The phylogenetic relationships of Caulobacter, Asticcacaulis and Brevundimonas species and their taxonomic implications

The phylogenetic relationships among the species of Caulobacter, Asticcacaulis and Brevundimonas were studied by comparison of their 16S rDNA sequences. The analysis of almost complete sequences confirmed the early evolutionary divergence of the freshwater and marine species of Caulobacter reported previously [Stahl, D. A., Key, R,, Flesher, B, & Smit, J. (1992), J Bacteriol 174, 2193-2198]. The freshwater species formed two distinct clusters. One cluster contained the species Caulobacter bacteroides, Caulobacter crescentus, Caulobacter fusiformis and Caulobacter henricii. C, bacteroides and C, fusiformis are very closely related (sequence identity 99.8%). The second cluster was not exclusive and contained the species Caulobacter intermedius, Caulobacter subvibrioides and Caulobacter variabilis, as well as Brevundimonas diminuta and Brevundimonas vesicularis, The marine species Caulobacter halobacteroides and Caulobacter maris were very closely related, with a sequence identity of 99.7%, These two species were most closely but distantly related to the marine hyphal/budding bacteria Hyphomonas jannaschiana and Hirschia baltica, which formed a deep phylogenetic line with Rhodobacter sphaeroides and Rhodobacter capsulatus, Caulobacter leidyia is unrelated to the other species of Caulobacter and belongs to the alpha-4 subclass of the Proteobacteria, forming a distinct cluster with Asticcacaulis excentricus and Asticcacaulis biprosthecium, The taxonomic implications of the polyphyletic nature of the genus Caulobacter and the absence of a type culture for the type species of the genus, Caulobacter vibrioides, are discussed.

Molecular recognition of macrocyclic peptidomimetic inhibitors by HIV-1 protease

High-resolution crystal structures are described for seven macrocycles complexed with HIV-1 protease (HIVPR). The macrocycles possess two amides and an aromatic group within 15-17 membered rings designed to replace N- or C-terminal tripeptides from peptidic inhibitors of HIVPR. Appended to each macrocycle is a transition state isostere and either an acyclic peptide, nonpeptide, or another macrocycle. These cyclic analogues are potent inhibitors of HIVPR, and the crystal structures show them to be structural mimics of acyclic peptides, binding in the active site of HIVPR via the same interactions. Each macrocycle is restrained to adopt a P-strand conformation which is preorganized for protease binding. An unusual feature of the binding of C-terminal macrocyclic inhibitors is the interaction between a positively charged secondary amine and a catalytic aspartate of HIVPR. A bicyclic inhibitor binds similarly through its secondary amine that lies between its component N-terminal and C-terminal macrocycles. In contrast, the corresponding tertiary amine of the N-terminal macrocycles does not interact with the catalytic aspartates. The amine-aspartate interaction induces a 1.5 Angstrom N-terminal translation of the inhibitors in the active site and is accompanied by weakened interactions with a water molecule that bridges the ligand to the enzyme, as well as static disorder in enzyme flap residues. This flexibility may facilitate peptide cleavage and product dissociation during catalysis. Proteases [Aba(67,95)]HIVPR and [Lys(7),Ile(33),Aba(67,95)]- HIVPR used in this work were shown to have very similar crystal structures.

Protein fold recognition score functions: Unusual construction strategies

We describe two ways of optimizing score functions for protein sequence to structure threading. The first method adjusts parameters to improve sequence to structure alignment. The second adjusts parameters so as to improve a score function's ability to rank alignments calculated in the first score function. Unlike those functions known as knowledge-based force fields, the resulting parameter sets do not rely on Boltzmann statistics, have no claim to representing free energies and are purely constructions for recognizing protein folds. The methods give a small improvement, but suggest that functions can be profitably optimized for very specific aspects of protein fold recognition, Proteins 1999;36:454-461. (C) 1999 Wiley-Liss, Inc.

Plant latex and first-instar monarch larval growth and survival on three North American milkweed species

First-instar larvae of the monarch butterfly, Danaus plexippus, a milkweed specialist, generally grew faster and survived better on leaves when latex flow was reduced by partial severance of the leaf petiole. The outcome depended on milkweed species and was related to the amount of latex produced. The outcome also may be related to the amount of cardenolide produced by the plants as a potential chemical defense against herbivory. Growth was more rapid, but survival was similar on partially severed compared with intact leaves of the high-latex/low-cardenolide milkweed, Asclepias syriaca, whereas both growth and survival were unaffected on the low-latex/low-cardenolide milkweed A. incarnata. On the low-latex/low-cardenolide milkweed A. tuberosa, both growth and survival of larvae were only marginally affected. These results contrast sharply to previous results with the milkweed, A. humistrata, in Florida, which has both high latex and high cardenolide. Larval growth and survival on A. humistrata were both increased by partially severing leaf petioles. Larval growth rates among all four milkweed species on leaves with partially severed petioles were identical, suggesting that latex and possibly the included cardenolides are important in first-instar monarch larval growth, development, and survivorship.

Description of Gluconacetobacter sacchari sp. nov., a new species of acetic acid bacterium isolated from the leaf sheath of sugar cane and from the pink sugar-cane mealy bug

A new species of the genus Gluconacetobacter, for which the name Gluconacetobacter sacchari sp. nov. is proposed, was isolated from the leaf sheath of sugar cane and from the pink sugar-cane mealy bug, Saccharicoccus sacchari, found on sugar cane growing in Queensland and northern New South Wales, Australia, The nearest phylogenetic relatives in the alpha-subclass of the Proteobacteria are Gluconacetobacter liquefaciens and Gluconacetobacter diazotrophicus, which have 98.8-99.3% and 97.9-98.5% 16S rDNA sequence similarity, respectively, to members of Gluconacetobacter sacchari. On the basis of the phylogenetic positioning of the strains, DNA reassociation studies, phenotypic tests and the presence of the Q10 ubiquinone, this new species was assigned to the genus Gluconacetobacter. No single phenotypic characteristic is unique to the species, but the species can be differentiated phenotypically from closely related members of the acetic acid bacteria by growth in the presence of 0.01% malachite green, growth on 30% glucose, an inability to fix nitrogen and an inability to grow with the L-amino acids asparagine, glycine, glutamine, threonine and tryptophan when D-mannitol was supplied as the sole carbon and energy source. The type strain of this species is strain SRI 1794(T) (= DSM 12717(T)).

Evolution of the genetic covariance between male and female components of mate recognition: An experimental test

The evolution of a positive genetic correlation between male and female components of mate recognition systems will result as a consequence of assortative mating and, in particular, is central to a number of theories of sexual selection. Although the existence of such genetic correlations has been investigated in a number of taxa, it has yet to be shown that such correlations evolve and whether they may evolve as rapidly as suggested by sexual selection models. In this study, I used a hybridization experiment to disrupt natural mate recognition systems and then observed the subsequent evolutionary dynamics of the genetic correlation between male and female components for 56 generations in hybrids between Drosophila serrata and Drosophila birchii. The genetic correlation between male and female components evolved from 0.388 at generation 5 to 1.017 at generation 37 and then declined to -0.040 after a further 19 generations. These results indicated that the genetic basis of the mate recognition system in the hybrid populations evolved rapidly. The initial rapid increase in the genetic correlation was consistent with the classic assumption that male and female components will coevolve under sexual selection. The subsequent decline in genetic correlation may be attributable to the fixation of major genes or, alternatively, may be a result of a cyclic evolutionary change in mate recognition.

Molecular characterization of the toxic cyanobacterium Cylindrospermopsis raciborskii and design of a species-specific PCR

Cylindrospermopsis raciborskii is a toxic-bloom-forming cyanobacterium that is commonly found in tropical to subtropical climatic regions worldwide, but it is also recognized as a common component of cyanobacterial communities in temperate climates. Genetic profiles of C. raciborskii were examined in 19 cultured isolates originating from geographically diverse regions of Australia and represented by two distinct morphotypes. A 609-bp region of rpoC1, a DNA-dependent RNA polymerase gene, was amplified by PCR from these isolates with cyanobacterium-specific primers. Sequence analysis revealed that all isolates belonged to the same species, including morphotypes with straight or coiled trichomes. Additional rpoC1 gene sequences obtained for a range of cyanobacteria highlighted clustering of C. raciborskii with other heterocyst-producing cyanobacteria (orders Nostocales and Stigonematales). In contrast, randomly amplified polymorphic DNA and short tandemly repeated repetitive sequence profiles revealed a greater level of genetic heterogeneity among C. raciborskii isolates than did rpoC1 gene analysis, and unique band profiles were also found among each of the cyanobacterial genera examined. A PCR test targeting a region of the rpoC1 gene unique to C. raciborskii was developed for the specific identification of C. raciborskii from both purified genomic DNA and environmental samples. The PCR was evaluated with a number of cyanobacterial isolates, but a PCR-positive result was only achieved with C, raciborskii. This method provides an accurate alternative to traditional morphological identification of C. raciborskii.

A review of the Arhythmacanthidae (Acanthocephala) with a description of Heterosentis hirsutus n. sp. from Cnidoglanis macrocephala (Plotosidae) in Australia

Heterosentis hirsutus n. sp. is described from Cnidoglanis macrocephalo (Siluriformes: Plotosidae) from the Swan Estuary, Western Australia. It is distinguished by having 14 longitudinal rows of 6-7 hooks per row on the proboscis, a trunk armed anteriorly and posteriorly (=genital spines) with minute spines and lemnisci that may extend to the poster;or margin of the proboscis receptacle The new species also has prominent fragmented nuclei in its trunk well. New information is given for Heterosentis plotosi Yamoguti, 1935 from Plotosus lineatus (Siluriformes: Plotosidae) and H. poraplagusiarum (Nickol, 1972) Amin, 1985 from Paraplogusia guttata (Pleuronectiformes: Cynoglossidoe), both from Queensland. A key to the species of Heterosentis Van Cleave, 1931 is provided. The Arhythmacanthidae subfamilies are reviewed: there is little utility in the recognition of these taxa because of the small number of genera involved and the validity/ of the characters on which they ore based is in doubt, particularly whether trunk spines are present or absent. Only Acanthocephaloides Meyer, 1932, Breizocanthus Golvon, 1969, Euzetocanthus Golvan & Houin, 1964, Heterosentis, Hypoechinorhynchus Yamaguti, 1939 and Paracanthocepholoides Golvan, 1969 of the Arhythmacanthidae are considered valid. A key to these genera is provided. The monotypic genus Neocanthocepholoides Cable & Quick, 1954 is considered a new synonym of Acanthocephaloides thus creating Acanthocephaloides spinicaudatus (Cable & Quick, 1954) n. comb. Arhythmocanthus Yamaguti, 1935 is maintained as a synonym of Heterosentis because the distinction between two and three hook types is made equivocal when the transition between the opical and subapical hooks is gradual.

1,9-dimethylhypoxanthine from a southern Australian marine sponge Spongosorites species

A Spongosorites sp. collected off southern Australia has yielded 1,9-dimethylhypoxanthine (4). The structure for 4 was solved by spectroscopic analysis.

Structural basis of recognition of monopartite and bipartite nuclear localization sequences by mammalian importin-alpha

Importin-alpha is the nuclear import receptor that recognizes cargo proteins which contain classical monopartite and bipartite nuclear localization sequences (NLSs), and facilitates their transport into the nucleus. To determine the structural basis of the recognition of the two classes of NLSs by mammalian importin-alpha, we co-crystallized an N-terminally truncated mouse receptor protein with peptides corresponding to the monopartite NLS from the simian virus 40 (SV40) large T-antigen, and the bipartite NLS from nucleoplasmin. We show that the monopartite SV40 large T-antigen NLS binds to two binding sites on the receptor, similar to what was observed in yeast importin-alpha. The nucleoplasmin NLS-importin-alpha complex shows, for the first time, the mode of binding of bipartite NLSs to the receptor. The two basic clusters in the NLS occupy the two binding sites used by the monopartite NLS, while the sequence linking the two basic clusters is poorly ordered, consistent with its tolerance to mutations. The structures explain the structural basis for binding of diverse NLSs to the sole receptor protein. (C) 2000 Academic Press.

A new species of Aponurus looss, 1907 (Digenea : Lecithasteridae) in butterflyfishes (Perciformes : Chaetodontidae) from New Caledonia

Aponurus chelebesoi n. sp. is described from Chaetodon auriga, C. citrinellus, C. ephippium, C. flavirostris, C. lineolatus, C. melannotus, C. mertensii, C. pelewensis, C. lunulatus, C. vagabundus, Coradion altivelis, Forcipiger flavissimus, Heniochus acuminatus, H. chrysostomus and H. monoceros from the southern coast of New Caledonia. It is distinguished from most species in the genera Aponurus (synonym Brachadena) and Lecithophyllum by its claviform (as opposed to oval to subglobular) vitelline lobes. Three species, A. pyriformis, Lecithophyllum vogeae and Brachadena cheilonis, have similar claviform vitelline lobes, but differ from A. chelebesoi in their tandem testes and the distinct egg-size.

Desiccation tolerance of three moss species from continental Antarctica

Tolerance of desiccation was examined in three species of moss, Grimmia antarctici Card., Ceratodon purpureus (Hedw.) Brid. and Bryum pseudotriquetrum (Hedw.) Gaertn., Meyer et Scherb. collected from two sites of contrasting water availability in the Windmill Islands, continental Antarctica. Physiological tolerance to desiccation was measured using chlorophyll fluorescence in plugs of moss during natural drying in the laboratory. Differences in relative water content, rate of drying and the response of photosynthesis to desiccation were observed among the three species and between sites. Of the three species studied, G. antarctici showed the lowest capacity to sustain photosynthetic processes during desiccation, B. pseudotriquetrum had an intermediate response and showed the greatest plasticity and C. purpureus showed the greatest capacity to sustain photosynthesis during desiccation. These results fit well with the known distribution of the three species with G. antarctici being limited to relatively wet sites, C. purpureus being common in the driest sites and B. pseudotriquetrum showing a wide distribution between these two extremes. Levels of soluble carbohydrates were also measured in these samples following desiccation and these indicate the presence of stachyose, an oligosaccharide known to be important in desiccation tolerance in seeds, in B. pseudotriquetrum. Both gross morphology and carbohydrate content are likely to contribute to differences in desiccation tolerance of the moss species. These results indicate that if the Casey region continues to dry out, as a result of local geological uplifting or global climate change, we would expect to see not only reductions in the moss community but also changes in community composition. G. antarctici is likely to become more limited in distribution as C. purpureus and B. pseudotriquetrum expand into drying areas.

Clathrins A-C: Metabolites from a southern Australian marine sponge, Clathria species

A Clathria sp. collected in the Great Australian Bight has yielded the novel metabolites clathrins A (6), B (7), and C (8). Structures were assigned to clathrins A-C on the basis of spectroscopic analysis. Clathrin A (6) represents a plausible biosynthetic intermediate that provides an inferred link between marine sesquiterpene/benzenoids and mixed terpene/shikimate biosynthesis.

The status of Petalocotyle Ozaki, 1934 (Digenea : Gyliauchenidae), including the description of two new species from acanthurid fishes in Queensland, Australia

The status of Petalocotyle Ozaki, 1934 within the Gyliauchenidae Goto & Matsudaira, 1918 is reviewed. Two new species, P. adenometra from Prionurus microlepidotus (Amity Point, Queensland, Australia) and P. diverticulata from Acanthurus nigrofuscus and A. lineatus (Heron Island, Queensland, Australia), are described. The body plan of Petalocotyle conforms to that of members of the Gyliauchenidae (oral sucker absent, well-developed pharynx, complex oesophagus and characteristic male terminal genitalia), indicating justifiable inclusion in this family. A new diagnosis is given for the genus, such that Petalocotyle is now identified by the presence of an anterior, protuberant ventral sucker, long caeca, a large, sigmoid cirrus-sac containing a coiled ejaculatory duct, and an extensive vitellarium. We suggest that, of all the known genera of gyliauchenids, Petalocotyle may most closely resemble the 'archaetypal gyliauchenid', that is, it may be placed basally within the radiation of the Gyliauchenidae. However, derived characters, like diverticula in the reproductive system, indicate that some characters of individual members of Petalocotyle may be considered advanced and do not reflect an archaetypal condition. Parallels in the structure of the male and female genitalia of Robphildollfusium Paggi & Orecchia, 1963 and Petalocotyle, along with the shared morphology of the digestive tract, indicate possible phylogenetic links between the two genera. This affinity is difficult to infer using morphology alone and recommend that Robphildollfusium remain detached from the Gyliauchenidae.

Species of Trifoliovarium Yamaguti, 1940 (Digenea : Lecithasteridae) from Australian waters, with a description of T-draconis n. sp and a cladistic study of the subfamily Trifoliovariinae Yamaguti, 1958

Three species of Trifoliovarium are described from marine fishes from Moreton Bay, Queensland: T. triacanthi (Parukhin, 1964) n. comb. (syns Hysterolecitha triacanthi Parukhin, 1964; T. triacanthi Bilqees, 1973; T. triacanthusi Gupta & Ahmad, 1976) from Tripodichthys angustifrons; T. ovarilobulus (Wang, 1989) n. comb. (syn. Hysterolecithia[sic]ovarilobulus) from Paramonacanthus japonicus and Pelates quadrilineatus; and T. draconis n. sp. from Callionymus sublaevis and C. belcheri. A list of the species of the subfamily Trifoliovariinae is given along with a key. A cladistic study of the subfamily based on 23 characters is presented, the results of which indicate the monophyly of the genus Assitrema and the paraphyly of Trifoliovarium.