Home About us Contact
|
Home About us Contact | ||
|
|
||
rRNA Operon (rrna + operon)
Selected AbstractsGenetic and functional properties of uncultivated thermophilic crenarchaeotes from a subsurface gold mine as revealed by analysis of genome fragmentsENVIRONMENTAL MICROBIOLOGY, Issue 12 2005Takuro Nunoura Summary Within a phylum Crenarchaeota, only some members of the hyperthermophilic class Thermoprotei, have been cultivated and characterized. In this study, we have constructed a metagenomic library from a microbial mat formation in a subsurface hot water stream of the Hishikari gold mine, Japan, and sequenced genome fragments of two different phylogroups of uncultivated thermophilic Crenarchaeota: (i) hot water crenarchaeotic group (HWCG) I (41.2 kb), and (ii) HWCG III (49.3 kb). The genome fragment of HWCG I contained a 16S rRNA gene, two tRNA genes and 35 genes encoding proteins but no 23S rRNA gene. Among the genes encoding proteins, several genes for putative aerobic-type carbon monoxide dehydrogenase represented a potential clue with regard to the yet unknown metabolism of HWCG I Archaea. The genome fragment of HWCG III contained a 16S/23S rRNA operon and 44 genes encoding proteins. In the 23S rRNA gene, we detected a homing-endonuclease encoding a group I intron similar to those detected in hyperthermophilic Crenarchaeota and Bacteria, as well as eukaryotic organelles. The reconstructed phylogenetic tree based on the 23S rRNA gene sequence reinforced the intermediate phylogenetic affiliation of HWCG III bridging the hyperthermophilic and non-thermophilic uncultivated Crenarchaeota. [source] Uncultured Archaea in a hydrothermal microbial assemblage: phylogenetic diversity and characterization of a genome fragment from a euryarchaeoteFEMS MICROBIOLOGY ECOLOGY, Issue 3 2006Hélène Moussard Abstract The polychaete Alvinella pompejana lives in organic tubes on the walls of active hydrothermal chimneys along the East Pacific Rise. To examine the diversity of the archaeal community associated with the polychaete tubes, we constructed libraries by direct PCR amplification and cloning of 16S rRNA genes. Almost half of the sequences of the 16S rRNA gene libraries clustered with uncultured archaeal groups. In an effort to access genomic information from uncultured archaeal members we further constructed a fosmid library from the same DNA source. One of the clones, Alv-FOS5, was sequenced completely. Its sequence analysis revealed an incomplete rRNA operon and 32 predicted ORFs. Seventeen of these ORFs have been assigned putative functions, including transcription and translation, cellular processes and signalling, transport systems and metabolic pathways. Phylogenetic analyses of the 16S rRNA gene suggested that Alv-FOS5 formed a new lineage related to members of Deep-Sea Hydrothermal Vent Euryarchaeota group II. Phylogenetic analyses of predicted proteins revealed the existence of likely cases of horizontal gene transfer, both between Crenarchaeota and Euryarchaeota and between Archaea and Bacteria. This study is the first step in using genomics to reveal the physiology of an as yet uncultured group of archaea from deep-sea hydrothermal vents. [source] Occurrence of the wattle wilt pathogen, Ceratocystis albifundus on native South African treesFOREST PATHOLOGY, Issue 5 2007J. Roux Summary Ceratocystis albifundus causes the disease known as wattle wilt of non-native Acacia mearnsii trees in South Africa, Uganda and Kenya. Infection results in rapid wilt and death of susceptible trees and stem cankers on more tolerant trees. It has been suggested that C. albifundus is indigenous to southern Africa, possibly having spread from native Protea spp. to non-native A. mearnsii and A. decurrens trees. Although C. albifundus has been collected from Protea spp., these reports are based on limited records for which only aged herbarium specimens exist. During surveys of wound-infecting fungi on native tree species in South Africa, a fungus resembling C. albifundus was collected from Protea gaguedi, Acacia caffra, Burkea africana, Combretum molle, C. zeyheri, Faurea saligna, Ochna pulchra, Ozoroa paniculosa and Terminalia sericea. The identity of the fungus was confirmed as C. albifundus, using comparisons of DNA sequence data for the ITS and 5.8S gene of the rRNA operon. In pathogenicity trials, lesions were produced on C. molle and A. caffra, with some trees beginning to die at the termination of the experiment. This study represents the first report of C. albifundus from native tree species in South Africa and provides unequivocal evidence that the fungus occurs naturally on native Protea spp. The wide host range of C. albifundus, as well as its abundance on these indigenous hosts lends further support to the view that it is a native African pathogen. [source] Mycosphaerella species associated with leaf disease of Eucalyptus globulus in EthiopiaFOREST PATHOLOGY, Issue 4 2006Alemu Gezahgne Summary Eucalyptus spp. are among the most widely planted exotic trees in Ethiopia. Several damaging leaf pathogens are known from Eucalyptus spp. worldwide. Of these, Mycosphaerella spp. are among the most important, causing the disease known as Mycosphaerella leaf disease (MLD). Characteristic symptoms of MLD include leaf spot, premature defoliation, shoot and twig dieback. Recent disease surveys conducted in Ethiopian Eucalyptus plantations have revealed disease symptoms similar to those caused by Mycosphaerella spp. These symptoms were restricted to E. globulus trees growing in several localities in south, south western and western Ethiopia. The aim of this study was to identify the fungi associated with this disease. This was achieved by examining ascospore germination patterns, anamorph associations and sequence data from the Internal Transcribed Spacer (ITS) region of the rRNA operon, for representative isolates. Several different ascospore germination patterns were observed, suggesting that more than one species of Mycosphaerella is responsible for MLD on E. globulus in Ethiopia. Analysis of sequence data showed that three Mycosphaerella spp., M. marksii, M. nubilosa and M. parva were present. This is the first report of these three species from Ethiopia and represents a valuable basis on which to build further studies in the region. Résumé Les Eucalyptus comptent parmi les essences d'arbres exotiques les plus plantées en Ethiopie. Plusieurs pathogènes foliaires sont connus dans le monde pour occasionner des dégâts sur Eucalyptus. Parmi ceux-ci, les espèces de Mycosphaerella sont parmi les plus importantes, causant la maladie connue comme Maladie Foliaire àMycosphaerella (MFM, MLD en anglais). Les symptômes caractéristiques de la MFM comprennent des taches foliaires, une défoliation précoce et des dépérissements de pousses et de rameaux. Des campagnes de surveillance menées récemment dans les plantations éthiopiennes d'Eucalyptus ont révélé la présence de tels symptômes. Ces symptômes sont uniquement observés sur E. globulus dans plusieurs localités du sud, sud-ouest et ouest de l'Ethiopie. L'objectif de cette étude était d'identifier les champignons associés à cette maladie. Pour cela, des isolats représentatifs ont étéétudiés pour les modalités de germination des ascospores, les anamorphes associés ainsi que les données de séquence de la région ITS de l'opéron ADNr. Différentes modalités de germination des ascospores ont été observées, suggérant que plusieurs espèces de Mycosphaerella seraient associées à la MFM sur E. globulus en Ethiopie. L'analyse des données de séquence a montré la présence de 3 espèces : M. marksii, M. nubilosa et M. parva. Ceci constitue la première mention de ces 3 espèces en Ethiopie et une première étape pour envisager d'autres études dans cette région. Zusammenfassung Eucalyptus -Arten sind die am häufigsten angepflanzten exotischen Bäume in Äthiopien. An Eucalyptus kommen verschiedene Blattkrankheiten vor, wobei die Mycosphaerella -Arten als Verursacher der Mycosphaerella -Blattkrankheit (MLD) am bedeutendsten sind. Charakteristische Symtpome der MLD sind Blattnekrosen und vorzeitiger Blattfall sowie Trieb- und Zweigsterben. Bei der Inventur von Krankheiten in äthiopischen Eucalyptusplantagen wurden Symptome entdeckt, die denen von Mycosphaerella spp. ähnlich waren. Diese traten nur an E. globulus lokal in S-, SW- und W-Äthiopien auf. Ziel dieser Untersuchung war es, die damit assoziierten Pilze zu identifizieren. Hierzu wurde an repräsentativen Isolaten das Keimverhalten der Ascosporen, das Vorkommen von Anamorphen und die ITS-Sequenz des rRNA-Operons untersucht. Es wurden verschiedene Keimungstypen der Ascosporen beobachtet, was darauf schliessen liess, dass mehr als eine Mycosphaerella -Art für die Krankheit an E. globulus in Äthiopien verantwortlich ist. Anhand der Sequenzen wurden M. marksii, M. nubilosa und M. parva identifiziert. Dies ist der Erstnachweis für diese drei Arten in Äthiopien und eine Grundlage für weitere Studien. [source] The root rot fungus Armillaria mellea introduced into South Africa by early Dutch settlersMOLECULAR ECOLOGY, Issue 2 2001Martin P. A. Coetzee Abstract Dead and dying oak (Quercus) and numerous other woody ornamental trees and shrubs showing signs and symptoms of Armillaria root rot were identified in the Company Gardens, Cape Town, South Africa, which were established in the mid-1600s by the Dutch East Indies Trading Company. Nineteen isolates from dying trees or from mushrooms were collected and analysed to identify and characterize the Armillaria sp. responsible for the disease. The AluI digestion of the amplified product of the first intergenic spacer region (IGS-1) of the rRNA operon of 19 isolates from the Company Gardens was identical to that of some of the European isolates of A. mellea s. s. The IGS-1 region and the internal transcribed spacers (ITS) were sequenced for some of the Cape Town isolates. Phylogenetic analyses placed the Cape Town isolates in the European clade of A. mellea, which is distinct from the Asian and North American clades of this species. Identification based on sexual compatibility was conducted using A. mellea tester strains in diploid,haploid pairings, which showed some compatibility between the Cape Town isolates and testers from Europe. Somatic compatibility tests (diploid,diploid pairings) and DNA fingerprinting with multilocus, microsatellite probes indicated that the Cape Town isolates were genetically identical and may have resulted from vegetative (clonal) spread from a single focus in the centre of the original Company Gardens (c. 1652). The colonized area is at least 345 m in diameter. Assuming a linear spread rate underground of 0.3 m/year to 1.6 m/year, the genet (clone) was estimated to be between 108 and 575 years old. These data suggest that A. mellea was introduced into Cape Town from Europe, perhaps on potted plants, such as grapes or citrus, planted in the Company Gardens more than 300 years ago. [source] Transfer of Nosema locustae (Microsporidia) to Antonospora locustae n. comb.THE JOURNAL OF EUKARYOTIC MICROBIOLOGY, Issue 2 2004Based on Molecular, Ultrastructural Data ABSTRACT. Nosema locustae is a microsporidian parasite of grasshopper pesthd that is used as a biological control agent, and is one of the emerging model systems for microsporidia. Due largely to its diplokaryotic nuclei, N. locustae has been classified in the genus Nosema, a large genus with members that infect a wide variety of insects. However, some molecular studies have cast doubt on the validity of certain Nosema species, and on the taxonomic position of N. locustae. To clarify the affinities of this important insect parasite we sequenced part of the rRNA operon of N. locustae and conducted a phylogenetic analysis using the complete small subunit rRNA gene. Nosema locustae is only distantly related to the nominotypic N. bombycis, and is instead closely related to Antonospora scoticae, a recently described parasite of bees. We examined the ultrastructure of mature N. locustae spores, and found the spore wall to differ from true Nosema species in having a multi-layered exospore resembling that of Antonospora (one of the distinguishing features of that genus). Based on both molecular and morphological evidence, therefore, we propose transferring N. locustae to the genus Antonospora, as Antonospora locustae n. comb. [source] Pneumocystis jirovecii multilocus genotyping profiles in patients from Portugal and SpainCLINICAL MICROBIOLOGY AND INFECTION, Issue 4 2008F. Esteves Abstract Pneumonia caused by the opportunistic organism Pneumocystis jirovecii is a clinically important infection affecting AIDS and other immunocompromised patients. The present study aimed to compare and characterise the frequency pattern of DNA sequences from the P. jirovecii mitochondrial large-subunit rRNA (mtLSU rRNA) gene, the dihydropteroate synthase (DHPS) gene and the internal transcribed spacer (ITS) regions of the nuclear rRNA operon in specimens from Lisbon (Portugal) and Seville (Spain). Total DNA was extracted and used for specific molecular sequence analysis of the three loci. In both populations, mtLSU rRNA gene analysis revealed an overall prevalence of genotype 1. In the Portuguese population, genotype 2 was the second most common, followed by genotype 3. Inversely, in the Spanish population, genotype 3 was the second most common, followed by genotype 2. The DHPS wild-type sequence was the genotype observed most frequently in both populations, and the DHPS genotype frequency pattern was identical to distribution patterns revealed in other European studies. ITS types showed a significant diversity in both populations because of the high sequence variability in these genomic regions. The most prevalent ITS type in the Portuguese population was Eg, followed by Cg. In contrast to other European studies, Bi was the most common ITS type in the Spanish samples, followed by Eg. A statistically significant association between mtLSU rRNA genotype 1 and ITS type Eg was revealed. [source] Variation in 16S-23S rRNA intergenic spacer regions among Bacillus subtilis 168 isolatesMOLECULAR MICROBIOLOGY, Issue 1 2001Yevette J. Shaver The genome of the Bacillus subtilis 168-type strain contains 10 ribosomal RNA (rRNA) operons. In the intergenic spacer region (ISR) between the 16S and 23S rRNA genes, five rRNA operons, rrnI-H-G and rrnJ-W, lack a trinucleotide signature region. Precise determination of molecular weight (MW), using electrospray mass spectrometry (MS), of the polymerase chain reaction (PCR) products from a segment of the ISR from the 168-type strain and B. subtilis 168-like strain 23071 demonstrated 114 and 111 basepair (bp) PCR products (due to the presence or absence of the insert in the operons) as predicted from sequence. However, PCR of the ISR segment for five other B. subtilis 168 isolates generated only a 114 bp PCR product, suggesting the presence of the trinucleotide signature region in all rRNA operons for these strains. Additional genetic variability between the seven B. subtilis 168 isolates was demonstrated by restriction fragment length polymorphism (RFLP) of the rRNA operons, with three distinct patterns found upon Southern blot analysis. The 168-type strain and three others (23066, 23067, and 23071) exhibited the same Southern pattern. Thus, operon deletion is not responsible for the absence of a 111 bp product on MS analysis for strains 23066 and 23067. Restriction analysis confirmed the presence of the trinucleotide signature region in the ISR of all rRNA operons for five B. subtilis 168 isolates; sequencing of rrnW/H from a representative strain also upheld this finding. These results help provide a better understanding of variations in sequence, operon number and chromosomal organization, both within a genome and among isolates of B. subtilis subgroup 168. It is also hypothesized that the presence of the trinucleotide insert in certain rRNA operons may play a role in rRNA maturation and protein synthesis. [source] | ||||||||||