | ID: mdl-34196266

RESUMO

An outbreak surveillance system for Salmonella integrating whole genome sequencing (WGS) and epidemiological data was developed in South East and London in 2016-17 to assess local WGS clusters for triage and investigation. Cases genetically linked within a 5 single-nucleotide polymorphism (SNP) single linkage cluster were assessed using a set of locally agreed thresholds based on time, person and place, for reporting to local health protection teams (HPTs). Between September 2016 and September 2017, 230 unique 5-SNP clusters (442 weekly reports) of non-typhoidal Salmonella 5-SNP WGS clusters were identified, of which 208 unique 5-SNP clusters (316 weekly reports) were not reported to the HPTs. In the remaining 22 unique clusters (126 weekly clusters) reported to HPTs, nine were known active outbreak investigations, seven were below locally agreed thresholds and six exceeded local thresholds. A common source or vehicle was identified in four of six clusters that exceeded locally agreed thresholds. This work demonstrates that a threshold-based surveillance system, taking into account time, place and genetic relatedness, is feasible and effective in directing the use of local public health resources for risk assessment and investigation of non-typhoidal Salmonella clusters.


Assuntos
Surtos de Doenças , Genoma Bacteriano/genética , Infecções por Salmonella/epidemiologia , Salmonella/genética , Análise por Conglomerados , DNA Bacteriano/genética , Notificação de Doenças , Inglaterra/epidemiologia , Monitoramento Epidemiológico , Humanos , Polimorfismo de Nucleotídeo Único , Saúde Pública , Medição de Risco , Salmonella/classificação , Salmonella/isolamento & purificação , Infecções por Salmonella/microbiologia , Sequenciamento Completo do Genoma
4.
Nat Commun ; 12(1): 4485, 2021 07 23.
Artigo em Inglês | MEDLINE | ID: mdl-34301928

RESUMO

High-throughput short-read metagenomics has enabled large-scale species-level analysis and functional characterization of microbial communities. Microbiomes often contain multiple strains of the same species, and different strains have been shown to have important differences in their functional roles. Recent advances on long-read based methods enabled accurate assembly of bacterial genomes from complex microbiomes and an as-yet-unrealized opportunity to resolve strains. Here we present Strainberry, a metagenome assembly pipeline that performs strain separation in single-sample low-complexity metagenomes and that relies uniquely on long-read data. We benchmarked Strainberry on mock communities for which it produces strain-resolved assemblies with near-complete reference coverage and 99.9% base accuracy. We also applied Strainberry on real datasets for which it improved assemblies generating 20-118% additional genomic material than conventional metagenome assemblies on individual strain genomes. We show that Strainberry is also able to refine microbial diversity in a complex microbiome, with complete separation of strain genomes. We anticipate this work to be a starting point for further methodological improvements on strain-resolved metagenome assembly in environments of higher complexities.


Assuntos
Biologia Computacional/métodos , Genoma Bacteriano/genética , Metagenoma/genética , Metagenômica/métodos , Bactérias/classificação , Bactérias/genética , Genômica/métodos , Sequenciamento de Nucleotídeos em Larga Escala , Especificidade da Espécie
5.
Nat Commun ; 12(1): 4347, 2021 07 23.
Artigo em Inglês | MEDLINE | ID: mdl-34301933

RESUMO

Heterologous expression of biosynthetic gene clusters (BGCs) avails yield improvements and mining of natural products, but it is limited by lacking of more efficient Gram-negative chassis. The proteobacterium Schlegelella brevitalea DSM 7029 exhibits potential for heterologous BGC expression, but its cells undergo early autolysis, hindering further applications. Herein, we rationally construct DC and DT series genome-reduced S. brevitalea mutants by sequential deletions of endogenous BGCs and the nonessential genomic regions, respectively. The DC5 to DC7 mutants affect growth, while the DT series mutants show improved growth characteristics with alleviated cell autolysis. The yield improvements of six proteobacterial natural products and successful identification of chitinimides from Chitinimonas koreensis via heterologous expression in DT mutants demonstrate their superiority to wild-type DSM 7029 and two commonly used Gram-negative chassis Escherichia coli and Pseudomonas putida. Our study expands the panel of Gram-negative chassis and facilitates the discovery of natural products by heterologous expression.


Assuntos
Produtos Biológicos/metabolismo , Burkholderiales/genética , Genoma Bacteriano/genética , Família Multigênica/genética , Proteobactérias/genética , Burkholderiaceae/genética , Burkholderiaceae/metabolismo , Burkholderiales/metabolismo , Escherichia coli/genética , Escherichia coli/metabolismo , Regulação Bacteriana da Expressão Gênica , Engenharia Genética/métodos , Mutação , Policetídeos/metabolismo , Proteobactérias/metabolismo , Pseudomonas putida/genética , Pseudomonas putida/metabolismo
6.
Bioresour Technol ; 337: 125473, 2021 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-34320753

RESUMO

Filamentous cyanobacteria, Jacksonvillea sp. ISTCYN1 was isolated from agriculture field and cultured in BG-11 medium. This study, report the genome sequence of cyanobacteria Jacksonvillea thatto the best of our knowledgeis the firstgenome sequenceof thisgenus. The 5.7 MB draft genome sequence of this cyanobacterium contains 5134 protein-coding genes. The phylogenetic tree was constructed based on genome and Desertifilum sp. IPPAS B-1220 validated the closest relationship with Jacksonvillea sp. ISTCYN1. The growth of strain ISTCYN1 has been reported in the presence of different types of plastic when used as a sole carbon source. SEM analysis revealed biofilm formation by cyanobacterial strain ISTCYN1 on the surface of high and low-density polyethylene and polypropylene. In the presence of these plastics, EPS production has also been reported by this strain. Whole genome sequence analysis reveals the presence of many genes involved in biofilm formation. The presence of key enzymes responsible for plastic degradation laccase, esterase, lipase, thioesterase, and peroxidase have been predicted in the genome analysis. Genome analysis also provides insight into the genes involved in biotin biosynthetic pathways. Furthermore, the presence of many selenoproteins reveals the selenium acquisition by this cyanobacterium.


Assuntos
Cianobactérias , Genoma Bacteriano , Sequência de Bases , Vias Biossintéticas , Cianobactérias/genética , Genoma Bacteriano/genética , Filogenia
7.
Nat Commun ; 12(1): 4649, 2021 07 30.
Artigo em Inglês | MEDLINE | ID: mdl-34330925

RESUMO

The bacterium Vibrio cholerae can colonize the human intestine and cause cholera, but spends much of its life cycle in seawater. The pathogen must adapt to substantial environmental changes when moving between seawater and the human intestine, including different availability of carbon sources such as fructose. Here, we use in vitro experiments as well as mouse intestinal colonization assays to study the mechanisms used by pandemic V. cholerae to adapt to these environmental changes. We show that a LacI-type regulator (FruI) and a fructose/H+ symporter (FruT) are important for fructose uptake at low fructose concentrations, as those found in seawater. FruT is downregulated by FruI, which is upregulated when O2 concentrations are low (as in the intestine) by ArcAB, a two-component system known to respond to changes in oxygen levels. As a result, the bacteria predominantly use FruT for fructose uptake under seawater conditions (low fructose, high O2), and use a known fructose phosphotransferase system (PTS, Fpr) for fructose uptake under conditions found in the intestine. PTS activity leads to reduced levels of intracellular cAMP, which in turn upregulate virulence genes. Our results indicate that the FruT/FruI system may be important for survival of pandemic V. cholerae in seawater.


Assuntos
Proteínas de Bactérias/metabolismo , Frutose/metabolismo , Simportadores/metabolismo , Vibrio cholerae/metabolismo , Animais , Proteínas de Bactérias/genética , Cólera/epidemiologia , Cólera/microbiologia , Feminino , Regulação Bacteriana da Expressão Gênica , Genoma Bacteriano/genética , Genômica/métodos , Humanos , Masculino , Camundongos , Viabilidade Microbiana/genética , Pandemias , Regiões Promotoras Genéticas/genética , Ligação Proteica , Água do Mar/microbiologia , Simportadores/genética , Vibrio cholerae/genética , Vibrio cholerae/patogenicidade , Virulência/genética
8.
Nat Microbiol ; 6(7): 885-898, 2021 07.
Artigo em Inglês | MEDLINE | ID: mdl-34127845

RESUMO

Extracellular DNA is a major macromolecule in global element cycles, and is a particularly crucial phosphorus, nitrogen and carbon source for microorganisms in the seafloor. Nevertheless, the identities, ecophysiology and genetic features of DNA-foraging microorganisms in marine sediments are largely unknown. Here, we combined microcosm experiments, DNA stable isotope probing (SIP), single-cell SIP using nano-scale secondary isotope mass spectrometry (NanoSIMS) and genome-centric metagenomics to study microbial catabolism of DNA and its subcomponents in marine sediments. 13C-DNA added to sediment microcosms was largely degraded within 10 d and mineralized to 13CO2. SIP probing of DNA revealed diverse 'Candidatus Izemoplasma', Lutibacter, Shewanella and Fusibacteraceae incorporated DNA-derived 13C-carbon. NanoSIMS confirmed incorporation of 13C into individual bacterial cells of Fusibacteraceae sorted from microcosms. Genomes of the 13C-labelled taxa all encoded enzymatic repertoires for catabolism of DNA or subcomponents of DNA. Comparative genomics indicated that diverse 'Candidatus Izemoplasmatales' (former Tenericutes) are exceptional because they encode multiple (up to five) predicted extracellular nucleases and are probably specialized DNA-degraders. Analyses of additional sediment metagenomes revealed extracellular nuclease genes are prevalent among Bacteroidota at diverse sites. Together, our results reveal the identities and functional properties of microorganisms that may contribute to the key ecosystem function of degrading and recycling DNA in the seabed.


Assuntos
Bactérias/metabolismo , DNA/metabolismo , Sedimentos Geológicos/microbiologia , Água do Mar/microbiologia , Anaerobiose , Bactérias/classificação , Bactérias/genética , Proteínas de Bactérias/genética , Biodegradação Ambiental , Vias Biossintéticas , Isótopos de Carbono/metabolismo , Temperatura Baixa , Genoma Bacteriano/genética , Metagenômica , Nucleosídeos/metabolismo , Filogenia
9.
Arch Microbiol ; 203(7): 4693-4703, 2021 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-34189594

RESUMO

Six different fermented vegetables were collected from Zhejiang Province, China, to explore the associated bacterial community using a high-throughput sequencing platform. A total of 24 phyla, 274 families and 569 genera were identified from 6 samples. Firmicutes and Proteobacteria were the main phyla in all of the samples. Brevibacterium was the major genus in Xiaoshan pickled radish. Lactobacillus-related genera and Vibrio were the major genera in fermented potherb mustard and its brine. Enterobacter and Cobetia were the major genera in fermented radish and its brine. Chromohalobacter was the major genus in the tuber mustard. These results indicated clear differences were there between the bacterial genera present in Xiaoshan pickled radish, fermented potherb mustard, fermented radish, and tuber mustard. This demonstrated the possible influences of raw materials and manufacturing processes. Furthermore, a large number of lactic acid bacteria were isolated and identified by culture-dependent and 16S rRNA gene sequence analysis, which accounted for more than 68% of all the isolates. In addition, whole-genome analysis of Levilactobacillus suantsaii, Latilactobacillus sakei subsp. sakei, and Weissella cibaria showed that they had large numbers of genes associated with carbohydrate metabolism. This may explain why these three bacterial strains can grow in fermented vegetable environments.


Assuntos
Alimentos e Bebidas Fermentados , Microbiologia de Alimentos , Lactobacillales , Microbiota , Verduras , China , Alimentos e Bebidas Fermentados/microbiologia , Genoma Bacteriano/genética , Genômica , Lactobacillales/genética , Microbiota/genética , RNA Ribossômico 16S/genética , Verduras/microbiologia
10.
Nat Commun ; 12(1): 3801, 2021 06 21.
Artigo em Inglês | MEDLINE | ID: mdl-34155204

RESUMO

The recent emergence of strains of Neisseria gonorrhoeae associated with treatment failures to ceftriaxone, the foundation of current treatment options, has raised concerns over a future of untreatable gonorrhea. Current global data on gonococcal strains suggest that several lineages, predominately characterized by mosaic penA alleles, are associated with elevated minimum inhibitory concentrations (MICs) to extended spectrum cephalosporins (ESCs). Here we report on whole genome sequences of 813 N. gonorrhoeae isolates collected through the Gonococcal Isolate Surveillance Project in the United States. Phylogenomic analysis revealed that one persisting lineage (Clade A, multi-locus sequence type [MLST] ST1901) with mosaic penA-34 alleles, contained the majority of isolates with elevated MICs to ESCs. We provide evidence that an ancestor to the globally circulating MLST ST1901 clones potentially emerged around the early to mid-20th century (1944, credibility intervals [CI]: 1935-1953), predating the introduction of cephalosporins, but coinciding with the use of penicillin. Such results indicate that drugs with novel mechanisms of action are needed as these strains continue to persist and disseminate globally.


Assuntos
Antibacterianos/farmacologia , Cefalosporinas/farmacologia , Genes Bacterianos/genética , Neisseria gonorrhoeae/efeitos dos fármacos , Neisseria gonorrhoeae/genética , Alelos , Resistência às Cefalosporinas/efeitos dos fármacos , Resistência às Cefalosporinas/genética , Variação Genética , Genoma Bacteriano/genética , Gonorreia/epidemiologia , Gonorreia/microbiologia , Humanos , Testes de Sensibilidade Microbiana , Tipagem de Sequências Multilocus , Neisseria gonorrhoeae/classificação , Neisseria gonorrhoeae/isolamento & purificação , Filogenia , Recombinação Genética , Análise de Sequência de DNA , Estados Unidos/epidemiologia
11.
J Med Microbiol ; 70(6)2021 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-34170219

RESUMO

Introduction. Members of the genus Citrobacter are facultative anaerobic Gram-negative bacilli belonging to the Enterobacterales [Janda J Clin Microbiol 1994; 32(8):1850-1854; Arens Clin Microbiol Infect 1997;3(1):53-57]. Formerly, Citrobacter species were occasionally reported as nosocomial pathogens with low virulence [Pepperell Antimicrob Agents Chemother 2002;46(11):3555-60]. Now, they are consistently reported to cause nosocomial infections of the urinary tract, respiratory tract, bone, peritoneum, endocardium, meninges, intestines, bloodstream and central nervous system. Among Citrobacter species, the most common isolates are C. koseri and C. freundii, while C. amalonaticus has seldom been isolated [Janda J Clin Microbiol 1994; 32(8):1850-1854; Marak Infect Dis (Lond) 2017;49(7):532-9]. Further, Citrobacter spp. are usually susceptible to carbapenems, aminoglycosides, tetracyclines and colistin [Marak Infect Dis (Lond) 2017;49(7):532-9].Hypothesis/Gap Statement. As C. amalonaticus is rare, only one clinical isolate, coharbouring carbapenem resistance gene bla IMP-4 and quinolone resistance gene qnrs1, has been reported.Aim. To characterize a carbapenem-resistant C. amalonaticus strain from PR China coharbouring bla IMP-4 and qnrs1.Methodology. Three hundred and forty nonrepetitive carbapenem-resistant Enterobacterales (CRE) strains were collected during 2011-2018. A carbapenem-resistant C. amalonaticus strain was detected and confirmed using a VITEK mass spectrometry-based microbial identification system and 16S rRNA sequencing. Minimum inhibitory concentrations (MICs) for clinical antimicrobials were obtained by the broth microdilution method. Whole-genome sequencing (WGS) was performed for antibiotic resistance gene analysis, and a phylogenetic tree of C. amalonaticus strains was constructed using the Bacterial Pan Genome Analysis (BPGA) tool. The transferability of the resistance plasmid was verified by conjugal transfer.Results. A rare carbapenem-resistant C. amalonaticus strain (CA71) was recovered from a patient with cerebral obstruction and the sequences of 16S rRNA gene shared more than 99 % similarity with C. amalonaticus CITRO86, FDAARGOS 165. CA71 is resistant to ß-lactam, quinolone and aminoglycoside antibiotics, and even imipenem and meropenem (MICs of 2 and 4 mg l-1 respectively), and is only sensitive to polymyxin B and tigecycline. Six antibiotic resistance genes were detected via WGS, including the ß-lactam genes bla IMP-4, bla CTX-M-18 and bla Sed1, the quinolone gene qnrs1, and the aminoglycoside genes AAC(3)-VIIIa, AadA24. Interestingly, bla IMP-4 and qnrs1 coexist on an IncN1-type plasmid (pCA71-IMP) and successfully transferred to Escherichia coli J53 via conjugal transfer. Phylogenetic analysis showed that CA71 is most similar to C. amalonaticus strain CJ25 and belongs to the same evolutionary cluster along with seven other strains.Conclusion. To the best of our knowledge, this is the first report of a carbapenem-resistant C. amalonaticus isolate coharbouring bla IMP-4 and qnrs1.


Assuntos
Proteínas de Bactérias/genética , Enterobacteriáceas Resistentes a Carbapenêmicos/genética , Citrobacter/genética , Resistência a Múltiplos Medicamentos/genética , Antibacterianos/farmacologia , Enterobacteriáceas Resistentes a Carbapenêmicos/classificação , Enterobacteriáceas Resistentes a Carbapenêmicos/efeitos dos fármacos , Enterobacteriáceas Resistentes a Carbapenêmicos/isolamento & purificação , Citrobacter/classificação , Citrobacter/efeitos dos fármacos , Citrobacter/isolamento & purificação , Conjugação Genética , DNA Bacteriano/genética , Resistência a Múltiplos Medicamentos/efeitos dos fármacos , Infecções por Enterobacteriaceae/microbiologia , Genoma Bacteriano/genética , Humanos , Testes de Sensibilidade Microbiana , Filogenia , Plasmídeos/genética , RNA Ribossômico 16S/genética , beta-Lactamases/genética
12.
F1000Res ; 10: 286, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34113437

RESUMO

Background: Synthetic engineering of bacteria to produce industrial products is a burgeoning field of research and application. In order to optimize genome design, designers need to understand which genes are essential, which are optimal for growth, and locations in the genome that will be tolerated by the organism when inserting engineered cassettes. Methods: We present a pan-genome based method for the identification of core regions in a genome that are strongly conserved at the species level. Results: We show that the core regions determined by our method contain all or almost all essential genes. This demonstrates the accuracy of our method as essential genes should be core genes. We show that we outperform previous methods by this measure. We also explain why there are exceptions to this rule for our method. Conclusions: We assert that synthetic engineers should avoid deleting or inserting into these core regions unless they understand and are manipulating the function of the genes in that region. Similarly, if the designer wishes to streamline the genome, non-core regions and in particular low penetrance genes would be good targets for deletion. Care should be taken to remove entire cassettes with similar penetrance of the genes within cassettes as they may harbor toxin/antitoxin genes which need to be removed in tandem. The bioinformatic approach introduced here saves considerable time and effort relative to knockout studies on single isolates of a given species and captures a broad understanding of the conservation of genes that are core to a species.


Assuntos
Bacillus subtilis , Escherichia coli , Bacillus subtilis/genética , Escherichia coli/genética , Genoma Bacteriano/genética
13.
Nat Commun ; 12(1): 3864, 2021 06 23.
Artigo em Inglês | MEDLINE | ID: mdl-34162873

RESUMO

Genetically encoded small molecules (secondary metabolites) play eminent roles in ecological interactions, as pathogenicity factors and as drug leads. Yet, these chemical mediators often evade detection, and the discovery of novel entities is hampered by low production and high rediscovery rates. These limitations may be addressed by genome mining for biosynthetic gene clusters, thereby unveiling cryptic metabolic potential. The development of sophisticated data mining methods and genetic and analytical tools has enabled the discovery of an impressive array of previously overlooked natural products. This review shows the newest developments in the field, highlighting compound discovery from unconventional sources and microbiomes.


Assuntos
Biologia Computacional/métodos , Mineração de Dados/métodos , Genoma Bacteriano/genética , Genoma de Planta/genética , Genômica/métodos , Produtos Biológicos/química , Produtos Biológicos/metabolismo , Vias Biossintéticas/genética , Descoberta de Drogas/métodos , Estrutura Molecular , Metabolismo Secundário/genética
14.
Nat Commun ; 12(1): 4021, 2021 06 29.
Artigo em Inglês | MEDLINE | ID: mdl-34188040

RESUMO

Chlamydiae are highly successful strictly intracellular bacteria associated with diverse eukaryotic hosts. Here we analyzed metagenome-assembled genomes of the "Genomes from Earth's Microbiomes" initiative from diverse environmental samples, which almost double the known phylogenetic diversity of the phylum and facilitate a highly resolved view at the chlamydial pangenome. Chlamydiae are defined by a relatively large core genome indicative of an intracellular lifestyle, and a highly dynamic accessory genome of environmental lineages. We observe chlamydial lineages that encode enzymes of the reductive tricarboxylic acid cycle and for light-driven ATP synthesis. We show a widespread potential for anaerobic energy generation through pyruvate fermentation or the arginine deiminase pathway, and we add lineages capable of molecular hydrogen production. Genome-informed analysis of environmental distribution revealed lineage-specific niches and a high abundance of chlamydiae in some habitats. Together, our data provide an extended perspective of the variability of chlamydial biology and the ecology of this phylum of intracellular microbes.


Assuntos
Chlamydia/genética , Ciclo do Ácido Cítrico/genética , Genoma Bacteriano/genética , Metagenoma/genética , Acanthamoeba/microbiologia , Animais , Chlamydia/classificação , Chlamydia/isolamento & purificação , Ecossistema , Peixes/parasitologia , Brânquias/parasitologia , Hidrolases/metabolismo , Filogenia , Ácido Pirúvico/metabolismo , Sequenciamento Completo do Genoma
15.
Nat Commun ; 12(1): 4024, 2021 06 29.
Artigo em Inglês | MEDLINE | ID: mdl-34188051

RESUMO

Pseudomonas aeruginosa can cause nosocomial infections, especially in ventilated or cystic fibrosis patients. Highly pathogenic isolates express the phospholipase ExoU, an effector of the type III secretion system that acts on plasma membrane lipids, causing membrane rupture and host cell necrosis. Here, we use a genome-wide screen to discover that ExoU requires DNAJC5, a host chaperone, for its necrotic activity. DNAJC5 is known to participate in an unconventional secretory pathway for misfolded proteins involving anterograde vesicular trafficking. We show that DNAJC5-deficient human cells, or Drosophila flies knocked-down for the DNAJC5 orthologue, are largely resistant to ExoU-dependent virulence. ExoU colocalizes with DNAJC5-positive vesicles in the host cytoplasm. DNAJC5 mutations preventing vesicle trafficking (previously identified in adult neuronal ceroid lipofuscinosis, a human congenital disease) inhibit ExoU-dependent cell lysis. Our results suggest that, once injected into the host cytoplasm, ExoU docks to DNAJC5-positive secretory vesicles to reach the plasma membrane, where it can exert its phospholipase activity.


Assuntos
Proteínas de Bactérias/metabolismo , Proteínas de Choque Térmico HSP40/metabolismo , Proteínas de Membrana/metabolismo , Transporte Proteico/fisiologia , Pseudomonas aeruginosa/patogenicidade , Animais , Membrana Celular/patologia , Infecção Hospitalar/microbiologia , Drosophila melanogaster/genética , Genoma Bacteriano/genética , Proteínas de Choque Térmico HSP40/genética , Humanos , Proteínas de Membrana/genética , Chaperonas Moleculares/metabolismo , Infecções por Pseudomonas/patologia , Pseudomonas aeruginosa/genética , Pseudomonas aeruginosa/metabolismo , Sistemas de Secreção Tipo III/metabolismo
16.
Genes (Basel) ; 12(5)2021 05 18.
Artigo em Inglês | MEDLINE | ID: mdl-34070083

RESUMO

Type I toxin-antitoxin (TA) systems are widespread genetic modules in bacterial genomes. They express toxic peptides whose overexpression leads to growth arrest or cell death, whereas antitoxins regulate the expression of toxins, acting as labile antisense RNAs. The Staphylococcus aureus (S. aureus) genome contains and expresses several functional type I TA systems, but their biological functions remain unclear. Here, we addressed and challenged experimentally, by proteomics, if the type I TA system, the SprG1/SprF1 pair, influences the overall gene expression in S. aureus. Deleted and complemented S. aureus strains were analyzed for their proteomes, both intracellular and extracellular, during growth. Comparison of intracellular proteomes among the strains points to the SprF1 antitoxin as moderately downregulating protein expression. In the strain naturally expressing the SprG1 toxin, cytoplasmic proteins are excreted into the medium, but this is not due to unspecific cell leakages. Such a toxin-driven release of the cytoplasmic proteins may modulate the host inflammatory response that, in turn, could amplify the S. aureus infection spread.


Assuntos
Antitoxinas/genética , Proteínas de Bactérias/genética , Regulação Bacteriana da Expressão Gênica/genética , Expressão Gênica/genética , Staphylococcus aureus/genética , Sistemas Toxina-Antitoxina/genética , Citoplasma/genética , Genoma Bacteriano/genética , Proteoma/genética , RNA Antissenso/genética
17.
Int J Mol Sci ; 22(10)2021 May 20.
Artigo em Inglês | MEDLINE | ID: mdl-34065296

RESUMO

Little is known about DNA tandem repeats across prokaryotes. We have recently described an enigmatic group of tandem repeats in bacterial genomes with a constant repeat size but variable sequence. These findings strongly suggest that tandem repeat size in some bacteria is under strong selective constraints. Here, we extend these studies and describe tandem repeats in a large set of Bacillus. Some species have very few repeats, while other species have a large number. Most tandem repeats have repeats with a constant size (either 52 or 20-21 nt), but a variable sequence. We characterize in detail these intriguing tandem repeats. Individual species have several families of tandem repeats with the same repeat length and different sequence. This result is in strong contrast with eukaryotes, where tandem repeats of many sizes are found in any species. We discuss the possibility that they are transcribed as small RNA molecules. They may also be involved in the stabilization of the nucleoid through interaction with proteins. We also show that the distribution of tandem repeats in different species has a taxonomic significance. The data we present for all tandem repeats and their families in these bacterial species will be useful for further genomic studies.


Assuntos
Bacillus/genética , Sequências de Repetição em Tandem/genética , Bactérias/genética , Eucariotos/genética , Genoma Bacteriano/genética , Genômica/métodos , Células Procarióticas/fisiologia , Especificidade da Espécie
18.
BMC Ecol Evol ; 21(1): 108, 2021 06 02.
Artigo em Inglês | MEDLINE | ID: mdl-34078265

RESUMO

BACKGROUND: Feather feeding lice are abundant and diverse ectoparasites that complete their entire life cycle on an avian host. The principal or sole source of nutrition for these lice is feathers. Feathers appear to lack four amino acids that the lice would require to complete development and reproduce. Several insect groups have acquired heritable and intracellular bacteria that can synthesize metabolites absent in an insect's diet, allowing insects to feed exclusively on nutrient-poor resources. Multiple species of feather feeding lice have been shown to harbor heritable and intracellular bacteria. We expected that these bacteria augment the louse's diet with amino acids and facilitated the evolution of these diverse and specialized parasites. Heritable symbionts of insects often have small genomes that contain a minimal set of genes needed to maintain essential cell functions and synthesize metabolites absent in the host insect's diet. Therefore, we expected the genome of a bacterial endosymbiont in feather lice would be small, but encode pathways for biosynthesis of amino acids. RESULTS: We sequenced the genome of a bacterial symbiont from a feather feeding louse (Columbicola wolffhuegeli) that parasitizes the Pied Imperial Pigeon (Ducula bicolor) and used its genome to predict metabolism of amino acids based on the presence or absence of genes. We found that this bacterial symbiont has a small genome, similar to the genomes of heritable symbionts described in other insect groups. However, we failed to identify many of the genes that we expected would support metabolism of amino acids in the symbiont genome. We also evaluated other gene pathways and features of the highly reduced genome of this symbiotic bacterium. CONCLUSIONS: Based on the data collected in this study, it does not appear that this bacterial symbiont can synthesize amino acids needed to complement the diet of a feather feeding louse. Our results raise additional questions about the biology of feather chewing lice and the roles of symbiotic bacteria in evolution of diverse avian parasites.


Assuntos
Iscnóceros , Parasitos , Animais , Bactérias/genética , Genoma Bacteriano/genética , Simbiose
19.
Int J Food Microbiol ; 351: 109269, 2021 Aug 02.
Artigo em Inglês | MEDLINE | ID: mdl-34102570

RESUMO

Microbial population heterogeneity contributes to differences in stress response between individual cells in a population, and can lead to the selection of genetically stable variants with increased stress resistance. We previously provided evidence that the multiple-stress resistant Listeria monocytogenes LO28 variant 15, carries a point mutation in the rpsU gene, resulting in an arginine-proline substitution in ribosomal protein RpsU (RpsU17Arg-Pro). Here, we investigated the trade-off between general stress sigma factor SigB-mediated stress resistance and fitness in variant 15 using experimental evolution. By selecting for higher fitness in two parallel evolving cultures, we identified two evolved variants: 15EV1 and 15EV2. Whole genome sequencing and SNP analysis showed that both parallel lines mutated in the same codon in rpsU as the original mutation resulting in RpsU17Pro-His (15EV1) and RpsU17Pro-Thr (15EV2). Using a combined phenotyping and proteomics approach, we assessed the resistance of the evolved variants to both heat and acid stress, and found that in both lines reversion to WT-like fitness also resulted in WT-like stress sensitivity. Proteome analysis of L. monocytogenes LO28 WT, variant 15, 15EV1, and 15EV2 revealed high level expression of SigB regulon members only in variant 15, whereas protein profiles of both evolved variants were highly similar to that of the LO28 WT. Experiments with constructed RpsU17Arg-Pro mutants in L. monocytogenes LO28 and EGDe, and RpsU17Arg-His and RpsU17Arg-Thr in LO28, confirmed that single amino acid substitutions in RpsU enable switching between multiple-stress resistant and high fitness states in L. monocytogenes.


Assuntos
Adaptação Fisiológica/genética , Proteínas de Bactérias/genética , Listeria monocytogenes/fisiologia , Proteínas Ribossômicas/genética , Ácidos/metabolismo , Substituição de Aminoácidos , Proteínas de Bactérias/metabolismo , Evolução Molecular Direcionada , Genoma Bacteriano/genética , Temperatura Alta , Listeria monocytogenes/genética , Mutação , Proteoma/metabolismo , Proteínas Ribossômicas/metabolismo , Fator sigma/genética , Fator sigma/metabolismo
20.
Curr Microbiol ; 78(8): 2935-2942, 2021 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-34047832

RESUMO

Genomic sequencing has vastly expedited our understanding of bacterial functions. However, the genomes of many plant-growth-promoting bacteria (PGPB) have yet to be sequenced and contextualized. To this end, I report the sequenced genome of a PGPB-Caulobacter segnis CBR1-and contextualize its genomic features with the genomic features of sequenced Caulobacter strains. Moreover, I demonstrate that the CBR1 genome harbors genomic features that have been shown to be necessary for select Caulobacter strains to enhance the growth and development of Arabidopsis plants. Together, these findings will help guide future investigations that seek to understand the molecular factors undergirding the positive interactions between plants and microbes.


Assuntos
Caulobacter , Bactérias , Caulobacter/genética , Genoma Bacteriano/genética , Desenvolvimento Vegetal , Plantas
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