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Results for “Ribosome Profiling”

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PubMed2006

Gene expression and survival changes in Saccharomyces cerevisiae during suspension culture.

This study explores the connection between changes in gene expression and the genes that determine strain survival during suspension culture, using the model eukaryotic organism, Saccharomyces cerevisiae. The Saccharomyces cerevisiae homozygous diploid deletion pool (HDDP), and the BY4743 parental strain were grown for 18 h in a rotating wall vessel (RWV), a suspension culture device optimized to minimize the delivered shear. In addition to the reduced shear conditions, the RWVs were also placed in a static position or in a shaker in order to change the amount of shear stress on the cells. Using simple linear regression, it was found that there were 140 differentially expressed genes for which >70% of the variation can be explained by shear stress alone. A significant number of these genes are involved in catalytic activity. In the HDDP, shear stress was associated with significant survival changes in 15 deletion strains (R(2>) > 0.7) Interestingly, both analyses uncovered changes in the ribosomal protein machinery. Comparing the changes in gene expression and strain survival under the different shear conditions allows for the insights into the molecular mechanisms behind the cells response to shear stress. This in turn can provide information for the optimization of suspension culture.

Cell Division↗

PubMed2005

Classification of oligonucleotide fingerprints: application for microbial community and gene expression analyses.

MOTIVATION: Oligonucleotide fingerprinting of ribosomal RNA genes (OFRG) is a procedure that sorts rRNA gene (rDNA) clones into taxonomic groups through a series of hybridization experiments. The hybridization signals are classified into three discrete values 0, 1 and N, where 0 and 1, respectively, specify negative and positive hybridization events and N designates an uncertain assignment. This study examined various approaches for classifying the values including Bayesian classification with normally distributed signal data, Bayesian classification with the exponentially distributed data, and with gamma distributed data, along with tree-based classification. All classification data were clustered using the unweighted pair group method with arithmetic mean. RESULTS: The performance of each classification/clustering procedure was compared with results from known reference data. Comparisons indicated that the approach using the Bayesian classification with normal densities followed by tree clustering out-performed all others. The paper includes a discussion of how this Bayesian approach may be useful for the analysis of gene expression data.

Algorithms↗

PubMed2003

Annotation pattern of ESTs from Spodoptera frugiperda Sf9 cells and analysis of the ribosomal protein genes reveal insect-specific features and unexpectedly low codon usage bias.

MOTIVATION: A whole set of Expressed Sequence Tags (ESTs) from the Sf9 cell line of Spodoptera frugiperda is presented here for the first time. By this way we want to identify both conserved and specific genes of this pest species. We also expect from this analysis to find a class of protein sequences providing a tool to explore genomic features and phylogeny of Lepidoptera. RESULTS: The ESTs display both housekeeping as well as developmentally regulated genes, and a high percentage of sequences with unknown function. Among the identified ORFs, almost all ribosomal proteins (RPs) were found with high EST redundancy and hence sequence accuracy. The codon usage found among RP genes is in average surprisingly much less biased in Lepidoptera than in other organisms. Other Spodoptera genes also displayed a low bias, suggesting a general genome expression feature in this Lepidoptera. We also found that the L35A and L36 RP sequences, respectively, display 40 and 10 amino-acid insertions, both being present only in insects. Sequence analysis suggests that they are probably not subjected to a strong selective pressure and may be good phylogenetic markers for Lepidoptera. Most interestingly, the Lepidoptera sequences of 9 RP genes displayed a specific signature different from the canonical one. We conclude that the RP family allows valuable comparative genomics and phylogeny of Lepidoptera. AVAILABILITY: All EST sequence data are available from the private 'Spodo-Base' upon request.

Abstracting and Indexing↗

PubMed1980

Poly(A)- and nonpoly(A)-RNA associated with rat brain microsomal fractions: in vivo labelling studies.

The time course of incorporation of radiolabelled precursor into RNA associated with rat brain free polyribosomes, rough membranes, and smooth membranes was measured following a single intracranial injection of [3H] orotic acid. Polyadenylated RNAs were separated from nonpolyadenylated RNAs by affinity chromatography on oligo (dT)-cellulose columns. Poly(A)-RNA associated with each of the microsomal fractions became more rapidly labelled than did the nonpoly(A)-RNA of the same fractions. While the labelling profiles of the nonpoly(A)-RNA isolated from the polyribosomes and rough membranes are similar from one fraction to another, the specific radioactivity of the poly(A)-RNA isolated from free polyribosomes increased much more drastically than that of the poly(A)-RNA associated with rough membranes. The labelling profiles of RNA species isolated from smooth membranes were very different in this respect from the two ribosomal fractions. There was a lag of more than four hours before significant label appeared in the RNA associated with the smooth membrane fraction. These studies demonstrate that the different populations of brain microsomal RNA are labelled at different rates, perhaps reflecting differences in the turnover of these RNAs and differences in their function.

Animals↗

PubMed2002

Comparison of selection for mutants with reduced susceptibility to ABT-773, erythromycin and rifampicin in respiratory tract pathogens.

Attempts were made to select mutants on agar media containing the new ketolide ABT-773, erythromycin or rifampicin, at concentrations above the MICs, from Staphylococcus aureus, Streptococcus pneumoniae, Streptococcus pyogenes and Haemophilus influenzae, including erythromycin-resistant strains. ABT-773 did not select for mutants in four strains, whereas in eight strains the frequencies at 72 h were < or = 10(-9). ABT-773 MICs were 0.015-4 mg/L for mutants, except those selected from inducible Erm(A) S. aureus. Mutants selected on ABT-773 or erythromycin were cross-resistant to ABT-773, erythromycin and, sometimes, clindamycin. The susceptibility profiles indicate that different mutations were selected and that ABT-773 and erythromycin may interact with the ribosome differently.

Anti-Bacterial Agents↗

PubMed1978

Effects of low temperature on in vivo and in vitro protein synthesis in Escherichia coli and Pseudomonas fluorescens.

The effects of temperature on protein synthesis by Escherichia coli, a mesophile, and Pseudomonas fluorescens, a psychotroph, were investigated by using whole-cell and cell extract preparations. After shifts to 5 degrees C, protein was synthesized at a slowly decreasing rate for 1 h by both organisms, after which P. fluorescens synthesized protein at a new rate corresponding to its 5 degrees growth rate, in contrast to E. coli which did not synthesize protein at a measurable rate. In vitro protein-synthesizing systems using MS-2 RNA, endogenous mRNA, and purified polysomes were utilized to investigate initiation of translation at 5 degrees C. In these systems, P. fluorescens cell extracts synthesized protein at linear rates for up to 2 h at 5 degrees C, whereas E. coli cell extracts synthesized protein for only 25 min at 5 degrees C. The rates of polypeptide elongation, as tested by the incorporation of phenylalanine into polyphenylalanine by cell extract protein-synthesizing systems from both organisms, were identical over the range of 25 to 0 degrees C. The polysome profiles of E. coli whole cells shifted from 37 to 5 degrees C showed accumulation of 70S ribosomal particles and ribosomal subunits at the expense of polysomes. Similar experiements done with P. fluorescens resulted in polysome reformation at 5 degrees C. In vitro experiments demonstrated that the 70S ribosomal particles, which accumulated in E. coli at 5 degrees C, were capable of synthesizing protein in vitro in the absence of added mRNA. These in vivo and in vitro results suggest that incubation of E. coli at subminimal temperatures results in a block in initiation of translation causing polysomal runoff and the accumulation of 70S particles, some of which are 70S monosomes.

Bacterial Proteins↗

PubMed2000

Expression pattern in a modified equalized kidney cDNA library of hypertensive rat.

BACKGROUND: Genes with important functions and rarely expressed would probably more easily be cloned from a modified equalized kidney cDNA library for further investigation. METHODS: A kidney cDNA library of a spontaneously hypertensive rat was synthesized by a modified equalization method. Inserts of random clones were amplified by PCR and sequenced. Sequences were compared against a nonredundant database in GenBank. The cDNA profile was compared with an expression profile of a mouse renal proximal tubule cDNA library. Seven clones were analyzed by Northern blot analysis. The cDNA ends of two novel genes were amplified by PCR, sequenced and analyzed. RESULTS: 336 cDNA clones were analyzed and grouped into 323 species of transcript with 77 species similar to previously reported genes. Northern blot analysis identified one kidney-specific, one rarely expressed and lung-specific, and another relatively testis-specific gene. Two novel genes were cloned. One was 4.1 kb in length and encoded a 390-amino acid zinc-finger protein. Another was 2.5 kb and encoded a 474-amino acid protein of unknown function. Compared with the expression profile of a mouse renal proximal tubule cDNA library, this kidney library had a lower proportion of ribosomal genes and had a greater proportion of genes for signal transduction and DNA or RNA binding. CONCLUSIONS: Rare or novel genes could be more easily isolated from this library for molecular study of hypertension and renal pathophysiology.

Amino Acid Sequence↗

PubMed1992

Molecular approaches to malaria and babesiosis diagnosis.

The development of additional methods for detecting and identifying Babesia and Plasmodium infections may be useful in disease monitoring, management and control efforts. The preliminary evaluate synthetic peptide-based serodiagnosis, a hydrophilic sequence (DDESEFDKEK) was selected from the published BabR gene of B. bovis. Immunization of rabbits and cattle with the hemocyanin-conjugated peptide elicited antibody responses that specifically detected both P. falciparum and B. bovis antigens by immunofluorescence and Western blots. Using a dot-ELISA with this peptide, antisera from immunized and naturally-infected cattle, and immunized rodents, were specifically detected. Reactivity was weak and correlated with peptide immunization or infection. DNA-based detection using repetitive DNA was species-specific in dot-blot formats for B. bovis DNA, and in both dot-blot and in situ formats for P. falciparum; a streamlined enzyme-linked synthetic DNA assay for P. falciparum detected 30 parasites/mm3 from patient blood using either colorimetric (2-15 h color development) or chemiluminescent detection (0.5-6-min exposures). Serodiagnostic and DNA hybridization methods may be complementary in the respective detection of both chronic and acute infections. However, recent improvements in the polymerase chain reaction (PCR) make feasible a more sensitive and uniform approach to the diagnosis of these and other infectious disease complexes, with appropriate primers and processing methods. An analysis of ribosomal DNA genes of Plasmodium and Toxoplasma identified Apicomplexa-conserved sequence regions. Specific and distinctive PCR profiles were obtained for primers spanning the internal transcribed spacer locus for each of several Plasmodium and Babesia species.

Amino Acid Sequence↗

PubMed2002

Conserved codon composition of ribosomal protein coding genes in Escherichia coli, Mycobacterium tuberculosis and Saccharomyces cerevisiae: lessons from supervised machine learning in functional genomics.

Genomics projects have resulted in a flood of sequence data. Functional annotation currently relies almost exclusively on inter-species sequence comparison and is restricted in cases of limited data from related species and widely divergent sequences with no known homologs. Here, we demonstrate that codon composition, a fusion of codon usage bias and amino acid composition signals, can accurately discriminate, in the absence of sequence homology information, cytoplasmic ribosomal protein genes from all other genes of known function in Saccharomyces cerevisiae, Escherichia coli and Mycobacterium tuberculosis using an implementation of support vector machines, SVM(light). Analysis of these codon composition signals is instructive in determining features that confer individuality to ribosomal protein genes. Each of the sets of positively charged, negatively charged and small hydrophobic residues, as well as codon bias, contribute to their distinctive codon composition profile. The representation of all these signals is sensitively detected, combined and augmented by the SVMs to perform an accurate classification. Of special mention is an obvious outlier, yeast gene RPL22B, highly homologous to RPL22A but employing very different codon usage, perhaps indicating a non-ribosomal function. Finally, we propose that codon composition be used in combination with other attributes in gene/protein classification by supervised machine learning algorithms.

Algorithms↗

PubMed2006

Restriction of rRNA synthesis by VHL maintains energy equilibrium under hypoxia.

Biological evolution abides by an unbending rule obligating organisms to maintain energy equilibrium. Hypoxia reduces cellular energy supply and is thus thought to be deleterious. We report that cells have evolved pH-sensitive mechanisms to maintain energy equilibrium by lowering energy demand. We found that fermentation-induced acidosis allows hypoxic cells to maintain energy equilibrium and viability under hypoxia by restricting ribosomal biogenesis, the most energy-demanding cellular process. Acidosis triggers nucleolar condensation, decreases precursor rRNA synthesis, reduces the dynamic profile of the RNA polymerase I preinitiation factor UBF1 and its interaction with the promoter of rRNA genes (rDNA). These changes require the pH-dependent interaction of the statically detained von Hippel-Lindau tumor suppressor protein (VHL) with rDNA. This phenomenon is promoted by, but does not require, activation of the hypoxia-inducible factor (HIF), a transcription factor implicated in extracellular acidification, energy production and oxygen homeostasis. Abrogating this program by silencing VHL expression, competing rDNA-VHL interaction or preventing environmental acidification triggers energy starvation and cell death under hypoxia. Our data suggest that oxygen-starved cells maintain energy equilibrium by gauging the environmental concentration of H(+) to statically detain VHL to nucleolar rDNA and restrict ribosome production. These findings also provide an explanation for the protective effect of acidosis in ischemic settings such as development, stroke and cancer.

3T3 Cells↗

PubMed2000

Interorganellar communication. Altered nuclear gene expression profiles in a yeast mitochondrial dna mutant.

Communication between mitochondria and the nucleus is important for a variety of cellular processes such as carbohydrate and nitrogen metabolism, mating and sporulation, and cell growth and morphogenesis. It has long been known that the functional state of mitochondria can influence nuclear gene expression. For example, in yeast cells lacking the mitochondrial genome, the expression of several nuclear genes, such as CIT2 (citrate synthase), MRP13 (mitochondrial ribosomal protein), and DLD3 (d-lactate dehydrogenase) has been reported to be altered. Here we show by microarray analysis of the genome-wide transcription profile of Saccharomyces cerevisiae that yeast petite mutants lacking mitochondrial DNA induce genes coding for mitochondrial proteins, enzymes of the glycolytic pathway and of the citric acid cycle, cell wall components, membrane transporters, and genes normally induced by nutrient deprivation and a variety of stresses. Consistent with the observed induction of genes related to cell stress and those encoding membrane transporters, yeast petite cells showed increased resistance to severe heat shock and exhibited a pleiotropic drug resistance phenotype. The observed changes in nuclear gene expression in cells lacking mitochondrial DNA may have implications for the role of mitochondria in processes such as carcinogenesis and aging.

Cell Nucleus↗

PubMed2005

An improved method for an efficient and easily accessible eukaryotic ribosome display technology.

Ribosome display is a powerful in vitro technology for the selection and directed evolution of proteins. However, this technology has so far been perceived as being technically challenging owing to comparatively difficult protocols and the absence of tailored commercial reagents, particularly when using prokaryotic cell-free expression systems. Eukaryotic ribosome display is potentially a more accessible alternative because of the availability of suitable commercial reagents, yet despite published protocols, this method has been less widely used. For eukaryotic ribosome display, a novel mechanism of mRNA recovery compared with that of the well-proven prokaryotic method has been proposed. We have examined the eukaryotic ribosome display process with the aims of investigating the proposed mechanism of sequence recovery and of identifying aspects of the protocol that may have lead to poor performance and therefore so far limited its use. We demonstrate that the proposed novel method is in fact mechanistically comparable to the prokaryotic method and we provide a step-by-step protocol for eukaryotic ribosome display that is 20-fold more efficient than current published methods. Our findings should increase the ease of operating ribosome display technology, making it more accessible to the scientific community.

Animals↗

PubMed2025

Global Profiling and Analysis of 5' Monophosphorylated mRNA Decay Intermediates.

During RNA turnover, the action of endo- and exo-ribonucleases can yield RNA decay intermediates with specific 5' ends. These RNA decay intermediates have been demonstrated to be the outcome of decapping, microRNA-directed endo-cleavage, or the protected fragments of ribosomes and exon-junction complexes. Therefore, global analysis of RNA decay intermediates can facilitate studies of many RNA decay pathways. In this chapter, we describe a high-throughput sequencing protocol named parallel analysis of RNA ends (PARE), which allows genome-wide profiling of 5' monophosphorylated mRNA decay intermediates from plants or other eukaryotes. Also, we present the tools and scripts necessary for the proper analysis of RNA degradome data obtained from the PARE method. Details and modifications of library construction procedures and bioinformatic analyses to optimize sequencing quality and cope with emerging sequencing platforms and findings are highlighted.

RNA Stability↗

PubMed2005

Response of 1,2-dichloroethane-adapted microbial communities to ex-situ biostimulation of polluted groundwater.

The microbial community of a groundwater system contaminated by 1,2-dichloroethane (1,2-DCA), a toxic and persistent chlorinated hydrocarbon, has been investigated for its response to biostimulation finalized to 1,2-DCA removal by reductive dehalogenation. The microbial population profile of samples from different wells in the aquifer and from microcosms enriched in the laboratory with different organic electron donors was analyzed by ARISA (Amplified Ribosomal Intergenic Spacer Analysis) and DGGE (Denaturing Gradient Gel Electrophoresis) of 16S rRNA genes. 1,2-DCA was completely removed with release of ethene from most of the microcosms supplemented with lactate, acetate plus formate, while cheese whey supported 1,2-DCA dehalogenation only after a lag period. Microbial species richness deduced from ARISA profiles of the microbial community before and after electron donor amendments indicated that the response of the community to biostimulation was heterogeneous and depended on the well from which groundwater was sampled. Sequencing of 16S rRNA genes separated by DGGE indicated the presence of bacteria previously associated with soils and groundwater polluted by halogenated hydrocarbons or present in consortia active in the removal of these compounds. A PCR assay specific for Desulfitobacterium sp. showed the enrichment of this genus in some of the microcosms. The dehalogenation potential of the microbial community was confirmed by the amplification of dehalogenase-related sequences from the most active microcosms. Cloning and sequencing of PCR products indicated the presence in the metagenome of the bacterial community of a new dehalogenase potentially involved in 1,2-DCA reductive dechlorination.

Amino Acid Sequence↗

PubMed2005

De novo ribosome biosynthesis is transcriptionally regulated in Eimeria tenella, dependent on its life cycle stage.

Protozoan parasites go through various developmental stages during their parasitic life, which requires the expression of different genes. To identify stage specific gene products in Eimeria tenella, a differential screening was performed comparing the intracellular schizont stage with the extracellular oocyst stage. De novo transcripts of 18S-5.8S-26S rRNA transcription units and of two ribosomal proteins (RPL5 and RPL23) were specifically identified in schizonts and were undetectable in oocysts. The stage specific transcription of pre-rRNAs (prior to processing) was confirmed with Northern blot analysis. Since the E. tenella genome contains a repeated gene cluster with an estimated 140 large rRNA transcription units, they all might be similarly regulated. Specific expression of RPL5 and RPL23 in E. tenella schizonts was also confirmed by Northern blotting. Furthermore, an analysis of the E. tenella EST database with 26,705 ESTs showed that 9.5% of all merozoite ESTs and only 0.2% of the sporozoite ESTs encoded ribosomal proteins (RPs). These ESTs encoded 69 different RPs, suggesting that most and possibly all RPs are differentially transcribed in E. tenella. Analysis of EST data from other Coccidia, such as Toxoplasma gondii, indicated a similar stage dependent transcription of RP genes. We conclude that ribosome biosynthesis is transcriptionally regulated in E. tenella and other Coccidia, such that rapidly growing parasite stages utilize much of their resources to de novo biosynthesis of ribosomes, and that "dormant" oocyst stages do not synthesize new ribosomes. The 50- to 100-fold reduction in transcription of RPs together with the reduced rRNA transcription prevents that unnecessary new ribosomes are synthesized in oocysts.

Animals↗

PubMed1998

Altered expression of mitochondrial 16S ribosomal RNA in p53-deficient mouse embryos revealed by differential display.

Inactivation of the tumor suppressor p53 is associated with neural tube defects and altered teratogenicity in early embryos. To gain insight into the function of p53 during early embryogenesis, RNA profiles of wild-type p53(+/+) and p53(-/-) null mutant mouse embryos were compared at the head-fold stage (day 8 post coitum) using HPLC-based mRNA differential display. The results of this screen revealed a deficiency of mitochondrial 16S ribosomal RNA in p53(-/-) embryos. RT-PCR showed abnormalities in 16S rRNA levels relative to some representative nuclear (COIV, beta-actin) and mitochondrial (COIII) transcripts in p53(-/-) embryos, and that 16S rRNA expression increased with development of p53(+/+) embryos during neurulation. Embryos that lack p53 also displayed weakened cytochrome c oxidase staining and reduced ATP content. During neurulation, the mouse embryo switches from an anaerobic (glycolytic) to an aerobic (oxidative) metabolism. The preliminary results of the present study suggest that p53 may be involved, directly or indirectly, in this transition.

Adenosine Diphosphate↗

PubMed1977

New class of ribonucleic acid in Neurospora associated with the outer cell envelope.

Extrinsic ribonucleic acid (RNA) can be isolated from a KCl extract of Neurospora crassa conidial cell surface products. It is heterogeneous in size. The bulk of this RNA travels as a broad band, trailing the 5.8S ribosomal marker RNA on electrophoretic gels. The extrinsic RNA, when denatured, exhibites several discrete lengths between 50,000 and 130,000 daltons. Melting profiles confirm the heterogeneity of the RNA and indicate that 58% of the bases are involved in hydrogen bonding. Analyses of alkaline hydrolysis products reveal no extensive methylation and few or none of the unusual bases present in transfer RNA. The bases are present in approximately equivalent amounts. Extrinsic RNA represents 2 to 3% of the total cellular RNA. Since this membrane-associated class of RNA does not resemble ribosomal RNA, messenger RNA, or transfer RNA and since it is extracted from the cell exterior by methods used to remove extrinsic membrane molecules, we have designated it extrinsic RNA.

Adenine↗

PubMed2005

Identification of highly specific localized sequence motifs in human ribosomal protein gene promoters.

For ribosomal protein (RP) genes the start of transcription is rigidly controlled to maintain the 5'-TOP signal on the messenger RNA. The responsible regulatory mechanism is not yet fully understood. Careful comparative analysis of their proximal promoter sequences reveals common characteristics and thus provides clues to the underlying mechanism. We have extracted the proximal promoters of the 80 human cytosolic ribosomal protein genes together with the orthologous mouse sequences. After annotating the set with transcription factor binding sites based on the available literature, we searched for over-represented sequence motifs. We uncovered a novel motif that is localized at a fixed distance downstream to the transcription start. 31 out of the 80 promoters contain the motif in the same orientation around position +62 (standard deviation 6). A second evolutionary conserved and palindromic motif is found 13 times in the RP promoter set, 9 instances of which are located upstream around position -40. In addition, we see a characteristic profile of the GC-content and of the CpG dinucleotide frequencies. Our results support a model for the transcription of ribosomal protein genes in which the maintenance of the accurate start of transcription is provided by specific transcription factors. Such a factor binds the target DNA at a fixed location relative to the TSS, and possibly interacts directly with the basal transcription machinery.

Amino Acid Motifs↗