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PubMed2005

Genetic control for light-induced carotenoid production in non-phototrophic bacteria.

Carotenoids are naturally occurring yellow or orange pigments that serve as a protectant against photo-oxidative damages. Among the wide variety of producers, the prokaryotes generate a broad spectrum of carotenoids with diverse chemical structures that are expected to have a high potential in biotechnological applications. Bacterial carotenogenesis occurs in a constitutive or light-induced manner, which suggests the diversity of the regulatory mechanism. The mechanism for light-induced carotenoid production in non-phototrophic bacteria has been studied in detail in Myxococcus xanthus, a Gram-negative gliding bacterium. The complicated mechanism involves the activation of an extracytoplasmic function (ECF) sigma factor (CarQ), which leads to the sequestration of a MerR family transcriptional regulator (CarA) that represses the expression of the carotenoid biosynthesis genes in the dark. Recently, we identified another regulatory mechanism for light-induced carotenogenesis in Streptomyces coelicolor A3(2), a Gram-positive soil bacterium. In this organism, the transcription of the carotenoid biosynthesis gene cluster is specified by LitS, a photo-inducible ECF sigma factor. The evidence indicates that the photo-dependent transcription of litS is mediated by LitR, a MerR family transcriptional regulator. In addition, it is suggested that the conformational alteration of LitR upon receiving the illumination signal determines its binding to DNA. The carboxy-terminal domain of LitR contains a possible binding site for Vitamin B12, which may serve as a capturing apparatus for the illumination signal.

Bacterial Proteins↗
PubMed1991

Nucleoside diphosphate kinase from Escherichia coli; its overproduction and sequence comparison with eukaryotic enzymes.

The gene encoding nucleoside diphosphate (NDP) kinase of Escherichia coli was identified by polymerase chain reaction using oligodeoxyribonucleotide primers synthesized on the basis of consensus sequences from Myxococcus xanthus and various eukaryotic NDP kinases. The gene (ndk), mapped at 54.2 min on the E. coli chromosome, was cloned and sequenced. The E. coli NDP kinase was found to consist of 143 amino acid residues that are 57, 45, 45, 42, 43, and 43% identical to the M. xanthus, Dictyostelium discoideum, Drosophila melanogaster, mouse, rat, and human enzymes, respectively. The ndk gene appears to be in a monocistronic operon and, when cloned in a pUC vector, NDP kinase was overproduced at a level of approx. 25% of total cellular proteins. The protein could be labeled with [gamma-32P]ATP and migrated at a 16.5 kDa when electrophoresed in SDS-polyacrylamide gel, which is in good agreement with the Mr of the purified E. coli NDP kinase previously reported.

Amino Acid Sequence↗
PubMed2005

A continuous fluorimetric assay for protoporphyrinogen oxidase by monitoring porphyrin accumulation.

A continuous spectrofluorimetric assay for protoporphyrinogen oxidase (PPO, EC 1.3.3.4) activity has been developed using a 96-well plate reader. Protoporphyrinogen IX, the tetrapyrrole substrate, is a colorless nonfluorescent compound. The evolution of the fluorescent tetrapyrrole product, protoporphyrin IX, was detected using a fluorescence plate reader. The apparent Km (Kapp) values for protoporphyrinogen IX were measured as 3.8+/-0.3, 3.6+/-0.5, and 1.0+/-0.1 microM for the enzymes from human, Myxococcus xanthus, and Aquifex aeolicus, respectively. The Ki for acifluorfen, a diphenylether herbicide, was measured as 0.53 microM for the human enzyme. Also, the specific activity of mouse liver mitochondrial PPO was measured as 0.043 nmol h-1/mg mitochondria, demonstrating that this technique is useful for monitoring low-enzyme activities. This method can be used to accurately measure activities as low as 0.5 nM min-1, representing a 50-fold increase in sensitivity over the currently used discontinuous assay. Furthermore, this continuous assay may be used to monitor up to 96 samples simultaneously. These obvious advantages over the discontinuous assay will be of importance for both the kinetic characterization of recombinant PPOs and the detection of low concentrations of this enzyme in biological samples.

Bacteria↗
PubMed2006

Taxonomic characterization of members of the genus Corallococcus: molecular divergence versus phenotypic coherency.

Corallococcus coralloides DSM 2259(T), Corallococcus exiguus DSM 14696(T), Corallococcus macrosporus DSM 14697(T) and more than 35 strains identified as members of Corallococcus on the basis of morphology were subjected to partial sequences analysis of three housekeeping genes (lepA, fusA and rpoB), complementing a recent phylogenetic analysis based on genes coding for 16S rRNA and gyrB. Phylogenetic analysis of each gene, generated by maximum likelihood and two different additive treeing algorithms, resulted in the separate position of C. macrosporus DSM 14697(T) and a few Corallococcus strains that were more closely related to Myxococcus xanthus than to the other members of Corallococcus. The latter strains formed three clearly separate clusters by 16S rRNA gene phylogeny. This relationship, however, was only partially recovered by the other gene trees. Group 1, embracing the type strains of C. coralloides and C. exiguus, only emerged as a coherent cluster in the 16S rRNA gene tree. In all other gene trees this cluster embraced organisms of cluster 3, which either formed coherent subclusters (gyrB, lepA) or which appeared polyphyletic (fusA, rpoB). Group 2 organisms consistently constituted a monophyletic cluster, though their branching within the gene trees differed. A concatenated tree, based on the analysis of about 5400 nucleotides of all five partial genes was most similar to the 16S rRNA gene tree. In order to determine whether the individual clusters that emerged by 16S rRNA gene analysis (>99.1% intracluster similarities) show phenetic properties that would allow their description as new species, a few strains of each group were subjected to the analysis of whole cell fatty acid and physiological properties. Riboprint patterns were generated for some members of group 1. While the DNA-DNA reassociation values and riboprint patterns confirmed the genomic heterogeneity of members of cluster 1, none of the other properties investigated were sufficiently discriminative to allow the formal description of strain clusters as new species.

Bacterial Proteins↗
PubMed2005

Making waves: pattern formation by a cell-surface-associated signal.

Starving Myxococcus xanthus cells organize into two strikingly different spatio-temporal patterns, either rippling or aggregation of cells into fruiting bodies. Formation of both patterns depends on a cell-surface-associated, non-diffusible signal, the C-signal. A key motility parameter modulated by the C-signal during pattern formation is the frequency at which cells reverse their gliding direction, with low and high levels of C-signalling causing an increase and a decrease in the reversal frequency, respectively. Recently, a simple yet elegant mathematical model was proposed to explain the mechanism underlying the non-linear dependence of the reversal frequency on C-signalling levels. The mathematical solution hinges on the introduction of a negative feedback loop into the biochemical circuit that regulates the reversal frequency. This system displays an oscillatory behaviour in which the oscillation frequency depends in a non-monotonic manner on the level of C-signalling. Thus, the biochemical oscillator recapitulates the effect of the C-signal on the reversal frequency. The challenge for biologists now is to test the mathematical model experimentally.

Bacterial Proteins↗
PubMed2006

A myxobacterial S-motility protein dances with poles.

Coordinated movement of packs of S-motile Myxococcus xanthus cells relies on extrusion and retraction of pili that are located at one cell pole. At regular intervals the pili switch their polar location and cells reverse direction. Recently, the FrzS S-motility protein was observed to localize predominantly to the piliated pole. In time, FrzS was redeployed to the opposite pole and its sequestration at the new site coincided with cell reversal. The C-terminal region of FrzS, a response regulator homolog, is rich in coiled-coil motifs and is required for dynamic localization and proper motility. These results raise the possibility that proper spatial control of FrzS has an important role in the regulation of cell reversal and S-motility.

Bacterial Proteins↗
PubMed1998

Kinetic stabilisation of a modular protein by domain interactions.

Protein S, a two-domain spore coat protein from Myxococcus xanthus, is structurally related to eye-lens Pr crystallins. No natural monomeric one-domain member of this protein superfamily is known. To determine the stability of the single domains and to explain the ubiquitous domain duplication, the isolated domains of protein S were constructed. The N-domain is thermodynamically more stable than the C-domain. In intact protein S, domain interactions lead to an apparent decrease in stability of the N-terminal domain, whereas the C-terminal domain is stabilised. In contrast, unfolding kinetics of both domains are decreased 100-fold due to interactions in the complete molecule.

Bacterial Proteins↗
PubMed1999

Cell fate and organogenesis in bacteria.

Intercellular signaling through the Notch receptor and its ligands leads to the spatial differentiation of cell fate in vertebrates and invertebrates. In Myxococcus xanthus, fruiting-body development requires the transmission of a cell-bound intercellular signal by the protein called C-factor, which is functionally equivalent to the eukaryotic Notch ligands. Functional parallels between these two signaling systems include strong positive and negative feedback, and a consequent role in spatial differentiation. Consideration of these parallels enables us to make testable experimental predictions about Notch and C-signaling.

Animals↗
PubMed1996

Positive-negative KG cassettes for construction of multi-gene deletions using a single drug marker.

Positive-negative KG cassettes were developed in order to create a number of independent deletion mutations on the bacterial chromosome using a single drug marker. These cassettes consist of a kanamycin-resistant (KmR) gene for positive screening and a galactokinase gene (galK) for negative screening. Both genes are in an operon driven by the native KmR promoter and are flanked by identical fragments of yeast chromosomal DNA approximately one kb in size. An internal region of a cloned target gene of a bacterium is replaced with a cassette, which is then transformed into the bacterium. The intact gene on the chromosome is replaced with the mutated gene by homologous recombination. From the KmR cells thus obtained, those cells which lose both KmR and galK genes by homologous recombination between the identical yeast DNA fragments are subsequently screened on plates containing 2-deoxygalactose, a non-metabolizable analogue of galactose. This method was applied to isolate a triple-deletion mutant of pkn3, pkn1, and pkn11 from Myxococcus xanthus.

Anti-Bacterial Agents↗
PubMed1992

Sporulation in prokaryotes and lower eukaryotes.

During the past year, highlights in sporulation research include the demonstration that phosphorylation of SpoOA is a critical factor in Bacillus subtilis development; the identification of C alpha proteins, adenylyl cyclase and protein kinase A genes in Dictyostelium; proof that an endogenous antisense RNA regulates gene expression in Dictyostelium; and characterization of a second type of differentiated cell in Myxococcus.

Animals↗
PubMed2002

How myxobacteria glide.

BACKGROUND: Many microorganisms, including myxobacteria, cyanobacteria, and flexibacteria, move by gliding. Although gliding always describes a slow surface-associated translocation in the direction of the cell's long axis, it can result from two very different propulsion mechanisms: social (S) motility and adventurous (A) motility. The force for S motility is generated by retraction of type 4 pili. A motility may be associated with the extrusion of slime, but evidence has been lacking, and how force might be generated has remained an enigma. Recently, nozzle-like structures were discovered in cyanobacteria from which slime emanated at the same rate at which the bacteria moved. This strongly implicates slime extrusion as a propulsion mechanism for gliding. RESULTS: Here we show that similar but smaller nozzle-like structures are found in Myxococcus xanthus and that they are clustered at both cell poles, where one might expect propulsive organelles. Furthermore, light and electron microscopical observations show that slime is secreted in ribbons from the ends of cells. To test whether the slime propulsion hypothesis is physically reasonable, we construct a mathematical model of the slime nozzle to see if it can generate a force sufficient to propel M. xanthus at the observed velocities. The model assumes that the hydration of slime, a cationic polyelectrolyte, is the force-generating mechanism. CONCLUSIONS: The discovery of nozzle-like organelles in various gliding bacteria suggests their role in prokaryotic gliding. Our calculations and our observations of slime trails demonstrate that slime extrusion from such nozzles can account for most of the observed properties of A motile gliding.

Cyanobacteria↗
PubMed2003

Taxing questions in development.

Bacteria use taxis-controlled movement to reach their optimum environment. Chemotaxis is probably the best understood behavioural system in biology, biasing the normal random movement of bacteria using a phospho-relay pathway from receptors to the motility organelles. The pathways are typified by signal recognition and receptor adaptation, enabling bacteria to sense and respond to changing environments. Models have been derived from the single chemosensory pathway of Escherichia coli but the sequencing of an increasing number of bacterial genomes is revealing genes that apparently encode multiple chemosensory pathways. Recently, data have accumulated suggesting that some of these pathways might not control motility, although the mechanisms by which this might happen remain unclear. Information from the soil bacterium Myxococcus xanthus could lead the way to an understanding of such mechanisms.

Models, Genetic↗
PubMed1994

NMR-derived three-dimensional solution structure of protein S complexed with calcium.

BACKGROUND: Protein S is a developmentally-regulated Ca(2+)-binding protein of the soil bacterium Myxococcus xanthus. It functions by forming protective, multilayer spore surface assemblies which may additionally act as a cell-cell adhesive. Protein S is evolutionarily related to vertebrate lens beta gamma-crystallins. RESULTS: The three-dimensional solution structure of Ca(2+)-loaded protein S has been determined using multi-dimensional heteronuclear NMR spectroscopy. (Sixty structures were calculated, from which thirty were selected with a root mean square difference from the mean of 0.38 A for backbone atoms and 1.22 A for all non-hydrogen atoms.) The structure was analyzed and compared in detail with X-ray crystallographic structures of beta gamma-crystallins. The two internally homologous domains of protein S were compared, and hydrophobic cores, domain interfaces, surface ion pairing, amino-aromatic interactions and potential modes of multimerization are discussed. CONCLUSIONS: Structural features of protein S described here help to explain its overall thermostability, as well as the higher stability and Ca2+ affinity of the amino-terminal domain relative to the carboxy-terminal domain. Two potential modes of multimerization are proposed involving cross-linking of protein S molecules through surface Ca(2+)-binding sites and formation of the intramolecular protein S or gamma B-crystallin interdomain interface in an intermolecular content. This structural analysis may also have implications for Ca(2+)-dependent cell-cell interactions mediated by the vertebrate cadherins and Dictyostelium discoideum protein gp24.

Amino Acid Sequence↗
PubMed1994

Unusual helix-containing greek keys in development-specific Ca(2+)-binding protein S. 1H, 15N, and 13C assignments and secondary structure determined with the use of multidimensional double and triple resonance heteronuclear NMR spectroscopy.

Multidimensional heteronuclear NMR spectroscopy has been used to determine almost complete backbone and side-chain 1H, 15N, and 13C resonance assignments of calcium loaded Myxococcus xanthus protein S (173 residues). Of the range of constant-time triple resonance experiments recorded, HNCACB and CBCA(CO)NH, which correlate C alpha and C beta with backbone amide resonances of the same and the succeeding residue respectively, proved particularly useful in resolving assignment ambiguities created by the 4-fold internal homology of the protein S amino acid sequence. Extensive side-chain 1H and 13C assignments have been obtained by analysis of HCCH-TOCSY and 15N-edited TOCSY-HMQC spectra. A combination of NOE, backbone amide proton exchange, 3JNH alpha coupling constant, and chemical shift data has been used to show that each of the protein S repeat units consists of four beta-strands in a Greek key arrangement. Two of the Greek keys contain a regular alpha-helix between the third and fourth strands, resulting in an unusual and possibly unique variation on this common folding motif. Despite similarity between two nine-residue stretches in the first and third domains of protein S and one of the Ca(2+)-binding sequences in bovine brain calmodulin [Inouye, S., Franceschini, T., & Inouye, M. (1983) Proc. Natl. Acad. Sci. U.S.A. 80, 6829-6833], the protein S topology in these regions is incompatible with an EF-hand calmodulin-type Ca(2+)-binding site.

Amino Acid Sequence↗
PubMed2001

Binding of nucleotides to nucleoside diphosphate kinase: a calorimetric study.

The source of affinity for substrates of human nucleoside diphosphate (NDP) kinases is particularly important in that its knowledge could be used to design more effective antiviral nucleoside drugs (e.g., AZT). We carried out a microcalorimetric study of the binding of enzymes from two organisms to various nucleotides. Isothermal titration calorimetry has been used to characterize the binding in terms of Delta G degrees, Delta H degrees and Delta S degrees. Thermodynamic parameters of the interaction of ADP with the hexameric NDP kinase from Dictyostelium discoideum and with the tetrameric enzyme from Myxococcus xanthus, at 20 degrees C, were similar and, in both cases, binding was enthalpy-driven. The interactions of ADP, 2'deoxyADP, GDP, and IDP with the eukaryotic enzyme differed in enthalpic and entropic terms, whereas the Delta G degrees values obtained were similar due to enthalpy--entropy compensation. The binding of the enzyme to nonphysiological nucleotides, such as AMP--PNP, 3'deoxyADP, and 3'-deoxy-3'-amino-ADP, appears to differ in several respects. Crystallography of the protein bound to 3'-deoxy-3'-amino-ADP showed that the drug was in a distorted position, and was unable to interact correctly with active site side chains. The interaction of pyrimidine nucleoside diphosphates with the hexameric enzyme is characterized by a lower affinity than that with purine nucleotides. Titration showed the stoichiometry of the interaction to be abnormal, with 9--12 binding sites/hexamer. The presence of supplementary binding sites might have physiological implications.

Adenosine Diphosphate↗
PubMed2005

A novel type of geosmin biosynthesis in myxobacteria.

The biosynthesis of geosmin (1) and (1(10)E,5E)-germacradien-11-ol (2), two volatile terpenoid compounds emitted by the myxobacteria Myxococcus xanthus and Stigmatella aurantiaca, was investigated in feeding experiments with different labeled precursors. In these experiments, the volatiles released by the cell cultures grown on agar plates were collected with a closed-loop stripping apparatus (CLSA) and analyzed by GC-MS. [(2)H(10)]Leucine and [4,4,4,5,5,5-(2)H(6)]dimethylacrylate were fed to wild-type strains and bkd mutant strains, which are impaired in the degradation of leucine to isovaleryl-CoA. [(2)H(10)]Leucine was incorporated into 1 and 2 only by the wild-type strains via the biosynthetic pathway that involves leucine degradation and branching into the mevalonate pathway. Dimethylacrylyl-CoA (DMA-CoA) is an intermediate in the leucine degradation and in the recently discovered pathway from HMG-CoA to isovaleryl-CoA. The corresponding free acid, [4,4,4,5,5,5-(2)H(6)]dimethylacrylic acid, was incorporated into 1 and 2 only by the mutants impaired in leucine degradation. [4,4,6,6,6-(2)H(5)]Mevalonic acid lactone (12) was synthesized and fed to M. xanthus and S. aurantiaca wild-type strains and a double mutant strain of M. xanthus. This strain does not degrade leucine and is impaired in the reduction of 3-hydroxy-3-methylglutaryl-CoA to mevalonic acid. The mass spectral analysis of labeled 1 and 2 obtained in these feeding experiments led to a biosynthetic scheme to 1 with intermediate 2. This pathway differs from that observed in the liverwort Fossombronia pusilla and thus suggests microbial geosmin biosynthesis following a route different from that in liverworts. Our results are supported by a 1,2-hydride shift of the tertiary hydrogen atom at C-4a into the ring opposite to that in F. pusilla.

Gas Chromatography-Mass Spectrometry↗
PubMed2006

Evolution of an obligate social cheater to a superior cooperator.

Obligate relationships have evolved many times and can be parasitic or mutualistic. Obligate organisms rely on others to survive and thus coevolve with their host or partner. An important but little explored question is whether obligate status is an evolutionarily terminal condition or whether obligate lineages can evolve back to an autonomous lifestyle. The bacterium Myxococcus xanthus survives starvation by the social development of spore-bearing fruiting bodies. Some M. xanthus genotypes defective at fruiting body development in isolation can nonetheless exploit proficient genotypes in chimaeric groups. Here we report an evolutionary transition from obligate dependence on an altruistic host to an autonomous mode of social cooperation. This restoration of social independence was caused by a single mutation of large effect that confers fitness superiority over both ancestral genotypes, including immunity from exploitation by the ancestral cheater. Thus, a temporary state of obligate cheating served as an evolutionary stepping-stone to a novel state of autonomous social dominance.

Acetyltransferases↗
PubMed2005

Functional genome annotation through phylogenomic mapping.

Accurate determination of functional interactions among proteins at the genome level remains a challenge for genomic research. Here we introduce a genome-scale approach to functional protein annotation--phylogenomic mapping--that requires only sequence data, can be applied equally well to both finished and unfinished genomes, and can be extended beyond single genomes to annotate multiple genomes simultaneously. We have developed and applied it to more than 200 sequenced bacterial genomes. Proteins with similar evolutionary histories were grouped together, placed on a three dimensional map and visualized as a topographical landscape. The resulting phylogenomic maps display thousands of proteins clustered in mountains on the basis of coinheritance, a strong indicator of shared function. In addition to systematic computational validation, we have experimentally confirmed the ability of phylogenomic maps to predict both mutant phenotype and gene function in the delta proteobacterium Myxococcus xanthus.

Bacterial Proteins↗