Distribution of polyamines in representative species of archaebacteria

Identification, chemical synthesis, and biological functions of unusual polyamines produced by extreme thermophiles

Unusual long polyamines such as caldopentamine and caldohexamine, and branched polyamines such as tetrakis(3-aminopropyl)ammonium and N (4)-aminopropylspermidine were often found in cells of extreme thermophiles and hyperthermophiles belonging to both Bacteria and Archaea domains. Some of these unusual polyamines are essential for life at extreme temperatures. In some cases, the unusual polyamines also exist in cells of nonthermophilic organisms and play important physiological roles under normal conditions. Methods for chromatographic analysis, isolation, and chemical syntheses of unusual polyamines as well as experimental methods for measuring their physiological roles are discussed. Especially, many newly improved methods for chemical syntheses are presented in this article.

The first agmatine/cadaverine aminopropyl transferase: biochemical and structural characterization of an enzyme involved in polyamine biosynthesis in the hyperthermophilic archaeon Pyrococcus furiosus

We report here the characterization of the first agmatine/cadaverine aminopropyl transferase (ACAPT), the enzyme responsible for polyamine biosynthesis from an archaeon. The gene PF0127 encoding ACAPT in the hyperthermophile Pyrococcus furiosus was cloned and expressed in Escherichia coli, and the recombinant protein was purified to homogeneity. P. furiosus ACAPT is a homodimer of 65 kDa. The broad substrate specificity of the enzyme toward the amine acceptors is unique, as agmatine, 1,3-diaminopropane, putrescine, cadaverine, and sym-nor-spermidine all serve as substrates. While maximal catalytic activity was observed with cadaverine, agmatine was the preferred substrate on the basis of the k(cat)/K(m) value. P. furiosus ACAPT is thermoactive and thermostable with an apparent melting temperature of 108 degrees C that increases to 112 degrees C in the presence of cadaverine. Limited proteolysis indicated that the only proteolytic cleavage site is localized in the C-terminal region and that the C-terminal peptide is not necessary for the integrity of the active site. The crystal structure of the enzyme determined to 1.8-A resolution confirmed its dimeric nature and provided insight into the proteolytic analyses as well as into mechanisms of thermal stability. Analysis of the polyamine content of P. furiosus showed that spermidine, cadaverine, and sym-nor-spermidine are the major components, with small amounts of sym-nor-spermine and N-(3-aminopropyl)cadaverine (APC). This is the first report in Archaea of an unusual polyamine APC that is proposed to play a role in stress adaptation.

Unique polyamines produced by an extreme thermophile, Thermus thermophilus

Recent research progress on polyamines in extreme thermophiles is reviewed. Extreme thermophiles produce two types of unique polyamines; one is longer polyamines such as caldopentamine and caldohexamine, and the other is branched polyamines such as tetrakis(3-aminopropyl)ammonium. The protein synthesis catalyzed by a cell-free extract of Thermus thermophilus, an extreme thermophile, required the presence of a polyamine and the highest activity was found in the presence of tetrakis(3-aminopropyl)ammonium. In vitro experiments, longer polyamines efficiently stabilized double stranded nucleic acids and a branched polyamine, tetrakis(3-aminropyl)ammonium, stabilized stem-and-loop structures. In T. thermophilus, polyamines are synthesized from arginine by a new metabolic pathway; arginine is converted to agmatine and then agmatine is aminopropylated to N(1)-aminopropylagmatine which is converted to spermidine by an enzyme coded by a gene homologous to speB (a gene for agmatinase). In this new pathway spermidine is not synthesized from putrescine. Reverse genetic studies indicated that the unique polyamines are synthesized from spermidine.

Stabilization of nucleic acids by unusual polyamines produced by an extreme thermophile, Thermus thermophilus

Extreme thermophiles produce two types of unusual polyamine: long linear polyamines such as caldopentamine and caldohexamine, and branched polyamines such as quaternary ammonium compounds [e.g. tetrakis(3-aminopropyl)ammonium]. To clarify the physiological roles of long linear and branched polyamines in thermophiles, we synthesized them chemically and tested their effects on the stability of ds (double-stranded) and ss (single-stranded) DNAs and tRNA in response to thermal denaturation, as measured by differential scanning calorimetry. Linear polyamines stabilized dsDNA in proportion to the number of amino nitrogen atoms within their molecular structure. We used the empirical results to derive formulae that estimate the melting temperature of dsDNA in the presence of polyamines of a particular molecular composition. ssDNA and tRNA were stabilized more effectively by tetrakis(3-aminopropyl)ammonium than any of the other polyamines tested. We propose that long linear polyamines are effective to stabilize DNA, and tetrakis(3-aminopropyl)ammonium plays important roles in stabilizing RNAs in thermophile cells.

Thermoadaptation trait revealed by the genome sequence of thermophilic Geobacillus kaustophilus

We present herein the first complete genome sequence of a thermophilic Bacillus-related species, Geobacillus kaustophilus HTA426, which is composed of a 3.54 Mb chromosome and a 47.9 kb plasmid, along with a comparative analysis with five other mesophilic bacillar genomes. Upon orthologous grouping of the six bacillar sequenced genomes, it was found that 1257 common orthologous groups composed of 1308 genes (37%) are shared by all the bacilli, whereas 839 genes (24%) in the G.kaustophilus genome were found to be unique to that species. We were able to find the first prokaryotic sperm protamine P1 homolog, polyamine synthase, polyamine ABC transporter and RNA methylase in the 839 unique genes; these may contribute to thermophily by stabilizing the nucleic acids. Contrasting results were obtained from the principal component analysis (PCA) of the amino acid composition and synonymous codon usage for highlighting the thermophilic signature of the G.kaustophilus genome. Only in the PCA of the amino acid composition were the Bacillus-related species located near, but were distinguishable from, the borderline distinguishing thermophiles from mesophiles on the second principal axis. Further analysis revealed some asymmetric amino acid substitutions between the thermophiles and the mesophiles, which are possibly associated with the thermoadaptation of the organism.

DNA topoisomerase III from the hyperthermophilic archaeon Sulfolobus solfataricus with specific DNA cleavage activity

We report the production, purification, and characterization of a type IA DNA topoisomerase, previously designated topoisomerase I, from the hyperthermophilic archaeon Sulfolobus solfataricus. The protein was capable of relaxing negatively supercoiled DNA at 75 degrees C in the presence of Mg2+. Mutation of the putative active site Tyr318 to Phe318 led to the inactivation of the protein. The S. solfataricus enzyme cleaved oligonucleotides in a sequence-specific fashion. The cleavage occurred only in the presence of a divalent cation, preferably Mg2+. The cofactor requirement of the enzyme was partially satisfied by Cu2+, Co2+, Mn2+, Ca2+, or Ni2+. It appears that the enzyme is active with a broader spectrum of metal cofactors in DNA cleavage than in DNA relaxation (Mg2+ and Ca2+). The enzyme-catalyzed oligonucleotide cleavage required at least 7 bases upstream and 2 bases downstream of the cleavage site. Analysis of cleavage by the S. solfataricus enzyme on a set of oligonucleotides revealed a consensus cleavage sequence of the enzyme: 5'-G(A/T)CA(T)AG(T)G(A)X / XX-3'. This sequence bears more resemblance to the preferred cleavage sites of topoisomerases III than to those of topoisomerases I. Based on these data and sequence analysis, we designate the enzyme S. solfataricus topoisomerase III.

Classification and identification of bacteria: current approaches to an old problem. Overview of methods used in bacterial systematics

Most of the bacterial species are still unknown. Consequently, our knowledge about bacterial ecology is poor and expectations about specialized species with novel enzymatic functions or new products are high. Thus, bacterial identification is a growing field of interest within microbiology. In this review, suitability of developments for identification based on miniaturized biochemical and physiological investigations of bacteria are evaluated. Special emphasis is given to chemotaxonomic methods such as analysis of quinone system, fatty acid profiles, polar lipid patterns, polyamine patterns, whole cell sugars, peptidoglycan diaminoacids, as well as analytical fingerprinting methods and cellular protein patterning. 16S rDNA sequencing introduced to investigate the phylogenetic relationships of bacteria, nucleic acids hybridization techniques and G + C content determination are discussed as well as restriction fragment length polymorphism (RFLP), macrorestriction analysis and random amplified polymorphic DNA (RAPD). The importance of the different approaches in classification and identification of bacteria according to phylogenetic relationships are demonstrated on selected examples.

Polyamines as a chemotaxonomic marker in bacterial systematics

Aliphatic linear polyamines, from diamines to hexaamines, tertiary branched tetraamines, and quaternary branched pentaamines are widely distributed in eubacteria, archaebacteria, and cyanobacteria. Twenty-four linear types and four branched types are acid extractable from bacterial cells and can be chromatographically analyzed and identified. The varieties of polyamines are due to the combination of amino acid decarboxylase activities to form diamines, aminopropyl- and aminobutyl-transfer activities mediated by aminopropyltransferases or Schiff-base complex formation, and hydroxylation activity. The absence or presence of spermidine, norspermidine or homospermidine and the occurrence of 2-hydroxyputrescine and diaminopropane are related to grouping into the alpha, beta, gamma, and delta subclasses within Proteobacteria. Flavobacterium complex and green bacteria contain putrescine and homospermidine. Gram-negative thermophiles contain long linear and branched polyamines; however, their distribution profiles are species specific. Gram-positive eubacteria, which comprise Bacillus cluster, anaerobes, and actinomycetes, ubiquitously contain putrescine and spermidine, while the occurrence of spermine is limited to thermophiles. Archaebacteria are separated into polyamine-absent methanogens and halophiles, homospermidine-dominant methanogens, spermidine-dominant methanogens, and spermidine- and norspermidine-containing thermophiles. Cyanobacteria comprise two types; one group contains homospermidine and the other spermidine. The polyamine distribution pattern can serve as a chemotaxonomic marker in bacterial classification and is associated with bacterial systematics on the level of order, family, or genus.

Increase in spermine content coordinated with siderophore production in Paracoccus denitrificans

Spermine is present in relatively low amounts in Paracoccus denitrificans cultured aerobically in an ammonium succinate minimal salts medium supplemented with 50 microM iron(III). However, in iron-deprived cultures [minimal salts medium containing 0.5 microM iron(III)], spermine content increases by an order of magnitude in coordination with the well-known responses to iron derivation, e.g., derepression of siderophore synthesis and siderophore excretion. When iron-deprived cultures exhibiting both high spermine content and strong siderophore production are reseeded into fresh minimal salts medium containing 50 microM iron[III], both siderophore production and spermine content fall rapidly. Five hours after iron supplementation, spermine is below limits of detection. These results suggest a specific role for spermine in the response of P. denitrificans to low-iron stress.

Effect of norspermidine and its related triamines on the cell-free polyphenylalanine synthesizing system from Vibrio parahaemolyticus

The effect of norspermidine and its structurally related triamines on the cell-free polyphenylalanine synthesizing system from Vibrio parahaemolyticus was examined in connection with the requirement of the system for monovalent cation. In the absence of norspermidine, the maximal incorporation of [14C]phenylalanine into hot trichloroacetic acid insoluble material was observed under ionic conditions of 12 mM Mg2+ and 50 mM NH4+. K+ could partially substitute for NH4+, but Na+ could not. The addition of norspermidine to the polyphenylalanine synthetic reaction mixture not only lowered the optimal Mg2+ concentration, but it also stimulated the polyphenylalanine synthesis up to 2-fold with no significant increase in misincorporation of [14C]leucine. Other triamines having one or two methylene chains more than norspermidine were also effective in eliciting these effects. Furthermore, Na+ could not support the polyphenylalanine synthesis even in the presence of norspermidine and, on the contrary, inhibited the polyphenylalanine synthesis induced by NH4+ regardless of whether norspermidine was present or not. These findings are discussed in comparison with the properties of other bacterial cell-free systems.

Methanocorpusculaceae fam. nov., represented by Methanocorpusculum parvum, Methanocorpusculum sinense spec. nov. and Methanocorpusculum bavaricum spec. nov

Two new methanogenic bacteria, Methanocorpusculum sinense spec. nov. strain DSM 4274 from a pilot plant for treatment of distillery wastewater in Chengdu (Province Sichuan, China), and Methanocorpusculum bavaricum spec. nov. strain DSM 4179, from a wastewater pond of the sugar factory in Regensburg (Bavaria, FRG) are described. Methanocorpusculum strains are weakly motile and form irregularly coccoid cells, about 1 micron in diameter. The cell envelope consists of a cytoplasmic membrane and a S-layer, composed of hexagonally arranged glycoprotein subunits with molecular weights of 90,000 (Methanocorpusculum parvum), 92,000 (M. sinense), and 94,000 (M. bavaricum). The center-to-center spacings are 14.3 nm, 15.8 nm and 16.0 nm, respectively. Optimal growth of strains is obtained in the mesophilic temperature range and at a pH around 7. Methane is produced from H2/CO2, formate, 2-propanol/CO2 and 2-butanol/CO2 by M. parvum and M. bavaricum, whereas M. sinense can only utilize H2/CO2 and formate. Growth of M. sinense and M. bavaricum is dependent on the presence of clarified rumen fluid. The G + C content of the DNA of the three strains is ranging from 47.7-53.6 mol% as determined by different methods. A similar, but distinct polar lipid pattern indicates a close relationship between the three Methanocorpusculum species. The polyamine patterns of M. parvum, M. sinense and M. bavaricum are similar, but distinct from those of other methanogens and are characterized by a high concentration of the otherwise rare 1,3-diaminopropane. Quantitative comparison of the antigenic fingerprint of members of Methanocorpusculum revealed no antigenic relationship with any one of the reference methanogens tested. On the basis of the distant phylogenetic position of M. parvum and the data presented in this paper a new family, the Methanocorpusculaceae fam. nov., is defined.

Polyamine biosynthesis and inhibition in Trichomonas vaginalis

Polyomines - particularly putrescine, spermidine and spermine - are ubiquitous components of eukaryote and most prokaryote cells, and are essential for optimal cell proliferation. But since routes of polyamine synthesis may differ, for example between parasites and their hosts, selective inhibition of polyamine metabolism offers an attractive target for chemotherapy - as already shown with the success of difluoromethylomithine (DFMO) as an inhibitor of polyamine synthesis in African trypanosomes. Parasitology Today has featured a series of articles reviewing research on polyamine metabolism of various parasites (eg. vol. 3, pp 190-192, pp 312-315; vol. 4, pp 18-20) and here, Nigel Yorlett discusses these metabolic aspects of Trichomonas vaginalis (Fig. 1)-a common parasite of the urogenital tract.

Polyamine metabolism in filarial worms

The human and animal filarial parasites Onchocerca volvulus, Dirofilaria immitis, Brugia patei and Litomosoides carinii contained low levels of putrescine but much higher levels of spermidine and spermine as estimated by ion-pair high pressure liquid chromatography; N-acetylated polyamines were present only in minute amounts. Enzyme activities of ornithine decarboxylase (EC 4.1.1.17) and arginine decarboxylase (EC 4.1.1.19), respectively, were not detectable. Experiments carried out with O. volvulus and D. immitis demonstrated the uptake and bioconversion of labeled polyamines. There is evidence for the existence of a complete reverse pathway generating putrescine from spermidine and spermine, respectively, in both worms. N-Acetylating enzyme activities were detected in 100,000 X g preparations of homogenates from D. immitis which were capable to acetylate putrescine, spermidine and spermine. Long term incubation of the worms in the presence of labeled polyamines resulted in the excretion of putrescine and N-acetylputrescine.