Neurospora crassa ribosomal DNA: sequence of internal transcribed spacer and comparison with N. intermedia and N. sitophila

Phenotypic, Molecular, and Pathological Characterization of Colletotrichum acutatum Associated with Andean Lupine and Tamarillo in the Ecuadorian Andes

Anthracnose is a serious problem of both Andean lupine and tamarillo in Ecuador. Morphological features, internal transcribed spacer (ITS) sequences, and host specificity were used to characterize Colletotrichum isolates from lupine and tamarillo. Based on phenotypic and molecular characterization, the causal agent of anthracnose on both hosts was Colletotrichum acutatum. All isolates were identified in a C. acutatum-specific polymerase chain reaction assay. Colony diameter, conidia shape, and insensitivity to benomyl also placed isolates from both hosts in the C. acutatum group. However, a detailed analysis of the ITS sequences placed the lupine and tamarillo isolates from the Ecuadorian Andean zone in two clades, with both lupine and tamarillo isolates in each clade. C. acutatum isolates from Andean lupine were distinct from other C. acutatum isolates on lupine around the world. In cross-infection studies, the diameter of lesions produced by isolates from each host was compared on the main stem of two tamarillo and three lupine cultivars. Some isolates produced larger lesions on the host from which they were isolated but others showed similar aggressiveness on their alternate host. Isolates from both hosts were biotrophic on lupine stems, producing little necrosis and abundant sporulation whereas, on tamarillo stems, they produced dark lesions with few conidia. The collection of C. acutatum isolates from lupine and tamarillo provides interesting material for the study quantitative host adaptation.

Spatial distribution of polygalacturonase-inhibiting proteins in Arabidopsis and their expression induced by Stemphylium solani infection

Disease-induced polygalacturonase-inhibiting proteins (PGIPs) are the major defense proteins which play an important role in resistance to infection of pathogens. To date, the AtPGIP expression in Arabidopsis induced by Stemphylium solani (S. solani) was not described. Here the distribution of AtPGIPs and their expression induced by S. solani infection in Arabidopsis was reported. Notably, immunofluorescence localization showed that the AtPGIPs were distributed in leaves, petioles, stems and roots of 5 week old Arabidopsis, but they were mainly localized in epidermis, vascular bundles and vascular cylinder. Further studies indicated that the transcription level of AtPGIP1 and AtPGIP2 was both up-regulated in response to infection with S. solani which caused hypersensitive cell death, but the transcription level of AtPGIP2 was less induced than AtPGIP1. Consistently, the bulk AtPGIPs of Arabidopsis showed a higher activity in leaves infected by S. solani. Taken together, our preliminary results showed that AtPGIPs were spatially distributed and AtPGIP expression might take part in resistance to infection of S. solani. This study might highlight the potential importance of AtPGIPs and plant disease resistance.

Genetic and Morphological Characterization of Colletotrichum acutatum Causing Anthracnose of Lupins

ABSTRACT Anthracnose, caused by Colletotrichum sp., is a serious problem of lupins (Lupinus spp.) worldwide. Morphological characters and molecular markers were used to characterize 43 Colletotrichum isolates from lupins, 8 isolates from other hosts, and 18 reference isolates representing related Colletotrichum spp., to assess the pathogen diversity and resolve its taxonomy. All lupin Colletotrichum isolates tested positive with C. acutatum-specific polymerase chain reaction (PCR) and did not test positive with C. gloeosporioides-specific PCR. Spore shape and colony diameter as well as insensitivity to benomyl grouped the lupin anthracnose isolates closer to C. acutatum than to C. gloeosporioides. Analysis of internal transcribed spacer (ITS) sequences of 57 Colletotrichum isolates grouped all lupin isolates with C. acutatum and distinct from C. gloeosporioides. Further, tub2 and his4 sequences revealed groups concordant with ITS, reducing the excessive dependence on the latter. Arbitrarily primed-PCR and amplified fragment length polymorphism analyses revealed intraspecific subgroups, but neither was useful to decipher species level relationships. ITS, tub2, and his4 results strongly support designating lupin anthracnose pathogen as C. acutatum or its subspecies. Most Colletotrichum isolates from lupins from worldwide locations are genetically homogeneous and form a distinct subgroup within C. acutatum. Present results also underline the potential of the C. acutatum-specific PCR for routine pathogen diagnosis.

Utilization of the internal transcribed spacer regions as molecular targets to detect and identify human fungal pathogens

Advances in molecular technology show great potential for the rapid detection and identification of fungi for medical, scientific and commercial purposes. Numerous targets within the fungal genome have been evaluated, with much of the current work using sequence areas within the ribosomal DNA (rDNA) gene complex. This section of the genome includes the 18S, 5.8S and 28S genes which code for ribosomal RNA (rRNA) and which have a relatively conserved nucleotide sequence among fungi. It also includes the variable DNA sequence areas of the intervening internal transcribed spacer (ITS) regions called ITS1 and ITS2. Although not translated into proteins, the ITS coding regions have a critical role in the development of functional rRNA, with sequence variations among species showing promise as signature regions for molecular assays. This review of the current literature was conducted to evaluate clinical approaches for using the fungal ITS regions as molecular targets. Multiple applications using the fungal ITS sequences are summarized here including those for culture identification, phylogenetic research, direct detection from clinical specimens or the environment, and molecular typing for epidemiological investigations. The breadth of applications shows that ITS regions have great potential as targets in molecular-based assays for the characterization and identification of fungi. Development of rapid and accurate amplification-based ITS assays to diagnose invasive fungal infections could potentially impact care and improve outcome for affected patients.

Inter- and intra-strain variation in the 5.8S ribosomal RNA and internal transcribed spacer sequences of Entamoeba histolytica and comparison with Entamoeba dispar, Entamoeba moshkovskii and Entamoeba invadens

The ribosomal RNA genes in Entamoeba histolytica are located on circular DNA molecules in about 200 copies per genome equivalent. Nucleotide sequence analysis of the 5.8S rRNA gene and the flanking internal transcribed spacers was carried out to determine the degree of sequence divergence in the multiple rRNA gene copies of a given strain; amongst three different E. histolytica strains (HM-1:IMSS, Rahman and HK-9); and amongst four species of Entamoeba (Entamoeba histolytica, Entamoeba dispar, Entamoeba moshkovskii and Entamoeba invadens). The results show that all rRNA gene copies of a given strain are identical. Few nucleotide positions varied between strains of a species but the differences were very pronounced amongst species. In general, the internal transcribed spacer 2 sequence was more variable and may be useful for strain- and species-identification. The 5.8S rRNA gene and the internal transcribed spacer 2 of E. invadens were unusually small in size.

Electrotransformation of the human pathogenic fungus Scedosporium prolificans mediated by repetitive rDNA sequences

The regions encoding the 5.8S rRNA and the flanking internal transcribed spacers (ITSI and ITSII) from two isolates of the human pathogenic fungus Scedosporium prolificans and one isolate of the taxonomically related species Pseudallescheria boydii (S. apiospermum) were sequenced. The sequences of the two S. prolificans isolates were identical. However, there were minor differences between both species. Phylogenetic analysis of known fungal sequences confirmed a close relationship between S. prolificans and P. boydii. An attempt was made to transform S. prolificans by electroporation using a plasmid vector, pMLF2, bearing the Escherichia coli hygromycin B phosphotransferase gene (hph) under the control of Aspergillus nidulans promoter and terminator sequences. To increase transformation efficiency, the sequenced ribosomal cluster of S. prolificans was used to construct a new vector for homologous recombination.

A comparison of the nucleotide sequence of the cerato-ulmin gene and the rDNA ITS between aggressive and non-aggressive isolates of Ophiostoma ulmi sensu lato, the causal agent of Dutch elm disease

Little genetic information exists comparing aggressive and non-aggressive isolates of the causal agent of Dutch elm disease, Ophiostoma ulmi. Two genetic elements were compared between the subgroups. The ceratoulmin cu gene product has been associated with disease symptoms. Nucleotide-sequence analysis of cu and the internal transcribed spacer (ITS) region of the rDNA were made from three aggressive and three non-aggressive isolates of the pathogen. Our results suggested uniformity within, and unique differences between, subgroups. Differences were detected for cu in the promoter, coding, and transcription termination regions. Sequence data for the ITS clearly distinguish the subgroups.

Comparison of fungi within the Gaeumannomyces-Phialophora complex by analysis of ribosomal DNA sequences

Four ascomycete species of the genus Gaeumannomyces infect roots of monocotyledons. Gaeumannomyces graminis contains four varieties, var. tritici, var. avenae, var. graminis, and var. maydis. G. graminis varieties tritici, avenae, and graminis have Phialophora-like anamorphs and, together with the other Gaeumannomyces and Phialophora species found on cereal roots, constitute the Gaeumannomyces-Phialophora complex. Relatedness of a number of Gaeumannomyces and Phialophora isolates was assessed by comparison of DNA sequences of the 18S rRNA gene, the 5.8S rRNA gene, and the internal transcribed spacers (ITS). G. graminis var. tritici, G. graminis var. avenae, and G. graminis var. graminis isolates can be distinguished from each other by nucleotide sequence differences in the ITS regions. The G. graminis var. tritici isolates can be further subdivided into R and N isolates (correlating with ability [R] or inability [N] to infect rye). Phylogenetic analysis of the ITS regions of several oat-infecting G. graminis var. tritici isolates suggests that these isolates are actually more closely related to G. graminis var. avenae. The isolates of Magnaporthe grisea included in the analysis showed a surprising degree of relatedness to members of the Gaeumannomyces-Phialophora complex. G. graminis variety-specific oligonucleotide primers were used in PCRs to amplify DNA from cereal seedlings infected with G. graminis var. tritici or G. graminis var. avenae, and these should be valuable for sensitive detection of pathogenic isolates and for diagnosis of take-all.

The phylogeny of the tomato leaf mould fungus Cladosporium fulvum syn. Fulvia fulva by analysis of rDNA sequences

The nucleotide sequence of part of the ribosomal DNA from races of the fungal tomato pathogen Cladosporium fulvum and other Cladosporium species have been determined. Comparisons of the internal transcribed spacer regions (ITS1 and ITS2) of several C. fulvum races showed complete sequence homology suggesting a recent evolutionary divergence. Comparisons of these nucleotide sequences in the ITS region with those of other Cladosporium species showed the close relationship within the Cladosporium genus. Using the nucleotide sequence of part of the 18s ribosomal subunit from these isolates and comparing them with sequences of some Ascomycetes, Basidiomycetes and Chytridiomycetes, obtained from GenBank, we infer the phylogeny of the Cladosporium species studied here. Our analysis shows that the Cladosporia form a monophyletic group which falls within the order Ascomycotina.

Processing of eukaryotic ribosomal RNA

In summary, it can be argued that the understanding of eukaryotic rRNA processing is no less important than the understanding of mRNA maturation, since the capacity of a cell to carry out protein synthesis is controlled, in part, by the abundance of ribosomes. Processing of pre-rRNA is highly regulated, involving many cellular components acting either alone or as part of a complex. Some of these components are directly involved in the modification and cleavage of the precursor rRNA, while others direct the packaging of the rRNA into ribosome subunits. As is the case for pre-mRNA processing, snoRNPs are clearly involved in eukaryotic rRNA processing, and have been proposed to assemble with other proteins into at least one complex called a "processosome" (17), which carries out the ordered processing of the pre-rRNA and its assembly into ribosomes. The formation of a processing complex clearly makes possible the regulation required to coordinate the abundance of ribosomes with the physiological and developmental changes of a cell. It may be that eukaryotic rRNA processing is even more complex than pre-mRNA maturation, since pre-rRNA undergoes extensive nucleotide modification and is assembled into a complex structure called the ribosome. Undoubtedly, features of the eukaryotic rRNA-processing pathway have been conserved evolutionarily, and the genetic approach available in yeast research (6) should provide considerable knowledge that will be useful for other investigators working with higher eukaryotic systems. Interestingly, it was originally hoped that the extensive work and understanding of bacterial ribosome formation would provide a useful paradigm for the process in eukaryotes. However, although general features of ribosome structure and function are highly conserved between bacterial and eukaryotic systems, the basic strategy in ribosome biogenesis seems to be, for the most part, distinctly different. Thus, the detailed molecular mechanisms for rRNA processing in each kingdom will have to be independently deciphered in order to elucidate the features and regulation of this important process for cell survival.

Comparison of the 5.8s rDNA and internal transcribed spacer sequences of isolates of Leptosphaeria maculans from different pathogenicity groups

The regions coding for the 5.8s rRNA and the flanking internal transcribed spacers (ITS1 and ITS2) from nine isolates of the blackleg pathogen Leptosphaeria maculans and one isolate of Sclerotinia sclerotiorum were amplified by the polymerase chain reaction and sequenced. Five of the L. maculans isolates were highly virulent to Brassica plants, two were weakly virulent and two were isolated from the cruciferous weed Thlaspi arvense. The 5.8s DNA sequences of all L. maculans isolates were identical. However, there were major differences in both ITS1 and ITS2 sequences that correlated with the pathogenicity grouping. Phylogenetic analysis of the ITS sequences by both parsimony and maximum-likelihood methods indicated that each pathogenicity group was statistically different from each other with the weakly-virulent isolates being more closely related to the Thlaspi than to the highly-virulent isolates. The relationships of L. maculans to other fungi, based on a comparison of the 5.8s rDNA sequences, are discussed.

Unusually compact ribosomal RNA gene cluster in Sphaeronaemella fimicola

The ribosomal DNA repeat unit of Sphaeronaemella fimicola was found to be a 13.7-kb tandem repeat with a relatively long nontranscribed spacer (NTS) and an unusually compact ribosomal RNA gene cluster. The DNA sequence of an 850-bp PCR amplification product containing the 3' end of the small subunit rRNA (SSrRNA) gene, the 5.8s gene, and the 5' end of the large subunit rRNA (LSrRNA) gene was determined. The putative internal spacers flanking the 5.8s RNA gene could be the shortest yet noted for any fungus, totaling only 102 bases.

Sequence and secondary structure comparisons of ITS rDNA in mosquitoes (Diptera: Culicidae)

Sequences of the internal transcribed spacers (ITS1 and ITS2) of the mosquito Aedes aegypti, and the ITS2 of six related species, A. simpsoni, A. albopictus, A. vexans, A. triseriatus, Haemagogus mesodentatus, and Psorophora ferox are reported. Intraspecific variation in A. aegypti ITS1 is 1.07% among four clones from three individuals, and in the ITS2 is 1.17% among 15 clones from four individuals. In A. simpsoni, intraspecific ITS2 variation is 0.46% among 10 clones from a single individual. Alignment of the ITS2 sequence of the seven species reveals several homologous domains. Secondary structure predictions for the ITS2 region indicate that these domains base pair to form a core region central to several stem features. The sequence outside the ITS2 homologous domains tends to be GC-rich and characteristically slippage generated; these areas preserve or add to the stem length of the predicted secondary structures. These ITS2 intraspacer variable regions resemble previously described expansion segments of the 28S gene region. Evolutionary analysis of the ITS2 of these species, using both sequence and secondary structure information, leads to the prediction of divergence in the mosquito tribe Aedini that is not clearly reflected in current taxonomic designations.

Length heterogeneity in ITS 2 and the methylation status of CCGG and GCGC sites in the rRNA genes of the genus Peronosclerospora

The polymerase chain reaction (PCR) was used with primers complementary to conserved flanking sequences to amplify the internal transcribed spacer 2 (ITS 2) of the rDNA repeat units of five Peronoscleropora isolates, one each of P. sorghi, P. maydis, P. sacchari and two of P. zeae. In contrast to the situation found in most-fungi that have been examined, length heterogeneity was evident in each sample. The rDNA composition of the amplified bands was confirmed by Southern hybridizations using an ITS 2 amplified from P. sorghi and cloned rDNA from Neurospora crassa as probes. Length heterogeneity was also detected in genomic DNA digests using the same probes. In addition to one dominant fragment for each isolate, there were several less frequent fragments of different sizes, and the isolate(s) for each species had a unique banding pattern for ITS 2. The absence of 5-methylcytosine residues in CCGG and GCGC sequences in the ribosomal genes of these four Peronosclerospora species was demonstrated by the production of identical banding patterns with ribosomal DNA probes following digestion of genomic DNA with MspI and HpaII, and by complete digestion with CfoI.

Ribosomal DNA internal transcribed spacers are highly divergent in the phytopathogenic ascomycete Fusarium sambucinum (Gibberella pulicaris)

Variation within the internal transcribed spacers (ITS1 and ITS2) and 5.8s ribosomal DNA gene of the heterothallic phytopathogenic filamentous fungus, Fusarium sambucinum (teleomorph = Gibberella pulicaris), was examined in 86 strains from diverse geographical locations by PCR amplification and direct sequencing in order to measure intraspecific divergence within the ITS region. Sequence analysis revealed three ITS types (A, B, C), within which divergence was extremely low (0-2.3%). Surprisingly, the level of intraspecific divergence observed between ITS types, A----B = 14.3%, A----C = 15%, and B----C = 4.6%, is much greater than that reported for any other species. The degree to which transition/transversions and insertion/deletions make up the pattern of ITS sequence evolution both within and between types was analyzed. The sequences of the ITS types exhibit a C-T transition bias together with a GC insertion/deletion bias. In comparison, the genic flanking sequences, including the 5.8s rDNA gene and 5' end of the 28s large nuclear rDNA, are highly conserved. By the criteria of mating and DNA-DNA hybridization, all the strains examined represent a single species. Discordance between the ITS sequence data and other molecular and genetic data on F. sambucinum is discussed.

Fourteen internal transcribed spacers in the circular ribosomal DNA of Euglena gracilis

Cytoplasmic ribosomes from Euglena gracilis contain 16 rRNA components. These include the typical 5 S, 5.8 S and 19 S rRNAs that are found in other eukaryotes as well as 13 discrete small RNAs that interact to form the equivalent of eukaryotic 25-28 S rRNA (accompanying paper). We have utilized DNA sequencing techniques to establish that genes for all of these RNAs, with the exception of 5 S rRNA, are encoded by the 11,500 base-pair circular rDNA of E. gracilis. We have determined the relative positions of the coding regions for the 19 S rRNA and the 14 components (including 5.8 S rRNA) of the large subunit rRNA, thereby establishing that the genes for each of these rRNAs are separated by internal transcribed spacers. We conclude that sequences corresponding to these spacers are removed post-transcriptionally from a high molecular weight pre-rRNA, resulting in a multiply fragmented large subunit rRNA. Internal transcribed spacers, in positions analogous to some of these additional Euglena rDNA spacers, have been found in the rDNA of other organisms and organelles. This finding supports the view that at least some internal transcribed spacers may have been present at an early stage in the evolution of rRNA genes.

Primary structure of the non-transcribed spacer region and flanking sequences of the ribosomal DNA of Neurospora crassa and comparison with other organisms

The non-transcribed spacer (NTS) region of the rDNA of Neurospora crassa contains the transcription regulatory sequences. We isolated a 3.4 kb EcoRI fragment from wild type N.crassa rDNA and cloned in the plasmid pBR325 at the EcoRI site. The insert contains the entire NTS region along with the flanking sequences. Nucleotide sequencing of 3592 nt shows many interesting features like: the NTS region is rich in G+C content (65% G+C); it contains the conserved rRNA processing site 6 (with the nucleotide sequence motif GGTGCGAGAACCCGG, from nt residue 226 to 240, a characteristic feature of most eukaryotic rDNA nontranscribed spacer region); and the NTS region also contains the transcription termination site with the representative Sal I box (from nt residue 1469 to 1477). The potential sequences of transcription termination site are located 288 nt downstream from the end of 26S rRNA gene, and another sequence motif CTTCCT (from nt residue 512 to 517) shows similarity with the human transcription termination site T-2 of its pre-rRNA. Nucleotide sequence homology matrix analysis suggests its relatedness to Saccharomyces cerevisiae and not to human, mouse, rat, Drosophila, Xenopus, wheat, rice and cucumber NTS region. The phylogenetic implication of the NTS region and exploitation of N.crassa NTS rDNA clone to correlate the otherwise indistinguishable species of Neurospora and the correlation with other organisms has been discussed. To the best of our knowledge this is the first report where the nucleotide sequence of the entire NTS region of a filamentous fungus has been determined.

Structural analysis of the internal transcribed spacer 2 of the precursor ribosomal RNA from Saccharomyces cerevisiae

Full-length precursor ribosomal RNA molecules (6440 bases) were produced in vitro using a plasmid containing the yeast 35 S pre-rRNA operon under the control of phage T7 promoter. The higher-order structure of the internal transcribed spacer 2 (ITS-2) region (between the 5.8 S and 25 S rRNA sequence) in the pre-rRNA molecule was investigated using a combination of enzymatic and chemical structural probes. The data were used to evaluate several structural models predicted by a minimum free-energy calculation. The results supported a model in which the 3' end of the 5.8 S rRNA and the 5' end of the 25 S rRNA are hydrogen-bonded better than the one in which the ends are not. The model contains a high degree of secondary structure with several stable hairpins. Similar structural models for the ITS-2 regions of Schizosaccharomyces pombe, Saccharomyces carlsbergensis, mung bean and Xenopus laevis were derived. Certain common folding features appear to be conserved, in spite of extensive sequence divergence. The yeast model should be useful as a prototype in future investigations of the structure, function and processing of pre-rRNA.

GC balance in the internal transcribed spacers ITS 1 and ITS 2 of nuclear ribosomal RNA genes

The internal transcribed spacer (ITS) 1 and 2, the 5.8S rRNA gene, and adjacent 18S rRNA and 25S rRNA coding regions of two Cucurbitaceae (Cucurbita pepo, zucchini, ITS 1: 187 bp, and ITS 2: 252 bp in length, and Cucumis sativus, cucumber, ITS 1: 229 bp, and ITS 2: 245 bp in length) have been sequenced. The evolutionary pattern shown by the ITSs of these plants is different from that found in vertebrates. Deletions, insertions, and base substitutions have occurred in both spacers; however, it is obvious that some selection pressure is responsible for the preservation of stem-loop structures. The dissimilarity of the 5' region of ITS 2 found in higher plants has consequences for proposed models on U3 snRNA-ITS 2 interaction in higher eukaryotes. The two investigated Cucurbitaceae species show a G + C content of ITS 1 that nearly equals that of ITS 2. An analysis of the ITS sequences reveals that in 19 out of 20 organisms published, the G + C content of ITS 1 nearly equals that of ITS 2, although it ranges from 20% to 90% in different organisms (GC balance). Moreover, the balanced G + C content of the ITSs in a given species seems to be similar to that of so-called expansion segments (ESs) in the 25/28S rRNA coding region. Thus, ITSs show a phenomenon called molecular coevolution with respect to each other and to the ESs. In the ITSs of Cucurbitaceae the balanced G + C composition is at least partly achieved by C to T transitions, via deamination of 5-methylcytosine. Other mutational events must be taken into account. The appearance of this phenomenon is discussed in terms of functional constraints linked to the structures of these spacers.