scholarly journals Multiple and Interconnected Pathways for l-Lysine Catabolism in Pseudomonas putida KT2440

2005 ◽  
Vol 187 (21) ◽  
pp. 7500-7510 ◽  
Author(s):  
Olga Revelles ◽  
Manuel Espinosa-Urgel ◽  
Tobias Fuhrer ◽  
Uwe Sauer ◽  
Juan L. Ramos
Keyword(s):  
Pseudomonas Putida ◽  
Nitrogen Source ◽  
Pseudomonas Putida Kt2440 ◽  
Carbon And Nitrogen ◽  
New Genes ◽  
In The Wild ◽  
Isogenic Mutants ◽  
Hydrolysis Of ◽  
Successful Colonization ◽  
Lysine Catabolism

ABSTRACT l-Lysine catabolism in Pseudomonas putida KT2440 was generally thought to occur via the aminovalerate pathway. In this study we demonstrate the operation of the alternative aminoadipate pathway with the intermediates d-lysine, l-pipecolate, and aminoadipate. The simultaneous operation of both pathways for the use of l-lysine as the sole carbon and nitrogen source was confirmed genetically. Mutants with mutations in either pathway failed to use l-lysine as the sole carbon and nitrogen source, although they still used l-lysine as the nitrogen source, albeit at reduced growth rates. New genes were identified in both pathways, including the davB and davA genes that encode the enzymes involved in the oxidation of l-lysine to δ-aminovaleramide and the hydrolysis of the latter to δ-aminovalerate, respectively. The amaA, dkpA, and amaB genes, in contrast, encode proteins involved in the transformation of Δ1-piperidine-2-carboxylate into aminoadipate. Based on l-[U-13C, U-15N]lysine experiments, we quantified the relative use of pathways in the wild type and its isogenic mutants. The fate of 13C label of l-lysine indicates that in addition to the existing connection between the d- and l-lysine pathways at the early steps of the catabolism of l-lysine mediated by a lysine racemase, there is yet another interconnection at the lower end of the pathways in which aminoadipate is channeled to yield glutarate. This study establishes an unequivocal relationship between gene and pathway enzymes in the metabolism of l-lysine, which is of crucial importance for the successful colonization of the rhizosphere of plants by this microorganism.

scholarly journals Identification of the Initial Steps in d-Lysine Catabolism in Pseudomonas putida

2007 ◽  
Vol 189 (7) ◽  
pp. 2787-2792 ◽  
Author(s):  
Olga Revelles ◽  
Rolf-Michael Wittich ◽  
Juan L. Ramos
Keyword(s):  
Pseudomonas Putida ◽  
Nitrogen Source ◽  
Culture Medium ◽  
Point Of View ◽  
Open Reading Frames ◽  
Gene Encoding ◽  
Carbon And Nitrogen ◽  
Extension Analysis ◽  
Reading Frames ◽  
Lysine Catabolism

ABSTRACT Pseudomonas putida uses l-lysine as the sole carbon and nitrogen source which preferentially requires its metabolism through two parallel pathways. In one of the pathways δ-aminovalerate is the key metabolite, whereas in the other l-lysine is racemized to d-lysine, and l-pipecolate and α-aminoadipate are the key metabolites. All the genes and enzymes involved in the d-lysine pathway, except for those involved in the conversion of d-lysine into Δ1-piperideine-2-carboxylate, have been identified previously (30). In this study we report that the conversion of d-lysine into Δ1-piperideine-2-carboxylate can be mediated by a d-lysine aminotransferase (PP3590) and a d-lysine dehydrogenase (PP3596). From a physiological point of view PP3596 plays a major role in the catabolism of d-lysine since its inactivation leads to a marked reduction in the growth rate with l- or d-lysine as the sole carbon and nitrogen source, whereas inactivation of PP3590 leads only to slowed growth. The gene encoding PP3590, called here amaC, forms an operon with dpkA, the gene encoding the enzyme involved in conversion of Δ1-piperideine-2-carboxylate to l-pipecolate in the d-lysine catabolic pathway. The gene encoding PP3596, called here amaD, is the fifth gene in an operon made up of seven open reading frames (ORFs) encoding PP3592 through PP3597. The dpkA amaC operon was transcribed divergently from the operon ORF3592 to ORF3597. Both promoters were mapped by primer extension analysis, which showed that the divergent −35 hexamers of these operon promoters were adjacent to each other. Transcription of both operons was induced in response to l- or d-lysine in the culture medium.

scholarly journals Proline Catabolism by Pseudomonas putida: Cloning, Characterization, and Expression of the put Genes in the Presence of Root Exudates

2000 ◽  
Vol 182 (1) ◽  
pp. 91-99 ◽  
Author(s):  
Susana Vílchez ◽  
Lázaro Molina ◽  
Cayo Ramos ◽  
Juan L. Ramos
Keyword(s):  
Pseudomonas Putida ◽  
Nitrogen Source ◽  
Root Exudates ◽  
Rhodobacter Capsulatus ◽  
Amino Acid Residues ◽  
Carbon And Nitrogen ◽  
Serovar Typhimurium ◽  
Induction Ratio ◽  
Inner Membrane Protein ◽  
Single Polypeptide

ABSTRACT Pseudomonas putida KT2442 is a root-colonizing strain which can use proline, one of the major components in root exudates, as its sole carbon and nitrogen source. A P. putida mutant unable to grow with proline as the sole carbon and nitrogen source was isolated after random mini-Tn5–Km mutagenesis. The mini-Tn5 insertion was located at the putAgene, which is adjacent to and divergent from the putPgene. The putA gene codes for a protein of 1,315 amino acid residues which is homologous to the PutA protein of Escherichia coli, Salmonella enterica serovar Typhimurium,Rhodobacter capsulatus, and several Rhizobiumstrains. The central part of P. putida PutA showed homology to the proline dehydrogenase of Saccharomyces cerevisiae and Drosophila melanogaster, whereas the C-terminal end was homologous to the pyrroline-5-carboxylate dehydrogenase of S. cerevisiae and a number of aldehyde dehydrogenases. This suggests that in P. putida, both enzymatic steps for proline conversion to glutamic acid are catalyzed by a single polypeptide. The putP gene was homologous to the putP genes of several prokaryotic microorganisms, and its gene product is an integral inner-membrane protein involved in the uptake of proline. The expression of both genes was induced by proline added in the culture medium and was regulated by PutA. In a P. putida putA-deficient background, expression of bothputA and putP genes was maximal and proline independent. Corn root exudates collected during 7 days also strongly induced the P. putida put genes, as determined by using fusions of the put promoters to ′lacZ. The induction ratio for the putA promoter (about 20-fold) was 6-fold higher than the induction ratio for the putPpromoter.

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 Transcriptome Changes in Pseudomonas putida KT2440 during Medium-Chain-Length Polyhydroxyalkanoate Synthesis Induced by Nitrogen Limitation

2020 ◽  
Vol 22 (1) ◽  
pp. 152
Author(s):  
Dorota Dabrowska ◽  
Justyna Mozejko-Ciesielska ◽  
Tomasz Pokój ◽  
Slawomir Ciesielski
Keyword(s):  
Chain Length ◽  
Nitrogen Limitation ◽  
Stringent Response ◽  
Wild Type ◽  
Pseudomonas Putida Kt2440 ◽  
Medium Chain ◽  
Environmental Stimuli ◽  
Medium Chain Length ◽  
In The Wild

Pseudomonas putida’s versatility and metabolic flexibility make it an ideal biotechnological platform for producing valuable chemicals, such as medium-chain-length polyhydroxyalkanoates (mcl-PHAs), which are considered the next generation bioplastics. This bacterium responds to environmental stimuli by rearranging its metabolism to improve its fitness and increase its chances of survival in harsh environments. Mcl-PHAs play an important role in central metabolism, serving as a reservoir of carbon and energy. Due to the complexity of mcl-PHAs’ metabolism, the manner in which P. putida changes its transcriptome to favor mcl-PHA synthesis in response to environmental stimuli remains unclear. Therefore, our objective was to investigate how the P. putida KT2440 wild type and mutants adjust their transcriptomes to synthesize mcl-PHAs in response to nitrogen limitation when supplied with sodium gluconate as an external carbon source. We found that, under nitrogen limitation, mcl-PHA accumulation is significantly lower in the mutant deficient in the stringent response than in the wild type or the rpoN mutant. Transcriptome analysis revealed that, under N-limiting conditions, 24 genes were downregulated and 21 were upregulated that were common to all three strains. Additionally, potential regulators of these genes were identified: the global anaerobic regulator (Anr, consisting of FnrA, Fnrb, and FnrC), NorR, NasT, the sigma54-dependent transcriptional regulator, and the dual component NtrB/NtrC regulator all appear to play important roles in transcriptome rearrangement under N-limiting conditions. The role of these regulators in mcl-PHA synthesis is discussed.

Access to 2-Arylquinazolines via Catabolism/Reconstruction of Amino Acids with Insertion of Dimethyl Sulfoxide

2021 ◽  
Author(s):  
Jin-Tian Ma ◽  
Li-Sheng Wang ◽  
Zhi Chai ◽  
Xin-Feng Chen ◽  
Bo-Cheng Tang ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Dimethyl Sulfoxide ◽  
Nitrogen Source ◽  
Carbon And Nitrogen ◽  
First Time

Quinazoline skeletons are synthesized by amino acids catabolism/reconstruction combined with dimethyl sulfoxide insertion/cyclization for the first time. The amino acid acts as a carbon and nitrogen source through HI-mediated catabolism...

scholarly journals Pseudomonas putida MPE, a manganese-dependent endonuclease of the binuclear metallophosphoesterase superfamily, incises single-strand DNA in two orientations to yield a mixture of 3′-PO4 and 3′-OH termini

2020 ◽  
Author(s):  
Shreya Ghosh ◽  
Anam Ejaz ◽  
Lucas Repeta ◽  
Stewart Shuman
Keyword(s):  
Pseudomonas Putida ◽  
Bound Water ◽  
Acid Catalyst ◽  
Nuclease Activity ◽  
Single Strand ◽  
Dna Endonuclease ◽  
Dependent Endonuclease ◽  
Leaving Group ◽  
Phosphodiester Hydrolysis ◽  
Hydrolysis Of

Abstract Pseudomonas putida MPE exemplifies a novel clade of manganese-dependent single-strand DNA endonuclease within the binuclear metallophosphoesterase superfamily. MPE is encoded within a widely conserved DNA repair operon. Via structure-guided mutagenesis, we identify His113 and His81 as essential for DNA nuclease activity, albeit inessential for hydrolysis of bis-p-nitrophenylphosphate. We propose that His113 contacts the scissile phosphodiester and serves as a general acid catalyst to expel the OH leaving group of the product strand. We find that MPE cleaves the 3′ and 5′ single-strands of tailed duplex DNAs and that MPE can sense and incise duplexes at sites of short mismatch bulges and opposite a nick. We show that MPE is an ambidextrous phosphodiesterase capable of hydrolyzing the ssDNA backbone in either orientation to generate a mixture of 3′-OH and 3′-PO4 cleavage products. The directionality of phosphodiester hydrolysis is dictated by the orientation of the water nucleophile vis-à-vis the OH leaving group, which must be near apical for the reaction to proceed. We propose that the MPE active site and metal-bound water nucleophile are invariant and the enzyme can bind the ssDNA productively in opposite orientations.

Sign in / Sign up

Export Citation Format

Share Document