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PubMed2026

Involvement of tRNA thiolation in uORF-mediated translational regulation during Xylogenesis in Arabidopsis thaliana.

Post-transcriptional modification of tRNAs is an important mechanism for regulating translation efficiency and cellular homeostasis, yet its contribution to upstream open reading frame (uORF)-mediated translational control remains largely unexplored. In this study, we investigated the role of tRNA thiolation in thermospermine-dependent regulation of xylem development in Arabidopsis thaliana. Using a suppressor screen of the thermospermine-deficient mutant acaulis5 (acl5), which exhibits dwarfism and excessive xylem differentiation, we identified suppressor-of-acl502 (sac502) as a recessive loss-of-function allele of CTU2, a gene encoding a key enzyme in the biosynthesis of the wobble uridine modification 5-methoxycarbonylmethyl-2-thiouridine. Mutations in other components of the same modification pathway, including ROL5 and TRM9, similarly suppressed the acl5 phenotype. Translational analyses using 5' leader-GUS reporter constructs revealed that the ctu2 mutation did not enhance translation of the mRNA containing a thermospermine-responsive uORF of SAC51, but instead significantly reduced translation of that of SACL3, a member of the SAC51 family, and that of LONESOME HIGHWAY (LHW), which contains another conserved uORF in the 5' leader region. Polysome profiling further demonstrated decreased association of SACL3 and LHW mRNAs with actively translating ribosomes in ctu2. Genetic interaction analyses supported the conclusion that the suppression of excessive xylem formation in acl5 by ctu2 is attributable to reduced LHW activity. In addition, ctu2 mutants displayed increased sensitivity to exogenous thermospermine, resembling the response of lhw mutants. Together, our results reveal that tRNA thiolation contributes to uORF-mediated translational regulation of key developmental regulators and identify tRNA modification as an important regulatory layer controlling vascular development.

Arabidopsis↗

PubMedDate not supplied

Biological parameters and molecular markers of clone CL Brener--the reference organism of the Trypanosoma cruzi genome project.

Clone CL Brener is the reference organism used in the Trypanosoma cruzi Genome Project. Some biological parameters of CL Brener were determined: (a) the doubling time of epimastigote forms cultured in liver infusion-tryptose (LIT) medium at 28 degrees C is 58 +/- 13 hr; (b) differentiation of epimastigotes to metacyclic trypomastigotes is obtained by incubation in LIT-20% Grace's medium; (c) trypomastigotes infect mammalian cultured cells and perform the complete intracellular cycle at 33 and 37 degrees C; (d) blood forms are highly infective to mice; (e) blood forms are susceptible to nifurtimox and benznidazole. The molecular typing of CL Brener has been determined: (a) isoenzymatic profiles are characteristic of zymodeme ZB; (b) PCR amplification of a 24S alpha ribosomal RNA sequence indicates it belongs to T. cruzi lineage 1; (c) schizodeme, randomly amplified polymorphic DNA (RAPD) and DNA fingerprinting analyses were performed.

Animals↗

PubMed1984

Stereological analysis of non-Hodgkins lymphomas.

A detailed stereological analysis was carried out on 30 lymph nodes at 2 ultrastructural levels. They were classified as follows: 10 were reactive lymph nodes, 10 were of low-grade non-Hodgkins lymphomas and 10 were of high-grade non-Hodgkins lymphomas. The mean and median values and interquartile ranges of nuclear profile diameter, nuclear volume, volume of cytoplasm, cell volume and absolute number of ribosomes were recorded for each case. The model proved very efficient in establishing several significant differences between the highgrade and lowgrade lymphomas and between the highgrade lymphomas and reactive lymph nodes but did not discriminate between lowgrade lymphomas and reactive nodes, nor did it distinguish neoplastic cells from reactive cells in the neoplastic group. The significance of these findings is discussed.

Humans↗

PubMed1977

Wheat embryo ribonucleates. VII. Rapid, efficient and selective formation of 5S-18S and 5.8S-26S hybrids in an aqueous solution of the four ribosomal polynucleotides, and the results of a search for the corresponding hybrids in wheat embryo ribosomes.

(1) If wheat embryo 5S and 5.8S rRNA are differentially labelled, it can be shown that there is highly selective association of 5S [14C]RNA with 18S rRNA, and of 5.8S [3H]RNA with 26S rRNA when a solution (0.3 M NaCl) that contains approximately equimolar amounts of the four ribosomal polynucleotides is heated briefly (3 min) at 60 degrees C. (2) Comparison of Tm values and melting profiles for laboratory-prepared and natural 5.8S-26S rRNA hybrids suggests that restoration of the natural union between 5.8S and 26 rRNA can be achieved with facility and fidelity in the laboratory. (3) Union between 5.8S rRNA remains intact when wheat embryo ribosomes are disintegrated either by digestion with pronase or by treatment with sodium dodecyl sulphate, but the same treatments release 5S and 18S rRNA as freely migrating electrophoretic components. (4) Intact 18S and 26S rRNA can be prepared from small and large subunits, respectively, when wheat embryo ribosomes are dissociated by treatment with 0.5 M KCl. (5) Incidental to the principal investigation, it has been shown that, even after storage for more than 6 years at -70 degrees C, commercial supplies of roller-milled wheat germ yield S23 extracts that are very active in the cell-free translation of globin mRNA. (6) The physicochemical and possible biochemical significance of various types of intermolecular complexing between pairs of ribosomal polynucleotides is a subject of discussion.

Molecular Weight↗

PubMed2003

Heat-stress-dependency and developmental modulation of gene expression: the potential of house-keeping genes as internal standards in mRNA expression profiling using real-time RT-PCR.

The potential of different house-keeping genes for their use as internal standards of gene expression under changing environmental conditions and in different organs of plants was assessed. Using real-time PCR mRNA levels were precisely quantified for preselected actin and ribosomal protein genes in Arabidopsis thaliana (L.) Heinh. and Nicotiana tabacum L. grown at normal temperature and following heat stress. In tobacco leaves the mRNA levels of the constitutively expressed ribosomal protein gene Nt-L25 and the actin genes Nt-ACT9 and At-ACT66 were strongly reduced (to approximately 10%) during heat stress. Heat stress applied at the temperature optimum (37 degrees C) for elicitation of a heat stress response to Arabidopsis leaves resulted in a strong induction (several thousand-fold) of the mRNA heat shock protein genes, At-HSP17.6 and At-HSP18.2. Concomitantly, the mRNA levels of constitutively expressed actin 2 (At-ACT2) and ribosomal protein L23 (At-L23a) genes were reduced to approximately 50% of the levels in leaves incubated at room temperature. Conversely, under severe heat stress conditions (44 degrees C), the induction of At-HSP17.6 and At-HSP18.2 mRNAs was insignificant, the mRNA levels of At-ACT2 remained at approximately the same levels as in leaves incubated at room temperature, whereas the mRNA level of At-L23 declined. The mRNA levels of At-ACT2 and At-L23a examined in stem, flower and siliques of Arabidopsis plants grown under non-stress condition showed differential alterations; the mRNA level of ribosomal protein L23 correlates with the metabolic activity of tissues. The potential use of house-keeping gene expression as standards in expression profiling and the mechanisms modulating the mRNA levels are discussed.

Actins↗

PubMed1998

Molecular characterization of susceptible and naturally resistant strains of Trypanosoma cruzi to benznidazole and nifurtimox.

Twenty-seven Trypanosoma cruzi strains, susceptible or naturally resistant to the nitroderivatives benznidazole and nifurtimox, were analyzed using the following molecular markers: (i) isoenzyme patterns of six enzymes; (ii) genetic variability assayed by randomly amplified polymorphic DNA (RAPD) with two different primers; and (iii) gene probes for P-glycoprotein (TcPGP), hypoxanthine-guanine phosphoribosyltransferase (HGPRT), the ribosomal RNA gene (rDNA) and the mini-exon gene (MEX), RAPD and isoenzyme profiles divided the T. cruzi strains into three groups, whereas the gene probes divided the T. cruzi strains in two groups. Strains classified as group I or II by RAPD or zymodemes Z1 or Z2 by isoenzyme analysis were either susceptible or naturally resistant to the nitroderivatives. In contrast, strains classified as group III by RAPD and zymodeme ZB by isoenzyme analysis were only drug susceptible and showed polymorphisms for HGPRT and TcPGP. No correlation was observed between drug susceptibility and polymorphisms of rDNA and MEX. Eighteen T. cruzi strains isolated from different geographic regions were included in this study. Thus, from a total of 45 T. cruzi strains analyzed, all 19 of zymodeme B were susceptible to the experimental treatment independent of their geographic origin.

ATP Binding Cassette Transporter, Subfamily B, Mem↗

PubMed2026

Histopathological evaluation of RPL5 expression in triple-negative breast cancer: an integrated immunohistochemical and transcriptomic study.

Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer characterized by high invasiveness, limited therapeutic options, and unfavorable clinical outcomes. Ribosomal protein L5 (RPL5), a component of the large ribosomal subunit, has been implicated in ribosome biogenesis, translational regulation, and p53-associated cellular processes. This study investigated the immunohistochemical expression pattern of RPL5 in TNBC tissues and explored its potential biological significance through integrated transcriptomic analyses. Tumor tissues from 37 patients with TNBC and 7 adjacent non-tumorous breast tissues were collected from the Affiliated Tumor Hospital of Xinjiang Medical University between December 2017 and December 2023. RPL5 protein expression was evaluated by immunohistochemistry, and its association with clinicopathological characteristics was analyzed. Public transcriptomic datasets from TCGA-BRCA and GEO were further used to validate RPL5 expression patterns in TNBC. Co-expression analysis and Gene Ontology (GO)/Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed to investigate potential biological functions and signaling pathways associated with RPL5. Immunohistochemical analysis demonstrated significantly lower RPL5 protein expression in TNBC tissues compared with adjacent normal breast tissues (p=0.001). In contrast, transcriptomic analyses revealed significantly higher RPL5 expression in TNBC compared with non-TNBC breast cancer subtypes (p<0.001). No significant associations were observed between RPL5 expression and clinicopathological parameters, including age, tumor size, menopausal status, TNM stage, histological grade, or lymph node metastasis (all p>0.05). Survival analysis showed no significant difference in overall survival between patients with high and low RPL5 expression. Functional enrichment analyses indicated that RPL5-related genes were predominantly involved in ribosome biogenesis, translational regulation, and p53-related signaling pathways. These findings suggest that abnormal RPL5 expression may be associated with TNBC biology through ribosome-related programs, although causal roles require functional validation. RPL5 may represent a potential histopathological and molecular indicator associated with TNBC biology, although its precise functional role requires further experimental validation.

Humans↗

PubMed1996

Restriction fragment length polymorphisms of rDNA and variation of essential oil composition in Atractylodes plants.

Total DNA was extracted from the leaves of Atractylodes lancea DE CANDOLLE, A. ovata DE CANDOLLE and A. japonica KOIDZUMI ex KITAMURA of various origins and hybridized with digoxigenin-labeled rice ribosomal DNA after digestion with eight different restriction endonucleases. The resulting restriction fragment length polymorphism (RFLP) profiles allowed us to distinguish the three Atractylodes species when DNA was digested with Sac I. Although atractylon was detected in the rhizomes of some of the cultivated strains of A. lancea, their RFLP profiles clearly indicate that these plants are not hybrids of A. ovata or A. japonica. RFLP analysis also revealed the presence of intraspecific variation in DNA sequence of rRNA locus among A. lancea as well as A. japonica.

DNA Restriction Enzymes↗

PubMed2003

Use of amplified ribosomal DNA restriction analysis for identification of Ralstonia and Pandoraea species: interest in determination of the respiratory bacterial flora in patients with cystic fibrosis.

The recovery of Ralstonia and Pandoraea species from respiratory tract cultures of patients with cystic fibrosis has recently been reported. These species are difficult to identify, and especially to differentiate from Burkholderia cepacia complex organisms, with classical methods. The discriminatory power of amplified ribosomal DNA restriction analysis (ARDRA) within the two genera was assessed by comparing the restriction profiles of reference strains of each species by using a panel of six enzymes already proven suitable for the identification of Burkholderia species. ARDRA provided differentiation of all the Ralstonia species tested and of Pandoraea norimbergensis. Pandoraea species P. pnomenusa, P. sputorum, P. pulmonicola, and P. apista were not discriminated to the species level. This method allowed the identification of five clinical isolates recovered from French cystic fibrosis patients as Ralstonia mannitolilytica.

Bacterial Typing Techniques↗

PubMed1990

Ribosomal protein L30 is dispensable in the yeast Saccharomyces cerevisiae.

In the yeast Saccharomyces cerevisiae, L30 is one of many ribosomal proteins that is encoded by two functional genes. We have cloned and sequenced RPL30B, which shows strong homology to RPL30A. Use of mRNA as a template for a polymerase chain reaction demonstrated that RPL30B contains an intron in its 5' untranslated region. This intron has an unusual 5' splice site, C/GUAUGU. The genomic copies of RPL30A and RPL30B were disrupted by homologous recombination. Growth rates, primer extension, and two-dimensional ribosomal protein analyses of these disruption mutants suggested that RPL30A is responsible for the majority of L30 production. Surprisingly, meiosis of a diploid strain carrying one disrupted RPL30A and one disrupted RPL30B yielded four viable spores. Ribosomes from haploid cells carrying both disrupted genes had no detectable L30, yet such cells grew with a doubling time only 30% longer than that of wild-type cells. Furthermore, depletion of L30 did not alter the ratio of 60S to 40S ribosomal subunits, suggesting that there is no serious effect on the assembly of 60S subunits. Polysome profiles, however, suggest that the absence of L30 leads to the formation of stalled translation initiation complexes.

Amino Acid Sequence↗

PubMed2006

Characteristics and clustering of human ribosomal protein genes.

BACKGROUND: The ribosome is a central player in the translation system, which in mammals consists of four RNA species and 79 ribosomal proteins (RPs). The control mechanisms of gene expression and the functions of RPs are believed to be identical. Most RP genes have common promoters and were therefore assumed to have a unified gene expression control mechanism. RESULTS: We systematically analyzed the homogeneity and heterogeneity of RP genes on the basis of their expression profiles, promoter structures, encoded amino acid compositions, and codon compositions. The results revealed that (1) most RP genes are coordinately expressed at the mRNA level, with higher signals in the spleen, lymph node dissection (LND), and fetal brain. However, 17 genes, including the P protein genes (RPLP0, RPLP1, RPLP2), are expressed in a tissue-specific manner. (2) Most promoters have GC boxes and possible binding sites for nuclear respiratory factor 2, Yin and Yang 1, and/or activator protein 1. However, they do not have canonical TATA boxes. (3) Analysis of the amino acid composition of the encoded proteins indicated a high lysine and arginine content. (4) The major RP genes exhibit a characteristic synonymous codon composition with high rates of G or C in the third-codon position and a high content of AAG, CAG, ATC, GAG, CAC, and CTG. CONCLUSION: Eleven of the RP genes are still identified as being unique and did not exhibit at least some of the above characteristics, indicating that they may have unknown functions not present in other RP genes. Furthermore, we found sequences conserved between human and mouse genes around the transcription start sites and in the intronic regions. This study suggests certain overall trends and characteristic features of human RP genes.

Amino Acids↗

PubMedDate not supplied

Abscence of changes in the protein profile of erythrocyte membranes in Duchenne patients.

Numerous authors have suggested an impairement in protein synthesis as a possible cause for the failure in growth with degeneration of the skeletal muscles protein content present in Duchenne muscular dystrophy (DMD). Others have supported the use of in vitro erythrocyte membranes as a model of the sarcolemmal changes in DMD. Very recently, in vitro decrease in protein synthesis of ribosomal proteins of skeletal muscle cells, fibroblasts and erythrocytes of DMD patients have been reported. We studied the protein profile of erythrocytic membranes of 5 patients with confirmed DMD by means of SDS-polyacrylamide discontinuous gels electrophoresis (method with which we detected changes in the electrophoretic profile of erythrocyte membrane proteins induced by myotonizing drugs) and compared it with the profile of 5 healthy subjects of a similar age range. No differences between the two groups were apparent, rising doubts about the appropriatness of the erythrocyte membrane as an in vivo model of molecular changes in DMD and about the limitations of unidimensional electrophoresis as a suitable method for the detection of such changes.

Erythrocyte Membrane↗

PubMed1995

The majority of yeast UPF1 co-localizes with polyribosomes in the cytoplasm.

In Saccharomyces cerevisiae the UPF1 protein is required for nonsense-mediated mRNA decay, the accelerated turnover of mRNAs containing a nonsense mutation. Several lines of evidence suggest that translation plays an important role in the mechanism of nonsense mRNA decay, including a previous report that nonsense mRNAs assemble in polyribosomes. In this study we show that UPF1 and ribosomal protein L1 co-localize in the cytoplasm and that UPF1 co-sediments with polyribosomes. To detect UPF1, three copies of the influenza hemagglutinin epitope were placed at the C-terminus. The tagged protein, UPF1-3EP, retains 86% (+/- 5%) of function. Using immunological detection, we found that UPF1-3EP is primarily cytoplasmic and was not detected either in the nucleus or in the mitochondrion. UPF1-3EP and L1 co-distributed with polyribosomes fractionated in a 7-47% sucrose gradient. The sucrose sedimentation profiles for UPF1-3EP and L1 exhibited similar changes using three different sets of conditions that altered the polyribosome profile. When polyribosomes were disaggregated, UPF1-3EP and L1 accumulated in fractions coincident with 80S ribosomal particles. These results suggest that UPF1-3EP associates with polyribosomes. L3 and S3 mRNAs, which code for ribosomal proteins of the 60S and 40S ribosomal subunits, respectively, were on average about 100-fold more abundant than UPF1 mRNA. Assuming that translation rates for L3, S3, and UPF1 mRNA are similar, this result suggests that there are far fewer UPF1 molecules than ribosomes per cell. Constraints imposed by the low UPF1 abundance on the functional relationships between UPF1, polyribosomes, and nonsense mRNA turnover are discussed.

Base Sequence↗

PubMed2006

Systemic analysis of the differential gene expression profile in a colonic adenoma-normal SSH library.

BACKGROUND: The discovery of differentially expressed genes of colonic adenoma minus normal mucosa enables the understanding of early molecular events in colorectal carcinogenesis. In our previous study, we have developed an adenoma minus normal mucosa suppression subtractive hybridization (SSH) library and identified 109 differentially expressed clones. METHODS: An in-house EST pipeline and the Gene Ontology web-based tool () were used to analyze these clones. Realtime quantitative RT-PCR (Q-PCR) was applied to detect the expression of 14-3-3 zeta, REG4 and 6 ribosomal protein genes (RPS2, RPS12, RPS27A, RPL5, RPL7a and RPL10a) in 14 adenomas (8 with concurrent cancers) and 44 colorectal adenocarcinomas with paired normal mucosa. RESULTS: Sixty-two candidate genes were obtained from this library. Bioinformatics analysis indicated that both ribosomal protein genes and immune-related genes were enriched. REG4 was significantly upregulated in colorectal adenomas (medium fold: 1.676, p<0.05, Wilcoxon test) and 14-3-3 zeta in cancers (medium fold: 1.202, p<0.01, Wilcoxon test), as compared with those of paired normal mucosa. However, all ribosomal protein genes were not significantly overexpressed in colorectal adenomas or cancers. CONCLUSIONS: A differential gene expression profile in A-N SSH library may be helpful in understanding the molecular mechanism of colorectal cancer initiation and progression. REG4 and 14-3-3 zeta may be potential biomarkers for early colorectal cancer detection.

Adenoma↗

PubMed2005

[Screening and identification of human nasopharyngeal carcinoma-associated antigens].

OBJECTIVE: The purpose of this study was to provide an informative marker for clinical immunopathological diagnosis of nasopharyngeal carcinoma (NPC) and to lay a foundation for furture study of immunotherapy. METHODS: The NPC cDNA expression library was screened by serological analysis of recombinant cDNA expression libraries (SEREX) technology using xenogenic immune sera. The positive nucleotide sequences of cDNA inserts were determined and analysed with DNASIS and BLAST software in EMBL and GenBank. RESULTS: Eighteen positive clones encoding antigen genes were obtained after immunoscreening. These antigen genes included known genes, such as MAGE gene, CREM gene, beta2-microglobulin, Ribosomal Protein, et al, and unknown genes or ESTs in GenBank. To characterize the expression profile of these genes, the antibodies in sera from 40 nasopharyngeal carcinoma patients and 40 healthy donors were assayed with three antigens to screen specific and relative serum markers for nasopharyngeal carcinoma. The results showed that the positive rates for These results indicate nasopharyngeal carcinoma patients were higher than those for healthy donors. CONCLUSION: that some of the antigens may be related to nasopharyngeal carcinoma and may be valuable tumor markers in the diagnosis of nasopharyngeal carcinoma.

Antigens, Neoplasm↗

PubMed2001

Physical and transcriptional organization of the ribosomal RNA genes of the savannah-type Trypanosoma congolense.

Ribosomal RNA genes have been cloned from the major species of African trypanosomes. Complete nucleotide sequence composition of the small subunit (SSU) and portions of the large subunit (LSU) ribosomal RNA genes was determined for each of these trypanosome species. In contrast to the situation in Trypanosoma brucei, in savannah-type T. congolense the LSU ribosomal RNA is cleaved twice, to generate two additional prominent fragments. This leads to the different profiles observed when the rRNA molecules from these two trypanosome species are resolved in agarose gels. From the nucleotide sequences of the 18S RNA, a phylogenetic tree was derived depicting the relationships among the T. congolense complex of trypanosomes and the other species of trypanosomes.

Animals↗

PubMed2002

Using expressed sequence tag databases to identify ovarian genes of interest.

GenBank contains 4879 expressed sequence tags (EST) derived from four non-normalized human ovarian cDNA libraries. Of these EST, 2646 are contributors to UniGene clusters and have UniGene numbers. The EST map to 1206 distinct UniGenes. A gene expression profile was established for the human ovary by identifying the abundance of each UniGene cluster and its corresponding annotation. The most highly expressed transcripts were for proteins associated with protein synthesis (ribosomal proteins, elongation factors, thymosins, etc.). However, there are also transcripts for genes of unknown function that are ovary-specific. This ovarian gene expression profile provides useful data for the design of DNA microarrays targeted at ovarian function and highlights novel sequences that warrant further investigation.

Databases, Nucleic Acid↗

PubMed2001

Hydrophobic moments of protein structures: spatially profiling the distribution.

It is generally accepted that globular proteins fold with a hydrophobic core and a hydrophilic exterior. Might the spatial distribution of amino acid hydrophobicity exhibit common features? The hydrophobic profile detailing this distribution from the protein interior to exterior has been examined for 30 relatively diverse structures obtained from the Protein Data Bank, for 3 proteins of the 30S ribosomal subunit, and for a simple set of 14 decoys. A second-order hydrophobic moment has provided a simple measure of the spatial variation. Shapes of the calculated spatial profiles of all native structures have been found to be comparable. Consequently, profile shapes as well as particular profile features should assist in validating predicted protein structures and in discriminating between different protein-folding pathways. The spatial profiles of the 14 decoys are clearly distinguished from the profiles of their native structures.

Amino Acids↗