Regulation of pyrimidine synthesis in Pseudomonas resinovorans

AIMS: To investigate the regulation of de novo pyrimidine biosynthesis in the bacterium Pseudomonas resinovorans ATCC 14235. METHODS AND RESULTS: The pyrimidine biosynthetic pathway enzymes were measured in cell extracts from P. resinovorans ATCC 14235 and from an auxotroph lacking orotate phosphoribosyltransferase activity. Pyrimidine biosynthetic pathway enzyme activities in ATCC 14235 were affected by the addition of pyrimidine bases to the culture medium. The de novo enzyme activities of the phosphoribosyltransferase mutant strain increased after pyrimidine starvation indicating possible repression of the pathway by a pyrimidine-related compound. Aspartate transcarbamoylase activity in ATCC 14235 was inhibited in vitro by ATP, UTP and pyrophosphate. CONCLUSIONS: Pyrimidine biosynthesis in P. resinovorans was regulated at the level of enzyme synthesis and at the level of activity for aspartate transcarbamoylase. Its regulation of enzyme synthesis seemed to be similar to what has been observed in the taxonomically related species Pseudomonas oleovorans. SIGNIFICANCE AND IMPACT OF THE STUDY: This study found that pyrimidine biosynthesis is regulated in P. resinovorans. This could prove helpful to future studies investigating polyhydroxyalkanoate production by the bacterium.     

Regulation of pyrimidine biosynthesis in Pseudomonas cepacia

Pyrimidine biosynthesis was investigated in Pseudomonas cepacia ATCC 17759. The presence of the de novo pyrimidine biosynthetic pathway enzyme activities was confirmed in this strain. Following transposon mutagenesis of the wild-type cells, a mutant strain deficient for orotidine 5-monophosphate decarboxylase activity (pyrF) was isolated. Uracil, cytosine or uridine supported the growth of this mutant. Uracil addition to minimal medium cultures of the wild-type strain diminished the levels of the de novo pyrimidine biosynthetic enzyme activities, while pyrimidine limitation of the mutant cells increased those de novo enzyme activities measured. It was concluded that regulation of pyrimidine biosynthesis at the lelel of enzyme synthesis in P. cepacia was present. Aspartate transcarbamoylase activity was found to be regulated in the wild-type cells. Its activity was shown to be controlled in vitro by inorganic pyrophosphate, adenosine 5-triphosphate and uridine 5-phosphate.     

Regulation of pyrimidine nucleotide biosynthesis in Pseudomonas synxantha

Regulation of pyrimidine nucleotide biosynthesis in Pseudomonas synxantha ATCC 9890 was investigated and the pyrimidine biosynthetic pathway enzyme activities were affected by pyrimidine supplementation in cells grown on glucose or succinate as a carbon source. In pyrimidine-grown ATCC 9890 cells, the activities of four de novo enzymes could be depressed which indicated possible repression of enzyme synthesis. To learn whether the pathway was repressible, pyrimidine limitation experiments were conducted using an orotate phosphoribosyltransferase (pyrE) mutant strain identified in this study. Compared to excess uracil growth conditions for the succinate-grown mutant strain cells, pyrimidine limitation of this strain caused dihydroorotase activity to increase about 3-fold while dihydroorotate dehydrogenase and orotidine 5'-monophosphate decarboxylase activities rose about 2-fold. Regulation of de novo pathway enzyme synthesis by pyrimidines appeared to be occurring. At the level of enzyme activity, aspartate transcarbamoylase activity in P. synxantha ATCC 9890 was strongly inhibited in vitro by pyrophosphate, UTP, ADP, ATP, CTP and GTP under saturating substrate concentrations.     

Control of the pyrimidine biosynthetic pathway in Pseudomonas pseudoalcaligenes

The five de novo enzyme activities unique to the pyrimidine biosynthetic pathway were found to be present in Pseudomonas pseudoalcaligenes ATCC 17440. A mutant strain with 31-fold reduced orotate phosphoribosyltransferase (encoded by pyrE) activity was isolated that exhibited a pyrimidine requirement for uracil or cytosine. Uptake of the nucleosides uridine or cytidine by wild-type or mutant cells was not detectable; explaining the inability of the mutant strain to utilize either nucleoside to satisfy its pyrimidine requirement. When the wildtype strain was grown in the presence of uracil, the activities of the five de novo enzymes were depressed. Pyrimidine limitation of the mutant strain led to the increase in aspartate transcarbamoylase and dihydroorotate dehydrogenase activities by more than 3-fold, and dihydroorotase and orotidine 5-monophosphate decarboxylase activities about 1.5-fold, as compared to growth with excess uracil. It appeared that the syntheses of the de novo enzymes were regulated by pyrimidines. In vitro regulation of aspartate transcarbamoylase activity in P. pseudoalcaligenes ATCC 17440 was investigated using saturating substrate concentrations; transcarbamoylase activity was inhibited by P_i, PP_i, uridine ribonucleotides, ADP, ATP, GDP, GTP, CDP, and CTP.     

Deciphering CAD: Structure and function of a mega‐enzymatic pyrimidine factory in health and disease

CAD is a 1.5 MDa particle formed by hexameric association of a 250 kDa protein divided into different enzymatic domains, each catalyzing one of the initial reactions for de novo biosynthesis of pyrimidine nucleotides: glutaminase‐dependent Carbamoyl phosphate synthetase, Aspartate transcarbamoylase, and Dihydroorotase. The pathway for de novo pyrimidine synthesis is essential for cell proliferation and is conserved in all living organisms, but the covalent linkage of the first enzymatic activities into a multienzymatic CAD particle is unique to animals. In other organisms, these enzymatic activities are encoded as monofunctional proteins for which there is abundant structural and biochemical information. However, the knowledge about CAD is scarce and fragmented. Understanding CAD requires not only to determine the three‐dimensional structures and define the catalytic and regulatory mechanisms of the different enzymatic domains, but also to comprehend how these domains entangle and work in a coordinated and regulated manner. This review summarizes significant progress over the past 10 years toward the characterization of CAD''s architecture, function, regulatory mechanisms, and cellular compartmentalization, as well as the recent finding of a new and rare neurometabolic disorder caused by defects in CAD activities.     

Pyrimidine biosynthesis in Pseudomonas stutzeri ATCC 17588

The de novo pyrimidine biosynthetic enzymes in the denitrifying bacterium Pseudomonas stutzeri ATCC 17588 were assayed and their activities were lower in glucose-grown cells than in succinate-grown cells. When P. stutzeri was grown in the presence of uracil, the de novo enzyme activities in succinate-grown cells were lowered while they remained largely unchanged in glucose-grown cells. A uracil auxotroph of P. stutzeri, deficient for aspartate transcarbamoylase activity, was isolated and its auxotrophic requirement was met by only uracil and cytosine. The inability of pyrimidine ribonucleosides to meet the auxotrophic requirement was related to the limited ability of P. stutzeri to transport uridine and cytidine. Pyrimidine limitation of the auxotroph elevated the de novo enzyme activities indicating that this pathway may be repressible by a uracil-related compound in succinate-grown P. stutzeri cells. Regulation of pyrimidine synthesis in P. stutzeri was similar to that observed for other pseudomonads classified within rRNA homology group I.     

Intersubunit communication in the dihydroorotase–aspartate transcarbamoylase complex of Aquifex aeolicus

Aspartate transcarbamoylase and dihydroorotase, enzymes that catalyze the second and third step in de novo pyrimidine biosynthesis, are associated in dodecameric complexes in Aquifex aeolicus and many other organisms. The architecture of the dodecamer is ideally suited to channel the intermediate, carbamoyl aspartate from its site of synthesis on the ATC subunit to the active site of DHO, which catalyzes the next step in the pathway, because both reactions occur within a large, internal solvent‐filled cavity. Channeling usually requires that the reactions of the enzymes are coordinated so that the rate of synthesis of the intermediate matches its rate of utilization. The linkage between the ATC and DHO subunits was demonstrated by showing that the binding of the bisubstrate analog, N‐phosphonacetyl‐L ‐aspartate to the ATC subunit inhibits the activity of the distal DHO subunit. Structural studies identified a DHO loop, loop A, interdigitating between the ATC domains that would be expected to interfere with domain closure essential for ATC catalysis. Mutation of the DHO residues in loop A that penetrate deeply between the two ATC domains inhibits the ATC activity by interfering with the normal reciprocal linkage between the two enzymes. Moreover, a synthetic peptide that mimics that part of the DHO loop that binds between the two ATC domains was found to be an allosteric or noncompletive ATC inhibitor (K_i = 22 μM). A model is proposed suggesting that loop A is an important component of the functional linkage between the enzymes.     

群体感应对铜绿假单胞菌生物被膜形成的调控

生物被膜是一种与浮游细胞相对应的生长方式,由细菌和自身分泌的包外基质组成。铜绿假单胞菌是研究这一生长方式的模式生物。在过去十年,对铜绿假单胞菌生物被膜的研究已取得显著进展。群体感应(QS)的细胞沟通机制在铜绿假单胞菌生物被膜形成中发挥着重要作用。介绍生物被膜的特点,并重点讨论了QS和生物被膜之间的关系。     

Crystal structure of the catalytic trimer of Methanococcus jannaschii aspartate transcarbamoylase

The catalytic trimer of Methanococcus jannaschii aspartate transcarbamoylase is extremely heat stable, maintaining 75% of its activity after heat treatment for 60 min at 75 degrees C. We undertook its structural analysis in order to understand the molecular basis of its thermostability and gain insight on how its catalytic function adapts to high temperature. Several structural elements potentially contributing to thermostability were identified. These include: (i) changes in the amino acid composition such as a decrease in the thermolabile residues Gln and Asn, an increase in the charged residues Lys and Glu, an increase in Tyr and a decrease in Ala residues; (ii) a larger number of salt bridges, in particular, the improvement of ion-pair networks; (iii) shortening of the N-terminus and shortening of three loops. An interesting feature of the crystal structure is the association of two crystallographically independent catalytic subunits into a staggered complex with an intertrimer distance of 33.8 A. The active site appears similar to Escherichia coli. Upon substrate binding, smaller changes in the global orientation of domains and larger conformational changes of the active site residues are expected as compared to E. coli.     

Regulation of the Pyrimidine Biosynthetic Pathway in <Emphasis Type="Italic">Pseudomonas mucidolens</Emphasis>

Control of pyrimidine biosynthesis was examined in Pseudomonas mucidolens ATCC 4685 and the five de novo pyrimidine biosynthetic enzyme activities unique to this pathway were influenced by pyrimidine supplementation in cells grown on glucose or succinate as a carbon source. When uracil was supplemented to glucose-grown ATCC 4685 cells, activities of four de novo enzymes were depressed which indicated possible repression of enzyme synthesis. To learn whether the pathway was repressible, pyrimidine limitation experiments were conducted using an orotate phosphoribosyltransferase (pyrE) mutant strain identified in this study. Compared to excess uracil growth conditions for the glucose-grown mutant strain cells, pyrimidine limitation of this strain caused aspartate transcarbamoylase, dihydroorotase and dihydroorotate dehydrogenase activities to increase by more than 3-fold while OMP decarboxylase activity increased by 2.7-fold. The syntheses of the de novo enzymes appeared to be regulated by pyrimidines. At the level of enzyme activity, aspartate transcarbamoylase activity in P. mucidolens ATCC 4685 was subject to inhibition at saturating substrate concentrations. Transcarbamoylase activity was strongly inhibited by UTP, ADP, ATP, GTP and pyrophosphate.     

The role of fatty acid biosynthesis and degradation in the supply of substrates for poly(3-hydroxyalkanoate) formation in Pseudomonas putida

Abstract The relationship between fatty acid metabolism and PHA biosynthesis in P. putida is described. Detailed ¹H and ¹³C NMR studies were performed to investigate the structures of poly(3-hydroxyalkanoates) (PHAs) formed from carbohydrates and fatty acids. On the basis of these results, it is proposed that during growth on glucose the 3-hydroxyacyl-acyl carrier protein intermediates of the de novo fatty acid biosynthetic pathway are diverted to PHA biosynthesis. Similarly, further evidence is presented that during cultivation on fatty acids, intermediates of the β-oxidation cycle serve as precursors of PHA biosynthesis.     

Optimization of octanoic acid and sulfur donor concentrations for lipoic acid production by Pseudomonas reptilivora

Using the optimal concentrations of octanoic acid (0.75 mM) and ethyl mercaptan (2 mM), as the most effective sulfur donor, Pseudomonas reptilivora produced 74 mug lipoic acid per dry cell weight at pH 7.5 and 30 degrees C in a fermenter over 9 h. The dry cell weight was 13.9 g l(-1).     

Pseudomonas pseudoalcaligenes B50铁载体合成相关基因pyrD的克隆与功能分析

从棉花根际分离的一株细菌B50在低铁条件下可以产生铁载体。通过形态学特征、生理生化特征及其16SrDNA序列分析,将其鉴定为Pseudomonas pseudoalcaligenes。采用三亲本杂交的方法将转座子Tn5-1063a(含luxAB)导入B50中,进行转座子插入诱变,获得突变株。用TAIL-PCR方法得到与铁吸收有关的pyrD基因序列。通过互补实验验证pyrD与铁载体的合成有关。Pseudomonas pseudoalcaligenes能够产生铁载体属于首次报道。     

Regulation of quorum sensing in Pseudomonas

Bacteria use small signal molecules in order to monitor their population density and coordinate gene regulation in a process called quorum sensing. In Gram-negative bacteria, the most common signal molecules are acylated homoserine lactones. Several Pseudomonas species produce acylated homoserine lactones that control important functions including pathogenicity and plant growth promotion. Many reports indicate that the quorum sensing systems of Pseudomonas are significantly regulated and interconnected with regulons of other global regulators. The integration of quorum sensing into additional regulatory circuits increases the range of environmental and metabolic signals beyond that of cell density, as well as further tuning the timing of the response. This review will focus on the regulation of quorum sensing in Pseudomonas, highlighting a complex response that might serve a given species to adapt in its particular environment.     

假单胞菌Quorum sensing调控体系

群体感应(Quorum sensing,QS)是近来受到广泛关注的一种细菌群体行为调控机制,通过感应一些信号分子如酰基高丝氨酸环内酯(acyl-homoserine lactone,AHL)来判断菌群密度和周围环境变化,假单胞菌中同样也有AHL信号分子,当信号达到一定的浓度阈值时,能启动菌体中相关基因的表达来适应环境中的变化,从而调节菌体的群体行为(如致病性及群体生长调节)。众多报道说明了假单胞菌的群体感应调节系统是由一些全面的调节子所调控的。本文系统介绍了假单胞菌群体感应调控系统,并分析假单胞菌在该系统中复杂的应答反应。