High Apparent Rate of Simultaneous Compensatory Base-Pair Substitutions in Ribosomal RNA

Genetics ◽  
1998 ◽  
Vol 148 (4) ◽  
pp. 1993-2002 ◽  
Author(s):  
Elisabeth R M Tillier ◽  
Richard A Collins
Keyword(s):  
Base Pair ◽  
Large Subunit ◽  
Small Subunit ◽  
High Ratio ◽  
Small Subunit Rrna ◽  
Rna Sequences ◽  
Instantaneous Rate ◽  
The Core ◽  
Rrna Sequences ◽  
Simultaneous Substitution

Abstract We present a model for the evolution of paired bases in RNA sequences. The new model allows for the instantaneous rate of substitution of both members of a base pair in a compensatory substitution (e.g., A-U→G-C) and expands our previous work by allowing for unpaired bases or noncanonical pairs. We implemented the model with distance and maximum likelihood methods to estimate the rates of simultaneous substitution of both bases, αd, vs. rates of substitution of individual bases, αs in rRNA. In the rapidly evolving D2 expansion segments of Drosophila large subunit rRNA, we estimate a low ratio of αd/αs, indicating that most compensatory substitutions involve a G-U intermediate. In contrast, we find a surprisingly high ratio of αd/αs in the core small subunit rRNA, indicating that the evolution of the slowly evolving rRNA sequences is modeled much more accurately if simultaneous substitution of both members of a base pair is allowed to occur approximately as often as substitution of individual bases. Using simulations, we have ruled out several potential sources of error in the estimation of αd/αs. We conclude that in the core rRNA sequences compensatory substitutions can be fixed so rapidly as to appear to be instantaneous.

scholarly journals Pre-AIDS Era Isolates of Pneumocystis carinii f. sp. hominis: High Genotypic Similarity with Contemporary Isolates

1998 ◽  
Vol 36 (1) ◽  
pp. 90-93 ◽  
Author(s):  
Anthony G. Tsolaki ◽  
Pieter Beckers ◽  
Ann E. Wakefield
Keyword(s):  
Large Subunit ◽  
Pneumocystis Carinii ◽  
Small Subunit ◽  
Its Sequence ◽  
Small Subunit Rrna ◽  
Aids Pandemic ◽  
Genes Encoding ◽  
Lsu Rrna ◽  
Large Subunit Rrna ◽  
Sequence Types

Isolates of Pneumocystis carinii f. sp.hominis were examined from six individuals who died ofP. carinii pneumonia between 1968 and 1981 and who had underlying immunodeficiencies which were not due to human immunodeficiency virus infection. DNA sequence variation was analyzed in the genes encoding the mitochondrial large subunit rRNA (mt LSU rRNA), the internal transcribed spacer (ITS) regions of the nuclear rRNA, the arom locus, and the mitochondrial small subunit rRNA. No major variations were observed when these isolates were compared to isolates from HIV-infected individuals. A small number of minor differences were detected. A new position at which variation occurred in the mt LSU rRNA was observed in one sample. Three new ITS sequence types were identified. A total of nine different ITS sequence types were found in the six samples. Mixed infection with different ITS sequence types of P. carinii f. sp. hominis was observed in four of the six samples. The ITS locus was the most informative of the four loci for distinguishing among the isolates ofP. carinii f. sp. hominis. The data suggest that isolates of P. carinii f. sp. hominis from before the AIDS pandemic are genetically very similar to those currently found in HIV-infected individuals.

scholarly journals Microbial Composition of Near-Boiling Silica-Depositing Thermal Springs throughout Yellowstone National Park

2002 ◽  
Vol 68 (10) ◽  
pp. 5123-5135 ◽  
Author(s):  
Carrine E. Blank ◽  
Sherry L. Cady ◽  
Norman R. Pace
Keyword(s):  
Yellowstone National Park ◽  
National Park ◽  
Hydrogen Oxidation ◽  
Large Subunit ◽  
Microbial Community Composition ◽  
Pcr Amplification ◽  
Small Subunit ◽  
Rrna Genes ◽  
Small Subunit Rrna ◽  
Microbial Composition

ABSTRACT The extent of hyperthermophilic microbial diversity associated with siliceous sinter (geyserite) was characterized in seven near-boiling silica-depositing springs throughout Yellowstone National Park using environmental PCR amplification of small-subunit rRNA genes (SSU rDNA), large-subunit rDNA, and the internal transcribed spacer (ITS). We found that Thermocrinis ruber, a member of the order Aquificales, is ubiquitous, an indication that primary production in these springs is driven by hydrogen oxidation. Several other lineages with no known close relatives were identified that branch among the hyperthermophilic bacteria. Although they all branch deep in the bacterial tree, the precise phylogenetic placement of many of these lineages is unresolved at this time. While some springs contained a fair amount of phylogenetic diversity, others did not. Within the same spring, communities in the subaqueous environment were not appreciably different than those in the splash zone at the edge of the pool, although a greater number of phylotypes was found along the pool's edge. Also, microbial community composition appeared to have little correlation with the type of sinter morphology. The number of cell morphotypes identified by fluorescence in situ hybridization and scanning electron microscopy was greater than the number of phylotypes in SSU clone libraries. Despite little variation in Thermocrinis ruber SSU sequences, abundant variation was found in the hypervariable ITS region. The distribution of ITS sequence types appeared to be correlated with distinct morphotypes of Thermocrinis ruber in different pools. Therefore, species- or subspecies-level divergences are present but not detectable in highly conserved SSU sequences.

Phylogeny of Trichomonads Inferred from Small-Subunit rRNA Sequences

1995 ◽  
Vol 42 (4) ◽  
pp. 411-415 ◽  
Author(s):  
JOHN GUNDERSON ◽  
GREGORY HINKLE ◽  
DETLEF LEIPE ◽  
HILARY G. MORRISON ◽  
SHAWN K. STICKEL ◽  
...  
Keyword(s):  
Small Subunit ◽  
Small Subunit Rrna ◽  
Rrna Sequences

Isolation of high-quality total RNA from rumen anaerobic bacteria and fungi, and subsequent detection of glycoside hydrolases

2011 ◽  
Vol 57 (7) ◽  
pp. 590-598 ◽  
Author(s):  
Pan Wang ◽  
Meng Qi ◽  
Perry Barboza ◽  
Mary Beth Leigh ◽  
Emilio Ungerfeld ◽  
...  
Keyword(s):  
Gene Expression ◽  
Solid Phase ◽  
Large Subunit ◽  
Rna Extraction ◽  
Small Subunit ◽  
Glycoside Hydrolases ◽  
Small Subunit Rrna ◽  
High Quality ◽  
Major Barrier ◽  
Total Rna

The rumen is one of the most powerful fibrolytic fermentation systems known. Gene expression analyses, such as reverse transcription PCR (RT-PCR), microarrays, and metatranscriptomics, are techniques that could significantly expand our understanding of this ecosystem. The ability to isolate and stabilize representative RNA samples is critical to obtaining reliable results with these procedures. In this study, we successfully isolated high-quality total RNA from the solid phase of ruminal contents by using an improved RNA extraction method. This method is based on liquid nitrogen grinding of whole ruminal solids without microbial detachment and acid guanidinium – phenol – chloroform extraction combined with column purification. Yields of total RNA were as high as 150 µg per g of fresh ruminal content. The typical large subunit/small subunit rRNA ratio ranged from 1.8 to 2.0 with an RNA integrity number (Agilent Technologies) greater than 8.5. By eliminating the detachment step, the resulting RNA was more representative of the complete ecosystem. Our improved method removed a major barrier limiting analysis of rumen microbial function from a gene expression perspective. The polyA-tailed eukaryotic mRNAs obtained have successfully been applied to next-generation sequencing, and metatranscriptomic analysis of the solid fraction of rumen contents revealed abundant sequences related to rumen fungi.

scholarly journals Three Small Nucleolar RNAs Identified from the Spliced Leader-Associated RNA Locus in Kinetoplastid Protozoans

1998 ◽  
Vol 18 (8) ◽  
pp. 4409-4417 ◽  
Author(s):  
T. Guy Roberts ◽  
Nancy R. Sturm ◽  
Billy K. Yee ◽  
Michael C. Yu ◽  
Toinette Hartshorne ◽  
...  
Keyword(s):  
Large Subunit ◽  
Small Subunit ◽  
Cell Fractionation ◽  
Small Nucleolar Rnas ◽  
Small Subunit Rrna ◽  
Base Pairs ◽  
Spliced Leader ◽  
Repeat Units ◽  
Large Subunit Rrna ◽  
Nucleolar Rnas

ABSTRACT First characterized in Trypanosoma brucei, the spliced leader-associated (SLA) RNA gene locus has now been isolated from the kinetoplastids Leishmania tarentolae and Trypanosoma cruzi. In addition to the T. brucei SLA RNA, bothL. tarentolae and T. cruzi SLA RNA repeat units also yield RNAs of 75 or 76 nucleotides (nt), 92 or 94 nt, and ∼450 or ∼350 nt, respectively, each with significant sequence identity to transcripts previously described from the T. brucei SLA RNA locus. Cell fractionation studies localize the three additional RNAs to the nucleolus; the presence of box C/D-like elements in two of the transcripts suggests that they are members of a class of small nucleolar RNAs (snoRNAs) that guide modification and cleavage of rRNAs. Candidate rRNA-snoRNA interactions can be found for one domain in each of the C/D element-containing RNAs. The putative target site for the 75/76-nt RNA is a highly conserved portion of the small subunit rRNA that contains 2′-O-ribose methylation at a conserved position (Gm1830) in L. tarentolae and in vertebrates. The 92/94-nt RNA has the potential to form base pairs near a conserved methylation site in the large subunit rRNA, which corresponds to position Gm4141 of small rRNA 2 in T. brucei. These data suggest that trypanosomatids do not obey the general 5-bp rule for snoRNA-mediated methylation.

Schistonchus hirtus n. sp. (Nematoda: Aphelenchoididae), an associate of Ficus hirta in China

Nematology ◽  
2010 ◽  
Vol 12 (4) ◽  
pp. 543-556 ◽  
Author(s):  
Yongsan Zeng ◽  
Weimin Ye ◽  
Robin M. Giblin-Davis ◽  
Changhui Li ◽  
Zhijian Du ◽  
...  
Keyword(s):  
Sequence Data ◽  
Large Subunit ◽  
Morphological Characters ◽  
Small Subunit ◽  
Rrna Gene ◽  
Small Subunit Rrna ◽  
Wasp Species ◽  
Dna Sequence Data ◽  
Ficus Hirta ◽  
Large Subunit Rrna

Abstract A nematode recovered from syconia of Ficus hirta from Guangzhou, P. R. China, during a survey of nematode biodiversity from 2007 to 2009, is described herein as Schistonchus hirtus n. sp. and is differentiated by a combination of morphological characters, including excretory pore (EP) located near the metacorpus, a short post-uterine sac (PUS) (0.5 vulval body diam. (VBD) long), rose thorn-shaped spicules, amoeboid sperm, absence of gubernaculum, three pairs of subventral papillae on the male tail, host-Ficus and host-wasp species and DNA sequence data. Morphologically, S. hirtus n. sp. is close to S. centerae, S. altermacrophylla, S. aureus, S. laevigatus and S. virens based upon the length of the PUS (about 0.5 VBD long). However, the relative position of the EP in S. hirtus n. sp. is very different from these species (near metacorpus vs near head). With regard to the EP character, S. hirtus n. sp. is very similar to S. macrophylla, S. guangzhouensis and S. caprifici where the EP is at metacorpus level. However, S. hirtus n. sp. differs from S. macrophylla and S. guangzhouensis by possessing a shorter PUS and smaller spicules, and differs from S. caprifici by a shorter female stylet and smaller spicules. Schistonchus hirtus n. sp. was easily differentiated from other sequenced species by the proportion of parsimony informative changes in the partial small subunit rRNA gene (SSU) and D2/D3 expansion segments of the large subunit rRNA gene (LSU). Phylogenetic analysis with SSU sequences suggests that S. hirtus n. sp. is in a highly supported monophyletic clade with Aphelenchoides and Laimaphelenchus and is polyphyletic to other sequenced Schistonchus species. With LSU sequence data, it forms a clade with S. caprifici and they appear polyphyletic relative to S. guangzhouensis, S. centerae, S. aureus, S. laevigatus and S. virens.

scholarly journals Abundant and Diverse Fungal Microbiota in the Murine Intestine

2006 ◽  
Vol 72 (1) ◽  
pp. 793-801 ◽  
Author(s):  
Alexandra J Scupham ◽  
Laura L. Presley ◽  
Bo Wei ◽  
Elizabeth Bent ◽  
Natasha Griffith ◽  
...  
Keyword(s):  
Small Subunit ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Small Subunit Rrna ◽  
Culture Independent ◽  
Specific Pathogen ◽  
Health And Disease ◽  
Oligonucleotide Fingerprinting ◽  
Rrna Sequences

ABSTRACT Enteric microbiota play a variety of roles in intestinal health and disease. While bacteria in the intestine have been broadly characterized, little is known about the abundance or diversity of enteric fungi. This study utilized a culture-independent method termed oligonucleotide fingerprinting of rRNA genes (OFRG) to describe the compositions of fungal and bacterial rRNA genes from small and large intestines (tissue and luminal contents) of restricted-flora and specific-pathogen-free mice. OFRG analysis identified rRNA genes from all four major fungal phyla: Ascomycota, Basidiomycota, Chytridiomycota, and Zygomycota. The largest assemblages of fungal rRNA sequences were related to the genera Acremonium, Monilinia, Fusarium, Cryptococcus/Filobasidium, Scleroderma, Catenomyces, Spizellomyces, Neocallimastix, Powellomyces, Entophlyctis, Mortierella, and Smittium and the order Mucorales. The majority of bacterial rRNA gene clones were affiliated with the taxa Bacteroidetes, Firmicutes, Acinetobacter, and Lactobacillus. Sequence-selective PCR analyses also detected several of these bacterial and fungal rRNA genes in the mouse chow. Fluorescence in situ hybridization analysis with a fungal small-subunit rRNA probe revealed morphologically diverse microorganisms resident in the mucus biofilm adjacent to the cecal and proximal colonic epithelium. Hybridizing organisms comprised about 2% of the DAPI (4′,6-diamidino-2-phenylindole, dihydrochloride)-positive organisms in the mucus biofilm, but their abundance in fecal material may be much lower. These data indicate that diverse fungal taxa are present in the intestinal microbial community. Their abundance suggests that they may play significant roles in enteric microbial functions.

Phylogenetic Relationships among Karyorelictids and Heterotrichs Inferred from Small Subunit rRNA Sequences: Resolution at the Base of the Ciliate Tree

1995 ◽  
Vol 4 (1) ◽  
pp. 77-87 ◽  
Author(s):  
Robert P. Hirt ◽  
Patricia L. Dyal ◽  
Mark Wilkinson ◽  
Bland J. Finlay ◽  
David McL. Roberts ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Small Subunit ◽  
Small Subunit Rrna ◽  
Rrna Sequences

Characterisation of, and entomopathogenic studies on, Pristionchus aerivorus (Cobb in Merrill & Ford, 1916) Chitwood, 1937 (Rhabditida: Diplogastridae) from North Carolina, USA

Nematology ◽  
2015 ◽  
Vol 17 (5) ◽  
pp. 567-580
Author(s):  
Weimin Ye ◽  
Qing Yu ◽  
Natsumi Kanzaki ◽  
Paul R. Adams ◽  
Yasmin J. Cardoza
Keyword(s):  
North Carolina ◽  
Helicoverpa Zea ◽  
Large Subunit ◽  
Small Subunit ◽  
Morphological Observation ◽  
Rrna Gene ◽  
Small Subunit Rrna ◽  
Morphological Studies ◽  
The Status ◽  
Molecular Phylogenetic

During a survey of entomopathogenic nematodes in North Carolina, USA, aPristionchusspecies was recovered using theGalleriabait method. Morphological studies with light microscopy and scanning electron microscopy, mating tests with reference strains, as well as molecular analyses of the near-full-length small subunit rRNA gene (18S) and D2-D3 expansion segments of the large subunit rRNA gene (28S) identified this isolate asPristionchus aerivorus. ExposedGallerialarvae were killed within 48 h and high numbers of nematodes were recovered from the cadavers about 5 days later. Preliminary tests revealed that this nematode is capable of infecting at least two other insect species (Helicoverpa zeaandTenebrio molitor) under laboratory conditions. The status of the genusChroniodiplogasteris discussed and confirmed as a junior synonym ofPristionchusbased on morphological observation and molecular phylogenetic analysis.

Sign in / Sign up

Export Citation Format

Share Document