334 research outputs found
Discovery of the teleomorph of the hyphomycete, Sterigmatobotrys macrocarpa, and epitypification of the genus to holomorphic status
Sterigmatobotrys macrocarpa is a conspicuous, lignicolous,
dematiaceous hyphomycete with macronematous, penicillate conidiophores with
branches or metulae arising from the apex of the stipe, terminating with
cylindrical, elongated conidiogenous cells producing conidia in a holoblastic
manner. The discovery of its teleomorph is documented here based on
perithecial ascomata associated with fertile conidiophores of S.
macrocarpa on a specimen collected in the Czech Republic; an identical
anamorph developed from ascospores isolated in axenic culture. The teleomorph
is morphologically similar to species of the genera Carpoligna and
Chaetosphaeria, especially in its nonstromatic perithecia, hyaline,
cylindrical to fusiform ascospores, unitunicate asci with a distinct apical
annulus, and tapering paraphyses. Identical perithecia were later observed on
a herbarium specimen of S. macrocarpa originating in New Zealand.
Sterigmatobotrys includes two species, S. macrocarpa, a
taxonomic synonym of the type species, S. elata, and S.
uniseptata. Because no teleomorph was described in the protologue of
Sterigmatobotrys, we apply Article 59.7 of the International Code of
Botanical Nomenclature. We epitypify (teleotypify) both Sterigmatobotrys
elata and S. macrocarpa to give the genus holomorphic status,
and the name S. macrocarpa is adopted for the holomorph. To evaluate
the ordinal and familial affinities of Sterigmatobotrys and its
relationships with the morphologically similar genera Carpoligna and
Chaetosphaeria, phylogenetic relationships were inferred based on
aligned sequences of the large subunit nuclear ribosomal DNA (ncLSU rDNA)
Monilochaetes and allied genera of the Glomerellales, and a reconsideration of families in the Microascales
We examined the phylogenetic relationships of two species that mimic
Chaetosphaeria in teleomorph and anamorph morphologies,
Chaetosphaeria tulasneorum with a Cylindrotrichum
anamorph and Australiasca queenslandica with a Dischloridium
anamorph. Four data sets were analysed: a) the internal transcribed spacer
region including ITS1, 5.8S rDNA and ITS2 (ITS), b) nc28S (ncLSU) rDNA, c)
nc18S (ncSSU) rDNA, and d) a combined data set of ncLSU-ncSSU-RPB2 (ribosomal
polymerase B2). The traditional placement of Ch. tulasneorum in the
Microascales based on ncLSU sequences is unsupported and
Australiasca does not belong to the Chaetosphaeriaceae. Both
holomorph species are nested within the Glomerellales. A new genus,
Reticulascus, is introduced for Ch. tulasneorum with
associated Cylindrotrichum anamorph; another species of
Reticulascus and its anamorph in Cylindrotrichum are
described as new. The taxonomic structure of the Glomerellales is
clarified and the name is validly published. As delimited here, it includes
three families, the Glomerellaceae and the newly described
Australiascaceae and Reticulascaceae. Based on ITS and ncLSU
rDNA sequence analyses, we confirm the synonymy of the anamorph genera
Dischloridium with Monilochaetes. Consequently
Dischloridium laeĂŤnse, type species of the genus, and three
related species are transferred to the older genus Monilochaetes. The
teleomorph of D. laeĂŤnse is described in Australiasca
as a new species. The Plectosphaerellaceae, to which the anamorph
genus Stachylidium is added, is basal to the Glomerellales
in the three-gene phylogeny. Stilbella annulata also belongs to this
family and is newly combined in Acrostalagmus. Phylogenetic analyses
based on ncLSU, ncSSU, and combined ncLSU-ncSSU-RPB2 sequences clarify family
relationships within the Microascales. The family
Ceratocystidaceae is validated as a strongly supported monophyletic
group consisting of Ceratocystis, Cornuvesica,
Thielaviopsis, and the type species of Ambrosiella. The new
family Gondwanamycetaceae, a strongly supported sister clade to the
Ceratocystidaceae, is introduced for the teleomorph genus
Gondwanamyces and its Custingophora anamorphs. Four families
are accepted in the Microascales, namely the
Ceratocystidaceae, Gondwanamycetaceae,
Halosphaeriaceae, and Microascaceae. Because of a suggested
affinity of a Faurelina indica isolate to the Microascales,
the phylogenetic position of the Chadefaudiellaceae is reevaluated.
Based on the results from a separate ncLSU analysis of the
Dothideomycetes, Faurelina is excluded from the
Microascales and placed in the Pleosporales
Long-Residency Hydration, Cation Binding, and Dynamics of Loop E/Helix IV rRNA-L25 Protein Complex
Molecular dynamics simulations of RNA-protein complex between Escherichia coli loop E/helix IV (LE/HeIV) rRNA and L25 protein reveal a qualitative agreement between the experimental and simulated structures. The major groove of LE is a prominent rRNA cation-binding site. Divalent cations rigidify the LE major groove geometry whereas in the absence of divalent cations LE extensively interacts with monovalent cations via inner-shell binding. The HeIV region shows bistability of its major groove explaining the observed differences between x-ray and NMR structures. In agreement with the experiments, the simulations suggest that helix-alpha1 of L25 is the least stable part of the protein. Inclusion of Mg2+ cations into the simulations causes perturbation of basepairing at the LE/HeIV junction, which does not, however, affect the protein binding. The rRNA-protein complex is mediated by a number of highly specific hydration sites with long-residing water molecules and two of them are bound throughout the entire 24-ns simulation. Long-residing water molecules are seen also outside the RNA-protein contact areas with water-binding times substantially enhanced compared to simulations of free RNA. Long-residency hydration sites thus represent important elements of the three-dimensional structure of rRNA
Taxonomy and pathology of Togninia (Diaporthales) and its Phaeoacremonium anamorphs.
The genus Togninia (Diaporthales, Togniniaceae) is here monographed along with its Phaeoacremonium (Pm.) anamorphs. Ten species of Togninia and 22 species of Phaeoacremonium are treated. Several new species of Togninia (T.) are described, namely T. argentinensis (anamorph Pm. argentinense), T. austroafricana (anamorph Pm. austroafricanum), T. krajdenii, T. parasitica, T. rubrigena and T. viticola. New species of Phaeoacremonium include Pm. novae-zealandiae (teleomorph T. novae-zealandiae), Pm. iranianum, Pm. sphinctrophorum and Pm. theobromatis. Species can be identified based on their cultural and morphological characters, supported by DNA data derived from partial sequences of the actin and Ă-tubulin genes. Phylogenies of the SSU and LSU rRNA genes were used to determine whether Togninia has more affinity with the Calosphaeriales or the Diaporthales. The results confirmed that Togninia had a higher affinity to the Diaporthales than the Calosphaeriales. Examination of type specimens revealed that T. cornicola, T. vasculosa, T. rhododendri, T. minima var. timidula and T. villosa, were not members of Togninia. The new combinations Calosphaeria cornicola, Calosphaeria rhododendri, Calosphaeria transversa, Calosphaeria tumidula, Calosphaeria vasculosa and Jattaea villosa are proposed. Species of Phaeoacremonium are known vascular plant pathogens causing wilting and dieback of woody plants. The most prominent diseases in which they are involved are Petri disease and esca, which occur on grapevines and are caused by a complex of fungi, often including multiple species of Phaeoacremonium. Various Phaeoacremonium species are opportunistic fungi on humans and cause phaeohyphomycosis. The correct and rapid identification of Phaeoacremonium species is important to facilitate the understanding of their involvement in plant as well as human disease. A rapid identification method was developed for the 22 species of Phaeacremonium. It involved the use of 23 species-specific primers, including 20 primers targeting the Ă-tubulin gene and three targeting the actin gene. These primers can be used in 14 multiplex reactions. Additionally, a multiple-entry electronic key based on morphological, cultural and Ă-tubulin sequence data was developed to facilitate phenotypic and sequence-based species identification of the different Phaeoacremonium species. Separate dichotomous keys are provided for the identification of the Togninia and Phaeoacremonium species. Keys for the identification of Phaeoacremonium-like fungi and the genera related to Togninia are also provided. The mating strategy of several Togninia species was investigated with ascospores obtained from fertile perithecia produced in vitro. Togninia argentinensis and T. novae-zealandiae have homothallic mating systems, whereas T. austroafricana, T. krajdenii, T. minima, T. parasitica, T. rubrigena and T. viticola were heterothallic.
Molecular taxonomy of bambusicolous fungi: Tetraplosphaeriaceae, a new pleosporalean family with Tetraploa-like anamorphs
A new pleosporalean family Tetraplosphaeriaceae is established to
accommodate five new genera; 1) Tetraplosphaeria with small ascomata
and anamorphs belonging to Tetraploa s. str., 2)
Triplosphaeria characterised by hemispherical ascomata with rim-like
side walls and anamorphs similar to Tetraploa but with three conidial
setose appendages, 3) Polyplosphaeria with large ascomata surrounded
by brown hyphae and anamorphs producing globose conidia with several setose
appendages, 4) Pseudotetraploa, an anamorphic genus, having
obpyriform conidia with pseudosepta and four to eight setose appendages, and
5) Quadricrura, an anamorphic genus, having globose conidia with one
or two long setose appendages at the apex and four to five short setose
appendages at the base. Fifteen new taxa in these genera mostly collected from
bamboo are described and illustrated. They are linked by their Tetraploa
s. l. anamorphs. To infer phylogenetic placement in the
Pleosporales, analyses based on a combined dataset of small- and
large-subunit nuclear ribosomal DNA (SSU+LSU nrDNA) was carried out.
Tetraplosphaeriaceae, however, is basal to the main pleosporalean
clade and therefore its relationship with other existing families was not
completely resolved. To evaluate the validity of each taxon and to clarify the
phylogenetic relationships within this family, further analyses using
sequences from ITS-5.8S nrDNA (ITS), transcription elongation factor 1-Îą
(TEF), and β-tubulin (BT), were also conducted. Monophyly of the family
and that of each genus were strongly supported by analyses based on a combined
dataset of the three regions (ITS+TEF+BT). Our results also suggest that
Tetraplosphaeria (anamorph: Tetraploa s. str.) is an
ancestral lineage within this family. Taxonomic placement of the bambusicolous
fungi in Astrosphaeriella, Kalmusia, Katumotoa, Massarina,
Ophiosphaerella, Phaeosphaeria, Roussoella, Roussoellopsis, and
Versicolorisporium, are also discussed based on the SSU+LSU
phylogeny
Understanding the Origins of Bacterial Resistance to Aminoglycosides through Molecular Dynamics Mutational Study of the Ribosomal A-Site
Paromomycin is an aminoglycosidic antibiotic that targets the RNA of the bacterial small ribosomal subunit. It binds in the A-site, which is one of the three tRNA binding sites, and affects translational fidelity by stabilizing two adenines (A1492 and A1493) in the flipped-out state. Experiments have shown that various mutations in the A-site result in bacterial resistance to aminoglycosides. In this study, we performed multiple molecular dynamics simulations of the mutated A-site RNA fragment in explicit solvent to analyze changes in the physicochemical features of the A-site that were introduced by substitutions of specific bases. The simulations were conducted for free RNA and in complex with paromomycin. We found that the specific mutations affect the shape and dynamics of the binding cleft as well as significantly alter its electrostatic properties. The most pronounced changes were observed in the U1406CâśU1495A mutant, where important hydrogen bonds between the RNA and paromomycin were disrupted. The present study aims to clarify the underlying physicochemical mechanisms of bacterial resistance to aminoglycosides due to target mutations
Molecular dynamics simulations suggest that RNA three-way junctions can act as flexible RNA structural elements in the ribosome
We present extensive explicit solvent molecular dynamics analysis of three RNA three-way junctions (3WJs) from the large ribosomal subunit: the 3WJ formed by Helices 90â92 (H90âH92) of 23S rRNA; the 3WJ formed by H42âH44 organizing the GTPase associated center (GAC) of 23S rRNA; and the 3WJ of 5S rRNA. H92 near the peptidyl transferase center binds the 3â˛-CCA end of amino-acylated tRNA. The GAC binds protein factors and stimulates GTP hydrolysis driving protein synthesis. The 5S rRNA binds the central protuberance and A-site finger (ASF) involved in bridges with the 30S subunit. The simulations reveal that all three 3WJs possess significant anisotropic hinge-like flexibility between their stacked stems and dynamics within the compact regions of their adjacent stems. The A-site 3WJ dynamics may facilitate accommodation of tRNA, while the 5S 3WJ flexibility appears to be essential for coordinated movements of ASF and 5S rRNA. The GAC 3WJ may support large-scale dynamics of the L7/L12-stalk region. The simulations reveal that H42âH44 rRNA segments are not fully relaxed and in the X-ray structures they are bent towards the large subunit. The bending may be related to L10 binding and is distributed between the 3WJ and the H42âH97 contact
Conformations of Flanking Bases in HIV-1 RNA DIS Kissing Complexes Studied by Molecular Dynamics
Explicit solvent molecular dynamics simulations (in total almost 800 ns including locally enhanced sampling runs) were applied with different ion conditions and with two force fields (AMBER and CHARMM) to characterize typical geometries adopted by the flanking bases in the RNA kissing-loop complexes. We focus on flanking base positions in multiple x-ray and NMR structures of HIV-1 DIS kissing complexes and kissing complex from the large ribosomal subunit of Haloarcula marismortui. An initial x-ray open conformation of bulged-out bases in HIV-1 DIS complexes, affected by crystal packing, tends to convert to a closed conformation formed by consecutive stretch of four stacked purine bases. This is in agreement with those recent crystals where the packing is essentially avoided. We also observed variants of the closed conformation with three stacked bases, while nonnegligible populations of stacked geometries with bulged-in bases were detected, too. The simulation results reconcile differences in positions of the flanking bases observed in x-ray and NMR studies. Our results suggest that bulged-out geometries are somewhat more preferred, which is in accord with recent experiments showing that they may mediate tertiary contacts in biomolecular assemblies or allow binding of aminoglycoside antibiotics
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