Fructification & antagonistic effect of myxobacteria on eubacteria: lytic effect & fruiting body formation of Myxococcus, Chondrococcus & Angiococcus spp.
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[On the distribution of myxobacteria in the temperate South America (author's transl)].
60 soil samples from Southern Chile, mainly from forests and grassland, yielded six species of myxobacteria. In forest soils Myxococcus coralloides and Myxococcus fulvus occur frequently, in grassland soils Myxococcus coralloides and Archangium gephyra are predominating. Myxococcus virescens, Melittangium lichenicola, and Cytobacter fuscus have been observed rarely. It is pointed out that due to climate factors a high soil acidity causes the low nuber of myxobacter species. A comparison with the number of species in substrates from important plant formations over various climates is given.
Chile↗
Refined X-ray structure of Dictyostelium discoideum nucleoside diphosphate kinase at 1.8 A resolution.
The X-ray structure of the nucleoside diphosphate kinase (NDP kinase) from Dictyostelium discoideum has been refined at 1.8 A resolution from a hexagonal crystal form with a 17 kDa monomer in its asymmetric unit. The atomic model was derived from the previously determined structure of a point mutant of the protein. It contains 150 amino acid residues out of 155, and 95 solvent molecules. The R-factor is 0.196 and the estimated accuracy of the average atomic position, 0.25 A. The Dictyostelium structure is described in detail and compared to those of Drosophila and Myxococcus xanthus NDP kinases. The protein is a hexamer with D3 symmetry. Residues 8 to 138 of each subunit form a globular alpha/beta domain. The four-stranded beta-sheet is antiparallel; its topology is different from other phosphate transfer enzymes, and also from the HPr protein which, like NDP kinase, carries a phosphorylated histidine. The same topology is nevertheless found in several other proteins that bind mononucleotides, RNA or DNA. Strand connections in NDP kinase involve alpha-helices and a 20-residue segment called the Kpn loop. The beta-sheet is regular except for a beta-bulge in edge strand beta 2 and a gamma-turn at residue Ile120 just preceding strand beta 4. The latter may induce strain in the main chain near the active site His122. The alpha 1 beta 2 motif participates in forming dimers within the hexamer, helices alpha 1 and alpha 3, the Kpn loop and C terminus, in forming trimers. The subunit fold and dimer interactions found in Dictyostelium are conserved in other NDP kinases. Trimer interactions probably occur in all eukaryotic enzymes. They are absent in the bacterial Myxococcus xanthus enzyme which is a tetramer, even though the subunit structure is very similar. In Dictyostelium, contacts between Kpn loops near the 3-fold axis block access to a central cavity lined with polar residues and filled with well-defined solvent molecules. Biochemical data on point mutants highlight the contribution of the Kpn loop to protein stability. In Myxococcus, the Kpn loops are on the tetramer surface and their sequence is poorly conserved. Yet, their conformation is maintained and they make a similar contribution to the substrate binding site.
Amino Acid Sequence↗
Phylogenetic comparison of retron elements among the myxobacteria: evidence for vertical inheritance.
Twenty-eight myxobacterial strains, representing members from all three subgroups, were screened for the presence of retron elements, which are novel prokaryotic retroelements encoding reverse transcriptase. The presence of retrons was determined by assaying strains for a small satellite DNA produced by reverse transcription called multicopy, single-stranded DNA (msDNA). An msDNA-producing retron appeared to be absent from only one of the strains surveyed. DNA hybridization experiments revealed that retron elements similar to retron Mx162, first identified in Myxococcus xanthus, were found only among members of the Myxococcus subgroup; that is, each of the seven different genera which constitute this subgroup contained a Mx162 homolog. Another retron element also appeared to have a clustered distribution, being found exclusively within the Nannocystis subgroup of the myxobacteria. A retron element of the Mx162 type was cloned from Melittangium lichenicola, and its DNA sequence was compared with those of similar elements in M. xanthus and Stigmatella aurantiaca. Together, the degree of sequence diversity, the codon bias of the reverse transcriptase genes, and the clustered distribution of these retrons suggest a possible evolutionary scenario in which a common ancestor of the Myxococcus subgroup may have acquired this retroelement.
Amino Acid Sequence↗
A microbial genetic journey.
Fortunately, I began research in 1950 when the basic concepts of microbial genetics could be explored experimentally. I began with bacteriophage lambda and tried to establish the colinearity of its linkage map with its DNA molecule. My students and I worked out the regulation of lambda repressor synthesis for the establishment and maintenance of lysogeny. We also investigated the proteins responsible for assembly of the phage head. Using cell extracts, we discovered how to package DNA inside the head in vitro. Around 1972, I began to use molecular genetics to understand the developmental biology of Myxococcus xanthus. In particular, I wanted to learn how myxococcus builds its multicellular fruiting body within which it differentiates spores. We identified two cell-to-cell signals used to coordinate development. We have elucidated, in part, the signal transduction pathway for C-signal that directs the morphogenesis of a fruiting body.
Bacterial Proteins↗
[Occurrence and distribution of fruiting body-forming myxobacteria in Siebengebirge. Comparative studies with special reference to characteristic biotypes].
In the region of the "Siebengebirge" near Bonn, six characteristic biotopes were studied with respect to the occurrence of fruiting body forming myxobacteria. 23 different species, belonging to the 8 known genera, were found. The number of species in the respective biotopes varied between 6 and 17, the average numbers of species per sampling area were between 2.1 and 10.0. 15 species were found on dung pellets of wild living herbivorous mammals. Deciduous forest soils contained 13 species in spring, 17 species in autumn. Rock coverings contained 14, creek slopes 16, bark of living trees 9, and rotting wood 16 fruiting myxobacterial species. Myxococcus fulvus, Myxococcus coralloides and Archangium gephyra occurred in all biotops studied. The rare species were Melittangium boletus, Polyangium vitellinum, Stigmatella aurantiaca, and Chondramyces apiculatus. The composition of the myxobacterial flora depends on ecological factors (kind of dung pellets, rock, bark and pH). The ecological influences upon the distribution are discussed.
Altitude↗
The correlation between morphological and phylogenetic classification of myxobacteria.
In order to determine whether morphological criteria are suitable to affiliate myxobacterial strains to species, a phylogenetic analysis of 16S rDNAs was performed on 54 myxobacterial strains that represented morphologically 21 species of the genera Angiococcus, Archangium, Chondromyces, Cystobacter, Melittangium, Myxococcus, Polyangium and Stigmatella, five invalid species and three unclassified isolates. The analysis included 12 previously published sequences. The branching pattern confirmed the deep trifurcation of the order Myxococcales. One lineage is defined by the genera Cystobacter, Angiococcus, Archangium, Melittangium, Myxococcus and Stigmatella. The study confirms the genus status of 'Corallococcus', previously 'Chondrococcus', within the family Myxococcaceae. The second lineage contains the genus Chondromyces and the species Polyangium ('Sorangium') cellulosum, while the third lineage is comprised of Nannocystis and a strain identified as Polyangium vitellinum. With the exception of a small number of strains that did not cluster phylogenetically with members of the genus to which they were assigned by morphological criteria ('Polyangium thaxteri' Pl t3, Polyangium cellulosum ATCC 25531T, Melittangium lichenicola ATCC 25947T and Angiococcus disciformis An d1), the phenotypic classification should provide a sound basis for the description of neotype species in those cases where original strain material is not available or is listed as reference material.
Bacterial Typing Techniques↗
Bacteriophage MX-1: properties of the phage and its structural proteins.
Bacteriophage MX-1 is a virulent DNA phage for Myxococcus. The host range includes strains of Myxococcus xanthus, M. fulvus and M. virescens. The phage has a sedimentation coefficient (S degrees 20,w) of 1145S and a density of 1-531 g/ml. By using SDS-polyacrylamide gel electrophoresis, 23 phage proteins with apparent mol. wt. between 10000 and 150000 were resolved. Gel filtration in the presence of non-ionic detergent partially resolved the proteins. The fraction excluded from Sephadex G-100, fraction 1, contains two glycoproteins. Fraction 1 was resolved into three fractions (1-1, 1-2 and 1-3) by chromatography on Sephadex G-200. The glycoproteins were present in fraction 1-2; all the proteins from this fraction were derived from the phage tail. Comparison of the amino-acid, hexosamine and neutral-sugar compositions of the two glycoproteins showed that they are distinct molecular species; the smaller molecule is not a subunit of the larger. The significance of these findings is discussed and compared with the proteins of the tails of T-even phage of Escherichia coli.
Amino Acids↗
Gene transfer to myxobacterium by Escherichia coli phage P1.
Myxococcus xanthus is a bacterium with an interest for studies of development because it has an organized multicellular phase in its life cycle. Bacteriophage Pl can adsorb to M. xanthus and inject its DNA into this organism despite the wide taxonomic gap separating myxococcus from Escherichia coli, the source of Pl. A specialized transducing derivative of Pl, called PlCM, can carry a gene for chloramphenicol resistance from E. coli into M. xanthus and generate unstable drug-resistant strains.
Chloramphenicol↗
Characterization and description of Anaeromyxobacter dehalogenans gen. nov., sp. nov., an aryl-halorespiring facultative anaerobic myxobacterium.
Five strains were isolated which form a physiologically and phylogenetically coherent group of chlororespiring microorganisms and represent the first taxon in the Myxobacteria capable of anaerobic growth. The strains were enriched and isolated from various soils and sediments based on their ability to grow using acetate as an electron donor and 2-chlorophenol (2-CPh) as an electron acceptor. They are slender gram-negative rods with a bright red pigmentation that exhibit gliding motility and form spore-like structures. These unique chlororespiring myxobacteria also grow with 2,6-dichlorophenol, 2,5-dichlorophenol, 2-bromophenol, nitrate, fumarate, and oxygen as terminal electron acceptors, with optimal growth occurring at low concentrations (<1 mM) of electron acceptor. 2-CPh is reduced by all strains as an electron acceptor in preference to nitrate, which is reduced to ammonium. Acetate, H(2), succinate, pyruvate, formate, and lactate were used as electron donors. None of the strains grew by fermentation. The 16S ribosomal DNA (rDNA) sequences of the five strains form a coherent cluster deeply branching within the family Myxococcaceae within the class Myxobacteria and are mostly closely associated with the Myxococcus subgroup. With the exception of anaerobic growth and lack of a characteristic fruiting body, these strains closely resemble previously characterized myxobacteria and therefore should be considered part of the Myxococcus subgroup. The anaerobic growth and 9.0% difference in 16S rDNA sequence from those of other myxobacterial genera are sufficient to place these strains in a new genus and species designated Anaeromyxobacter dehalogenans. The type strain is 2CP-1 (ATCC BAA-258).
Acetates↗
Distribution of multicopy single-stranded DNA among myxobacteria and related species.
Multicopy single-stranded DNA (msDNA) is a short single-stranded linear DNA originally discovered in Myxococcus xanthus and subsequently found in Stigmatella aurantiaca. It exists at an estimated 500 to 700 copies per chromosome (T. Yee, T. Furuichi, S. Inouye, and M. Inouye, Cell 38:203-209, 1984). We found msDNA in other myxobacteria, including Myxococcus coralloides, Cystobacter violaceus, Cystobacter ferrugineus (Cbfe17), Nannocystis exedens, and nine independently isolated strains of M. xanthus. The presence of msDNA in N. exedens would extend its phylogenetic distribution into another family of myxobacteria. Flexibacter elegans, a Cytophaga-like gliding bacteria which may be even more distantly related, also contained an msDNA but at a much lower copy number. msDNA was not detected in closely related strains of the myxobacteria Cystobacter fuscus and C. ferrugineus (Cbfe16 and Cbfe18) and the more distantly related eubacteria Herpetosiphon giganteus, Taxeobacter ocellatus, Lysobacter antibioticus, Lysobacter enzymogenes, Cytophaga johnsonae, Rhodopseudomonas sphaeroides, and Rhodospirillum rubrum. Thus far, msDNA has been found in certain gliding bacteria but not in others.
Cytophaga↗
Myxovirescin A biosynthesis is directed by hybrid polyketide synthases/nonribosomal peptide synthetase, 3-hydroxy-3-methylglutaryl-CoA synthases, and trans-acting acyltransferases.
Myxococcus xanthus DK1622 is shown to be a producer of myxovirescin (antibiotic TA) antibiotics. The myxovirescin biosynthetic gene cluster spans at least 21 open reading frames (ORFs) and covers a chromosomal region of approximately 83 kb. In silico analysis of myxovirescin ORFs in conjunction with genetic studies suggests the involvement of four type I polyketide synthases (PKSs; TaI, TaL, TaO, and TaP), one major hybrid PKS/NRPS (Ta-1), and a number of monofunctional enzymes similar to the ones involved in type II fatty-acid biosynthesis (FAB). Whereas deletion of either taI or taL causes a dramatic drop in myxovirescin production, deletion of both genes (DeltataIL) leads to the complete loss of myxovirescin production. These results suggest that both TaI and TaL PKSs might act in conjunction with a methyltransferase, reductases, and a monooxygenase to produce the 2-hydroxyvaleryl-S-ACP starter that is proposed to act as the biosynthetic primer in the initial condensation reaction with glycine. Polymerization of the remaining 11 acetates required for lactone formation is directed by 12 modules of Ta-1, TaO, and TaP megasynthetases. All modules, except for the first module of TaL, lack cognate acyltransferase (AT) domains. Furthermore, deletion of a discrete tandem AT-encoded by taV-blocks myxovirescin production; this suggests an "in trans" mode of action. To embellish the macrocycle with methyl and ethyl moieties, assembly of the myxovirescin scaffold is proposed to switch twice from PKS to 3-hydroxy-3-methylglutaryl-CoA (HMG-CoA)-like biochemistry during biosynthesis. Disruption of the S-adenosylmethionine (SAM)-dependent methyltransferase, TaQ, shifts production toward two novel myxovirescin analogues, designated myxovirescin Q(a) and myxovirescin Q(c). NMR analysis of purified myxovirescin Q(a) revealed the loss of the methoxy carbon atom. This novel analogue lacks bioactivity against E. coli.
Acyltransferases↗
Growth phase dependence of the activation of a bacterial gene for carotenoid synthesis by blue light.
Myxococcus xanthus responds to blue light by producing carotenoid pigments. A mutation at a gene named carC is known to block the metabolism of phytoene, a carotenoid precursor, and this gene has now been cloned and sequenced. We show here that gene carC, which is homologous to phytoene dehydrogenase genes from other organisms, is tightly regulated by light through a mechanism that operates only when the cells have reached the stationary phase or are starved of a carbon source. A genetic element that mediates the effect of the growth phase has been identified. Gene carC is integrated with another unlinked carotenogenic gene in a single 'light regulon' controlled by common trans-acting genetic elements. A potential -35 site for the binding of sigma factors has been found upstream of the carC transcriptional start. However, the -10 region shows no similarity with analogous sites at promoters of other Gram-negative bacteria.
Amino Acid Sequence↗
The 1.9 A crystal structure of a nucleoside diphosphate kinase complex with adenosine 3',5'-cyclic monophosphate: evidence for competitive inhibition.
The X-ray structure of Myxococcus xanthus nucleoside diphosphate (NDP) kinase complexed with adenosine 3',5'-cyclic monophosphate (cAMP) has been determined. The structure was solved by difference Fourier analysis. The refined structure has a crystallographic R-factor of 0.17 at 1.9 A resolution. The phosphoryl group and ribose moiety make extensive polar interactions with the protein, whereas the base interacts only with two hydrophobic residues. The comparison with the structure of the enzyme complex with the substrate adenosine diphosphate (ADP) reported earlier shows that cAMP and ADP interact similarly with the enzyme. The base of the cAMP is present in two conformations, syn and anti, with respect to the sugar. The syn conformer is dominant. Based on the effect of cAMP on phosphorylation of the human NDP kinase NM23, it had been proposed that cAMP might interact with NDP kinase in a manner distinct from other nucleotides. However, the structure of the M. xanthus NDP kinase/cAMP complex indicates that the nucleotide is a competitive inhibitor of the enzyme and occupies the usual nucleotide site. Kinetic assays of the NDP kinase activity in the presence of cAMP were done. Their results are consistent with a competitive character of the cAMP inhibition.
Adenosine Diphosphate↗
A transposition of the reverse transcriptase gene reveals unexpected structural homology to E. coli DNA polymerase I.
The rational design of antiviral agents targeting the reverse transcriptase (RT) of the human immunodeficiency virus (HIV) would greatly benefit from a more intimate knowledge of the structure of RT. Until now, the degree of sequence similarity between RT and E. coli DNA polymerase I (Pol I) has been thought to be confined to several small regions, suggesting little basis for homology molecular modeling. However, we have found that a region in the C terminal of the RT polymerase domain is homologous to a central region of Pol I that lies between the universal polymerase motifs A and C (specifically, helices N-O-P of the Pol I crystal structure); a single transposition closely aligns the RT and Pol I genes, revealing a similar domain structure with 20% residue identity, as well as the possible structural correlates of several RNA-dependent polymerase motifs. The RT from Myxococcus xanthus (a bacterium believed to have diverged from other species 2 billion years ago), if similarly transposed, shows homology to both HIV-1 and E. coli, suggesting the possibility of a very ancient divergence between the RT and Pol I polymerase genes. A second even more significant match to this E. coli region was found in the retroviral ribonuclease H (RNase H) domain, and corresponds precisely to a region that has been aligned by previous investigators with the E. coli RNase H, suggesting that Pol I helices O and P are homologous to helices A and D of the RNase H crystal structure, respectively. These results are consistent with a modular theory of molecular evolution.
Amino Acid Sequence↗
Nutrient regulation of epothilone biosynthesis in heterologous and native production strains.
Fermentation media with different initial concentrations of ammonium and phosphate salts were used to study the inhibitory effects of those ions on growth and production of epothilone in Sorangium cellulosum and Myxococcus xanthus. The native epothilone producer, S. cellulosum was more sensitive to ammonium and phosphate than the heterologous producer, M. xanthus. An ammonium concentration of 12 mM reduced epothilone titers by 90% in S. cellulosum but by only 40% in M. xanthus. When 5 mM phosphate was added to the medium, production in both strains was 60% lower. Higher phosphate concentrations had little additional effect on M. xanthus titers, but epothilone production with 17 mM extra-cellular phosphate in S. cellulosum was 95% lower than in the control condition. The effect of iron supplementation to the fermentation medium was also investigated. Both strains showed best production with 20 microM iron added to the medium.
Antineoplastic Agents↗
A novel regulation on developmental gene expression of fruiting body formation in Myxobacteria.
Myxobacteria are Gram-negative soil microorganisms that prey on other microorganisms. Myxobacteria have significant potential for applications in biotechnology because of their extraordinary ability to produce natural products such as secondary metabolites. Myxobacteria also stand out as model organisms for the study of cell-cell interactions and multicellular development during their complex life cycle. Cellular morphogenesis during multicellular development in myxobacteria is very similar to that in the eukaryotic soil amoebae. Recent studies have started uncovering molecular mechanisms directing the myxobacterial life cycle. We describe recent studies on signal transduction and gene expression during multicellular development in the myxobacterium Myxococcus xanthus. We provide our current model for signal transduction pathways mediated by a two-component His-Asp phosphorelay system and a Ser/Thr kinase cascade.
Gene Expression Regulation, Bacterial↗
Grouping myxococci (Corallococcus) strains by Matrix-Assisted Laser Desorption Ionization Time-of-Flight (MALDI TOF) mass spectrometry: comparison with gene sequence phylogenies.
Nine Corallococcus isolates and three type strains of Corallococcus species were characterized by Intact Cell Mass Spectrometry using Matrix Assisted Laser Desorption Ionization Time-of-Flight (MALDI-TOF) mass spectrometry. The resulting phenetic clustering was compared to the phylogenetic grouping based upon sequences of two housekeeping genes. The three dendrograms of relatedness resembled each other in that the isolates were highly similar to the type strains of Corallococcus exiguus and Corallococcus coralloides, while Corallococcus macrosporus and Myxococcus xanthus were more distantly related. While certain pairs of organisms were recovered by spectrometry and genes sequence analysis, others were detected by two of the three approaches. The degree of similarity determined by sequence analysis of the two genes was not higher than that revealed by MALDI-TOF analysis. The results show that the spectral profile, consisting of about 25 to 45 masses ranging between 2 and 20 kDa, have indeed taxonomic significance, confirming literature data that ribosomal proteins and certain housekeeping proteins are responsible for the masses obtained. Provided the availability of a database of type strains, MALDI-TOF analysis of unknown strains appears to be a rapid and inexpensive method to taxonomically cluster environmental isolates, expanding the spectrum to strains other than those of medical importance predominantly investigated so far.
Bacterial Typing Techniques↗