Phylogenetic Analysis of the Complete rRNA Gene Sequence of Nosema sp. SE Isolated from the Beet Armyworm Spodoptera exigua.

The microsporidium Nosema sp. SE is a pathogen that infects the beet armyworm Spodoptera exigua. The complete sequence of its 4,302-base pair (bp) ribosomal ribonucleic acid (rRNA) gene region was obtained by polymerase chain reaction amplification and sequencing. The rRNA organization of Nosema sp. SE was 5'-large subunit (LSU) rRNA-internal transcribed spacer-small subunit (SSU) rRNA-intergenic spacer-5S-3', which corresponded to the pattern of Nosema bombycis. Phylogenetic analysis based on LSU rRNA and SSU rRNA both indicated that the parasite had a close relationship with other true Nosema species, confirming that Nosema sp. SE belongs to true Nosema group of the genus Nosema.

Diel population and functional synchrony of microbial communities on coral reefs.

On coral reefs, microorganisms are essential for recycling nutrients to primary producers through the remineralization of benthic-derived organic matter. Diel investigations of reef processes are required to holistically understand the functional roles of microbial players in these ecosystems. Here we report a metagenomic analysis characterizing microbial communities in the water column overlying 16 remote forereef sites over a diel cycle. Our results show that microbial community composition is more dissimilar between day and night samples collected from the same site than between day or night samples collected across geographically distant reefs. Diel community differentiation is largely driven by the flux of Psychrobacter sp., which is two-orders of magnitude more abundant during the day. Nighttime communities are enriched with species of Roseobacter, Halomonas, and Alteromonas encoding a greater variety of pathways for carbohydrate catabolism, further illustrating temporal patterns of energetic provisioning between different marine microbes. Dynamic diel fluctuations of microbial populations could also support the efficient trophic transfer of energy posited in coral reef food webs.

Investigating the ion dependence of the first unfolding step of GTPase-Associating Center ribosomal RNA.

The interactions in the tertiary structure of a ribosomal RNA fragment in the GTPase Associating Center (GAC) have been experimentally studied, but the roles of the bound and diffuse cations in its folding pathway have not yet been fully elucidated. Melting experiments have shown that the temperature of the first of the two distinguishable transitions in the unfolding pathway of the GAC RNA can be regulated by altering the magnesium concentration, yet the physical interpretation of such ion-dependent effects on folding have not been clearly understood in spite of the availability of crystal structures that depict many GAC RNA-ion interactions. Here, we use umbrella sampling and molecular dynamics (MD) simulations to provide a physical description for the first transition in this unfolding pathway, with a focus on the role of a chelated magnesium ion. Our results indicate that the presence of cations mediating the local interaction of two loops stabilizes the folded state relative to the unfolded or partially folded states. Also, our findings suggest that a bridging magnesium ion between the two loops improves the stabilizing effect. This is consistent with the multistep unfolding pathway proposed for the GAC RNA and highlights the importance of ions in the first unfolding step. The results suggest how MD simulations can provide insight into RNA unfolding pathways as a complementary approach to experiments.

Structure of the Ribosomal RNA Decoding Site Containing a Selenium-Modified Responsive Fluorescent Ribonucleoside Probe.

Comprehensive understanding of the structure-function relationship of RNA both in real time and at atomic level will have a profound impact in advancing our understanding of RNA functions in biology. Here, we describe the first example of a multifunctional nucleoside probe, containing a conformation-sensitive fluorophore and an anomalous X-ray diffraction label (5-selenophene uracil), which enables the correlation of RNA conformation and recognition under equilibrium and in 3D. The probe incorporated into the bacterial ribosomal RNA decoding site, fluorescently reports antibiotic binding and provides diffraction information in determining the structure without distorting native RNA fold. Further, by comparing solution binding data and crystal structure, we gained insight on how the probe senses ligand-induced conformational change in RNA. Taken together, our nucleoside probe represents a new class of biophysical tool that would complement available tools for functional RNA investigations.

The complete chloroplast genome sequence of Cynanchum auriculatum Royle ex Wight (Apocynaceae).

Cynanchum auriculatum is a climbing vine belonging to the Apocynaceae family and shows very similar morphology to Cynanchum wilfordii, a medicinal plant. The complete chloroplast genome of C. auriculatum was generated by de novo assembly using the small amount of whole genome sequencing data. The chloroplast genome of C. auriculatum was 160 840 bp in length and consisted of four distinct regions, such as large single copy region (91 973 bp), small single copy region (19 667 bp), and a pair of inverted repeat regions (24 600 bp). The overall GC contents of the chloroplast genome were 37.8%. A total of 114 genes were predicted and included 80 protein-coding genes, 30 tRNA genes, and four rRNA genes. Phylogenetic analysis with the reported chloroplast genomes revealed that C. auriculatum is most closely related to Cynanchum wilfordii, a medicinal plant.

Molecular identification and characterization of ileal and cecal fungus communities in broilers given probiotics, specific essential oil blends, and under mixed Eimeria infection.

Broiler digestive tract fungal communities have gained far less scrutiny than that given corresponding bacterial communities. Attention given poultry-associated fungi have focused primarily on feed-associated toxin-producers, yeast, and yeast products. The current project focused on the use of pyrosequencing and denaturing gradient gel electrophoresis (DGGE) to identify and monitor broiler digestive fungal communities. Eight different treatments were included. Four controls were an Uninfected-Unmedicated Control, an Unmedicated-Infected Control, the antibiotic bacitracin methylene disalicylate plus the ionophore monensin as Positive Control, and the ionophore monensin alone as a Negative Control. Four treatments were two probiotics (BC-30 and Calsporin) and two specific essential oil blends (Crina Poultry Plus and Crina Poultry AF). All chickens except the Unmedicated-Uninfected Control were given, at 15 days of age, a standard oral Eimeria inoculum of sporulated oocysts. Ileal and cecal digesta were collected at pre-Eimeria infection at 14 days of age and at 7 days post-Eimeria infection at 22 days of age. Extracted cecal DNA was analyzed by pyrosequencing to examine the impact of diet supplements and Eimeria infection on individual constituents in the fungal community, while DGGE was used to compare more qualitative changes in ileal and cecal communities. Pyrosequencing identified three phyla, seven classes, eight orders, 13 families, 17 genera, and 23 fungal species. Ileal and cecal DGGE patterns showed fungal communities were clustered mainly into pre- and post-infection patterns. Post-infection Unmedicated-Uninfected patterns were clustered with pre-infection groups demonstrating a strong effect of Eimeria infection on digestive fungal populations. These combined techniques offered added versatility towards unraveling the effects of enteropathogen infection and performance enhancing feed additives on broiler digestive microflora.

The origins of the Redfield nitrogen-to-phosphorus ratio are in a homoeostatic protein-to-rRNA ratio.

One of the most intriguing patterns in the biosphere is the similarity of the atomic nitrogen-to-phosphorus ratio (N:P) = 16 found in waters throughout the deep ocean and in the plankton in the upper ocean. Although A.C. Redfield proposed in 1934 that the intracellular properties of plankton were central to this pattern, no theoretical significance for N:P = 16 in cells had been found. Here, we use theoretical modelling and a compilation of literature data for prokaryotic and eukaryotic microbes to show that the balance between two fundamental processes, protein and rRNA synthesis, results in a stable biochemical attractor that homoeostatically produces a given protein:rRNA ratio. Furthermore, when biochemical constants and reasonable kinetic parameters for protein synthesis and ribosome production under nutrient-replete conditions are applied in the model, it predicts a stable protein:rRNA ratio of 3 ± 0.7, which corresponds to N:P = 16 ± 3. The model also predicts that N-limitation, by constraining protein synthesis rates, will result in N:P ratios below the Redfield value while P-limitation, by constraining RNA production rates, will produce ratios above the Redfield value. Hence, one of most biogeochemically significant patterns on Earth is inherently rooted in the fundamental structure of life.

Characteristics of the microbial community associated with ammonia oxidation in a full-scale rockwool biofilter treating malodors from livestock manure composting.

The relationship between the activity and community structure of microbes associated with the oxidation of ammonia in a full-scale rockwool biofilter was examined by kinetic, denaturing gradient gel electrophoresis (DGGE), and sequence analyses. The packing materials were sampled from two different depths at 3 sites. Estimated K(m) values were similar among depths at same sampling sites, while V(max) differed in the mid-point sample. The lower depth of this site had the highest V(max). A correspondence analysis showed the DGGE profile of ammonia-oxidizing bacterial amoA of the lower depth of the mid-point sample to be distinguishable from the others. Banding patterns at other sites were similar among depths. Banding patterns of ammonia-oxidizing archaeal amoA of the mid-point sample were also similar among depths. The results suggested an association between the ammonia-oxidizing bacterial community's composition and ammonium oxidation kinetics in samples. Sequence analysis indicated that the ammonia-oxidizing bacterial community mainly belonged to the Nitrosomonas europaea lineage and Nitrosospira cluster 3. The ammonia-oxidizing archaeal amoA-like sequences were related to those belonging to soil and sediment groups, including one with 84% nucleotide similarity with Nitrosopumilus maritimus.

Polygalacturonase secreted by yeasts from Brazilian semi-arid environments.

Microbial pectinolytic enzymes are known to play a commercially important role in a number of industrial processes. The objective of this study was to investigate the extracellular polygalacturonases of yeasts isolated from Brazilian semi-arid environments. Among the 250 colonies tested, only 33 produced extracellular polygalacturonases: Aureobasidium pullulans (18 isolates), Candida boidinii (one isolate), Trichosporonoides sp. (three isolates), Kluyveromyces marxianus (one isolate), Cryptococcus liquefaciens (one isolate), Pseudozyma sp. (four isolates), and yeast-like related to fungal endophyte (five isolates). The highest activity of polygalacturonase was observed in Pseudozyma sp. CCMB 300 (14.17+/-0.08 micromol acid galacturonic released/min/mg protein). This study shows the potential of yeasts and yeast-like organisms isolated from Brazilian semi-arid environments to produce pectinolytic enzymes.

Isospora orlovi infection in suckling dromedary camel calves (Camelus dromedarius) in Kenya.

Outbreaks of isosporosis in young suckling dromedary camel calves (Camelus dromedarius) in Dubai, UAE and in Kenya were recently described. In the former outbreak the pathogen was shown to be Isospora orlovi by morphological features and was later characterized molecularly. In the present study, we have made a longitudinal investigation of 159 suckling dromedary calves < or =12 weeks of age belonging to 8 ranched camel herds (M1) in Northern Kenya. The study was carried out during 18 months. In three of the herds frequent samples were taken irregularly every 1-6 weeks. All calves < or =12 weeks of age present in the respective herds were sampled during the visits. In addition, 91 calves of the same age group but belonging to 42 pastoral herds (M2) in Northern Kenya were point sampled at convenience. Faecal samples from each calf were taken and the faeces were investigated for coccidia. Samples found with coccidian oocysts were suspended in a 2% potassium dichromate solution. Isospora sp. was identified and samples with relatively high numbers of Isospora sp. were analysed molecularly. The SSU rRNA gene and internal transcribed spacer 1 (ITS1) were amplified with primers complementary to conserved regions of the SSU rRNA gene in eukaryotes as well as a conserved part of the 5.8S rRNA gene of Eimeria. A relatively high number of the calves exhibited diarrhoea, 30.2% and 41.8% in the M1 and M2 herds, respectively. Isospora sp. was only found in diarrhoeic calves or in calves convalescent from recent scouring periods. No calf >8 weeks of age was found to be excreting Isospora sp. The parasite was only found in calves < or =4 weeks of age in the M1 herds and in the M2 herds in calves <8 weeks of age. Of the M1 and M2 calves exhibiting diarrhoea, 20.8% and 26.3% excreted Isospora sp., respectively. Morphologically the Isospora sp. was similar to I. orlovi and sequence analysis of the SSU rRNA gene from four Kenyan isolates (unfortunately only from the pastoral herds, M2) and ITS 1 segments from three of the isolates from Kenya and one from Dubai, confirmed that the Isospora isolates belonged to the species I. orlovi, and that the sequences were similar to the Dubai isolates.

Quantifying microbial utilization of petroleum hydrocarbons in salt marsh sediments by using the 13C content of bacterial rRNA.

Natural remediation of oil spills is catalyzed by complex microbial consortia. Here we took a whole-community approach to investigate bacterial incorporation of petroleum hydrocarbons from a simulated oil spill. We utilized the natural difference in carbon isotopic abundance between a salt marsh ecosystem supported by the 13C-enriched C4 grass Spartina alterniflora and 13C-depleted petroleum to monitor changes in the 13C content of biomass. Magnetic bead capture methods for selective recovery of bacterial RNA were used to monitor the 13C content of bacterial biomass during a 2-week experiment. The data show that by the end of the experiment, up to 26% of bacterial biomass was derived from consumption of the freshly spilled oil. The results contrast with the inertness of a nearby relict spill, which occurred in 1969 in West Falmouth, MA. Sequences of 16S rRNA genes from our experimental samples also were consistent with previous reports suggesting the importance of Gamma- and Deltaproteobacteria and Firmicutes in the remineralization of hydrocarbons. The magnetic bead capture approach makes it possible to quantify uptake of petroleum hydrocarbons by microbes in situ. Although employed here at the domain level, RNA capture procedures can be highly specific. The same strategy could be used with genus-level specificity, something which is not currently possible using the 13C content of biomarker lipids.

Biological stoichiometry in human cancer.

BACKGROUND: A growing tumor in the body can be considered a complex ecological and evolutionary system. A new eco-evolutionary hypothesis (the "Growth Rate Hypothesis", GRH) proposes that tumors have elevated phosphorus (P) demands due to increased allocation to P-rich nucleic acids, especially ribosomal RNA, to meet the protein synthesis demands of accelerated proliferation. METHODOLOGY/PRINCIPAL FINDINGS: We determined the elemental (C, N, P) and nucleic acid contents of paired malignant and normal tissues from colon, lung, liver, or kidney for 121 patients. Consistent with the GRH, lung and colon tumors were significantly higher (by approximately two-fold) in P content (fraction of dry weight) and RNA content and lower in nitrogen (N):P ratio than paired normal tissue, and P in RNA contributed a significantly larger fraction of total biomass P in malignant relative to normal tissues. Furthermore, patient-specific differences for %P between malignant and normal tissues were positively correlated with such differences for %RNA, both for the overall data and within three of the four organ sites. However, significant differences in %P and %RNA between malignant and normal tissues were not seen in liver and kidney and, overall, RNA contributed only approximately 11% of total tissue P content. CONCLUSIONS/SIGNIFICANCE: Data for lung and colon tumors provide support for the GRH in human cancer. The two-fold amplification of P content in colon and lung tumors may set the stage for potential P-limitation of their proliferation, as such differences often do for rapidly growing biota in ecosystems. However, data for kidney and liver do not support the GRH. To account for these conflicting observations, we suggest that local environments in some organs select for neoplastic cells bearing mutations increasing cell division rate ("r-selected," as in colon and lung) while conditions elsewhere may select for reduced mortality rate ("K-selected," as in liver and kidney).

Application of PCR-DGGE to analyse the yeast population dynamics in slurry reactors during degradation of polycyclic aromatic hydrocarbons in weathered oil.

Slurry-phase reactors have been used to investigate the biodegradation feasibility of polycyclic aromatic hydrocarbons (PAHs) in weathered crude oil, by mixed culture containing five PAHs-degrading yeast strains. Yeasts were isolated from the oily soil by enrichment culture, using phenanthrene as a sole carbon source, and identified based on the 26S ribosomal DNA (rDNA) sequence. Yeast strains belonged to the genera Candida, Pichia, Rhodotorula and Sporidiobolus. The experiment was carried out for a period of 6 weeks at room temperature with a solid : liquid ratio of 50% w/w. The results showed that high removal efficiency was obtained for all PAHs, including low molecular weight (LMW) and high molecular weight (HMW) compounds (89.3-98.6% and 66.3-89.4% within 6 weeks, respectively). The higher removal efficiency for HMW-PAHs obtained in this work suggested that yeast strains mixture could play an important role to reclaim oil-contaminated sites. Denaturing gradient gel electrophoresis (DGGE) of polymerase chain reaction (PCR)-amplified 26S rRNA genes was used to follow the changes of yeast populations during the slurry reactor process. The results of DGGE indicated that Candida maltosa-like and Pichia guilliermondii were the dominant species but Rhodotorula dairenensis appeared as a weak band and Sporidiobolus salmonicolor and Pichia anomala disappeared during the study. Moreover, the results showed that all of the five strains, including the two belonging to the same genus, could be differentiated from each other in the DGGE profile.

Indirect NMR spin-spin coupling constants 3J(P,C) and 2J(P,H) across the P-O...H-C link can be used for structure determination of nucleic acids.

Calculated indirect NMR spin-spin coupling constants (3)J(P,C) and (2)J(P,H) were correlated with the local structure of the P-O...H-C linkage between the nucleic acid (NA) backbone phosphate and the H-C group(s) of a nucleic acid base. The calculations were carried out for selected nucleotides from the large ribosomal subunit (Ban et al. Science 2000, 289, 905) with the aim of identifying NMR parameters suitable for detection of certain noncanonical RNA structures. As calculations in the model system, dimethyl-phosphate-guanine, suggest, the calculated indirect spin-spin couplings across the linkage are sensitive to the mutual orientation and distance between the phosphate and nucleic acid base. A short distance between the nucleic acid base and phosphate group and the angles C...P-O and P...C-H smaller than 50 degrees are prerequisites for a measurable spin-spin interaction of either coupling (|J| > 1 Hz). A less favorable arrangement of the P-O...H-C motif, e.g., in nucleotides of the canonical A-RNA, results in an effective dumping of both spin-spin interactions and insignificant values of the NMR coupling constants. The present work indicates that quantum chemical calculations of the indirect spin-spin couplings across the P-O...H-C motif can help detect some rare but important backbone topologies, as seen for example in the reverse kink-turn. Measuring of (3)J(P,C) and (2)J(P,H) couplings can therefore provide critical constraints on the NA base and phosphate geometry and help to determine the structure of NAs.

The ribosome as a drug target.

The elucidation of the crystal structure of the ribosome and its subunits has dramatically increased our understanding of this organelle and the molecular interactions that determine its functional capabilities. Two recent publications, one on the structure of the bacterial ribosome at 3.5A resolution and one on the identification of functionally relevant sites within the small subunit rRNA, illustrate the importance of interdisciplinary approaches in exploiting the ribosome as a drug target.

Expression of silicatein in spicules from the Baikalian sponge Lubomirskia baicalensis.

Lake Baikal harbors the largest diversity of sponge species [phylum Porifera] among all freshwater biotopes. The abundantly occurring species Lubomirskia baicalensis was used to study the seasonal silicatein metabolism; the spicules of this species have an unusually thick axial filament, consisting of silicatein, which remains constant in diameter during their growth. In the course of maturation, the size of the silicic acid shell grows, until the final diameter of the spicules of about 8 microm is reached. The seasonal content of silicatein was assessed by use of antibodies raised against silicatein; they stained specifically the axial filaments. In addition we determined, by application of the enzyme-linked immunosorbent assay system, that the proteinaceous content of the spicules, the silicatein, increases from spring to late summer by 8-fold. As molecular markers to quantify the seasonal changes in expression levels of genes coding for proteins/enzymes, the genes for the calumenin-like protein and the kinesin-related protein, were selected. The expression of calumenin-like gene, involved in the intracellular signaling, is highest during September, whereas the expression of the kinesin-related protein does not change during the annual course. These results suggest that the highest metabolic activity of L. baicalensis occurs in late summer (September), in parallel with the highest accumulation of silicatein, a structural protein/enzyme of the spicules.

A nonribosomal landscape in the nucleolus revealed by the stem cell protein nucleostemin.

Nucleostemin is a p53-interactive cell cycle progression factor that shuttles between the nucleolus and nucleoplasm, but it has no known involvement in ribosome synthesis. We found the dynamic properties of nucleostemin differed strikingly from fibrillarin (a protein directly involved in rRNA processing) both in response to rRNA transcription inhibition and in the schedule of reentry into daughter nuclei and the nucleolus during late telophase/early G1. Furthermore, nucleostemin was excluded from the nucleolar domains in which ribosomes are born--the fibrillar centers and dense fibrillar component. Instead it was concentrated in rRNA-deficient sites within the nucleolar granular component. This finding suggests that the nucleolus may be more subcompartmentalized than previously thought. In support of this concept, electron spectroscopic imaging studies of the nitrogen and phosphorus distribution in the nucleolar granular component revealed regions that are very rich in protein and yet devoid of nucleic acid. Together, these results suggest that the ultrastructural texture of the nucleolar granular component represents not only ribosomal particles but also RNA-free zones populated by proteins or protein complexes that likely serve other functions.

Expression and localization studies of hSDA, the human ortholog of the yeast SDA1 gene.

The yeast SDA1 gene was reported to play a critical role in G(1) events and to be involved in 60S ribosome biogenesis. Although the basic cellular mechanisms appear conserved from yeast to man, the human genes may have more diversified functions. In this view we obtained the first experimental evidences about the human ortholog of the yeast SDA1, i.e., hSDA. The gene is localized at the chromosomal region 4q21 and encodes for a 627a.a. long protein highly homologous to the yeast Sda1. Subcellular localization experiments indicate that the human protein behaves similarly to nucleolar proteins involved in rRNA processing machinery but not in RNA PolI transcriptional events. hSda appears localized in the granular component of the nucleolus and in the nucleoplasm, which is consistent with a role in early-intermediate steps of ribosome biogenesis. hSDA appears preferentially expressed in fetal tissues, pinpointing its role during development. Different expression levels in different tumor cell lines might suggest that the gene is involved also in tumorigenesis. However our preliminary results indicate that hSDA does not behave like a proapoptotic gene and its involvement in tumorigenesis is still to be clarified.

A structure-based strategy to identify new molecular scaffolds targeting the bacterial ribosomal A-site.

The need for novel antibiotics is widely recognized. A well validated target of antibiotics is the bacterial ribosome. Recent X-ray structures of the ribosome bound to antibiotics have shed new light on the binding sites of these antibiotics, providing fresh impetus for structure-based strategies aiming at identifying new ribosomal ligands. In that respect, the ribosomal decoding region of the aminoacyl-tRNA acceptor site (A-site) is of particular interest because oligonucleotide model systems of this site are available for crystallography, NMR and compound binding assays. This work presents how these different resources can be combined in a hierarchical screening strategy which has led to the identification of new A-site ligands. The approach exploits an X-ray structure of the A-site against which large and diverse libraries of compounds were computationally docked. The complementarity of the compounds to the A-site was assessed using a scoring function specifically calibrated for RNA targets. Starting from approximately 1 million compounds, the computational selection of candidate ligands allowed us to focus the experimental work on 129 compounds, 34 of which showed affinity for the A-site in a FRET-based binding assay. NMR experiments confirmed binding to the A-site for some compounds. For the most potent compound in the FRET assay, a tentative binding mode is suggested, which is compatible with the NMR data and the limited SAR in this series. Overall, the results validate the screening strategy.

Role of human ribosomal RNA (rRNA) promoter methylation and of methyl-CpG-binding protein MBD2 in the suppression of rRNA gene expression.

The methylation status of the CpG island located within the ribosomal RNA (rRNA) promoter in human hepatocellular carcinomas and pair-matched liver tissues was analyzed by bisulfite genomic sequencing. Significant hypomethylation of methyl-CpGs in the rRNA promoter was observed in the tumor samples compared with matching normal tissues, which was consistent with the relatively high level of rRNA synthesis in rapidly proliferating tumors. To study the effect of CpG methylation on RNA polymerase I (pol I)-transcribed rRNA genes, we constructed pHrD-IRES-Luc (human rRNA promoter-luciferase reporter). In this plasmid, Kozak sequence of the pGL3-basic vector was replaced by the internal ribosome entry site (IRES) of encephalomyocarditis viral genome to optimize pol I-driven reporter gene expression. Transfection of this plasmid into HepG2 (human) cells revealed reduced pol I-driven luciferase activity with an increase in methylation density at the promoter. Markedly reduced luciferase activity in Hepa (mouse) cells compared with HepG2 (human) cells showed that pHrD-IRES-Luc is transcribed by pol I. Site-specific methylation of human rRNA promoter demonstrated that methylation of CpG at the complementary strands located in the promoter (-9, -102, -347 with respect to the +1 site) inhibited luciferase activity, whereas symmetrical methylation of a CpG in the transcribed region (+152) did not affect the promoter activity. Immunofluorescence studies showed that the methyl-CpG-binding proteins, MBD1, MBD2, MBD3, and MeCP2, are localized both in the nuclei and nucleoli of HepG2 cells. Transient overexpression of MBD2 suppressed luciferase activity specifically from the methylated rRNA promoter, whereas MBD1 and MBD3 inhibited rRNA promoter activity irrespective of the methylation status. Chromatin immunoprecipitation analysis confirmed predominant association of MBD2 with the endogenous methylated rRNA promoter, which suggests a selective role for MBD2 in the methylation-mediated inhibition of ribosomal RNA gene expression.