Showing papers in "Fems Microbiology Reviews in 1998"

The anaerobic oxidation of ammonium

Abstract: From recent research it has become clear that at least two different possibilities for anaerobic ammonium oxidation exist in nature. 'Aerobic' ammonium oxidizers like Nitrosomonas eutropha were observed to reduce nitrite or nitrogen dioxide with hydroxylamine or ammonium as electron donor under anoxic conditions. The maximum rate for anaerobic ammonium oxidation was about 2 nmol NH4+ min-1 (mg protein)-1 using nitrogen dioxide as electron acceptor. This reaction, which may involve NO as an intermediate, is thought to generate energy sufficient for survival under anoxic conditions, but not for growth. A novel obligately anaerobic ammonium oxidation (Anammox) process was recently discovered in a denitrifying pilot plant reactor. From this system, a highly enriched microbial community with one dominating peculiar autotrophic organism was obtained. With nitrite as electron acceptor a maximum specific oxidation rate of 55 nmol NH4+ min-1 (mg protein)-1 was determined. Although this reaction is 25-fold faster than in Nitrosomonas, it allowed growth at a rate of only 0.003 h-1 (doubling time 11 days). 15N labeling studies showed that hydroxylamine and hydrazine were important intermediates in this new process. A novel type of hydroxylamine oxidoreductase containing an unusual P468 cytochrome has been purified from the Anammox culture. Microsensor studies have shown that at the oxic/anoxic interface of many ecosystems nitrite and ammonia occur in the absence of oxygen. In addition, the number of reports on unaccounted high nitrogen losses in wastewater treatment is gradually increasing, indicating that anaerobic ammonium oxidation may be more widespread than previously assumed. The recently developed nitrification systems in which oxidation of nitrite to nitrate is prevented form an ideal partner for the Anammox process. The combination of these partial nitrification and Anammox processes remains a challenge for future application in the removal of ammonium from wastewater with high ammonium concentrations.

Exocellular polysaccharides from cyanobacteria and their possible applications

Abstract: Cyanobacteria are photoautotrophic prokaryotes which include a large variety of species of widespread occurrence and with diverse morphological, physiological and biochemical properties. Many cyanobacteria are known to be able to synthesise outermost slimy investments and to release polysaccharidic material into the culture medium during cell growth. These released polysaccharides (RPSs), being easily recoverable from the culture medium, are attracting much interest in view of their possible uses in several industrial applications. In this paper, an overview of the current knowledge on both RPS-producing cyanobacterial strains (including the possible roles of the exopolysaccharides) and chemical characteristics of the cyanobacterial RPSs is given, with particular emphasis on RPS properties and possible industrial applications. On the whole, cyanobacterial RPSs are characterised by a great variety in both number (from two to 10) and type of constitutive monosaccharides (various arrangements of acidic and neutral sugars). Most polymers show an anionic nature due to the presence of uronic acids and/or other charged groups such as pyruvyl or sulfate. Polypeptide moieties as well as acetyl substituents have also sometimes been found, causing additional structural complexity. All the cyanobacterial RPSs so far tested showed a pseudoplastic behaviour, but with marked differences in both viscosity values and shear thinning. In terms of RPS production, the responses of cyanobacteria to changes of culture conditions appear strain-dependent. RPS productivities shown by some cyanobacteria are well comparable with those reported for other photosynthetic microorganisms proposed for polysaccharide production, but very low in comparison with those of heterotrophic microorganisms. Nevertheless, cyanobacteria may be regarded as a very abundant source of structurally diverse polysaccharides, some of which may possess unique properties for special applications, not fulfilled by the polymers currently available. However, much work has still to be done to bridge the wide gap existing between data on the biology of the RPS-producer strains and information concerning technological and other useful properties of the cyanobacterial RPS.

Anaerobic bacterial metabolism of hydrocarbons

Abstract: The capacity of some bacteria to metabolize hydrocarbons in the absence of molecular oxygen was first recognized only about ten years ago. Since then, the number of hydrocarbon compounds shown to be catabolized anaerobically by pure bacterial cultures has been steadily increasing. This review summarises the current knowledge of the bacterial isolates capable of anaerobic mineralization of hydrocarbons, and of the biochemistry and molecular biology of enzymes involved in the catabolic pathways of some of these substrates. Several alkylbenzenes, alkanes or alkenes are anaerobically utilized as substrates by several species of denitrifying, ferric iron-reducing and sulfate-reducing bacteria. Another group of anaerobic hydrocarbon degrading bacteria are ‘proton reducers’ that depend on syntrophic associations with methanogens. For two alkylbenzenes, toluene and ethylbenzene, details of the biochemical pathways involved in anaerobic mineralization are known. These hydrocarbons are initially attacked by novel, formerly unknown reactions and oxidized further to benzoyl-CoA, a common intermediate in anaerobic catabolism of many aromatic compounds. Toluene degradation is initiated by an unusual addition reaction of the toluene methyl group to the double bond of fumarate to form benzylsuccinate. The enzyme catalyzing this first step has been characterized at both the biochemical and molecular level. It is a unique type of glycyl-radical enzyme, an enzyme family previously represented only by pyruvate-formate lyases and anaerobic ribonucleotide reductases. Based on the nature of benzylsuccinate synthase as a radical enzyme, a hypothetical reaction mechanism for the addition of toluene to fumarate is proposed. The further catabolism of benzylsuccinate to benzoyl-CoA and succinyl-CoA appears to occur via reactions of a modified β-oxidation pathway. Ethylbenzene is first oxidized at the methylene carbon to 1-phenylethanol and subsequently to acetophenone, which is then carboxylated to 3-oxophenylpropionate and converted to benzoyl-CoA and acetyl-CoA. Anaerobic mineralization of alkanes involves an oxygen-independent oxidation to fatty acids, followed by β-oxidation. In one strain of an alkane-mineralizing sulfate-reducing bacterium, the activation appears to proceed via a chain-elongation, possibly by addition of a C1-group at the terminal methyl group of the alkane. Finally, aspects concerned with the regulation and ecological significance of anaerobic hydrocarbon catabolic pathways are discussed.

Eubacterial sigma‐factors

Abstract: The initiation of transcription is the most important step for gene regulation in eubacteria To initiate transcription, RNA polymerase has to associate with a small protein, known as a σ-factor The σ-factor directs RNA polymerase to a specific class of promoter sequences Most bacterial species synthesize several different σ-factors that recognize different consensus sequences This variety in σ-factors provides bacteria with the opportunity to maintain basal gene expression as well as for regulation of gene expression in response to altered environmental or developmental signals This review focuses on the function, regulation and distribution of the 14 different classes of σ-factors that are presently known

ATP‐binding‐cassette (ABC) transport systems: Functional and structural aspects of the ATP‐hydrolyzing subunits/domains

Abstract: Members of the superfamily of adenosine triphosphate (ATP)-binding-cassette (ABC) transport systems couple the hydrolysis of ATP to the translocation of solutes across a biological membrane. Recognized by their common modular organization and two sequence motifs that constitute a nucleotide binding fold, ABC transporters are widespread among all living organisms. They accomplish not only the uptake of nutrients in bacteria but are involved in diverse processes, such as signal transduction, protein secretion, drug and antibiotic resistance, antigen presentation, bacterial pathogenesis and sporulation. Moreover, some human inheritable diseases, like cystic fibrosis, adrenoleukodystrophy and Stargardt's disease are caused by defective ABC transport systems. Thus, albeit of major significance, details of the molecular mechanism by which these systems exert their functions are still poorly understood. In this review, recent data concerning the properties and putative role of the ATP-hydrolyzing subunits/domains are summarized and compared between bacterial and eukaryotic systems.

Reductive dechlorination in the energy metabolism of anaerobic bacteria

Abstract: Within the last few decades, several anaerobic bacteria have been isolated which are able to reductively dechlorinate chlorinated aliphatic and aromatic compounds at catabolic rates. For some of these bacteria, it has been shown that the reductive dechlorination is coupled to energy conservation, a process designated as ‘dehalorespiration’. Somewhat simple respiratory chains seem to be involved that utilize the free energy that could be gained from the exergonic dechlorination reaction quite inefficiently. With one exception, all reductive dehalogenases isolated to date contain a corrinoid and iron–sulfur clusters as cofactors. During the course of the catalytic reaction cycle, the cobalt of the corrinoid is subjected to a change in its redox state. Hence, reductive dechlorination represents a new type of biochemical reaction.

Anaerobic metabolism of aromatic compounds via the benzoyl‐CoA pathway

Abstract: Aromatic compounds are important growth substrates for microorganisms They form a large group of diverse compounds including lignin monomers, amino acids, quinones, and flavonoids Aerobic aromatic metabolism is characterized by the extensive use of molecular oxygen which is essential for the hydroxylation and cleavage of aromatic ring structures The anaerobic metabolism of low molecular mass soluble aromatic compounds requires, of necessity, a quite different strategy In most known cases, aromaticity is broken by reduction and the ring is subsequently opened hydrolytically A small number of different central aromatic intermediates can be reduced, the most common of which is benzoyl-CoA, a compound that is formed as a central intermediate in the degradation of a large number of aromatic growth substrates This review concentrates on the anaerobic aromatic metabolism via the benzoyl-CoA pathway The peripheral pathways that transform growth substrates to benzoyl-CoA include various types of novel reactions, for example carboxylation of phenolic compounds, reductive elimination of ring substituents like hydroxyl or amino groups, oxidation of methyl substituents, O-demethylation reactions and shortening of aliphatic side chains The central benzoyl-CoA pathway differs in several aspects in the denitrifying, phototrophic and fermenting bacteria studied In denitrifying and phototrophic bacteria it starts with the two-electron reduction of benzoyl-CoA to a cyclic dienoyl-CoA driven by the hydrolysis of two molecules of ATP to ADP+Pi This ring reduction is catalyzed by benzoyl-CoA reductase and requires a low-potential ferredoxin as an electron donor In Rhodopseudomonas palustris the cyclic diene is further reduced to cyclohex-1-ene-1-carboxyl-CoA In the denitrifying species Thauera aromatica, the cyclic diene is hydrated to give 6-hydroxycyclohex-1-ene-1-carboxyl-CoA Subsequent β-oxidation results in the formation of a cyclic β-oxo compound, followed by hydrolytic carbon ring opening yielding 3-hydroxypimelyl-CoA in the case of T aromatica and pimelyl-CoA in the case of R palustris These intermediates are further β-oxidized via glutaryl-CoA; final products are 3 acetyl-CoA and 1 CO2 In fermenting bacteria benzoyl-CoA may possibly be reduced to the level of cyclohex-1-ene-1-carboxyl-CoA in an ATP-independent reaction The genes coding for the enzymes of the central benzoyl-CoA pathway have been cloned and sequenced from R palustris, T aromatica, and Azoarcus evansii Sequence analyses of the genes support the concept that phototrophic and denitrifying bacteria use two slightly different pathways to metabolize benzoyl-CoA The gene sequences have in some cases been very helpful for the identification of possible catalytic mechanisms that were not obvious from initial characterizations of purified enzymes

Physiology of organic nitrogen acquisition by ectomycorrhizal fungi and ectomycorrhizas

Abstract: Ectomycorrhizal fungi are symbiotically associated microorganisms which ecological importance has been repeatedly demonstrated. There has been a considerable amount of research aimed at assessing the ability of ectomycorrhizal fungi and ectomycorrhizas to utilize organic nitrogen sources. The fate of soil proteins, peptides and amino acids has been studied from a number of perspectives. Exocellular hydrolytic enzymes have been detected and characterized in a number of ectomycorrhizal and ericoid fungi. Studies on amino acid transport through the plasma membrane have demonstrated the ability of ectomycorrhizal fungi to take up the products of proteolytic activities. Investigations on intracellular metabolism of amino acids have allowed the identification of the metabolic pathways involved. Possible intracellular compartmentation of amino acids will be examined by immunocytochemistry. Further translocation of amino acids in symbiotic tissues has been established by experiments using isotopic tracers, although the exact nature of the nitrogenous compounds transferred at the symbiotic interface remained unclear. One of the main future challenges in the physiology of organic nitrogen acquisition is to determine the nature, the regulation and the location of N-compound transporters at the soil-fungus and fungus-plant interfaces. The molecular approach which is just emerging in this particular research area will greatly improve our knowledge. Future research should also address the extent of competition between different ectomycorrhizal species and between different microbial populations for organic nitrogen.

Oxygen sensing by the global regulator, FNR: the role of the iron-sulfur cluster.

Abstract: FNR is a global regulator that controls transcription of genes whose functions facilitate adaptation to growth under O2 limiting conditions. It has long been appreciated that the activity of FNR must be regulated by O2 availability, since FNR dependent gene expression is observed in vivo only under anaerobic conditions, while similar levels of this protein are present in both aerobic and anaerobic grown cells. Recent progress in this field has shown that anaerobically purified FNR contains a [4Fe-4S]2+ cluster and that this [4Fe-4S]2+ cluster is sufficiently unstable toward O2 to make it suitable as an O2 sensor. The presence of the [4Fe-4S] cluster increases dimerization of FNR which is correlated with an increase in site-specific DNA binding of FNR, a property expected of transcription factors of the FNR/CRP family. According to Mossbauer spectroscopy on purified FNR and cells containing overexpressed FNR, the [4Fe-4S]2+ cluster of FNR is converted by O2 to a [2Fe-2S]2+ in high yield. The [2Fe-2S]2+ cluster can be reconverted to the [4Fe-4S]2+ cluster on reduction with dithionite in vitro raising the possibility that the [2Fe-2S]2+ cluster is a biologically inactive intermediate which may be more readily available for reconstitution into the [4Fe-4S]2+ form than the Fe-free apoform. The ability to observe, by Mossbauer spectroscopy, the Fe-S clusters of FNR in cells containing high levels of FNR should be of value in further unraveling how FNR functions in vivo. Attempts to reduce the [4Fe-4S]2+ cluster of FNR with dithionite indicated that the redox potential of the +1/+2 couple is ≤−650 mV and that the [4Fe-4S]+ cluster form is, therefore, not likely to occur in vivo.

Anaerobic respiration with elemental sulfur and with disulfides

Abstract: Anaerobic respiration with elemental sulfur/polysulfide or organic disulfides is performed by several bacteria and archaea, but has only been investigated in a few organisms in detail. The electron transport chain that catalyzes polysulfide reduction in the Gram-negative bacterium Wolinella succinogenes consists of a dehydrogenase (formate dehydrogenase or hydrogenase) and polysulfide reductase. The enzymes are integrated in the cytoplasmic membrane with the catalytic subunits exposed to the periplasm. The mechanism of electron transfer from formate dehydrogenase or hydrogenase to polysulfide reductase is discussed. The catalytic subunit of polysulfide reductase belongs to the family of molybdopterin-dinucleotide-containing oxidoreductases. From the hyperthermophilic archaeon Pyrodictium abyssi isolate TAG11 an integral membrane complex has been isolated which catalyzes the reduction of sulfur with H2 as electron donor. This enzyme complex, which is composed of a hydrogenase and a sulfur reductase, contains heme groups and several iron-sulfur clusters, but does not contain molybdenum or tungsten. In methanogenic archaea, the heterodisulfide of coenzyme M and coenzyme B is the terminal electron acceptor of the respiratory chain. In methanogens belonging to the order Methanosarcinales, this respiratory chain is composed of a dehydrogenase, the membrane-soluble electron carrier methanophenazine, and heterodisulfide reductase. The catalytic subunit of heterodisulfide reductase contains only iron-sulfur clusters. An iron-sulfur cluster may directly be involved in the reduction of the disulfide substrate.

The serine, threonine, and/or tyrosine-specific protein kinases and protein phosphatases of prokaryotic organisms: a family portrait

Abstract: Inspection of the genomes for the bacteria Bacillus subtilis 168, Borrelia burgdorferi B31, Escherichia coli K-12, Haemophilus influenzae KW20, Helicobacter pylori 26695, Mycoplasma genitalium G-37, and Synechocystis sp PCC 6803 and for the archaeons Archaeoglobus fulgidus VC-16 DSM4304, Methanobacterium thermoautotrophicum delta H, and Methanococcus jannaschii DSM2661 revealed that each contains at least one ORF whose predicted product displays sequence features characteristic of eukaryote-like protein-serine/threonine/tyrosine kinases and protein-serine/threonine/tyrosine phosphatases. Orthologs for all four major protein phosphatase families (PPP, PPM, conventional PTP, and low molecular weight PTP) were present in the bacteria surveyed, but not all strains contained all types. The three archaeons surveyed lacked recognizable homologs of the PPM family of eukaryotic protein-serine/threonine phosphatases; and only two prokaryotes were found to contain ORFs for potential protein phosphatases from all four major families. Intriguingly, our searches revealed a potential ancestral link between the catalytic subunits of microbial arsenate reductases and the protein-tyrosine phosphatases; they share similar ligands (arsenate versus phosphate) and features of their catalytic mechanism (formation of arseno- versus phospho-cysteinyl intermediates). It appears that all prokaryotic organisms, at one time, contained the genetic information necessary to construct protein phosphorylation–dephosphorylation networks that target serine, threonine, and/or tyrosine residues on proteins. However, the potential for functional redundancy among the four protein phosphatase families has led many prokaryotic organisms to discard one, two, or three of the four.

Horizontal gene transfer from transgenic plants to terrestrial bacteria--a rare event?

Abstract: Today, 12 years after the first field release of a genetically modified plant (GMP), over 15 000 field trials at different locations have been performed. As new and unique characteristics are frequently introduced into GMPs, risk assessment has to be performed to assess their ecological impact. The possibilities of horizontal gene transfer (HGT; no parent-to-offspring transfer of genes) from plants to microorganisms are frequently evaluated in such risk assessments of GMPs before release into the field. In this review we indicate why putative HGT from plants to terrestrial (soil and plant associated) bacteria has raised concern in biosafety evaluations. Further, we discuss possible pathways of HGT from plants to bacteria, outline the barriers to HGT in bacteria, describe the strategies used to investigate HGT from plants to bacteria and summarize the results obtained. Only a few cases of HGT from eukaryotes such as plants to bacteria have been reported to date. These cases have been ascertained after comparison of DNA sequences between plants and bacteria. Although experimental approaches in both field and laboratory studies have not been able to confirm the occurrence of such HGT to naturally occurring bacteria, recently two studies have shown transfer of marker genes from plants to bacteria based on homologous recombination. The few examples of HGT indicated by DNA sequence comparisons suggest that the frequencies of evolutionarily successful HGT from plants to bacteria may be extremely low. However, this inference is based on a small number of experimental studies and indications found in the literature. Transfer frequencies should not be confounded with the likelihood of environmental implications, since the frequency of HGT is probably only marginally important compared with the selective force acting on the outcome. Attention should therefore be focused on enhancing the understanding of selection processes in natural environments. Only an accurate understanding of these selective events will allow the prediction of possible consequences of novel genes following their introduction into open environments.

GSP-dependent protein secretion in Gram-negative bacteria: the Xcp system of Pseudomonas aeruginosa

Abstract: Bacteria have evolved several secretory pathways to release proteins into the extracellular medium. In Gram-negative bacteria, the exoproteins cross a cell envelope composed of two successive hydrophobic barriers, the cytoplasmic and outer membranes. In some cases, the protein is translocated in a single step across the cell envelope, directly from the cytoplasm to the extracellular medium. In other cases, outer membrane translocation involves an extension of the signal peptide-dependent pathway for translocation across the cytoplasmic membrane via the Sec machinery. By analogy with the so-called general export pathway (GEP), this latter route, including two separate steps across the inner and the outer membrane, was designated as the general secretory pathway (GSP) and is widely conserved among Gram-negative bacteria. In their great majority, exoproteins use the main terminal branch (MTB) of the GSP, namely the Xcp machinery in Pseudomonas aeruginosa, to reach the extracellular medium. In this review, we will use the P. aeruginosa Xcp system as a basis to discuss multiple aspects of the GSP mechanism, including machinery assembly, exoprotein recognition, energy requirement and pore formation for driving through the outer membrane.

Biotransformation of monoterpenes, bile acids, and other isoprenoids in anaerobic ecosystems

Abstract: Isoprenoic compounds play a major part in the global carbon cycle. Biosynthesis and mineralization by aerobic bacteria have been intensively studied. This review describes our knowledge on the anaerobic metabolism of isoprenoids, mainly by denitrifying and fermentative bacteria. Nitrate-reducing β-Proteobacteria were isolated on monoterpenes as sole carbon source and electron donor. Thauera spp. were obtained on the oxygen-containing monoterpenes linalool, menthol, and eucalyptol. Several strains of Alcaligenes defragrans were isolated on unsaturated monoterpenes as growth substrates. A novel denitrifying β-Proteobacterium, strain 72Chol, mineralizes cholesterol completely to carbon dioxide. Physiological studies showed the presence of several oxidative pathways in these microorganisms. Investigations by organic geochemists indicate possible contributions of anaerobes to early diagenetic processes. One example, the formation of p-cymene from monoterpenes, could indeed be detected in methanogenic enrichment cultures. In man, cholic acid (CA) and chenodeoxycholic acid (CDCA), are synthesized in the liver from cholesterol. During their enterohepatic circulation, bile acids are biotransformed by the intestinal microflora into a variety of metabolites. Known bacterial biotransformations of conjugated bile acids include: deconjugation, oxidation of hydroxy groups at C-3, C-7 and C-12 with formation of oxo bile acids and reduction of these oxo groups to either α- or β-configuration. Quantitatively, the most important bacterial biotransformation is the 7α-dehydroxylation of CA and CDCA yielding deoxycholic acid and lithocholic acid, respectively. The 7α-dehydroxylation of CA occurs via a novel six-step biochemical pathway. The genes encoding several enzymes that either transport bile acids or catalyze various reactions in the 7α-dehydroxylation pathway of Eubacterium sp. strain VPI 12708 have been cloned, expressed in Escherichia coli, purified, and characterized.

Biochemistry of coenzyme B12-dependent glycerol and diol dehydratases and organization of the encoding genes

Abstract: Glycerol and diol dehydratases exhibit a subunit composition of α2β2γ2 and contain coenzyme B12 in the base-on form. The dehydratase reaction proceeds via a radical mechanism. The dehydratases are subject to reaction inactivation by the substrate glycerol which is caused by a cessation of the catalytic cycle because coenzyme B12 is not regenerated, instead 5′-deoxyadenosine and a catalytically inactive cobalamin are formed. The genetic organization of the dehydratase genes is quite similar in all organisms. Downstream of the dehydratase genes an open reading frame encoding a polypeptide of approximately 600 amino acids was identified which is apparently involved in the reactivation of suicide-inactivated enzyme.

A structural comparison of molybdenum cofactor-containing enzymes

Abstract: This work gives an overview of the recent achievements which have contributed to the understanding of the structure and function of molybdenum and tungsten enzymes. Known structures of molybdo-pterin cofactor-containing enzymes will be described briefly and the structural differences between representatives of the same and different families will be analyzed. This comparison will show that the molybdo-pterin cofactor-containing enzymes represent a very heterogeneous group with differences in overall enzyme structure, cofactor composition and stoichiometry, as well as differences in the immediate molybdenum environment. Two recently discovered molybdo-pterin cofactor-containing enzymes will be described with regard to molecular and EPR spectroscopic properties, pyrogallol-phloroglucinol transhydroxylase from Pelobacter acidigallici and acetylene hydratase from Pelobacter acetylenicus. On the basis of its amino acid sequence, transhydroxylase can be classified as a member of the dimethylsulfoxide reductase family, whereas classification of the tungsten/molybdenum-containing acetylene hydratase has to await the determination of its amino acid sequence.

Control of genes for conjugative transfer of plasmids and other mobile elements

Abstract: Conjugative transfer is a primary means of spread of mobile genetic elements (plasmids and transposons) between bacteria. It leads to the dissemination and evolution of the genes (such as those conferring resistance to antibiotics) which are carried by the plasmid. Expression of the plasmid genes needed for conjugative transfer is tightly regulated so as to minimise the burden on the host. For plasmids such as those belonging to the IncP group this results in downregulation of the transfer genes once all bacteria have a functional conjugative apparatus. For F-like plasmids (apart from F itself which is a derepressed mutant) tight control results in very few bacteria having a conjugative apparatus. Chance encounters between the rare transfer-proficient bacteria and a potential recipient initiate a cascade of transfer which can continue until all potential recipients have acquired the plasmid. Other systems express their transfer genes in response to specific stimuli. For the pheromone-responsive plasmids of Enterococcus it is small peptide signals from potential recipients which trigger the conjugative transfer genes. For the Ti plasmids of Agrobacterium it is the presence of wounded plants which are susceptible to infection which stimulates T-DNA transfer to plants. Transfer and integration of T-DNA induces production of opines which the plasmid-positive bacteria can utilise. They multiply and when they reach an appropriate density their plasmid transfer system is switched on to allow transfer of the Ti plasmid to other bacteria. Finally some conjugative transfer systems are induced by the antibiotics to which the elements confer resistance. Understanding these control circuits may help to modify management of microbial communities where plasmid transfer is either desirable or undesirable.

Rolling‐circle plasmids from Bacillus subtilis: complete nucleotide sequences and analyses of genes of pTA1015, pTA1040, pTA1050 and pTA1060, and comparisons with related plasmids from Gram‐positive bacteria

Abstract: Most small plasmids of Gram-positive bacteria use the rolling-circle mechanism of replication and several of these have been studied in considerable detail at the DNA level and for the function of their genes. Although most of the common laboratory Bacillus subtilis 168 strains do not contain plasmids, several industrial strains and natural soil isolates do contain rolling-circle replicating (RCR) plasmids. So far, knowledge about these plasmids was mainly limited to: (i) a classification into seven groups, based on size and restriction patterns; and (ii) DNA sequences of the replication region of a limited number of them. To increase the knowledge, also with respect to other functions specified by these plasmids, we have determined the complete DNA sequence of four plasmids, representing different groups, and performed computer-assisted and experimental analyses on the possible function of their genes. The plasmids analyzed are pTA1015 (5.8 kbp), pTA1040 (7.8 kbp), pTA1050 (8.4 kbp), and pTA1060 (8.7 kbp). These plasmids have a structural organization similar to most other known RCR plasmids. They contain highly related replication functions, both for leading and lagging strand synthesis. pTA1015 and pTA1060 contain a mobilization gene enabling their conjugative transfer. Strikingly, in addition to the conserved replication modules, these plasmids contain unique module(s) with genes which are not present on known RCR plasmids of other Gram-positive bacteria. Examples are genes encoding a type I signal peptidase and genes encoding proteins belonging to the family of response regulator aspartate phosphatases. The latter are likely to be involved in the regulation of post-exponential phase processes. The presence of these modules on plasmids may reflect an adaptation to the special conditions to which the host cells were exposed.

Tricarboxylic acid cycle and anaplerotic enzymes in rhizobia

Abstract: Rhizobia are a diverse group of Gram-negative bacteria comprised of the genera Rhizobium, Bradyrhizobium, Mesorhizobium, Sinorhizobium and Azorhizobium. A unifying characteristic of the rhizobia is their capacity to reduce (fix) atmospheric nitrogen in symbiotic association with a compatible plant host. Symbiotic nitrogen fixation requires a substantial input of energy from the rhizobial symbiont. This review focuses on recent studies of rhizobial carbon metabolism which have demonstrated the importance of a functional tricarboxylic acid (TCA) cycle in allowing rhizobia to efficiently colonize the plant host and/or develop an effective nitrogen fixing symbiosis. Several anaplerotic pathways have also been shown to maintain TCA cycle activity under specific conditions. Biochemical and physiological characterization of carbon metabolic mutants, along with the analysis of cloned genes and their corresponding gene products, have greatly advanced our understanding of the function of enzymes such as citrate synthase, oxoglutarate dehydrogenase, pyruvate carboxylase and malic enzymes. However, much remains to be learned about the control and function of these and other key metabolic enzymes in rhizobia.

Elucidation of novel biosynthetic pathways and metabolite flux patterns by retrobiosynthetic NMR analysis

Abstract: The labelling patterns of metabolites from experiments with stable isotope-labelled precursors can be determined by NMR spectroscopy. Complex isotopomer mixtures are found when general metabolites such as glucose are used as stable isotope-labelled precursors which are diverted to all branches of intermediary metabolism. The complex results can be interpreted by a pattern recognition approach based on comparison between the labelling patterns of secondary metabolites and primary metabolites such as amino acids and ribonucleosides. The isotope labelling patterns of intermediates in central metabolic pools such as carbohydrate phosphates, dicarboxylic acids, and acetyl CoA can be obtained by biosynthetic retroanalysis. Biosynthetic pathways as well as metabolite flux patterns can be determined from these data. The method is illustrated using the classical mevalonate pathway and the more recently discovered deoxyxylulose pathway of terpenoid biosynthesis as examples. Applications of the retrobiosynthetic method of the biosynthesis of molybdopterin and of riboflavin are also discussed. Stable isotope experiments monitored by NMR spectroscopy have also been shown to be a powerful tool for the elucidation of metabolic flux in microorganisms with unusual lifestyles and in fermentation processes.

Radical species in the catalytic pathways of enzymes from anaerobes

Abstract: Radicals are reactive intermediates of growing importance in enzymatic catalysis. There are reactions in which neutral radicals participate and those where radical anions are involved. The former class is illustrated by lysine 2,3-aminomutase and also by enzymes dependent on coenzyme B12, that catalyse carbon skeleton rearrangements (e.g. glutamate mutase). A substrate-based radical for both lysine 2,3-aminomutase and glutamate mutase has been characterised by EPR spectroscopy. Representatives of the second class are 2-hydroxyglutaryl-CoA dehydratase, benzoyl-CoA reductase, DNA photolyase and chorismate synthase, all of which may generate the radical anion by one-electron reduction. 4-Hydroxybutyryl-CoA dehydratase, pyruvate formate lyase, and the coenzyme B12-dependent eliminases (ribonucleotide reductase, ethanolamine ammonia lyase and diol dehydratase) could be examples of radical anion formation by one-electron oxidation. The electron-rich ketyl-like radical anions cause the elimination of an adjacent group. The advantages of using radicals as intermediates in enzymatic transformations are their high reactivity and special properties. However, this reactivity includes rapid bimolecular combination with dioxygen and radicals are therefore primarily utilised as intermediates by anaerobic organisms.

Comparing genomes in terms of protein structure: surveys of a finite parts list

Abstract: We give an overview of the emerging field of structural genomics, describing how genomes can be compared in terms of protein structure. As the number of genes in a genome and the total number of protein folds are both quite limited, these comparisons take the form of surveys of a finite parts list, similar in respects to demographic censuses. Fold surveys have many similarities with other whole-genome characterizations, e.g., analyses of motifs or pathways. However, structure has a number of aspects that make it particularly suitable for comparing genomes, namely the way it allows for the precise definition of a basic protein module and the fact that it has a better defined relationship to sequence similarity than does protein function. An essential requirement for a structure survey is a library of folds, which groups the known structures into 'fold families.' This library can be built up automatically using a structure comparison program, and we described how important objective statistical measures are for assessing similarities within the library and between the library and genome sequences. After building the library, one can use it to count the number of folds in genomes, expressing the results in the form of Venn diagrams and 'top-10' statistics for shared and common folds. Depending on the counting methodology employed, these statistics can reflect different aspects of the genome, such as the amount of internal duplication or gene expression. Previous analyses have shown that the common folds shared between very different microorganisms, i.e., in different kingdoms, have a remarkably similar structure, being comprised of repeated strand-helix-strand super-secondary structure units. A major difficulty with this sort of 'fold-counting' is that only a small subset of the structures in a complete genome are currently known and this subset is prone to sampling bias. One way of overcoming biases is through structure prediction, which can be applied uniformly and comprehensively to a whole genome. Various investigators have, in fact, already applied many of the existing techniques for predicting secondary structure and transmembrane (TM) helices to the recently sequenced genomes. The results have been consistent: microbial genomes have similar fractions of strands and helices even though they have significantly different amino acid composition. The fraction of membrane proteins with a given number of TM helices falls off rapidly with more TM elements, approximately according to a Zipf law. This latter finding indicates that there is no preference for the highly studied 7-TM proteins in microbial genomes. Continuously updated tables and further information pertinent to this review are available over the web at http://bioinfo.mbb.yale.edu/genome.

Mechanistic aspects of molybdenum-containing enzymes

Abstract: In the past several years, the number of enzymes known to possess mononuclear molybdenum centers in their active sites has increased significantly, and well over 50 such enzymes have been identified that catalyze a variety of hydroxylation, oxygen atom transfer and other oxidation-reduction reactions. Many of these enzymes have been isolated from either obligate anaerobes or facultative anaerobes grown under anaerobic or microaerobic conditions, and are involved in a variety of anabolic, catabolic and energy-conserving metabolic pathways. There are now several enzymes having known crystal structure, and this new structural information has provided the basis for an increasingly detailed understanding of the mechanisms of action of these enzymes. In the present review, an overview of our present understanding of the mechanism of action of these enzymes will be presented, and those of a few selected enzymes will be considered in greater detail. Several alternative classification schemes have been suggested for these molybdenum-containing enzymes, but for the purposes of the present discussion they will be considered to fall into three families, based on the structures of their molybdenum centers in their oxidized Mo(VI) state (Fig. 1) [1]. These families include: (i) the molybdenum hydroxylases, a large and broadly dispersed family of enzymes that possess an MoOS unit and catalyze the hydroxylation of a broad range of aldehydes and aromatic heterocycles; (ii) the eukaryotic oxo transferases, a family that at present includes only sulfite oxidase and the assimilatory nitrate reductases, enzymes which possess an MoO2 unit in their active sites and which catalyze oxygen atom transfer to or from a substrate; and finally (iii) a diverse group of prokaryotic enzymes that catalyze either oxo atom transfer or other oxidation-reduction reactions. As will be seen below, however, some may catalyze …

Genome evolution within the alpha Proteobacteria: why do some bacteria not possess plasmids and others exhibit more than one different chromosome?

Abstract: Animal intracellular Proteobacteria of the alpha subclass without plasmids and containing one or more chromosomes are phylogenetically entwined with opportunistic, plant-associated, chemoautotrophic and photosynthetic alpha Proteobacteria possessing one or more chromosomes and plasmids. Local variations in open environments, such as soil, water, manure, gut systems and the external surfaces of plants and animals, may have selected alpha Proteobacteria with extensive metabolic alternatives, broad genetic diversity, and more flexible and larger genomes with ability for horizontal gene flux. On the contrary, the constant and isolated animal cellular milieu selected heterotrophic alpha Proteobacteria with smaller genomes without plasmids and reduced genetic diversity as compared to their plant-associated and phototrophic relatives. The characteristics and genome sizes in the extant species suggest that a second chromosome could have evolved from megaplasmids which acquired housekeeping genes. Consequently, the genomes of the animal cell-associated Proteobacteria evolved through reductions of the larger genomes of chemoautotrophic ancestors and became rich in adenosine and thymidine, as compared to the genomes of their ancestors. Genome organisation and phylogenetic ancestor–descendent relationships between extant bacteria of closely related genera and within the same monophyletic genus and species suggest that some strains have undergone transition from two chromosomes to a single replicon. It is proposed that as long as the essential information is correctly expressed, the presence of one or more chromosomes within the same genus or species is the result of contingency. Genetic drift in clonal bacteria, such as animal cell-associated alpha Proteobacteria, would depend almost exclusively on mutation and internal genetic rearrangement processes. Alternatively, genomic variations in reticulate bacteria, such as many intestinal and plant cell-associated Proteobacteria, will depend not only on these processes, but also on their genetic interactions with other bacterial strains. Common pathogenic domains necessary for the invasion and survival in association with cells have been preserved in the chromosomes of the animal and plant-associated alpha Proteobacteria. These pathogenic domains have been maintained by vertical inherence, extensively ameliorated to match the chromosome G+C content and evolved within chromosomes of alpha Proteobacteria.

Hydropathy profile alignment: a tool to search for structural homologues of membrane proteins

Abstract: Hydropathy profile alignment is introduced as a tool in functional genomics. The architecture of membrane proteins is reflected in the hydropathy profile of the amino acid sequence. Both secondary and tertiary structural elements determine the profile which provides enough sensitivity to detect evolutionary links between membrane proteins that are based on structural rather than sequence similarities. Since structure is better conserved than amino acid sequence, the hydropathy profile can detect more distant evolutionary relationships than can be detected by the primary structure. The technique is demonstrated by two approaches in the analysis of a subset of membrane proteins coded on the Escherichia coli and Bacillus subtilis genomes. The subset includes secondary transporters of the 12 helix type. In the first approach, the hydropathy profiles of proteins for which no function is known are aligned with the profiles of all other proteins in the subset to search for structural paralogues with known function. In the second approach, family hydropathy profiles of 8 defined families of secondary transporters that fall into 4 different structural classes (SC-ST1–4) are used to screen the membrane protein set for members of the structural classes. The analysis reveals that over 100 membrane proteins on each genome fall in only two structural classes. The largest structural class, SC-ST1, correlates largely with the Major Facilitator Superfamily defined before, but the number of families within the class has increased up to 57. The second large structural class, SC-ST2 contains secondary transporters for amino acids and amines and consists of 12 families.

To be or not to be: the ultimate decision of the growth‐arrested bacterial cell

Abstract: The evolutionary survival of prokaryotes has depended not only on their performance during conditions that allow rapid growth, but also on their ability to adjust their internal affairs to enhance survival during prolonged periods of growth arrest. The small size of prokaryotes limits their ability to control their environment, and instead, their ability to cope with environmental challenges must rely on rapid and efficient control of gene expression. The majority of genes responding to a specific environmental condition causing growth arrest are, in general, uniquely induced by one specific stimulus. However, many genes, operons and regulons do not exclusively respond to one particular stress condition, and some regulons appear to be related in the sense that they share member genes. Furthermore, growth-arrest conditions activate several seemingly unlinked regulatory networks and several genes/proteins seem to respond to growth arrest in general. These proteins are interesting because we know very little about why growth-arrested, stationary phase cells ultimately die, and functional analysis of such general responders to growth arrest may help us to understand the genetic/biochemical basis for the bacterial defence against ageing processes. In this paper I review recent findings suggesting that several general responders to stasis form an integral part of a defence system aimed at avoiding the damaging effects of endogenously generated oxygen radicals. In addition, the curious finding that some proteins of a regulon are involved in enhancing the life-span of the growth-arrested cell while other members of the same regulon are devoted to killing it will be discussed.

The genome of Treponema pallidum: new light on the agent of syphilis

Abstract: Treponema pallidum subsp, pallidum, the causative agent of the sexually transmitted disease syphilis, is a fastidious, microaerophilic obligate parasite of humans. This bacterium is one of the few prominent infectious agents that has not been cultured continuously in vitro and consequently relatively little is known about its virulence mechanisms at the molecular level. T. pallidum therefore represented an attractive candidate for genomic sequencing. The complete genome sequence of T. pallidum has now been completed and comprises 1,138,006 base pairs containing 1041 predicted protein coding sequences. An important goal of this project is to identify possible virulence factors. Analysis of the genome indicates a number of potential virulence factors including a family of 12 proteins related to the Msp protein of Treponema denticola, a number of putative hemolysins, as well as several other classes of proteins of interest. The results of this analysis are reviewed in this article and indicate the value of whole genome sequences for rapidly advancing knowledge of infectious agents.

Indigo: a World-Wide-Web review of genomes and gene functions.

Abstract: The present article describes a genome database reviewing gene-related knowledge of two model bacteria, Bacillus subtilis and Escherichia coli. The database, Indigo, is open through the World-Wide Web (http://indigo.genetique.uvsq.fr). The concept used for organising the data, the concept of neighbourhood, allows one to explore the database content in an efficient although somewhat unusual way. Here, genes are related to each other by a variety of neighbourhoods, including proximity in the chromosome, phylogenetic kinship, participation in a common metabolic pathway, common presence in an article of the literature, or similar use of the genetic code. Several examples illustrate how this concept of neighbourhood permits one to review the available knowledge about a given gene or gene family, and elaborate unexpected, but revealing, analyses about gene functions.

Adhesive interactions between medically important yeasts and bacteria

Abstract: Yeasts are being increasingly identified as important organisms in human infections. Adhesive interactions between yeasts and bacteria may contribute to yeast retention at body sites. Methods for studying adhesive interactions between bacterial strains are well known, and range from simple macroscopic methods to flow chamber systems with complex image analysis capabilities. The adhesive interactions between bacteria and yeasts have been studied employing several of the methods originally developed for studying adhesive interactions between bacteria. However, in many of the methods employed the larger size of the yeasts as compared with bacteria results in strong sedimentation of the yeasts, often invalidating the method adapted. In addition, most methods are semi-quantitative and do not properly control mass transport. Consequently, adhesive interaction mechanisms between yeasts and bacteria identified hitherto, including lectin binding and protein-protein interactions, must be regarded with caution. Extensive physico-chemical characteristics of yeast cell surfaces are not available and a physico-chemical mechanism has not yet been put forth. A new method for quantifying adhesive interactions between yeasts and bacteria is proposed, based on the use of a parallel plate flow chamber, in which the influence of adhering bacteria upon the kinetics of yeast adhesion and aggregation of the adhering yeasts is quantitatively evaluated, under carefully controlled mass transport.

Adhesin–receptor interactions in Pasteurellaceae

Abstract: The ability of bacteria to adhere to mucosal epithelium is dependent on the expression of adhesive molecules or structures, called adhesins, that allow attachment of the organisms to complementary molecules on mucosal surfaces, the receptors. Important human and animal pathogens are found among the Pasteurellaceae family which includes Haemophilus, Actinobacillus, and Pasteurella organisms. The purpose of this paper is to review the adhesin-receptor systems found in Pasteurellaceae, with an emphasis on recent developments in this specific area. Most of these organisms can employ multiple molecular mechanisms of adherence (or multiple adhesins) to initiate infection. Indeed, a wide variety of adhesins are expressed by members of the Pasteurellaceae, and different proteins (e.g. fimbriae, fibrils, outer membrane proteins) as well as polysaccharides (lipooligosaccharides, lipopolysaccharides, capsular polysaccharides) were clearly shown to play an important role in adherence. In many instances, these adhesins have proved to represent good vaccine candidates. Surprisingly, the receptors on host mucosal surfaces have yet been identified in very few cases.