R. De Wachter

18S RRNA SUGGESTS THAT ENTOPROCTA ARE PROTOSTOMES, UNRELATED TO ECTOPROCTA

The Ento- and Ectoprocta are sometimes placed together in the Bryozoa, which have variously been regarded as proto- or deuterostomes. However, Entoprocta have also been allied to the pseudocoelomates, while Ectoprocta are often united with the Brachiopoda and Phoronida in the (super)phylum Lophophorata. Hence, the phylogenetic relationships of these taxa are still much debated. We determined complete 18S rRNA sequences of two entoprocts, an ectoproct, an inarticulate brachiopod, a phoronid, two annelids, and a platyhelminth. Phylogenetic analyses of these data show that (1) entoprocts and lophophorates have spiralian, protostomous affinities, (2) Ento- and Ectoprocta are not sister taxa, (3) phoronids and brachiopods form a monophyletic clade, and (4) neither Ectoprocta or Annelida appear to be monophyletic. Both deuterostomous and pseudocoelomate features may have arisen at least two times in evolutionary history. These results advocate a Spiralia-Radialia-based classification rather than one based on the Protostomia-Deuterostomia concept.

Proposal of Virgibacillus proomii sp. nov. and emended description of Virgibacillus pantothenticus (Proom and Knight 1950) Heyndrickx et al. 1998

A polyphasic study of strains originally received as Bacillus (now Virgibacillus) pantothenticus, along with strains representing species belonging to Bacillus, Halobacillus and Paenibacillus, was undertaken using amplified rDNA restriction analysis (ARDRA), fatty acid methyl ester (FAME) analysis, SDS-PAGE of whole-cell proteins and routine diagnostic characters comprising 61 biochemical tests in the API system and 15 observations of vegetative cell and sporangial morphology. It revealed the presence within Virgibacillus of an as yet undescribed new species, for which the name Virgibacillus proomii is proposed; V. proomii can be distinguished from V. pantothenticus and members of Bacillus sensu stricto, and from members of Paenibacillus and other aerobic endospore-forming bacteria, by routine phenotypic tests. The type strain of Virgibacillus proomii is LMG 12370T.

Primary structures of the 5S ribosomal RNAs of 11 arthropods and applicability of 5S RNA to the study of metazoan evolution

Summary5S Ribosomal RNA sequences have proven to be useful tools in the study of evolutionary relationships among species. However, in reviewing previously published trees constructed from alignments of metazoan 5S RNAs, we noticed several discrepancies with classical evolutionary views. One such discrepancy concerned the phylum Arthropoda, where a crustacean,Artemia salina, seemed to be evolutionarily very remote from four insects. The cause of this phenomenon was studied by determining the 5S RNA sequences of additional arthropods, viz.Limulus polyphemus, Eurypelma californica, Lasiodora erythrocythara, Areneus diadematus, Daphnia magna, Ligia oceanica, Homarus gammarus, Cancer pagurus, Spirobolus sp.,Locusta migratoria, andTenebrio molitor. A tree was then constructed from a dissimilarity matrix by a clustering method known as weighted pair grouping. Application of a correction for unequal evolutionary rates improved the apparent evolutionary position of the arthropods and of some other metazoan species. However, neither the uncorrected nor the corrected tree permitted a completely acceptable reconstruction of metazoan evolution. We presume that this phenomenon is due to random deviations in the evolutionary rate of 5S RNA.

RP4::Mu3A-mediated in vivo cloning and transfer of a chlorobiphenyl catabolic pathway

Chromosomal DNA fragments encoding the ability to utilize biphenyl as sole carbon source (Bph+) were mobilized by means of plasmid RP4::Mu3A from strain JB1 (tentatively identified as Burkholderia sp.) to Alcaligenes eutrophus CH34 at a frequency of 10(-3) per transferred plasmid. The mobilized DNA integrated into the recipient chromosome or was recovered as catabolic prime plasmids. Three Bph+ prime plasmids were transferred from A. eutrophus to Escherichia coli and back to A. eutrophus without modification of the phenotype. The transferred Bph+ DNA segments allowed metabolism of biphenyl, 2-, 3- and 4-chlorobiphenyl, and diphenylmethane. Genes involved in biphenyl degradation were identified on the prime plasmids by DNA-DNA hybridization and by gene cloning. Bph+ prime plasmids were transferred to Burkholderia cepacia, Pseudomonas aeruginosa, Comamonas testosteroni and A. eutrophus and the catabolic genes were expressed in those hosts. Transfer of the plasmid to the 3-chlorobenzoate-degrading bacterium Pseudomonas sp. B13 allowed the recipient to mineralize 3-chlorobiphenyl. Other catabolic prime plasmids were obtained from JB1 by selection on m-hydroxybenzoate and tyrosine as carbon sources. 16S rRNA sequence data demonstrated that the in vivo transfer of bph was achieved between bacteria belonging to two different branches of the beta-Proteobacteria.

5S ribosomal ribonucleic acid sequences in Bacteroides and Fusobacterium: evolutionary relationships within these genera and among eubacteria in general

The 5S ribosomal ribonucleic acid (rRNA) sequences were determined for Bacteroides fragilis, Bacteroides thetaiotaomicron, Bacteroides capillosus, Bacteroides veroralis, Porphyromonas gingivalis, Anaerorhabdus furcosus, Fusobacterium nucleatum, Fusobacterium mortiferum, and Fusobacterium varium. A dendrogram constructed by a clustering algorithm from these sequences, which were aligned with all other hitherto known eubacterial 5S rRNA sequences, showed differences as well as similarities with respect to results derived from 16S rRNA analyses. In the 5S rRNA dendrogram, Bacteroides clustered together with Cytophaga and Fusobacterium, as in 16S rRNA analyses. Intraphylum relationships deduced from 5S rRNAs suggested that Bacteroides is specifically related to Cytophaga rather than to Fusobacterium, as was suggested by 16S rRNA analyses. Previous taxonomic considerations concerning the genus Bacteroides, based on biochemical and physiological data, were confirmed by the 5S rRNA sequence analysis.

High-pressure liquid chromatography analysis of oligo- and monoribonucleotide mixtures, with special reference to ribosomal RNA constituents

Abstract High-pressure liquid chromatography on columns of commercial anion exchangers, with aqueous buffers as eluents, is used in two types of separation. Oligonucleotide mixtures are fractionated according to chain length at neutral pH in the presence of urea, and mononucleotides are separated according to base composition using acidic buffers. These procedures are applied to the quantitative assay of alkali-resistant oligonucleotides, and to the determination of base composition and pseudouridylic acid content, of Artemia salina ribosomal RNA. High-pressure liquid chromatography permits rapid and extremely sensitive assays not requiring a radioactive label, and therefore compares favorably with other fractionation procedures for RNA components in some specific applications.

Location of the hidden break in large subunit ribosomal RNA of Artemia salina

z.B. ein ganzer Gew/issertyp (dystroph, n/ihrstoffund kalkarm) beseitigt: Fische sind ausgestorben; die Unterwasservegetation hat sich zugunsten yon Torfmoosen und der Rasenbinse (Juncus bulbosus) ver/indert [71; die Seen sind aufgeklart; dutch den Eintrag von Aluminium aus dem Einzugsgebiet ist der Humusgehalt in den Seen verringert worden; auch bei Diatomeen, Cladoceren und Chironomiden (Zuckmficken) traten dramatische Ver/inderungen in den Populationen auf [4]. Als Ursache fiir die rezente Versauerung muB in den moisten F/illen die atmosph/irische Deposition versauernder Schadstoffe (und ihrer Begleitstoffe) angesehen werden. Entgegen einer oft aufgestellten Vermutung, die Versauerung sei ein neues Problem in Mitteleuropa, ist mit dem palfiolimnologischen Ansatz nachgewiesen, dab die Versauerung bei uns so neu nicht ist. Sie ist h/iufig so alt wie die in den Seen in Skandinavien odor Nordamerika. Sic wurde aber auBer beim Kleinen Bullensee [8] iibersehen. Diese Arbeit wurde vom Umweltbundesamt unter Ufo-Plan-Nr. Wasser 10204333 gef6rdert.

Inferring Eubacterial Phylogeny from SS Ribosomal RNA Structure Analysis

Based on analysis of 165 ribosomal RNA oligonucleotide catalogs of about 400 eubacterial species Woese et al. (1985) made a proposal to divide the eubacterial primary kingdom into 10 major phyla. Two years later with over 500 species characterized and with more than 50 nearly complete sequences, the earlier conclusions were significantly refined and extended (Woese, 1967). The picture obtained is substantially different from the classification system based on morphological and metabolic data In the 8th edition of Bergey’s Manual (Buchanan and Gibbons, 1974). Investigation of another universally occurring molecule such as 55 ribosomal RNA ought to help clarify this matter. So far about 160 eubacterial 55 RNA sequences have been published, but the distribution over the 10 major phyla is very uneven as can be seen from Table 1. For example, in the phylum of purple bacteria and relatives almost 80 species have been examined, whereas in the phylum of green sulfur bacteria, along with 4 other major phyla, no representatives whatsoever have been investigated. It is our aim to Lessen these gaps, in order to make possible a comparison with the view based on 165 ribosomal RNA. Rt present, progress has been made for several phyla, while work has started on others (Table 1). In this paper we present a tree derived from the weighted pairwise grouping of over 180 eubacterial 55 RNA sequences including several sequences of formerly undocumented phyla.