scholarly journals Pyrroloquinoline Quinone Biosynthesis GenepqqC, a Novel Molecular Marker for Studying the Phylogeny and Diversity of Phosphate-Solubilizing Pseudomonads

2011 ◽  
Vol 77 (20) ◽  
pp. 7345-7354 ◽  
Author(s):  
Joana Beatrice Meyer ◽  
Michele Frapolli ◽  
Christoph Keel ◽  
Monika Maurhofer
Keyword(s):  
Molecular Marker ◽  
Phylogenetic Trees ◽  
Phosphate Solubilization ◽  
Glucose Dehydrogenase ◽  
Housekeeping Genes ◽  
Pyrroloquinoline Quinone ◽  
Rock Phosphates ◽  
Content Type ◽  
Strain Collection ◽  
Phosphate Solubilizing

ABSTRACTMany root-colonizing pseudomonads are able to promote plant growth by increasing phosphate availability in soil through solubilization of poorly soluble rock phosphates. The major mechanism of phosphate solubilization by pseudomonads is the secretion of gluconic acid, which requires the enzyme glucose dehydrogenase and its cofactor pyrroloquinoline quinone (PQQ). The main aim of this study was to evaluate whether a PQQ biosynthetic gene is suitable to study the phylogeny of phosphate-solubilizing pseudomonads. To this end, two new primers, which specifically amplify thepqqCgene of thePseudomonasgenus, were designed.pqqCfragments were amplified and sequenced from aPseudomonasstrain collection and from a natural wheat rhizosphere population using cultivation-dependent and cultivation-independent approaches. Phylogenetic trees based onpqqCsequences were compared to trees obtained with the two concatenated housekeeping genesrpoDandgyrB. For bothpqqCandrpoD-gyrB, similar main phylogenetic clusters were found. However, in thepqqCbut not in therpoD-gyrBtree, the group of fluorescent pseudomonads producing the antifungal compounds 2,4-diacetylphloroglucinol and pyoluteorin was located outside thePseudomonas fluorescensgroup.pqqCsequences from isolated pseudomonads were differently distributed among the identified phylogenetic groups thanpqqCsequences derived from the cultivation-independent approach. ComparingpqqCphylogeny and phosphate solubilization activity, we identified one phylogenetic group with high solubilization activity. In summary, we demonstrate that the genepqqCis a novel molecular marker that can be used complementary to housekeeping genes for studying the diversity and evolution of plant-beneficial pseudomonads.

scholarly journals Regulation of Pyrroloquinoline Quinone-Dependent Glucose Dehydrogenase Activity in the Model Rhizosphere-Dwelling Bacterium Pseudomonas putida KT2440

2016 ◽  
Vol 82 (16) ◽  
pp. 4955-4964 ◽  
Author(s):  
Ran An ◽  
Luke A. Moe
Keyword(s):  
Gene Expression ◽  
Pseudomonas Putida ◽  
Sole Carbon Source ◽  
Phosphate Solubilization ◽  
Specific Activity ◽  
Glucose Dehydrogenase ◽  
Growth Conditions ◽  
Pyrroloquinoline Quinone ◽  
Soluble Phosphate ◽  
Content Type

ABSTRACTSoil-dwelling microbes solubilize mineral phosphates by secreting gluconic acid, which is produced from glucose by a periplasmic glucose dehydrogenase (GDH) that requires pyrroloquinoline quinone (PQQ) as a redox coenzyme. While GDH-dependent phosphate solubilization has been observed in numerous bacteria, little is known concerning the mechanism by which this process is regulated. Here we use the model rhizosphere-dwelling bacteriumPseudomonas putidaKT2440 to explore GDH activity and PQQ synthesis, as well as gene expression of the GDH-encoding gene (gcd) and PQQ biosynthesis genes (pqqoperon) while under different growth conditions. We also use reverse transcription-PCR to identify transcripts from thepqqoperon to more accurately map the operon structure. GDH specific activity and PQQ levels vary according to growth condition, with the highest levels of both occurring when glucose is used as the sole carbon source and under conditions of low soluble phosphate. Under these conditions, however, PQQ levels limitin vitrophosphate solubilization. GDH specific activity data correlate well withgcdgene expression data, and the levels of expression of thepqqFandpqqBgenes mirror the levels of PQQ synthesized, suggesting that one or both of these genes may serve to modulate PQQ levels according to the growth conditions. Thepqqgene cluster (pqqFABCDEG) encodes at least two independent transcripts, and expression of thepqqFgene appears to be under the control of an independent promoter and terminator.IMPORTANCEPlant growth promotion can be enhanced by soil- and rhizosphere-dwelling bacteria by a number of different methods. One method is by promoting nutrient acquisition from soil. Phosphorus is an essential nutrient that plants obtain through soil, but in many cases it is locked up in forms that are not available for plant uptake. Bacteria such as the model bacteriumPseudomonas putidaKT2440 can solubilize insoluble soil phosphates by secreting gluconic acid. This chemical is produced from glucose by the activity of the bacterial enzyme glucose dehydrogenase, which requires a coenzyme called PQQ. Here we have studied how the glucose dehydrogenase enzyme and the PQQ coenzyme are regulated according to differences in bacterial growth conditions. We determined that glucose dehydrogenase activity and PQQ production are optimal under conditions when the bacterium is grown with glucose as the sole carbon source and under conditions of low soluble phosphate.

scholarly journals Complete Genome Sequence of Burkholderia cenocepacia CR318, a Phosphate-Solubilizing Bacterium Isolated from Corn Root

2017 ◽  
Vol 5 (23) ◽  
Author(s):  
Filip Zekic ◽  
Brian Weselowski ◽  
Ze-Chun Yuan
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Phosphate Solubilization ◽  
Burkholderia Cenocepacia ◽  
Ecological Sustainability ◽  
Content Type ◽  
Phosphate Solubilizing ◽  
Circular Chromosomes ◽  
Insight Into

ABSTRACT Here, we report the complete genome sequence of the phosphate-solubilizing bacterium Burkholderia cenocepacia CR318, consisting of three circular chromosomes of 3,511,146 bp, 3,097,552 bp, and 1,056,069 bp. The data presented will facilitate further insight into the mechanisms of phosphate solubilization and its application for agricultural and ecological sustainability.

scholarly journals Burkholderia sprentiae sp. nov., isolated from Lebeckia ambigua root nodules

2013 ◽  
Vol 63 (Pt_11) ◽  
pp. 3950-3957 ◽  
Author(s):  
Sofie E. De Meyer ◽  
Margo Cnockaert ◽  
Julie K. Ardley ◽  
Garth Maker ◽  
Ron Yates ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Sequence Similarity ◽  
Root Nodules ◽  
Distinct Group ◽  
Housekeeping Genes ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
Phenotypic Differentiation ◽  
Content Type ◽  
Link Type

Seven Gram-stain-negative, rod-shaped bacteria were isolated from Lebeckia ambigua root nodules and authenticated on this host. Based on the 16S rRNA gene phylogeny, they were shown to belong to the genus Burkholderia , with the representative strain WSM5005T being most closely related to Burkholderia tuberum (98.08 % sequence similarity). Additionally, these strains formed a distinct group in phylogenetic trees based on the housekeeping genes gyrB and recA. Chemotaxonomic data including fatty acid profiles and analysis of respiratory quinones supported the assignment of the strains to the genus Burkholderia . Results of DNA–DNA hybridizations, and physiological and biochemical tests allowed genotypic and phenotypic differentiation of our strains from the closest species of the genus Burkholderia with a validly published name. Therefore, these strains represent a novel species for which the name Burkholderia sprentiae sp. nov. (type strain WSM5005T = LMG 27175T = HAMBI 3357T) is proposed.

scholarly journals A Novel Pyrroloquinoline Quinone-Dependent 2-Keto-d-Glucose Dehydrogenase from Pseudomonas aureofaciens

2015 ◽  
Vol 197 (8) ◽  
pp. 1322-1329 ◽  
Author(s):  
Kiwamu Umezawa ◽  
Kouta Takeda ◽  
Takuya Ishida ◽  
Naoki Sunagawa ◽  
Akiko Makabe ◽  
...  
Keyword(s):  
Glucose Dehydrogenase ◽  
Expression System ◽  
Pyrroloquinoline Quinone ◽  
Recombinant Enzyme ◽  
Reaction Products ◽  
Gene Encoding ◽  
Multiple Sequence ◽  
Content Type ◽  
Pseudomonas Aureofaciens ◽  
Arginine Residues

A gene encoding an enzyme similar to a pyrroloquinoline quinone (PQQ)-dependent sugar dehydrogenase from filamentous fungi, which belongs to new auxiliary activities (AA) family 12 in the CAZy database, was cloned fromPseudomonas aureofaciens. The deduced amino acid sequence of the cloned enzyme showed only low homology to previously characterized PQQ-dependent enzymes, and multiple-sequence alignment analysis showed that the enzyme lacks one of the three conserved arginine residues that function as PQQ-binding residues in known PQQ-dependent enzymes. The recombinant enzyme was heterologously expressed in anEscherichia coliexpression system for further characterization. The UV-visible (UV-Vis) absorption spectrum of the oxidized form of the holoenzyme, prepared by incubating the apoenzyme with PQQ and CaCl2, revealed a broad peak at approximately 350 nm, indicating that the enzyme binds PQQ. With the addition of 2-keto-d-glucose (2KG) to the holoenzyme solution, a sharp peak appeared at 331 nm, attributed to the reduction of PQQ bound to the enzyme, whereas no effect was observed upon 2KG addition to authentic PQQ. Enzymatic assay showed that the recombinant enzyme specifically reacted with 2KG in the presence of an appropriate electron acceptor, such as 2,6-dichlorophenol indophenol, when PQQ and CaCl2were added.1H nuclear magnetic resonance (1H-NMR) analysis of reaction products revealed 2-keto-d-gluconic acid (2KGA) as the main product, clearly indicating that the recombinant enzyme oxidizes the C-1 position of 2KG. Therefore, the enzyme was identified as a PQQ-dependent 2KG dehydrogenase (Pa2KGDH). Considering the high substrate specificity, the physiological function ofPa2KGDH may be for production of 2KGA.

scholarly journals Draft Genome Sequence of the Phosphate-Solubilizing Rhizobacterium Burkholderia pseudomultivorans Strain MPSB1, Isolated from a Copper Mined-Out Site

2021 ◽  
Vol 10 (1) ◽  
Author(s):  
Berna Lou L. Aba-Regis ◽  
Kristel Mae P. Oliveros ◽  
Cherry Ibarra-Romero ◽  
Asuncion K. Raymundo ◽  
Nelly S. Aggangan ◽  
...  
Keyword(s):  
Heavy Metal ◽  
Soil Sample ◽  
Genome Sequence ◽  
Phosphate Solubilization ◽  
Metal Tolerance ◽  
Draft Genome ◽  
Heavy Metal Tolerance ◽  
Draft Genome Sequence ◽  
Content Type ◽  
Phosphate Solubilizing

ABSTRACT Burkholderia pseudomultivorans MPSB1 was isolated from a copper mined-out soil sample collected from Mogpog, Marinduque, Philippines. Here, we report the draft genome sequence with predicted gene inventories supporting rhizosphere bioremediation, such as heavy metal tolerance, phosphate solubilization, and siderophore production.

Mesorhizobium shonense sp. nov., Mesorhizobium hawassense sp. nov. and Mesorhizobium abyssinicae sp. nov., isolated from root nodules of different agroforestry legume trees

2013 ◽  
Vol 63 (Pt_5) ◽  
pp. 1746-1753 ◽  
Author(s):  
Tulu Degefu ◽  
Endalkachew Wolde-meskel ◽  
Binbin Liu ◽  
Ilse Cleenwerck ◽  
Anne Willems ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Type Species ◽  
Phylogenetic Trees ◽  
Novel Species ◽  
Root Nodules ◽  
Housekeeping Genes ◽  
Content Type ◽  
Link Type ◽  
Wide Range ◽  
Type Strains

A total of 18 strains, representing members of the genus Mesorhizobium , obtained from root nodules of woody legumes growing in Ethiopia, have been previously shown, by multilocus sequence analysis (MLSA) of five housekeeping genes, to form three novel genospecies. In the present study, the phylogenetic relationship between representative strains of these three genospecies and the type strains of their closest phylogenetic neighbours Mesorhizobium plurifarium , Mesorhizobium amorphae , Mesorhizobium septentrionale and Mesorhizobium huakuii was further evaluated using a polyphasic taxonomic approach. In line with our earlier MLSA of other housekeeping genes, the phylogenetic trees derived from the atpD and glnII genes grouped the test strains into three well-supported, distinct lineages that exclude all defined species of the genus Mesorhizobium . The DNA–DNA relatedness between the representative strains of genospecies I–III and the type strains of their closest phylogenetic neighbours was low (≤59 %). They differed from each other and from their closest phylogenetic neighbours by the presence/absence of several fatty acids, or by large differences in the relative amounts of particular fatty acids. While showing distinctive features, they were generally able to utilize a wide range of substrates as sole carbon and nitrogen sources. The strains belonging to genospecies I, II and III therefore represent novel species for which we propose the names Mesorhizobium shonense sp. nov., Mesorhizobium hawassense sp. nov. and Mesorhizobium abyssinicae sp. nov. The isolates AC39aT ( = LMG 26966T = HAMBI 3295T), AC99bT ( = LMG 26968T = HAMBI 3301T) and AC98cT ( = LMG 26967T = HAMBI 3306T) are proposed as type strains for the respective novel species.

scholarly journals Performance of pineapple slips inoculated with diazotrophic phosphate-solubilizing bacteria and rock phosphate

Revista CERES ◽  
2014 ◽  
Vol 61 (3) ◽  
pp. 414-423
Author(s):  
Lílian Estrela Borges Baldotto ◽  
Marihus Altoé Baldotto ◽  
Fábio Lopes Olivares ◽  
Adriane Nunes de Souza
Keyword(s):  
Rock Phosphate ◽  
Phosphate Solubilization ◽  
P Availability ◽  
Phosphate Solubilizing Bacteria ◽  
Diazotrophic Bacteria ◽  
Rock Phosphates ◽  
Combined Application ◽  
Phosphate Solubilizing ◽  
Biological Nitrogen

Besides fixing N2, some diazotrophic bacteria or diazotrophs, also synthesize organic acids and are able to solubilize rock phosphates, increasing the availability of P for plants. The application of these bacteria to pineapple leaf axils in combination with rock phosphate could increase N and P availability for the crop, due to the bacterial activity of biological nitrogen fixation and phosphate solubilization. The objectives of this study were: (i) to select and characterize diazotrophs able to solubilize phosphates in vitro and (ii) evaluate the initial performance of the pineapple cultivars Imperial and Pérola in response to inoculation with selected bacteria in combination with rock phosphate. The experiments were conducted at Universidade Estadual do Norte Fluminense Darcy Ribeiro, in 2009. In the treatments with bacteria the leaf contents of N, P and K were higher than those of the controls, followed by an increase in plant growth. These results indicate that the combined application of diazotrophic phosphate-solubilizing bacteria Burkholderia together with Araxá rock phosphate can be used to improve the initial performance of pineapple slips.

scholarly journals Amphritea ceti sp. nov., isolated from faeces of Beluga whale (Delphinapterus leucas)

2014 ◽  
Vol 64 (Pt_12) ◽  
pp. 4068-4072 ◽  
Author(s):  
Young-Ok Kim ◽  
Sooyeon Park ◽  
Doo Nam Kim ◽  
Bo-Hye Nam ◽  
Sung-Min Won ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Sequence Similarity ◽  
Beluga Whale ◽  
Delphinapterus Leucas ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Content Type ◽  
Link Type ◽  
Beluga Whale Delphinapterus Leucas ◽  
Type Strains

A Gram-stain-negative, aerobic, non-spore-forming, non-flagellated and rod-shaped or ovoid bacterial strain, designated RA1T, was isolated from faeces collected from Beluga whale (Delphinapterus leucas) in Yeosu aquarium, South Korea. Strain RA1T grew optimally at 25 °C, at pH 7.0–8.0 and in the presence of 2.0 % (w/v) NaCl. Neighbour-joining, maximum-likelihood and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences revealed that strain RA1T joins the cluster comprising the type strains of three species of the genus Amphritea , with which it exhibited 95.8–96.0 % sequence similarity. Sequence similarities to the type strains of other recognized species were less than 94.3 %. Strain RA1T contained Q-8 as the predominant ubiquinone and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C18 : 1ω7c and C16 : 0 as the major fatty acids. The major polar lipids of strain RA1T were phosphatidylethanolamine, phosphatidylglycerol, two unidentified lipids and one unidentified aminolipid. The DNA G+C content of strain RA1T was 47.4 mol%. The differential phenotypic properties, together with the phylogenetic distinctiveness, revealed that strain RA1T is separated from other species of the genus Amphritea . On the basis of the data presented, strain RA1T is considered to represent a novel species of the genus Amphritea , for which the name Amphritea ceti sp. nov. is proposed. The type strain is RA1T ( = KCTC 42154T = NBRC 110551T).

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