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Results for “Ribosome Profiling”

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PubMed1986

Translational profiles of alpha 1-, alpha 2-, and beta-globin messenger ribonucleic acids in human reticulocytes.

In human reticulocytes, the critical balancing of alpha- and beta-globin synthesis may be controlled in part by differential translation of the three major adult globin messenger RNAs (mRNAs), alpha 1, alpha 2, and beta. In this study, we determined, as a parameter of translational efficiency, the relative ribosome loading of these three mRNAs. Using oligonucleotide probes specific for the alpha 1- and alpha 2-globin mRNAs, we find that these two mRNAs have identical translational profiles. Their distribution contrasts with that of beta-globin mRNA, which is present on heavier polyribosomes and is less prevalent in pre-80S messenger ribonucleoprotein fractions. The relative distribution of alpha- vs. beta-globin mRNA is consistent with more efficient beta-globin translation. In contrast, the parallel distributions of alpha 1- and alpha 2-globin mRNAs suggests they are translated with equal efficiencies. Considering the relative concentrations of the two alpha-globin mRNAs in normal reticulocytes, this result predicts a dominant role for the alpha 2-globin locus in human alpha-globin expression.

Base Sequence↗

PubMed2001

[Isolation and study of one novel full-length gene related to human glioma].

OBJECTIVES: To obtain differentially expressed genes related to human glioma using cDNA microarray and make a preliminary study of one novel full-length gene. METHODS: Total RNA was extracted from human glioma tissues and normal brain tissues, and mRNA was used to make probes. After hybridization and washing procedure, the results of hybridization were scanned using computer system. One gene named 507E08 clone was subsequently analyzed by northern blotting, in situ hybridization, bioinformatics and radiation hybridization. RESULTS: Fifteen differentially expressed novel genes related to human glioma were obtained through four times of hybridization and scanning. Northern blotting and in situ hybridization confirmed that 507E08 clone was lowly expressed in normal human brain tissue and over-expressed in human glioma tissue. BLASTn and BLASTx analysis showed that the clone 507E08 was a novel full-length gene with the length of 2002 bp. This gene, called human ribosomal protein 14.22 gene, codes 203 amino acids and is located on chromosome 14 between D14S1066 Marker and D14S265 Marker. CONCLUSION: cDNA microarray technology can be successfully applied to identify differentially expressed genes with small amount of specimen, high quality, high speed, and high sensitivity. The novel full-length human ribosomal protein 14.22 gene may correlate with formation of human glioma.

Adult↗

PubMed1993

Genotype analysis of faecal and blood isolates of Salmonella dublin from humans in England and Wales.

An analysis of genotype was made for representative strains of Salmonella dublin. The collection consisted primarily of strains isolated from humans in England and Wales, and were of both intestinal and extra-intestinal origin. Three genetic elements were characterized by DNA hybridization. They were the spvBC genes, extrachromosomal virulence determinants, the salmonella-specific insertion sequence IS200, and the 16S ribosomal RNA genes, a phylogenetic marker. Two clones of S. dublin (SdRI and SdRII) which shared an identical IS200 profile, were identified on the basis of restriction fragment length polymorphism at the 16S rRNA locus. With one exception, all strains harboured a 52 MDa plasmid which contained a conserved 3.7 kbp Hind III fragment homologous to the spvBC mouse-virulence genes of S. typhimurium. However, a single plasmid-free strain of SdRI, isolated from a patient with septicaemia exhibited no spc homology. In SdRI there was no observable genotype distinction between strains causing gastroenteritis or bacteraemia. In contrast, none of the strains of SdRII were from cases of bacteraemia, and all human isolates of this clone were from cases of gastroenteritis.

Bacteremia↗

PubMed1989

Ferritin mRNA is found on bound as well as on free polyribosomes in rat heart.

Free and endoplasmic reticulum-bound polyribosomes from rat heart were examined for their ferritin mRNA content. A procedure for separation and purification of the two ribosome populations that produced good yields of homogeneous mono- and polyribosomes with no contaminating ultrastructures and gave distinctive sedimentation profiles in 15-50% sucrose gradients was developed. 14C-labeled free and bound polyribosomes added to heart preparations indicated that only 3% of free and 5.5% of bound polyribosomes cross-contaminated the bound and free fractions, respectively. RNA from both polyribosome populations hybridized with [32P]cDNA for rat ferritin. The extent of hybridization with mRNA from endoplasmic reticulum (ER)-derived polyribosomes was much greater than what could be accounted for by cross-contamination with free polyribosomes. This indicates that heart ferritin is synthesized not only on free polyribosomes for internal use in iron storage but also on ER-bound polyribosomes, where it may be destined for secretion into the plasma.

Animals↗

PubMed2003

Maize BMS cultured cell lines survive with massive plastid gene loss.

As part of developing an ex planta model system for the study of maize plastid and mitochondrial gene expression, a series of established Black Mexican Sweet (BMS) suspension cell lines was characterized. Although the initial assumption was that their organelle biochemistry would be similar enough to normal in planta cells to facilitate future work, each of the three lines was found to have plastid DNA (ptDNA) differing from control maize plants, in one case lacking as much as 70% of the genome. The other two BMS lines possessed either near-wild-type ptDNA or displayed an intermediate state of gene loss, suggesting that these clonal lines are rapidly evolving. Gene expression profiles of BMS cells varied dramatically from those in maize leaf chloroplasts, but resembled those of albino plants lacking plastid ribosomes. In spite of lacking most plastid gene expression and apparently mature rRNAs, BMS cells appear to import proteins from the cytoplasm in a normal manner. The regions retained in BMS ptDNAs point to a set of tRNA genes universally preserved among even highly reduced plastid genomes, whereas the other preserved regions may illuminate which plastid genes are truly indispensable for plant cell survival.

Biolistics↗

PubMedDate not supplied

Enhanced expression of S8, L12, L23a, L27 and L30 ribosomal protein mRNAs in human hepatocellular carcinoma.

Differential display (DD) analysis using surgically resected human hepatocellular carcinoma (HCC) and adjacent non-tumorous liver tissues was performed. We identified 5 cDNAs up-regulated in human hepatocellular carcinoma, encoding S8, L12, L23a, L27 and L30 ribosomal protein mRNAs. Northern blot analysis, using total RNAs from thirteen pairs of HCC and abjacent non-tumorous liver tissues demonstrated that these mRNA levels were up-regulated along with the histological grading of tumors. The expression of these mRNAs was also high in three human HCC cell lines (HuH-7, HepG2 and HLF), irrespective of the growth state. These results suggest that activation of these genes is an important manifestation of HCC phenotypes.

Blotting, Northern↗

PubMed2006

Selection of reference genes for quantitative real-time PCR analysis in canine mammary tumors using the GeNorm algorithm.

Eleven reference genes (18s ribosomal ribonucleic acid [RNA], 28s ribosomal RNA, ubiquitin, beta-actin, glycerine aldehyde dehydrogenase, ATP-synthase subunit 5B, hydroxymethyl-bilane synthase, hypoxanthine-phosphoribosyl transferase, ribosomal protein L32, tryptophan 5-monooxygenase activation protein (zeta polypeptide), and TATA-Box binding protein) were analyzed in use as references for gene expression profiling experiments using quantitative reverse transcription polymerase chain reaction (qRT-PCR) in canine mammary tumors. The transcription level of the candidates was measured in 22 histologically characterized excised tumor specimens from mammary gland tissue and 22 samples of non-neoplastic mammary tissue samples from the same individuals. Results were used to rank candidate reference genes using the GeNorm tool. It was determined that in samples of canine mammary gland tissue, a combination of hypoxanthine-phosphoribosyl transferase, ATP-synthase subunit 5B, ribosomal protein L32 and ubiquitin yields stable reference gene expression levels, whereas the use of glycerin aldehyde dehydrogenase or ribosomal RNA is unsuitable for normalization of qRT-PCR results in this tissue type.

Algorithms↗

PubMed2005

Analysis of the large bowel microbiota of colitic mice using PCR/DGGE.

AIM: To test combined polymerase chain reaction amplification of 16S rRNA gene sequences and denaturing gradient gel electrophoresis (PCR/DGGE) as an analytical method to investigate the composition of the large bowel microbiota of mice during the development of colitis. METHODS AND RESULTS: The colonic microbiota of formerly germfree interleukin 10 (IL-10)-deficient mice that had been exposed to the faecal microbiota of specific pathogen-free animals was screened using PCR/DGGE. The composition of the large bowel microbiota of IL-10-deficient mice changed as colitis progressed. DNA fragments originating from four bacterial populations ('Bacteroides sp.', Bifidobacterium animalis, Clostridium cocleatum, enterococci) were more apparent in PCR/DGGE profiles of colitic mice relative to non-colitic animals, whereas two populations were less apparent (Eubacterium ventriosum, Acidophilus group lactobacilli). Specific DNA:RNA dot blot analysis showed that bifidobacterial ribosomal RNA (rRNA) abundance increased as colitis developed. CONCLUSIONS: PCR/DGGE was shown to be an effective method to demonstrate changes in the composition of the large bowel microbiota of mice in relation to progression of inflammatory disease. The intensity of staining of DNA fragments in DGGE profiles reflected increased abundance of bifidobacterial rRNA in the microbiota of colitic animals. As bifidobacterial fragments in PCR/DGGE profiles generated from microbiota DNA showed increased intensity of fragment staining, an increase in bifidobacterial numbers in colitic mice was indicated. SIGNIFICANCE AND IMPACT OF THE STUDY: PCR/DGGE analysis demonstrated an altered composition of the large bowel microbiota of colitic mice. This work will allow specific groups of bacteria to be targeted in future research concerning the pathogenesis of colitis.

Animals↗

PubMed2002

Complexities in ETS-domain transcription factor function and regulation: lessons from the TCF (ternary complex factor) subfamily. The Colworth Medal Lecture.

The ETS-domain transcription factor family can be divided into a series of subfamilies. Elk-1 represents the founding member of the ternary complex factor (TCF) subfamily. By focusing on the TCF subfamily, we can demonstrate the complexities that exist in the function and regulation of ETS-domain transcription factors. This article focuses on Elk-1 in detail and summarizes the functions of other TCFs. The key themes covered include the domain structure of the TCFs, the mechanisms of complex formation with serum response factor, regulation of TCFs by mitogen-activated protein kinase cascades, and transcriptional regulatory properties of the TCFs. Finally, the emerging role of the TCFs in vivo is discussed. A picture is developing indicating that, while these proteins exhibit significant sequence and functional conservation, key differences in their structure and regulation are being identified which may relate to unique functions of these proteins in vivo.

Amino Acid Sequence↗

PubMed2004

A PCR-based approach to distinguish important Diadegma species (Hymenoptera: Ichneumonidae) associated with diamondback moth, Plutella xylostella (Lepidoptera: Plutellidae).

The diamondback moth, Plutella xylostella (Linnaeus) has a cosmopolitan distribution and is one of the major pests on cruciferous plants. Biological control, especially with species of the genus Diadegma, has been successfully employed in several parts of the world, mainly in South East Asia. The taxonomy of this genus based on classical morphological characters is still unclear and misidentifications are reported. In the present study seven Diadegma species associated with P. xylostella were separated using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analyses. The second internal transcribed spacer (ITS2) of the ribosomal DNA (rDNA) was successfully amplified in all 167 individuals and digested using 11 different restriction enzymes. One restriction enzyme (CfoI) showed different restriction profiles in all species and also between two population samples of D. mollipla (Holmgren) from eastern and southern Africa. In addition, a new Diadegma species associated with P. xylostella from Ethiopia was discovered.

Animals↗

PubMed1977

Coordination of ribosome content and polysome formation during estradiol stimulation of vitellogenin synthesis in immature male chick livers.

To elucidate the mechanisms by which protein synthesis is affected by estradiol, we characterized cockerel liver polysomal profiles during hormone induction and withdrawal. We describe a method for isolating intact polysomes which results in preparations that are stable even after storage in solution at 10 degrees for 16 hr. In addition, our procedure eliminates the necessity for starving animals prior to experiments. Recovery of radioactive polysomes indicated that yield is about 90% and that our polysomal preparations appear to represent polysome distribution in vivo. Using this approach we show that estradiol injection stimulates ribosome content 6-fold and that formation of polysomes is coincident with the induction of vitellogenin synthesis. We also demonstrate that the size and number of polysomes increase and decrease in a coordinated fashion with the rate of vitellogenin synthesis. The kinetics of ribosome synthesis and the fact that at least 80% of the newly synthesized ribosomes are directly recruited into polysomes indicate that ribosomes might be limiting the rate of protein synthesis during the stimulatory phase of the hormone cycle.

Animals↗

PubMed2000

Modulation of cardiocyte functional activity by antibodies against trypanosoma cruzi ribosomal P2 protein C terminus.

Antibodies against the Trypanosoma cruzi ribosomal P2beta protein (TcP2beta) have been associated with the chronic cardiac pathology of Chagas' disease in humans. Using synthetic peptides spanning the entire TcP2beta molecule, we investigated their epitope recognition by antibodies from mice chronically infected with T. cruzi and from mice immunized with two recombinant TcP2betas. We found clear differences in epitope recognition between antibodies from T. cruzi-infected mice and mice immunized with two different recombinant TcP2betas associated with different schedules of immunization. Major epitopes recognized by antibodies from mice immunized with recombinant glutathione S-transferase (GST) or histidine (Hist) fusion TcP2beta (GST-TcP2beta or Hist-TcP2beta) are located in the central and hinge regions of the molecule. Nevertheless, mice immunized with Hist-TcP2beta were also able to elicit antibodies against the TcP2beta C terminus, a region which is highly conserved in both T. cruzi and mammal ribosomal P proteins. Strikingly, antibodies from infected animals recognized only the TcP2beta C terminus. By using these antisera with distinct profiles of epitope recognition, it could be shown that only C terminus-specific antibodies were able to increase the beating frequency of cardiomyocytes from neonatal rats in vitro by selective stimulation of the beta1-adrenergic receptor. Thus, antibodies against the TcP2beta C terminus elicited in the absence of infection are able to modulate a functional activity of host cells through a molecular mimicry mechanism.

Amino Acid Sequence↗

PubMed2005

Conservation and evolvability in regulatory networks: the evolution of ribosomal regulation in yeast.

Transcriptional modules of coregulated genes play a key role in regulatory networks. Comparative studies show that modules of coexpressed genes are conserved across taxa. However, little is known about the mechanisms underlying the evolution of module regulation. Here, we explore the evolution of cis-regulatory programs associated with conserved modules by integrating expression profiles for two yeast species and sequence data for a total of 17 fungal genomes. We show that although the cis-elements accompanying certain conserved modules are strictly conserved, those of other conserved modules are remarkably diverged. In particular, we infer the evolutionary history of the regulatory program governing ribosomal modules. We show how a cis-element emerged concurrently in dozens of promoters of ribosomal protein genes, followed by the loss of a more ancient cis-element. We suggest that this formation of an intermediate redundant regulatory program allows conserved transcriptional modules to gradually switch from one regulatory mechanism to another while maintaining their functionality. Our work provides a general framework for the study of the dynamics of promoter evolution at the level of transcriptional modules and may help in understanding the evolvability and increased redundancy of transcriptional regulation in higher organisms.

Computational Biology↗

PubMed2003

Messenger RNA profiling of human platelets by microarray hybridization.

Platelets are generally believed to be inactive in terms of de novo protein synthesis. On the other hand, the presence of ribosomes and mRNA molecules is well established. Many studies have used reverse transcriptase (RT) -PCR for detection of gene transcripts in platelets. As RT-PCR is a very sensitive method, any leukocyte contamination of platelet preparations can lead to false results. We performed three filtration procedures to minimize leukocyte contamination of pooled buffy-coat platelet concentrates prior to RNA isolation. Furthermore, by applying a genomic PCR approach with 50 amplification cycles we demonstrated that nucleated cells were not detectable. Microarray hybridization was used to analyze 9,850 individual human genes in RNA from purified platelets. In total we identified 1,526 (15.5%) positive genes. The data were confirmed in six individual experiments each performed on a PC pooled from four individual blood donations. Genes specific for nucleated blood cells such as CD4, CD83 and others were negative and verified the purity of PC. Overrepresentation of positive genes was found in the functional categories of glycoproteins/integrins (22.6% vs. 15.5%, p=0.029) and receptors (20.7% vs. 15.5%, p<0.001). Gene transcripts encoding RANTES, GRO-alpha, MIP-1alpha, MIP-1beta, and others were found at high levels of signal intensity and confirmed literature data. This work provides a mRNA profile of human platelets and a complete list of results can be downloaded from the website of our institute www.ma.uni-heidelberg.de/inst/iti/plt_array.xls. The knowledge about gene transcripts may have an impact on the characterization of novel proteins and their functions in platelets.

Adult↗

PubMed1991

The cell cycle dependence of protein synthesis during Xenopus laevis development.

The regulation of early embryonic development in the amphibian Xenopus laevis depends largely upon translational and post-translational regulatory mechanisms to direct the complex cytodifferentiations that take place during early cleavage and blastula formation. The cell cycle dependence of protein synthesis was examined in developing Xenopus embryos as well as in cycling cell-free lysates from Xenopus eggs. In both cases M-phase and the activation of the M-phase kinase were found to be correlated with an inhibition of translation. Translation in both the rough endoplasmic reticulum and cytosolic-free ribosomes were affected by this inhibition. Since elongation was found to be unaffected by M-phase, shifts in the polysome profiles during M-phase indicated that the inhibition affected initiation processes. The activity of the M-phase kinase may inhibit initiation through the modification of initiation factors or some other component during this process. The cell cycle dependence of translation may affect developmental mechanisms controlled by the titration of regulatory proteins.

Animals↗

PubMed2005

Analysis of tumor progression by transcriptional profiling of mouse MK16 cell lines transformed with human papillomavirus type 16 E6 and E7 oncogenes and activated H-ras.

A better understanding of the molecular basis of tumor progression and invasion is needed to improve therapy for malignant tumors. Recently, we established a mouse metastatic MK16 model by transduction of secondary kidney cells with human papillomavirus type 16 (HPV16) E6 and E7 oncogenes and human H-ras activated by G12V mutation. In this study, we extended the model to MK16 cell lines derived from lung metastases and compared the oncogenicity of seven cell lines successively isolated from primary tumors or metastases. By observing the formation and growth of subcutaneous tumors and generation of lung metastasis, we showed a gradual increase in oncogenicity of MK16 cell lines. Interestingly, we demonstrated metastatic potential of MK16/A cells with low oncogenic potential in primary tumor development. To detect changes in gene expression associated with increasing oncogenicity of MK16 cell lines, we performed transcriptional profiling with the Atlas Plastic Mouse 5K microarray. We found that a substantial proportion of up-regulated genes encoded ribosomal proteins. Among the down-regulated genes, the highest number (n=10) belonged to a group coding for transcription factors. Expression of two of these, Pou3f2 and Gtl3, was reduced both in cells derived from primary tumors and those isolated from metastases. Furthermore, microarray hybridization suggested that the down-regulation of cyclin-dependent kinase inhibitors p16(Ink4a) and p57(Kip2) and up-regulation of A6 and A10 members of the S100 protein family might play a role in the increase of MK16 oncogenicity.

Animals↗

PubMed2001

Molecular epidemiology of Arthroderma benhamiae, an emerging pathogen of dermatophytoses in Japan, by polymorphisms of the non-transcribed spacer region of the ribosomal DNA.

In Japan, several isolates of Arthroderma benhamiae, a teleomorphic member of Trichophyton mentagrophytes complex, which were not found by earlier mating studies, have recently been recovered from human and animal dermatophytoses. In the present study, intraspecies polymorphism of A. benhamiae isolated in Japan was investigated using restriction fragment length polymorphisms (RFLP) of the non-transcribed spacer (NTS) region of the ribosomal DNA (rDNA), a method introduced to detect intraspecies polymorphisms of other dermatophyte species, such as T. rubrum. Based on their restriction profiles, there were five DNA types out of eight strains of A. benhamiae isolated in Japan. None of the five DNA types were found among the registered tester strains of A. benhamiae. Therefore, several different strains of A. benhamiae may have been brought into Japan separately.

Arthrodermataceae↗

PubMed1990

Characterization of differentiated Syrian golden hamster pancreatic duct cells maintained in extended monolayer culture.

Epithelial cells isolated from fragments of hamster pancreas interlobular ducts were freed of fibroblast contamination by plating them on air-dried collagen, maintaining them in serum-free Dulbecco's modified Eagle's (DME):F12 medium supplemented with growth factors, and selecting fibroblast-free aggregates of duct cells with cloning cylinders. Duct epithelial cells plated on rat type I collagen gel and maintained in DME:F12 supplemented with Nu Serum IV, bovine pituitary extract, epidermal growth factor, 3,3',5-triiodothyronine, dexamethasone, and insulin, transferrin, selenium, and linoleic acid conjugated to bovine serum albumin (ITS+), showed optimal growth as monolayers with a doubling time of about 20 h and were propagated for as long as 26 wk. Early passage cells consisted of cuboidal cells with microvilli on their apical surface, complex basolateral membranes, numerous elongated mitochondria, and both free and membrane-bound ribosomes. Cells grown as monolayers for 3 mo. were more flattened and contained fewer apical microvilli, mitochondria, and profiles of rough surfaced endoplasmic reticulum; in addition, there were numerous autophagic vacuoles. Functional characteristics of differentiated pancreatic duct cells which were maintained during extended monolayer culture included intracellular levels of carbonic anhydrase and their capacity to generate cyclic AMP (cAMP) after stimulation by 1 X 10(-6) M secretin. From 5 to 7 wk in culture, levels of carbonic anhydrase remained stable but after 25 to 26 wk decreased by 1.9-fold. At 5 to 7 wk of culture, cyclic AMP increased 8.7-fold over basal levels after secretin stimulation. Although pancreatic duct cells cultured for 25 to 26 wk showed lower basal levels of cAMP, they were still capable of generating significant levels of cAMP after exposure to secretin with a 7.0-fold increase, indicating that secretin receptors and the adenyl cyclase system were both present and functional. These experiments document that pancreatic duct monolayer cultures can be maintained in a differentiated state for up to 6 mo. and suggest that this culture system may be useful for in vitro physiologic and pathologic studies.

Animals↗