scholarly journals Genome Analysis ofFimbriiglobus ruberSP5T, a Planctomycete with Confirmed Chitinolytic Capability

2018 ◽  
Vol 84 (7) ◽  
Author(s):  
Nikolai V. Ravin ◽  
Andrey L. Rakitin ◽  
Anastasia A. Ivanova ◽  
Alexey V. Beletsky ◽  
Irina S. Kulichevskaya ◽  
...  
Keyword(s):  
Sole Source ◽  
Major Constituent ◽  
Special Importance ◽  
Gene Encoding ◽  
Fungal Cell ◽  
Content Type ◽  
Carbon And Nitrogen ◽  
Type Iv ◽  
The Family ◽  
Weak Growth

ABSTRACTMembers of the bacterial orderPlanctomycetaleshave often been observed in associations with Crustacea. The ability to degrade chitin, however, has never been reported for any of the cultured planctomycetes although utilization ofN-acetylglucosamine (GlcNAc) as a sole carbon and nitrogen source is well recognized for these bacteria. Here, we demonstrate the chitinolytic capability of a member of the familyGemmataceae,Fimbriiglobus ruberSP5T, which was isolated from a peat bog. As revealed by metatranscriptomic analysis of chitin-amended peat, the pool of 16S rRNA reads fromF. ruberincreased in response to chitin availability. Strain SP5Tdisplayed only weak growth on amorphous chitin as a sole source of carbon but grew well with chitin as a source of nitrogen. The genome ofF. ruberSP5Tis 12.364 Mb in size and is the largest among all currently determined planctomycete genomes. It encodes several enzymes putatively involved in chitin degradation, including two chitinases affiliated with the glycoside hydrolase (GH) family GH18, GH20 family β-N-acetylglucosaminidase, and the complete set of enzymes required for utilization of GlcNAc. The gene encoding one of the predicted chitinases was expressed inEscherichia coli, and the endochitinase activity of the recombinant enzyme was confirmed. The genome also contains genes required for the assembly of type IV pili, which may be used to adhere to chitin and possibly other biopolymers. The ability to use chitin as a source of nitrogen is of special importance for planctomycetes that inhabit N-depleted ombrotrophic wetlands.IMPORTANCEPlanctomycetes represent an important part of the microbial community inSphagnum-dominated peatlands, but their potential functions in these ecosystems remain poorly understood. This study reports the presence of chitinolytic potential in one of the recently described peat-inhabiting members of the familyGemmataceae,Fimbriiglobus ruberSP5T. This planctomycete uses chitin, a major constituent of fungal cell walls and exoskeletons of peat-inhabiting arthropods, as a source of nitrogen in N-depleted ombrotrophicSphagnum-dominated peatlands. This study reports the chitin-degrading capability of representatives of the orderPlanctomycetales.

Description of bacteria able to degrade isoquinoline in pure culture

1994 ◽  
Vol 40 (7) ◽  
pp. 555-560 ◽  
Author(s):  
J. Aislabie ◽  
N. K. Richards ◽  
T. C. Lyttle
Keyword(s):  
Heterocyclic Compound ◽  
Pure Culture ◽  
Sole Source ◽  
Broth Culture ◽  
Gram Negative ◽  
Carbon And Nitrogen ◽  
The Family ◽  
Nitrogen Heterocyclic

Isoquinoline is a nitrogen heterocyclic compound that is associated with coal- and oil-derived wastes. Four strains of bacteria able to degrade isoquinoline in pure culture were isolated from sites known to be contaminated with oil. Isoquinoline was used as the sole source of carbon and nitrogen by these isolates. Isoquinoline was initially transformed to 1-hydroxyisoquinoline, which accumulated in the broth culture, and then disappeared. The four strains isolated were Gram negative, aerobic, rod-shaped bacteria with polar flagella. The strains have been presumptively identified as members of the family Comamonadaceae.Key words: isoquinoline degradation, Comamonadaceae.not available

scholarly journals Neisseria meningitidis Polynucleotide Phosphorylase Affects Aggregation, Adhesion, and Virulence

2016 ◽  
Vol 84 (5) ◽  
pp. 1501-1513 ◽  
Author(s):  
Jakob Engman ◽  
Aurel Negrea ◽  
Sara Sigurlásdóttir ◽  
Miriam Geörg ◽  
Jens Eriksson ◽  
...  
Keyword(s):  
Neisseria Meningitidis ◽  
Posttranslational Modifications ◽  
Human Cells ◽  
Bacterial Attachment ◽  
Polynucleotide Phosphorylase ◽  
Gene Encoding ◽  
Content Type ◽  
Type Iv ◽  
Transcriptional Changes

Neisseria meningitidisautoaggregation is an important step during attachment to human cells. Aggregation is mediated by type IV pili and can be modulated by accessory pilus proteins, such as PilX, and posttranslational modifications of the major pilus subunit PilE. The mechanisms underlying the regulation of aggregation remain poorly characterized. Polynucleotide phosphorylase (PNPase) is a 3′–5′ exonuclease that is involved in RNA turnover and the regulation of small RNAs. In this study, we biochemically confirm that NMC0710 is theN. meningitidisPNPase, and we characterize its role inN. meningitidispathogenesis. We show that deletion of the gene encoding PNPase leads to hyperaggregation and increased adhesion to epithelial cells. The aggregation induced was found to be dependent on pili and to be mediated by excessive pilus bundling. PNPase expression was induced following bacterial attachment to human cells. Deletion of PNPase led to global transcriptional changes and the differential regulation of 469 genes. We also demonstrate that PNPase is required for full virulence in anin vivomodel ofN. meningitidisinfection. The present study shows that PNPase negatively affects aggregation, adhesion, and virulence inN. meningitidis.

scholarly journals Selection for Growth on 3-Nitrotoluene by 2-Nitrotoluene-Utilizing Acidovorax sp. Strain JS42 Identifies Nitroarene Dioxygenases with Altered Specificities

2014 ◽  
Vol 81 (1) ◽  
pp. 309-319 ◽  
Author(s):  
Kristina M. Mahan ◽  
Joseph T. Penrod ◽  
Kou-San Ju ◽  
Natascia Al Kass ◽  
Watumesa A. Tan ◽  
...  
Keyword(s):  
Active Site ◽  
Sole Source ◽  
Degradation Pathway ◽  
Short Term ◽  
Gene Encoding ◽  
Α Subunit ◽  
Content Type ◽  
Term Selection ◽  
Genes Encoding ◽  
Related Enzyme

ABSTRACTAcidovoraxsp. strain JS42 uses 2-nitrotoluene as a sole source of carbon and energy. The first enzyme of the degradation pathway, 2-nitrotoluene 2,3-dioxygenase, adds both atoms of molecular oxygen to 2-nitrotoluene, forming nitrite and 3-methylcatechol. All three mononitrotoluene isomers serve as substrates for 2-nitrotoluene dioxygenase, but strain JS42 is unable to grow on 3- or 4-nitrotoluene. Using both long- and short-term selections, we obtained spontaneous mutants of strain JS42 that grew on 3-nitrotoluene. All of the strains obtained by short-term selection had mutations in the gene encoding the α subunit of 2-nitrotoluene dioxygenase that changed isoleucine 204 at the active site to valine. Those strains obtained by long-term selections had mutations that changed the same residue to valine, alanine, or threonine or changed the alanine at position 405, which is just outside the active site, to glycine. All of these changes altered the regiospecificity of the enzymes with 3-nitrotoluene such that 4-methylcatechol was the primary product rather than 3-methylcatechol. Kinetic analyses indicated that the evolved enzymes had enhanced affinities for 3-nitrotoluene and were more catalytically efficient with 3-nitrotoluene than the wild-type enzyme. In contrast, the corresponding amino acid substitutions in the closely related enzyme nitrobenzene 1,2-dioxygenase were detrimental to enzyme activity. When cloned genes encoding the evolved dioxygenases were introduced into a JS42 mutant lacking a functional dioxygenase, the strains acquired the ability to grow on 3-nitrotoluene but with significantly longer doubling times than the evolved strains, suggesting that additional beneficial mutations occurred elsewhere in the genome.

Parasulfuritortus cantonensis gen. nov., sp. nov., a microaerophilic sulfur-oxidizing bacterium isolated from freshwater sediment

2021 ◽  
Vol 71 (2) ◽  
Author(s):  
Zhangzhang Xie ◽  
Surong Li ◽  
Weitie Lin ◽  
Jianfei Luo
Keyword(s):  
Sulfide Oxidation ◽  
Draft Genome ◽  
Anaerobic Growth ◽  
Freshwater Sediment ◽  
Rrna Gene ◽  
Gene Encoding ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Sulfur Oxidizing

A novel sulfur-oxidizing bacterium, designated strain LSR1T, was enriched and isolated from a freshwater sediment sample collected from the Pearl River in Guangzhou, PR China. The strain was an obligate chemolithoautotroph, using thiosulfate or sulfide as an electron donor and energy source. Growth of strain LSR1T was observed at 15–40 °C, pH 6.0–7.5 and NaCl concentrations of 0–1.5 %. Strain LSR1T was microaerophilic, with growth only at oxygen content less than 10 %. Anaerobic growth was also observed when using nitrate as the sole electron acceptor. The major cellular fatty acids were C16 : 0 and summed feature 3 (comprising C16 : 1 ω7c and/or C16 : 1 ω6c). The DNA G+C content of the draft genome sequence was 67.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain LSR1T formed a lineage within the family Thiobacillaceae , showing sequence identities of 92.87, 92.33 and 90.80 % with its closest relative genera Sulfuritortus , Annwoodia and Thiobacillus , respectively. The genome of strain LSR1T contained multiple genes encoding sulfur-oxidizing enzymes that catalyse thiosulfate and sulfide oxidation, and the gene encoding cbb 3-type cytochrome c oxidase and bd-type quinol oxidase, which enables strain LSR1T to perform sulphur oxidation under microaerophilic conditions. On the basis of phenotypic, genotypic and phylogenetic results, strain LSR1T is considered to represent a novel species of a new genus Parasulfuritortus within the family Thiobacillaceae , for which the name Parasulfuritortus cantonensis gen. nov., sp. nov. is proposed. The type strain is LSR1T (=GDMCC 1.1549=JCM 33645).

scholarly journals Key Enzymes Enabling the Growth of Arthrobacter sp. Strain JBH1 with Nitroglycerin as the Sole Source of Carbon and Nitrogen

2012 ◽  
Vol 78 (10) ◽  
pp. 3649-3655 ◽  
Author(s):  
Johana Husserl ◽  
Joseph B. Hughes ◽  
Jim C. Spain
Keyword(s):  
Heterologous Expression ◽  
Nitrogen Source ◽  
Sole Source ◽  
Glycerol Kinase ◽  
Enzyme Assays ◽  
Content Type ◽  
Key Enzymes ◽  
Carbon And Nitrogen ◽  
Subsequent Transformation

ABSTRACTFlavoprotein reductases that catalyze the transformation of nitroglycerin (NG) to dinitro- or mononitroglycerols enable bacteria containing such enzymes to use NG as the nitrogen source. The inability to use the resulting mononitroglycerols limits most strains to incomplete denitration of NG. Recently,Arthrobacterstrain JBH1 was isolated for the ability to grow on NG as the sole source of carbon and nitrogen, but the enzymes and mechanisms involved were not established. Here, the enzymes that enable theArthrobacterstrain to incorporate NG into a productive pathway were identified. Enzyme assays indicated that the transformation of nitroglycerin to mononitroglycerol is NADPH dependent and that the subsequent transformation of mononitroglycerol is ATP dependent. Cloning and heterologous expression revealed that a flavoprotein catalyzes selective denitration of NG to 1-mononitroglycerol (1-MNG) and that 1-MNG is transformed to 1-nitro-3-phosphoglycerol by a glycerol kinase homolog. Phosphorylation of the nitroester intermediate enables the subsequent denitration of 1-MNG in a productive pathway that supports the growth of the isolate and mineralization of NG.

scholarly journals An Atypical Phr Peptide Regulates the Developmental Switch Protein RapH

2011 ◽  
Vol 193 (22) ◽  
pp. 6197-6206 ◽  
Author(s):  
Nicolas Mirouze ◽  
Vijay Parashar ◽  
Melinda D. Baker ◽  
David A. Dubnau ◽  
Matthew B. Neiditch
Keyword(s):  
Mobile Genetic Element ◽  
Developmental Pathways ◽  
Luciferase Reporter ◽  
Gene Encoding ◽  
Content Type ◽  
Signaling Systems ◽  
The Family ◽  
Developmental Switch

Under conditions of nutrient limitation and high population density, the bacterium Bacillus subtilis can initiate a variety of developmental pathways. The signaling systems regulating B. subtilis differentiation are tightly controlled by switch proteins called Raps, named after the founding members of the family, which were shown to be r esponse regulator a spartate p hosphatases. A phr gene encoding a secreted pentapeptide that regulates the activity of its associated Rap protein was previously identified downstream of 8 of the chromosomally encoded rap genes. We identify and validate here the sequence of an atypical Phr peptide, PhrH, by in vivo and in vitro analyses. Using a luciferase reporter bioassay combined with in vitro experiments, we found that PhrH is a hexapeptide (TDRNTT), in contrast to the other characterized Phr pentapeptides. We also determined that phrH expression is driven by a promoter lying within rapH . Unlike the previously identified dedicated σ H -driven phr promoters, it appears that phrH expression most likely requires σ A . Furthermore, we show that PhrH can antagonize both of the known activities of RapH: the dephosphorylation of Spo0F and the sequestration of ComA, thus promoting the development of spores and the competent state. Finally, we propose that PhrH is the prototype of a newly identified class of Phr signaling molecules consisting of six amino acids. This class likely includes PhrI, which regulates RapI and the expression, excision, and transfer of the mobile genetic element ICE Bs 1.

scholarly journals Genes of theN-Methylglutamate Pathway Are Essential for Growth of Methylobacterium extorquens DM4 with Monomethylamine

2014 ◽  
Vol 80 (11) ◽  
pp. 3541-3550 ◽  
Author(s):  
Christelle Gruffaz ◽  
Emilie E. L. Muller ◽  
Yousra Louhichi-Jelail ◽  
Yella R. Nelli ◽  
Gilles Guichard ◽  
...  
Keyword(s):  
Carbon Source ◽  
Nitrogen Source ◽  
Gene Clusters ◽  
Sole Source ◽  
Nadh:Ubiquinone Oxidoreductase ◽  
Methylotrophic Bacteria ◽  
Methylobacterium Extorquens ◽  
Content Type ◽  
Carbon And Nitrogen ◽  
In The Wild

ABSTRACTMonomethylamine (MMA, CH3NH2) can be used as a carbon and nitrogen source by many methylotrophic bacteria.Methylobacterium extorquensDM4 lacks the MMA dehydrogenase encoded bymaugenes, which inM. extorquensAM1 is essential for growth on MMA. Identification and characterization of minitransposon mutants with an MMA-dependent phenotype showed that strain DM4 grows with MMA as the sole source of carbon, energy, and nitrogen by theN-methylglutamate (NMG) pathway. Independent mutations were found in a chromosomal region containing the genesgmaS,mgsABC, andmgdABCDfor the three enzymes of the pathway, γ-glutamylmethylamide (GMA) synthetase, NMG synthase, and NMG dehydrogenase, respectively. Reverse transcription-PCR confirmed the operonic structure of the two divergent gene clustersmgsABC-gmaSandmgdABCDand their induction during growth with MMA. The genesmgdABCDandmgsABCwere found to be essential for utilization of MMA as a carbon and nitrogen source. The genegmaSwas essential for MMA utilization as a carbon source, but residual growth of mutant DM4gmaSgrowing with succinate and MMA as a nitrogen source was observed. Plasmid copies ofgmaSand thegmaShomolog METDI4690, which encodes a protein 39% identical to GMA synthetase, fully restored the ability of mutants DM4gmaSand DM4gmaSΔmetdi4690 to use MMA as a carbon and nitrogen source. Similarly, chemically synthesized GMA, the product of GMA synthetase, could be used as a nitrogen source for growth in the wild-type strain, as well as in DM4gmaSand DM4gmaSΔmetdi4690 mutants. The NADH:ubiquinone oxidoreductase respiratory complex component NuoG was also found to be essential for growth with MMA as a carbon source.

scholarly journals Rouxiella chamberiensis gen. nov., sp. nov., a member of the family Enterobacteriaceae isolated from parenteral nutrition bags

2015 ◽  
Vol 65 (Pt_6) ◽  
pp. 1812-1818 ◽  
Author(s):  
Anne Le Flèche-Matéos ◽  
Marion Levast ◽  
Fabienne Lomprez ◽  
Yolande Arnoux ◽  
Clément Andonian ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Parenteral Nutrition ◽  
Gas Production ◽  
New Taxon ◽  
16S Rrna Sequence ◽  
Gene Encoding ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
16S Rrna Sequence Analysis

Parenteral nutrition bags for newborns were found contaminated by a previously undescribed member of the family Enterobacteriaceae . The six isolates studied by rrs gene (encoding 16S rRNA) sequence analysis and multi-locus sequence analysis (MLSA) formed a discrete branch close to the genera Ewingella , Rahnella , Yersinia , Hafnia and Serratia . Phenotypically, the new taxon was distinct from these five genera. The new taxon gave positive results in Voges–Proskauer, Simmons citrate and o-nitrophenyl-β-galactoside hydrolysis tests; fermented d-glucose, d-mannitol, l-rhamnose, melibiose, l-arabinose and d-xylose; hydrolysed aesculin; and did not ferment maltose, trehalose, raffinose, d-sorbitol, sucrose or cellobiose. Tests for motility, gas production, urease, gelatinase and nitrate reduction were also negative. All isolates failed to grow at 37 °C. The DNA G+C content of strain 130333T was 53 mol%. On the basis of data obtained in this study, the six isolates represent a novel species of a new genus in the family Enterobacteriaceae , named Rouxiella chamberiensis gen. nov., sp. nov. The type strain of the type species is 130333T ( = CIP 110714T = DSM 28324T).

scholarly journals Implications of Chitin Attachment for the Environmental Persistence and Clinical Nature of the Human Pathogen Vibrio vulnificus

2013 ◽  
Vol 80 (5) ◽  
pp. 1580-1587 ◽  
Author(s):  
Tiffany C. Williams ◽  
Mesrop Ayrapetyan ◽  
James D. Oliver
Keyword(s):  
Vibrio Vulnificus ◽  
Protein A ◽  
Aquatic Organisms ◽  
The United States ◽  
Major Constituent ◽  
Marine Snow ◽  
Pathogenic Potential ◽  
Content Type ◽  
Type Iv ◽  
Type Iv Pilin

ABSTRACTVibrio vulnificusnaturally inhabits a variety of aquatic organisms, including oysters, and is the leading cause of seafood-related death in the United States. Strains of this bacterium are genetically classified into environmental (E) and clinical (C) genotypes, which correlate with source of isolation. E-genotype strains integrate into marine aggregates more efficiently than do C-genotype strains, leading to a greater uptake of strains of this genotype by oysters feeding on these aggregates. The causes of this increased integration of E-type strains into marine “snow” have not been demonstrated. Here, we further investigate the physiological and genetic causalities for this genotypic heterogeneity by examining the ability of strains of each genotype to attach to chitin, a major constituent of marine snow. We found that E-genotype strains attach to chitin with significantly greater efficiency than do C-genotype strains when incubated at 20°C. Type IV pili were implicated in chitin adherence, and even in the absence of chitin, the expression level of type IV pilin genes (pilA,pilD, andmshA) was found to be inherently higher by E genotypes than by C genotypes. In contrast, the level of expression ofN-acetylglucosamine binding protein A (gbpA) was significantly higher in C-genotype strains. Interestingly, incubation at a clinically relevant temperature (37°C) resulted in a significant increase in C-genotype attachment to chitin, which subsequently provided a protective effect against exposure to acid or bile, thus offering a clue into their increased incidence in human infections. This study suggests that C- and E-genotype strains have intrinsically divergent physiological programs, which may help explain the observed differences in the ecology and pathogenic potential between these two genotypes.

Exposure of protein VP7 on the surface of bluetongue virus

1990 ◽  
Vol 48 (3) ◽  
pp. 600-601
Author(s):  
A.D. Hyatt
Keyword(s):  
Bluetongue Virus ◽  
Structural Proteins ◽  
Major Constituent ◽  
Outer Coat ◽  
Virus Particles ◽  
Antibody Recognition ◽  
The Core ◽  
The Family ◽  
Electron Microscopical ◽  
Physical Accessibility

Bluetongue virus (BTV) is the type species os the genus orbivirus in the family Reoviridae. The virus has a fibrillar outer coat containing two major structural proteins VP2 and VP5 which surround an icosahedral core. The core contains two major proteins VP3 and VP7 and three minor proteins VP1, VP4 and VP6. Recent evidence has indicated that the core comprises a neucleoprotein center which is surrounded by two protein layers; VP7, a major constituent of capsomeres comprises the outer and VP3 the inner layer of the core . Antibodies to VP7 are currently used in enzyme-linked immunosorbant assays and immuno-electron microscopical (JEM) tests for the detection of BTV. The tests involve the antibody recognition of VP7 on virus particles. In an attempt to understand how complete viruses can interact with antibodies to VP7 various antibody types and methodologies were utilized to determine the physical accessibility of the core to the external environment.

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