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Biotechnology Reports (Amsterdam,... Dec 2020We report the complete genome sequencing of novel strain MP4687 isolated from cattle rumen. Various strains of have been reported from different environmental samples...
We report the complete genome sequencing of novel strain MP4687 isolated from cattle rumen. Various strains of have been reported from different environmental samples including oil-contaminated sites, crop roots, air, and human clinical samples, but not from rumen samples, which is being reported here for the first time. The genome of P. stutzeri MP4687 has a single replicon, 4.75 Mb chromosome and a G + C content of 63.45%. The genome encodes for 4,790 protein coding genes including 164 CAZymes and 345 carbohydrate processing genes. The isolate MP4687 harbors LCB hydrolyzing potential through endoglucanase (4.5 U/mL), xylanase (3.1 U/mL), β-glucosidase (3.3 U/mL) and β-xylosidase (1.9 U/mL) activities. The pangenome analysis further revealed that MP4687 has a very high number of unique genes (>2100) compared to other genomes, which might have an important role in rumen functioning.
PubMed: 32983925
DOI: 10.1016/j.btre.2020.e00530 -
Journal of Bacteriology May 1994The carAB operons from Pseudomonas aeruginosa PAO1 and Pseudomonas stutzeri JM300 were characterized by Southern and DNA sequence analyses. The results show that the... (Comparative Study)
Comparative Study
The carAB operons from Pseudomonas aeruginosa PAO1 and Pseudomonas stutzeri JM300 were characterized by Southern and DNA sequence analyses. The results show that the previously reported sequence for carA (S. C. Wong and A. T. Abdelal, J. Bacteriol. 172:630-642, 1990) is derived from P. stutzeri and not P. aeruginosa, as originally reported. Therefore, the amino-terminal sequence of the purified carA product is identical to that derived from the nucleotide sequence in both organisms, P. stutzeri having four additional amino acids. The results also show that while carA and carB are contiguous in P. stutzeri, as is the case in other bacteria, they are surprisingly separated by an open reading frame (ORF) of 216 amino acids in P. aeruginosa. S1 nuclease mapping experiments with RNA extracted under a variety of growth conditions, as well as experiments using different lacZ fusions, indicate that the carA-ORF-carB operon of P. aeruginosa is transcribed from a single promoter. Moreover, these experiments demonstrate that expression of this single transcript is controlled by both arginine and pyrimidines and that variation in arginine levels specifically modulates transcriptional initiation, while pyrimidine regulation is exerted subsequent to transcriptional initiation. Modification of a rho-independent terminator-like structure, which is present upstream of carA in P. aeruginosa, removed all transcriptional sensitivity of a carA::lacZ fusion to pyrimidines. This result, when coupled with the finding that translation of an 18-amino-acid leader polypeptide (associated with this putative rho-independent terminator), is inversely proportional to pyrimidine concentration in the cell, strongly suggests that regulation of carA by pyrimidines is mediated through an attenuation-type mechanism in P. aeruginosa.
Topics: Amino Acid Sequence; Base Sequence; Carbamoyl-Phosphate Synthase (Glutamine-Hydrolyzing); Cloning, Molecular; DNA Mutational Analysis; Gene Expression Regulation, Bacterial; Molecular Sequence Data; Operon; Protein Biosynthesis; Pseudomonas; Pseudomonas aeruginosa; RNA, Messenger; Recombinant Fusion Proteins; Sequence Analysis, DNA; Sequence Homology, Amino Acid; Sequence Homology, Nucleic Acid; Transcription, Genetic
PubMed: 8169201
DOI: 10.1128/jb.176.9.2532-2542.1994 -
NPJ Biofilms and Microbiomes Jul 2021Biofilm and nitrogen fixation are two competitive strategies used by many plant-associated bacteria; however, the mechanisms underlying the formation of nitrogen-fixing...
Biofilm and nitrogen fixation are two competitive strategies used by many plant-associated bacteria; however, the mechanisms underlying the formation of nitrogen-fixing biofilms remain largely unknown. Here, we examined the roles of multiple signalling systems in the regulation of biofilm formation by root-associated diazotrophic P. stutzeri A1501. Physiological analysis, construction of mutant strains and microscale thermophoresis experiments showed that RpoN is a regulatory hub coupling nitrogen fixation and biofilm formation by directly activating the transcription of pslA, a major gene involved in the synthesis of the Psl exopolysaccharide component of the biofilm matrix and nifA, the transcriptional activator of nif gene expression. Genetic complementation studies and determination of the copy number of transcripts by droplet digital PCR confirmed that the regulatory ncRNA RsmZ serves as a signal amplifier to trigger biofilm formation by sequestering the translational repressor protein RsmA away from pslA and sadC mRNAs, the latter of which encodes a diguanylate cyclase that synthesises c-di-GMP. Moreover, RpoS exerts a braking effect on biofilm formation by transcriptionally downregulating RsmZ expression, while RpoS expression is repressed posttranscriptionally by RsmA. These findings provide mechanistic insights into how the Rpo/Gac/Rsm regulatory networks fine-tune nitrogen-fixing biofilm formation in response to the availability of nutrients.
Topics: Bacterial Proteins; Biofilms; Gene Expression Regulation, Bacterial; Gene Order; Gene Regulatory Networks; Nitrogen Fixation; Nitrogenase; Pseudomonas stutzeri; Repetitive Sequences, Nucleic Acid; Transcriptional Activation
PubMed: 34210981
DOI: 10.1038/s41522-021-00230-7 -
Journal of Clinical Microbiology Jul 1987
Topics: Humans; Pseudomonas Infections; Renal Dialysis; Sepsis
PubMed: 3611326
DOI: 10.1128/jcm.25.7.1343-.1987 -
Data in Brief Apr 2018Plant growth-promoting bacterial endophytes (PGPBEs) produce volatile and diffusible compounds that inhibit phytopathogens (Santoyo et al., 2016) [1]. A recent work by...
Plant growth-promoting bacterial endophytes (PGPBEs) produce volatile and diffusible compounds that inhibit phytopathogens (Santoyo et al., 2016) [1]. A recent work by Rojas-Solis and colleagues [2] demonstrated the antifungal effect of volatile organic compounds exerted by the E25 and CR71 endophytes, highlighting the production of sulfur-containing compounds such as the antimicrobial volatile dimethyl disulfide (DMDS). The data presented in this article include the effect of two culture supernatants from the same strains, E25 and CR71, on the mycelial growth of the gray mold phytopathogen . These data may help to further evaluate the specific compounds produced by endophyte isolates E25 and CR71 with antifungal activity. This article is submitted as a companion paper to Rojas-Solís et al. (2018) [2].
PubMed: 29387737
DOI: 10.1016/j.dib.2018.01.023 -
Journal of Biochemistry Aug 1988The complete primary structure of Pseudomonas stutzeri strain ZoBell ferredoxin was determined by a combination of protease digestion, Edman degradation, and... (Comparative Study)
Comparative Study
The complete primary structure of Pseudomonas stutzeri strain ZoBell ferredoxin was determined by a combination of protease digestion, Edman degradation, and carboxypeptidase digestion and was: TFVVTDNCIKCKYTDCVEVCPVDCFYEGPNFLVIH PDECIDCALCEPECPAQAIFSEDEVPEDQQEFIELNADLAEVWPNITE KKDALADAEEWDGVKDKLQYLER. The calculated molecular weight was 12,110 excluding iron and sulfur atoms. The amino acid sequence was highly homologous to those of Azotobacter vinelandii and Pseudomonas ovalis ferredoxins. It showed, like the other two, a Tyr-Thr insertion between the second and third Cys, and extra Cys at position 24 and, compared to Clostridium- and Bacillus-type ferredoxins, an extended C-terminal sequence.
Topics: Amino Acid Sequence; Amino Acids; Azotobacter; Chymotrypsin; Ferredoxins; Molecular Sequence Data; Peptide Hydrolases; Peptides; Pseudomonas; Staphylococcus
PubMed: 3053681
DOI: 10.1093/oxfordjournals.jbchem.a122450 -
The Journal of Biological Chemistry Oct 2018is a very large bacterial genus in which several species can use d-malate for growth. However, the enzymes that can metabolize d-malate, such as d-malate dehydrogenase,...
is a very large bacterial genus in which several species can use d-malate for growth. However, the enzymes that can metabolize d-malate, such as d-malate dehydrogenase, appear to be absent in most species. d-3-Phosphoglycerate dehydrogenase (SerA) can catalyze the production of d-2-hydroxyglutarate (d-2-HG) from 2-ketoglutarate to support d-3-phosphoglycerate dehydrogenation, which is the initial reaction in bacterial l-serine biosynthesis. In this study, we show that SerA of the strain A1501 reduces oxaloacetate to d-malate and that d-2-HG dehydrogenase (D2HGDH) from displays d-malate-oxidizing activity. Of note, D2HGDH participates in converting a trace amount of d-malate to oxaloacetate during bacterial l-serine biosynthesis. Moreover, D2HGDH is crucial for the utilization of d-malate as the sole carbon source for growth of A1501. We also found that the D2HGDH expression is induced by the exogenously added d-2-HG or d-malate and that a flavoprotein functions as a soluble electron carrier between D2HGDH and electron transport chains to support d-malate utilization by These results support the idea that D2HGDH evolves as an enzyme for both d-malate and d-2-HG dehydrogenation in In summary, D2HGDH from A1501 participates in both a core metabolic pathway for l-serine biosynthesis and utilization of extracellular d-malate.
Topics: Alcohol Oxidoreductases; Bacterial Proteins; Electron Transport; Enzyme Assays; Gene Expression; Glutarates; Glyceric Acids; Ketoglutaric Acids; Kinetics; Malates; Oxaloacetic Acid; Oxidation-Reduction; Pseudomonas stutzeri; Serine; Stereoisomerism; Substrate Specificity
PubMed: 30131334
DOI: 10.1074/jbc.RA118.003897 -
Microbiology (Reading, England) Aug 2003The Pseudomonas stutzeri strain A1501 (formerly known as Alcaligenes faecalis) fixes nitrogen under microaerobic conditions in the free-living state and colonizes rice...
The Pseudomonas stutzeri strain A1501 (formerly known as Alcaligenes faecalis) fixes nitrogen under microaerobic conditions in the free-living state and colonizes rice endophytically. The authors characterized a region in strain A1501, corresponding to most of the nif genes and the rnf genes, involved in electron transport to nitrogenase in Rhodobacter capsulatus. The region contained three groups of genes arranged in the same order as in Azotobacter vinelandii: (1) nifB fdx ORF3 nifQ ORF5 ORF6; (2) nifLA-rnfABCDGEF-nifY2/nafY; (3) ORF13 ORF12-nifHDK-nifTY ORF1 ORF2-nifEN. Unlike in A. vinelandii, where these genes are not contiguous on the chromosome, but broken into two regions of the genome, the genes characterized here in P. stutzeri are contiguous and present on a 30 kb region in the genome of this organism. Insertion mutagenesis confirmed that most of the nif and the rnf genes in A1501 were essential for nitrogen fixation. Using lacZ fusions it was found that nif and rnf gene expression was under the control of ntrBC, nifLA and rpoN and that the rnf gene products were involved in the regulation of the nitrogen fixation process.
Topics: Ammonia; Base Sequence; Chromosome Mapping; DNA, Bacterial; Gene Deletion; Gene Expression Regulation, Bacterial; Genes, Bacterial; Molecular Sequence Data; Nitrogen Fixation; Oryza; Oxygen; Plasmids; Pseudomonas
PubMed: 12904565
DOI: 10.1099/mic.0.26270-0 -
Journal of Bacteriology Jul 1985Unlike enteric bacteria, Pseudomonas spp. generally lack thymidine phosphorylase and thymidine kinase activities, thus preventing their utilization of exogenous thymine...
Unlike enteric bacteria, Pseudomonas spp. generally lack thymidine phosphorylase and thymidine kinase activities, thus preventing their utilization of exogenous thymine or thymidine and precluding specific radioactive labeling of their DNA in vivo. To overcome this limitation, a DNA fragment encoding thymidine kinase (EC 2.7.1.21) from Escherichia coli was cloned into pKT230, a small, broad-host-range plasmid derived from plasmid RSF1010. From transformed E. coli colonies, the recombinant plasmid bearing the thymidine kinase gene was conjugally transferred to Pseudomonas stutzeri, Pseudomonas aeruginosa, Pseudomonas mendocina, Pseudomonas alcaligenes, and Pseudomonas pseudoalcaligenes. Thymidine kinase activity was expressed in all of these species, and all gained the ability to incorporate exogenous [2-14C]thymidine into their DNA. Thymidine incorporation into P. stutzeri was enhanced 12-fold more in mutants lacking thymidylate synthetase activity. These mutants produced higher levels of thymidine kinase and were thymidine auxotrophs; thymineless death resulted from removal of thymidine from a growing culture.
Topics: DNA Replication; Escherichia coli; Gene Expression Regulation; Genes; Genes, Bacterial; Plasmids; Pseudomonas; Pseudomonas aeruginosa; Thymidine; Thymidine Kinase
PubMed: 3924894
DOI: 10.1128/jb.163.1.291-295.1985 -
Journal of Environmental and Public... 2019Overuse of pesticides in agriculture may harm environmental and agricultural yields. Sustainable maintenance of soil fertility and management of the environment have...
Overuse of pesticides in agriculture may harm environmental and agricultural yields. Sustainable maintenance of soil fertility and management of the environment have become a concern due to the persistence of pesticides in the soil. Microbes have various mechanisms for the bioremediation of persistent organic pollutants from the environment. A bacterium that degrades clothianidin was isolated from the pesticide and applied to agricultural soil by the enrichment technique. The identity of the bacterium was determined by studying morphological, cultural, and biochemical characteristics and 16S rRNA gene sequences. The ability to metabolize clothianidin was confirmed using UV-visible spectrophotometric, chromatographic, and spectroscopic analyses. A Gram-negative bacterium, designated smk, isolated from clothianidin-contaminated soil was confirmed to be a member of . The biodegradation of clothianidin was studied using smk. Approximately 62% degradation of clothianidin was achieved within two weeks when grown at 30°C and pH 7. The effects of various physicochemical parameters, including pH, temperature, and clothianidin concentrations, on catabolic rates were studied. The biodegradation studies using UV-Vis spectrophotometry, HPLC, FTIR, and LC-MS indicated the production of the following metabolites: 2-chloro-5-methyl thiazole (CMT), methyl nitroguanidine (MNG), methyl 3-[thiazole-yl], and methyl guanidine (TMG). Identification of specific degradation metabolites indicates that bioremediation of toxic neonicotinoid insecticides may be achieved by application of smk.
Topics: Agriculture; Biodegradation, Environmental; Guanidines; Insecticides; Neonicotinoids; Pseudomonas stutzeri; RNA, Ribosomal, 16S; Soil Microbiology; Soil Pollutants; Thiazoles
PubMed: 30944570
DOI: 10.1155/2019/4807913