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1.
J Biosci Bioeng ; 132(2): 174-182, 2021 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-34074597

RESUMO

Alcaligenaceae and Chromatiaceae were previously reported as the specific pollution bioindicators in the receiving river water contaminated by palm oil mill effluent (POME) final discharge. Considering the inevitable sensitivity of bacteria under environmental stresses, it is crucial to assess the survivability of both bacteria in the fluctuated environmental factors, proving their credibility as POME pollution bioindicators in the environment. In this study, the survivability of Alcaligenaceae and Chromatiaceae from facultative pond, algae (aerobic) pond and final discharge were evaluated under varying sets of temperature (25-40°C), pH (pH 7-9) and low/high total suspended solid (TSS) contents of POME collected during low/high crop seasons of oil palm, respectively. Following treatment, the viability status and compositions of the bacterial community were assessed using flow cytometry-based assay and high-throughput Illumina MiSeq, respectively, in correlation with the changes of physicochemical properties. The changes in temperature, pH and TSS indeed changed the physicochemical properties of POME. The functionality of bacterial cells was also shifted where the viable cells and high nucleic acid contents reduced at elevated levels of temperature and pH but increased at high TSS content. Interestingly, the Alcaligenaceae and Chromatiaceae continuously detected in the samples which accounted for more than 0.5% of relative abundance, with a positive correlation with biological oxygen demand (BOD5) concentration. Therefore, either Alcaligenaceae or Chromatiaceae or both could be regarded as the reliable and specific bacterial indicators to indicate the pollution in river water due to POME final discharge despite the fluctuations in temperature, pH and TSS.


Assuntos
Alcaligenaceae , Chromatiaceae , Biomarcadores Ambientais , Concentração de Íons de Hidrogênio , Resíduos Industriais , Óleo de Palmeira , Óleos Vegetais , Temperatura , Eliminação de Resíduos Líquidos
2.
FEBS J ; 288(16): 4905-4917, 2021 08.
Artigo em Inglês | MEDLINE | ID: mdl-33630388

RESUMO

Recently, CxaP, a sugar acid substrate binding protein (SBP) from Advenella mimigardefordensis strain DPN7T , was identified as part of a novel sugar uptake strategy. In the present study, the protein was successfully crystallized. Although several SBP structures of tripartite ATP-independent periplasmic transporters have already been solved, this is the first structure of an SBP accepting multiple sugar acid ligands. Protein crystals were obtained with bound d-xylonic acid, d-fuconic acid d-galactonic and d-gluconic acid, respectively. The protein shows the typical structure of an SBP of a tripartite ATP-independent periplasmic transporter consisting of two domains linked by a hinge and spanned by a long α-helix. By analysis of the structure, the substrate binding site of the protein was identified. The carboxylic group of the sugar acids interacts with Arg175, whereas the coordination of the hydroxylic groups at positions C2 and C3 is most probably realized by Arg154 and Asn151. Furthermore, it was observed that 2-keto-3-deoxy-d-gluconic acid is bound in protein crystals that were crystallized without the addition of any ligand, indicating that this molecule is prebound to the protein and is displaced by the other ligands if they are available. DATABASE: Structural data of CxaP complexes are available in the worldwide Protein Data Bank (https://www.rcsb.org) under the accession codes 7BBR (2-keto-3-deoxy-d-gluconic acid), 7BCR (d-galactonic acid), 7BCN (d-xylonic acid), 7BCO (d-fuconic acid) and 7BCP (d-gluconic acid).


Assuntos
Alcaligenaceae/química , Proteínas de Bactérias/química , Proteínas de Membrana Transportadoras/química , Açúcares Ácidos/química , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Cristalografia por Raios X , Proteínas de Membrana Transportadoras/metabolismo , Modelos Moleculares , Açúcares Ácidos/metabolismo
3.
J Mol Evol ; 89(1-2): 81-94, 2021 02.
Artigo em Inglês | MEDLINE | ID: mdl-33462639

RESUMO

Despite extensive use in the biofuel industry, only butyryl co-A dehydrogenase enzymes from the Clostridia group have undergone extensive structural and genetic characterization. The present study, portrays the characterization of structural, functional and phylogenetic properties of butyryl co-A dehydrogenase identified within the genome of Pusillimonas ginsengisoli SBSA. In silico characterization, homology modelling and docking data indicates that this protein is a homo-tetramer and 388 amino acid residue long, rich in alanine and leucine residue; having molecular weight of 42347.69 dalton. Its isoelectric point value is 5.78; indicate its neutral nature while 38.38 instability index value indicate its stable nature. Its thermostable nature evidenced by its high aliphatic index (93.14); makes its suitable for industry-based use. The secondary structure prediction analysis of butyryl co-A dehydrogenase unveiled that the proteins has secondary arrangements of 54% α-helix, 13% ß-stand and 5% disordered conformation. However, phylogenetic analysis clearly indicates that probably horizontal gene transfer is the primary mechanism of spreading of this gene in this organism. Notably, multiple sequence alignment study of phylogenetically diverse butyryl co-A dehydrogenase sequence highlighted the presence of conserved amino acid residues i.e. YXV/LGXKXWXS/T. Physicochemical characterization of other relevant proteins involved in butanol metabolism of SBSA also has been carried out. However, metabolic construction of functional butanol biosynthesis pathway in SBSA, enlightened its cost-effective potential use in biofuel industry as an alternate to Clostridia system.


Assuntos
Alcaligenaceae , Butanóis , Clostridium/genética , Filogenia
4.
J Infect Chemother ; 27(5): 740-746, 2021 May.
Artigo em Inglês | MEDLINE | ID: mdl-33386260

RESUMO

Bordetella trematum and Kerstersia gyiorum are rare gram-negative bacilli that are not frequently detected in human infections. In this report, we describe a case of a 48-year-old man who presented to our hospital with an infected wound on his leg. Discharges from the cracks of the granulation were collected and evaluated in our microbiology laboratory. Gram staining of the specimen showed polymorphonuclear leukocytes and abundant gram-negative bacilli. Three types of colonies were isolated on blood agar and were identified as B. trematum and Alcaligenes faecalis using VITEK MS. Moreover, K. gyiorum and B. trematum were identified and confirmed via 16S ribosomal RNA (rRNA) gene sequencing. The patient successfully recovered following application of meropenem antibacterial therapy and surgical debridement. This is the first reported case of complex wound infection caused by both B. trematum and K. gyiorum. Identification of B. trematum has recently been made possible by routine bacterial identification using matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (MALDI-TOF MS). However, K. gyiorum isolation is still rare, and species identification requires 16S rRNA sequencing. Thus, this case highlighted the importance of using multiple methods, such as MALDI-TOF MS and 16S rRNA gene sequencing, for identification of rarely isolated species from clinical specimens.


Assuntos
Bordetella , Dermatite , Alcaligenaceae , Bordetella/genética , Humanos , Masculino , Pessoa de Meia-Idade , RNA Ribossômico 16S/genética , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz
5.
Bioresour Technol ; 323: 124641, 2021 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-33429316

RESUMO

Organophosphorus pesticides are highly toxic phosphate compounds with the general structure of O = P(OR)3 and threaten human health seriously. Methyl parathion hydrolase from microbial is an important enzyme to degrade organophosphorus pesticides (OPs) into less toxic or nontoxic compounds like. p-nitrophenol and diethyl phosphate. Here, a gene encoding methyl parathion hydrolase from Azohydromonas australica was firstly cloned and expressed in Escherichia coli. The recombinant hydrolase showed its optimal pH and temperature at pH 9.5 and 50 °C. Leveraging 1 mM Mn2+, the enzyme activity was significantly enhanced by 29.3-fold, and the thermostability at 40 and 50 °C was also improved. The recombinant MPH showed the specific activity of 4.94 and 16.0 U/mg towards methyl parathion and paraoxon, respectively. Moreover, A. australica MPH could effectively degrade various of OPs pesticides including methyl parathion, paraoxon, dichlorvos and chlorpyrifos in a few minutes, suggesting a great potential in the bioremediation of OPs pesticides.


Assuntos
Clorpirifos , Metil Paration , Praguicidas , Alcaligenaceae , Humanos , Hidrolases , Compostos Organofosforados
6.
J Hazard Mater ; 408: 124880, 2021 04 15.
Artigo em Inglês | MEDLINE | ID: mdl-33388628

RESUMO

Microbial fuel cells (MFCs) are capable of removing tetracycline in soils, in which the degradation efficiency of tetracycline is hindered by its strong adsorption capacity. Phosphate was chosen as a competitor for tetracycline adsorption to improve its removal rate in soil MFCs. The results showed that 42-50% of tetracycline was degraded within 7 days, which was 42-67% higher than open-circuit treatments. Compared with closed-circuit treatments without phosphate addition, the removal efficiencies of tetracycline after phosphate addition increased by 19-25% on day 51, and accumulated charge outputs were enhanced by 31-52%, while the abundance of antibiotic resistance genes decreased by 19-27%. Like Geobacter, the abundance of Desulfurispora and Anaeroomyxobacter in the anode showed similar tendencies with current densities, suggesting their dominant roles in bioelectricity generation. Gemmatimonadetes bacterium SCN 70-22, Azohydromonas australica, Steroidobacter denitrificans and Gemmatirosa kalamazoonesis were found to be potential electrotrophic microbes in the cathode. The expressed flavoprotein 2,3-oxidoreductase, quinol oxidase and fumarate reductase might have promoted the transfer efficiency of electrons from cathodes to cells, which finally accelerated the biodegradation rate of tetracycline in addition to the polyphenol oxidase. This study provides an insight into functional enzyme genes in the soil microbial electrochemical remediation.


Assuntos
Fontes de Energia Bioelétrica , Solo , Alcaligenaceae , Bactérias , Eletrodos , Gammaproteobacteria , Microbiologia do Solo , Tetraciclina
7.
Wound Manag Prev ; 66(10): 42-45, 2020 10.
Artigo em Inglês | MEDLINE | ID: mdl-33048830

RESUMO

The presence of Kerstersia gyiorum in lower leg wounds has been reported in case studies from several countries. OBJECTIVE: This study evaluated the antimicrobial susceptibility profile of K gyiorum isolated from a chronic wound. METHODS: An 85-year-old woman with chronic venous insufficiency presented to an intermediate care unit in Niteroi City, Rio de Janeiro, Brazil, with an instep chronic wound of 14 cm² with wound duration of 6 months. K gyiorum was identified by matrix-assisted laser desorption ionization-time of flight, confirmed by 16S rRNA partial sequence analysis, and classified as resistant for ciprofloxacin by reagent strips(minimum inhibitory concentration [MIC] = 32 µg/mL) and the broth macrodilution method (MIC = 8 µg/mL). Intermediate resistance for ciprofloxacin was verified by microscan (MIC = 2 µg/mL). CONCLUSION: The authors identified the first, to their knowledge, lower leg wound with K gyiorum in Brazil and verified that it was ciprofloxacin resistant.


Assuntos
Alcaligenaceae/efeitos dos fármacos , Ciprofloxacina/uso terapêutico , Resistência à Doença/efeitos dos fármacos , Úlcera da Perna/tratamento farmacológico , Cicatrização/efeitos dos fármacos , Idoso de 80 Anos ou mais , Alcaligenaceae/patogenicidade , Brasil , Feminino , Humanos , Úlcera da Perna/fisiopatologia , Testes de Sensibilidade Microbiana/estatística & dados numéricos , Cicatrização/fisiologia
8.
Viruses ; 12(10)2020 10 06.
Artigo em Inglês | MEDLINE | ID: mdl-33036277

RESUMO

Bacteriophages (phages), viruses that infect bacteria, are considered to be highly host-specific. To add to the knowledge about the evolution and development of bacteriophage speciation toward its host, we conducted a 21-day experiment with the broad host-range bacteriophage Aquamicrobium phage P14. We incubated the phage, which was previously isolated and enriched with the Alphaproteobacteria Aquamicrobium H14, with the Betaproteobacteria Alcaligenaceae H5. During the experiment, we observed an increase in the phage's predation efficacy towards Alcaligenaceae H5. Furthermore, genome analysis and the comparison of the bacteriophage's whole genome indicated that rather than being scattered evenly along the genome, mutations occur in specific regions. In total, 67% of the mutations with a frequency higher than 30% were located in genes that encode tail proteins, which are essential for host recognition and attachment. As control, we incubated the phage with the Alphaproteobacteria Aquamicrobium H8. In both experiments, most of the mutations appeared in the gene encoding the tail fiber protein. However, mutations in the gene encoding the tail tubular protein B were only observed when the phage was incubated with Alcaligenaceae H5. This highlights the phage's tail as a key player in its adaptation to different hosts. We conclude that mutations in the phage's genome were mainly located in tail-related regions. Further investigation is needed to fully characterize the adaptation mechanisms of the Aquamicrobium phage P14.


Assuntos
Adaptação Biológica/genética , Alcaligenaceae/virologia , Bacteriófagos/genética , Especificidade de Hospedeiro/genética , Phyllobacteriaceae/virologia , Proteínas da Cauda Viral/genética , Sequência de Aminoácidos/genética , Bacteriófagos/fisiologia , Evolução Molecular , Variação Genética/genética , Genoma Viral/genética , Mutação/genética
9.
Int J Syst Evol Microbiol ; 70(12): 6381-6389, 2020 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-33112223

RESUMO

A novel Gram-negative, aerobic, non-motile, ovoid to rod-shaped bacterium, designated NBD-18T, was isolated from a freshwater river in Taiwan. Optimal growth occurred at 30 °C, at pH 6 and in the absence of NaCl. The predominant fatty acids of strain NBD-18T were C16 : 0, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), C17 : 0 cyclo and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c). The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and phosphatidyldimethylethanolamine. The major polyamine was putrescine. The major isoprenoid quinone was Q-8. The genomic DNA G+C content of strain NBD-18T was 50.9 %. Strain NBD-18T was most closely related to Orrella dioscoreae LMG 29303T and Algicoccus marinus HZ20T at a 16S rRNA gene sequence similarity of 97.7 %. 16S rRNA gene sequence similarity between O. dioscoreae LMG 29303T and A. marinus HZ20T was 97.7 %. Phylogenetic analyses based on 16S rRNA gene sequences and an up-to-date bacterial core gene set indicated that strain NBD-18T, O. dioscoreae LMG 29303T and A. marinus HZ20T are affiliated with the same genus. Digital DNA-DNA hybridization, average nucleotide identity and average amino acid identity values among these three strains supported that they belong to the same genus and that strain NBD-18T represents a novel species. Thus, A. marinus HZ20T should be reclassified as Orrella marina comb. nov. based on the rules for priority of publication and validation. On the basis of the genotypic, chemotaxonomic and phenotypic data, strain NBD-18T represents a novel species in the genus Orrella, for which the name Orrella amnicola sp. nov. is proposed. The type strain is NBD-18T (=BCRC 81197T=LMG 31338T).


Assuntos
Alcaligenaceae/classificação , Filogenia , Rios/microbiologia , Alcaligenaceae/genética , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Genes Bacterianos/genética , Hibridização de Ácido Nucleico , RNA Ribossômico 16S/genética , Especificidade da Espécie
10.
Lett Appl Microbiol ; 71(4): 351-358, 2020 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-32654157

RESUMO

In a 2018 survey, U.S. Food and Drug Administration (FDA) identified microbial contamination in 42 (49%) of 85 unopened tattoo and permanent makeup (PMU) inks purchased from 13 manufacturers in the US between November 2015 and April 2016. To confirm the results of our previous survey, we evaluated the level of microbial contamination in an additional 27 samples from 10 manufacturers from September 2017 to December 2017, including 21 unopened tattoo and PMU inks which were selected based on our previous survey results and 6 ink diluents that were not previously analysed. Aerobic plate count and enrichment culture methods from the FDA's Bacteriological Analytical Manual revealed 11 (52%) out of 21 inks, from six manufacturers, were contaminated with micro-organisms, with contamination levels up to 3·6 × 108  CFU per gram, consistent with our previous survey results. We identified 25 bacterial strains belonging to nine genera and 19 species. Strains of Bacillus sp. (11 strains, 44%) were dominant, followed by Paenibacillus sp. (5 strains, 20%). Clinically relevant strains, such as Kocuria rhizophila and Oligella ureolytica, were also identified, as similar to the findings in our previous survey. No microbial contamination was detected in any of the six ink diluents.


Assuntos
Bactérias/isolamento & purificação , Corantes/química , Tinta , Tatuagem/efeitos adversos , Alcaligenaceae/genética , Alcaligenaceae/isolamento & purificação , Bactérias/classificação , Bactérias/genética , Corantes/efeitos adversos , Contaminação de Medicamentos , Seguimentos , Humanos , Micrococcaceae/genética , Micrococcaceae/isolamento & purificação
11.
Microbiome ; 8(1): 107, 2020 07 15.
Artigo em Inglês | MEDLINE | ID: mdl-32669127

RESUMO

BACKGROUND: In a pilot study, we found that feces transplantation from elderly individuals to mice significantly caused cognitive impairment. Paenalcaligenes hominis and Escherichia coli are increasingly detected in the feces of elderly adults and aged mice. Therefore, we isolated Paenalcaligenes hominis and Escherichia coli from the feces of elderly individuals and aged mice and examined their effects on the occurrence of age-related degenerative cognitive impairment and colonic inflammation in mice. RESULTS: The transplantation of feces collected from elderly people and aged mice caused significantly more severe cognitive impairment in transplanted young mice than those from young adults and mice. Oral gavage of Paenalcaligenes hominis caused strong cognitive impairment and colitis in specific pathogen-free (SPF) and germ-free mice. Escherichia coli also induced cognitive impairment and colitis in SPF mice. Oral gavage of Paenalcaligenes hominis, its extracellular vesicles (EVs), and/or lipopolysaccharide caused cognitive impairment and colitis in mice. However, celiac vagotomy significantly inhibited the occurrence of cognitive impairment, but not colitis, in mice exposed to Paenalcaligenes hominis or its EVs, whereas its lipopolysaccharide or Escherichia coli had no such effects. Vagotomy also inhibited the infiltration of EVs into the hippocampus. CONCLUSIONS: Paenalcaligenes hominis, particularly its EVs, can cause cognitive function-impaired disorders, such as Alzheimer's disease, and its EVs may penetrate the brain through the blood as well as the vagus nerve. Video Abstract.


Assuntos
Alcaligenaceae/patogenicidade , Disfunção Cognitiva/etiologia , Disfunção Cognitiva/microbiologia , Vesículas Extracelulares , Intestinos/microbiologia , Nervo Vago , Envelhecimento/metabolismo , Animais , Colite/etiologia , Colite/microbiologia , Escherichia coli/patogenicidade , Transplante de Microbiota Fecal , Fezes/microbiologia , Feminino , Microbioma Gastrointestinal , Humanos , Masculino , Camundongos , Camundongos Endogâmicos C57BL , Pessoa de Meia-Idade , Projetos Piloto , Fatores de Risco , Vagotomia , Adulto Jovem
12.
Int J Pediatr Otorhinolaryngol ; 136: 110165, 2020 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-32570062

RESUMO

Tympanostomy tube otorrhea (TTO) is a common complication of tympanostomy tubes. The most common bacteria associated with TTO include Haemophalis influenza, Moraxella catarrhalis, Streptococcus pneumoniae, Staphylococcus aureus, and Pseudomonas aeruginosa. We present the first case of a 9 year-old female with a history of 22q11 syndrome, hemifacial microsomia, Tetralogy of Fallot, and hearing aid dependence with left-sided profound sensorineural and right-sided moderate conductive hearing loss who presented with TTO caused by the bacteria Pigmentiphaga daeguenesis/kulla, a gram-negative bacteria often found in soil. This patient's otorrhea did not respond to typical otic antibiotic formulations, but was ultimately treated successfully with intramuscular ceftriaxone. We describe the natural history, presentation and management for a case of TTO caused by a rare bacteria from the genus Pigmentiphaga.


Assuntos
Síndrome da Deleção 22q11/complicações , Alcaligenaceae , Otopatias/microbiologia , Ventilação da Orelha Média/efeitos adversos , Antibacterianos/uso terapêutico , Ceftriaxona/uso terapêutico , Criança , Otopatias/diagnóstico , Otopatias/tratamento farmacológico , Feminino , Humanos , Pseudomonas aeruginosa , Staphylococcus aureus
13.
J Microbiol ; 58(7): 543-549, 2020 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-32594456

RESUMO

A grey pink colored bacterium, strain t3-1-3T, was isolated from the air at the foot of the Xiangshan Mountain in Beijing, China. The cells are aerobic, Gram-stain-negative, non-spore-forming, motile and coccoid-rod shaped (0.9-1.2 × 1.9-2.1 µm). Strain t3-1-3T was catalase-positive and oxidase-negative and this strain grew at 4-42°C (optimum 28°C), a pH of 4.0-9.0 (optimum pH 7.0) and under 0-2% (w/v) NaCl (optimum 0-1% NaCl). A phylogenetic analysis based on 16S rRNA gene sequences revealed that strain t3-1-3T was closely related to Azohydromonas riparia UCM-11T (97.4% similarity), followed by Azohydromonas australica G1-2T (96.8%) and Azohydromonas ureilytica UCM-80T (96.7%). The genome of strain t3-1-3T contains 6,895 predicted protein-encoding genes, 8 rRNA genes, 62 tRNA genes and one sRNA gene, as well as five potential biosynthetic gene clusters, including clusters of genes coding for non-ribosomal peptide synthetase (NRPS), bacteriocin and arylpolyene and two clusters of genes for terpene. The predominant cellular fatty acids (> 10.0% of the total) in strain t3-1-3T were summed feature 3 (C16:1ω7c and/or C16:1ω6c, 37.8%), summed feature 8 (C18:1ω7c and/or C18:1ω6c, 29.7%) and C16:0 (17.3%). Strain t3-1-3T contained ubiquinone-8 (Q-8) as the predominant respiratory quinone. The polar lipids of strain t3-1-3T comprised phosphatidyl ethanolamine (PE), phosphatidyl glycerol (PG), diphosphatidyl glycerol (DPG), an unidentified glycolipid (GL), an unidentified aminophospholipid (APL), two unidentified phospholipid (PL1-2) and five unidentified lipid (L1-5). The DNA G + C content of the type strain is 70.3%. The broader range of growth temperature, assimilation of malic acid and trisodium citrate, presence of C18:3ω6c and an unidentified glycolipid and absence of C12:0 2-OH and C16:0iso differentiate strain t3-1-3T from related species. Based on the taxonomic data presented in this study, we suggest that strain t3-1-3T represents a novel species within the genus Azohydromonas, for which the name Azohydromonas aeria sp. nov. is proposed. The type strain of Azohydromonas aeria is t3-1-3T (= CFCC 13393T = LMG 30135T).


Assuntos
Microbiologia do Ar , Alcaligenaceae/classificação , Alcaligenaceae/isolamento & purificação , Alcaligenaceae/genética , Técnicas de Tipagem Bacteriana , Bacteriocinas/genética , Composição de Bases/genética , DNA Bacteriano/genética , Ácidos Graxos/genética , Ácidos Graxos/metabolismo , Genoma Bacteriano/genética , Filogenia , RNA Ribossômico 16S/genética , Terpenos/metabolismo
14.
Int J Syst Evol Microbiol ; 70(5): 3483-3490, 2020 May.
Artigo em Inglês | MEDLINE | ID: mdl-32369004

RESUMO

Two Gram-stain-negative, short rod-shaped and non-flagellated strains, designated 17-4AT and L52-1-41, were isolated from the surface seawater of the Indian Ocean and South China Sea, respectively. The 16S rRNA genes of the two strains shared sequence similarity of 99.45 %. Strain 17-4AT shared the highest 16S rRNA gene similarity of 98.02 % with Pusillimonas caeni EBR-8-1T, followed by Pusillimonas noertemannii BN9T (97.47 %), Pusillimonas soli MJ07T (96.93 %), Parapusillimonas granuli Ch07T (96.68 %), Pusillimonas ginsengisoli DCY25T (96.65 %), Eoetvoesia caeni PB3-7BT (96.63 %), Paracandidimonas caeni 24T (96.34 %), Castellaniella defragrans 54PinT (96.28 %) and Pusillimonas harenae B201T (96.05 %). L52-1-41 shared the highest 16S rRNA gene similarity of 97.74 % with Pusillimonas caeni EBR-8-1T, followed by Pusillimonas noertemannii BN9T (97.47 %), Pusillimonas soli MJ07T (96.65 %), Parapusillimonas granuli Ch07T (96.41 %), Pusillimonas ginsengisoli DCY25T (96.37 %), Eoetvoesia caeni PB3-7BT (96.35 %), Pusillimonas harenae B201T (96.28 %), and Paracandidimonas caeni 24T (96.06 %). The results of phylogenetic analyses indicated that 17-4AT and L52-1-41 formed a stable, distinct and highly supported lineage affiliated to the genus Pusillimonas. The results of the digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) analyses indicated that they represented a single species. They featured similar genomic DNA G+C contents of 53.2-53.4 mol%. Activities of catalase and oxidase were negative for both strains. The fatty acids patterns of 17-4AT and L52-1-41 were most similar, mostly comprised of C16 : 0, C17 : 0cyclo, C18 : 0, C18 : 1ω9c and summed feature 8 (C18 : 1ω7c and/or C18 : 1 ω6c). The major polar lipids of the two strains were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and unidentified aminolipids. The respiratory quinone of the two strains was Q-8. Hence, on the basis of the phenotypic, chemotaxonomic and genotypic data presented in this study, we proposed the classification of both strains as representatives of a novel species named Pusillimonas maritima sp. nov., with the type strain 17-4AT (=MCCC 1A12670T=KCTC 62121T=NBRC 113794T), and another strain L52-1-41 (=MCCC 1A05046=KCTC 52313).


Assuntos
Alcaligenaceae/classificação , Filogenia , Água do Mar/química , Alcaligenaceae/isolamento & purificação , Técnicas de Tipagem Bacteriana , Composição de Bases , China , DNA Bacteriano/genética , Ácidos Graxos/química , Oceano Índico , Hibridização de Ácido Nucleico , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Ubiquinona/química
15.
Biochemistry ; 59(16): 1592-1603, 2020 04 28.
Artigo em Inglês | MEDLINE | ID: mdl-32242662

RESUMO

Tautomerase superfamily (TSF) members are constructed from a single ß-α-ß unit or two consecutively joined ß-α-ß units. This pattern prevails throughout the superfamily consisting of more than 11000 members where homo- or heterohexamers are localized in the 4-oxalocrotonate tautomerase (4-OT) subgroup and trimers are found in the other four subgroups. One exception is a subset of sequences that are double the length of the short 4-OTs in the 4-OT subgroup, where the coded proteins form trimers. Characterization of two members revealed an interesting dichotomy. One is a symmetric trimer, whereas the other is an asymmetric trimer. One monomer is flipped 180° relative to the other two monomers so that three unique protein-protein interfaces are created that are composed of different residues. A bioinformatics analysis of the fused 4-OT subset shows a further division into two clusters with a total of 133 sequences. The analysis showed that members of one cluster (86 sequences) have more salt bridges if the asymmetric trimer forms, whereas the members of the other cluster (47 sequences) have more salt bridges if the symmetric trimer forms. This hypothesis was examined by the kinetic and structural characterization of two proteins within each cluster. As predicted, all four proteins function as 4-OTs, where two assemble into asymmetric trimers (designated R7 and F6) and two form symmetric trimers (designated W0 and Q0). These findings can be extended to the other sequences in the two clusters in the fused 4-OT subset, thereby annotating their oligomer properties and activities.


Assuntos
Proteínas de Bactérias/química , Isomerases/química , Estrutura Quaternária de Proteína , Alcaligenaceae/enzimologia , Sequência de Aminoácidos , Sítios de Ligação , Bordetella/enzimologia , Burkholderia/enzimologia , Burkholderiaceae/enzimologia , Biologia Computacional , Cinética , Alinhamento de Sequência
16.
Appl Environ Microbiol ; 86(6)2020 03 02.
Artigo em Inglês | MEDLINE | ID: mdl-31924619

RESUMO

Acetamiprid, a chloronicotinyl neonicotinoid insecticide, is among the most commonly used insecticides worldwide, and its environmental fate has caused considerable concern. The compound 1-(6-chloropyridin-3-yl)-N-methylmethanamine (IM 1-4) has been reported to be the main intermediate during acetamiprid catabolism in microorganisms, honeybees, and spinach. However, the molecular mechanism underlying the hydrolysis of acetamiprid to IM 1-4 has not yet been elucidated. In this study, a novel amidase (AceAB) that initially hydrolyzes the C-N bond of acetamiprid to generate IM 1-4 was purified and characterized from the acetamiprid-degrading strain Pigmentiphaga sp. strain D-2. Based on peptide profiling of the purified AceAB and the draft genome sequence of strain D-2, aceA (372 bp) and aceB (2,295 bp), encoding the α and ß subunits of AceAB, respectively, were cloned and found to be necessary for acetamiprid hydrolysis in strain D-2. The characteristics of AceAB were also systematically investigated. Though AceA and AceB showed 35% to 56% identity to the α and ß subunits of the N,N-dimethylformamidase from Paracoccus aminophilus, AceAB was specific for the hydrolysis of acetamiprid and showed no activities to N,N-dimethylformamide or its structural analogs.IMPORTANCE Acetamiprid, among the top neonicotinoid insecticides used worldwide, is one of the most important commercial insecticides. Due to its extensive use, the environmental fate of acetamiprid, especially its microbial degradation, has caused considerable concern. Although the catabolic pathways of acetamiprid in microorganisms have been extensively studied, the molecular mechanisms underlying acetamiprid biodegradation (except for a nitrile hydratase) remain largely unknown, and the enzyme responsible for the biotransformation of acetamiprid into its main intermediate, IM 1-4, have not yet been elucidated. The amidase AceAB and its encoding genes, aceA and aceB, characterized in this study, were found to be necessary and specific for the initial hydrolysis of the C-N bond of acetamiprid to generate IM 1-4 in Pigmentiphaga sp. strain D-2. The finding of the novel amidase AceAB will greatly enhance our understanding of the microbial catabolism of the widely used insecticide acetamiprid at the molecular level.


Assuntos
Alcaligenaceae/metabolismo , Amidoidrolases/metabolismo , Proteínas de Bactérias/metabolismo , Inseticidas/metabolismo , Neonicotinoides/metabolismo , Hidrólise
17.
J Microbiol ; 58(2): 99-104, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-31993985

RESUMO

An obligately anaerobic, Gram-stain-negative, non-motile, non-spore-forming, and coccobacilli-shaped bacterial strain, designated KGMB03119T, was isolated from human faeces from a Korean. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that the isolate was a member of the genus Sutterella and most closely related to Sutterlla wadsworthensis KCTC 15691T (96.8% 16S rRNA gene sequence similarity). The DNA G + C content of strain KGMB03119T was 58.3 mol% as determined from its whole genome sequence. Strain KGMB03119T was asaccharolytic, catalase-positive, oxidase- and urease-negative. Furthermore, the isolate was positive for alkaline phosphatase, leucine arylamidase, acid phosphatase, arginine arylamidase, alanine arylamidase, and glycine arylamidase. The major cellular fatty acids (> 10%) of the isolate were C18:1ω9c and C16:0. Methylmenaquinone-5 (MMK-5, 100%) was the predominant isoprenoid quinone in the isolate. Based on the phylogenetic, physiological, and chemotaxonomic characteristics, strain KGMB03119T represents a novel species, for which the name Sutterella faecalis sp. nov. is proposed. The type strain is KGMB03119T (= KCTC 15823T = NBRC 114254T).


Assuntos
Alcaligenaceae/classificação , Alcaligenaceae/isolamento & purificação , Fezes/microbiologia , Alcaligenaceae/genética , Alcaligenaceae/metabolismo , Classificação , DNA Bacteriano/genética , Microbioma Gastrointestinal , Humanos , Filogenia , RNA Ribossômico 16S/genética
18.
Microbiology (Reading) ; 166(4): 386-397, 2020 04.
Artigo em Inglês | MEDLINE | ID: mdl-31999239

RESUMO

Chemolithotrophic sulfur oxidation represents a significant part of the biogeochemical cycling of this element. Due to its long evolutionary history, this ancient metabolism is well known for its extensive mechanistic and phylogenetic diversification across a diverse taxonomic spectrum. Here we carried out whole-genome sequencing and analysis of a new betaproteobacterial isolate, Pusillimonas ginsengisoli SBSA, which is found to oxidize thiosulfate via the formation of tetrathionate as an intermediate. The 4.7 Mb SBSA genome was found to encompass a soxCDYZAXOB operon, plus single thiosulfate dehydrogenase (tsdA) and sulfite : acceptor oxidoreductase (sorAB) genes. Recombination-based knockout of tsdA revealed that the entire thiosulfate is first converted to tetrathionate by the activity of thiosulfate dehydrogenase (TsdA) and the Sox pathway is not functional in this bacterium despite the presence of all necessary sox genes. The ∆soxYZ and ∆soxXA knockout mutants exhibited a wild-type-like phenotype for thiosulfate/tetrathionate oxidation, whereas ∆soxB, ∆soxCD and soxO::KanR mutants only oxidized thiosulfate up to tetrathionate intermediate and had complete impairment in tetrathionate oxidation. The substrate-dependent O2 consumption rate of whole cells and the sulfur-oxidizing enzyme activities of cell-free extracts, measured in the presence/absence of thiol inhibitors/glutathione, indicated that glutathione plays a key role in SBSA tetrathionate oxidation. The present findings collectively indicate that the potential glutathione : tetrathionate coupling in P. ginsengisoli involves a novel enzymatic component, which is different from the dual-functional thiol dehydrotransferase (ThdT), while subsequent oxidation of the sulfur intermediates produced (e.g. glutathione : sulfodisulfane molecules) may proceed via the iterative action of soxBCD .


Assuntos
Alcaligenaceae/metabolismo , Crescimento Quimioautotrófico/genética , Enxofre/metabolismo , Alcaligenaceae/genética , Proteínas de Bactérias/genética , Genoma Bacteriano/genética , Glutationa/metabolismo , Mutação , Oxirredução , Oxirredutases/genética , Oxigênio/metabolismo , Compostos de Sulfidrila/metabolismo , Sulfitos/metabolismo , Ácido Tetratiônico/metabolismo , Tiossulfatos/metabolismo
19.
J Basic Microbiol ; 60(3): 253-267, 2020 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-31750957

RESUMO

A new bacterial strain producing extracellular cholesterol oxidase (ChOx) was isolated and identified as Castellaniella sp. COX. The ChOx was purified by salting-out and ion-exchange chromatography up to 10.4-fold, with a specific activity of 15 U/mg with a molecular mass of 59 kDa. The purified ChOx exhibited pH 8.0 and temperature 40°C for its optimum activity. The enzyme showed stability over a wide pH range and was most stable at pH value 7.0, and at pH 8.0, it retained almost 86% of its initial activity after 3 h of incubation at 37°C. The enzyme possessed a half-life of 8 h at 37°C, 7 h at 40°C, and 3 h at 50°C. A Lineweaver-Burk plot was calibrated to determine its Km (0.16 mM) and Vmax (18.7 µmol·mg-1 ·min-1 ). The ChOx activity was enhanced with Ca2+ , Mg2+ , and Mn2+ while it was inhibited by Hg2+ , Ba2+ , Fe2+ , Cu2+ , and Zn2+ ions. Organic solvents like acetone, n-butanol, toluene, dimethyl sulfoxide, chloroform, benzene, and methanol were well tolerated by the enzyme while iso-propanol and ethanol were found to enhance the activity of purified ChOx. ChOx induced cytotoxicity with an IC50 value of 1.78 and 1.88 U/ml against human RD and U87MG established cell lines, respectively, while broadly sparing the normal human cells.


Assuntos
Alcaligenaceae/enzimologia , Proteínas de Bactérias/química , Proteínas de Bactérias/farmacologia , Colesterol Oxidase/química , Colesterol Oxidase/farmacologia , Alcaligenaceae/classificação , Alcaligenaceae/genética , Alcaligenaceae/isolamento & purificação , Proteínas de Bactérias/isolamento & purificação , Cátions/química , Linhagem Celular , Sobrevivência Celular/efeitos dos fármacos , Colesterol Oxidase/isolamento & purificação , Detergentes/química , Estabilidade Enzimática , Humanos , Concentração de Íons de Hidrogênio , Concentração Inibidora 50 , Cinética , Peso Molecular , Oxirredução , Solventes/química , Temperatura
20.
Antonie Van Leeuwenhoek ; 113(2): 233-252, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-31560092

RESUMO

Our aim was to identify less common non-fermenting gram-negative rods during the bioremediation process. Five genera were found: Advenella, Castellaniella, Kaistia, Pusillimonas and Sphingobacterium, for a total of 15 isolates. Therefore, we evaluated the applicability of four methods currently available for bacteria identification: (1) conventional biochemical methods, (2) the VITEK®-2 system, (3) MALDI-TOF mass spectrometry and (4) 16S rRNA gene sequencing. The biochemical methods and the VITEK®-2 system were reliable only for the Sphingobacterium isolate and solely at the genus level. Both MALDI-TOF mass spectrometry platforms (Bruker and VITEK® MS) did not achieve reliable identification results for any of these genera. 16S rRNA gene sequencing identified eight isolates to the species level but not to the subspecies level, when applicable. The remaining seven isolates were reliably identified through 16S rRNA gene sequencing to the genus level only. Our findings suggest that the detection and identification of less common genera (and species) that appeared at certain moments during the bioremediation process can be a challenge to microbiologists considering the most used techniques. In addition, more studies are required to confirm our results.


Assuntos
Alcaligenaceae/genética , Rhizobiaceae/genética , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz/métodos , Sphingobacterium/genética , Alcaligenaceae/classificação , Técnicas de Tipagem Bacteriana , RNA Ribossômico 16S/genética , Rhizobiaceae/classificação , Sphingobacterium/classificação
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