Molecular analysis of the in situ growth rates of subsurface Geobacter species.

Molecular tools that can provide an estimate of the in situ growth rate of Geobacter species could improve understanding of dissimilatory metal reduction in a diversity of environments. Whole-genome microarray analyses of a subsurface isolate of Geobacter uraniireducens, grown under a variety of conditions, identified a number of genes that are differentially expressed at different specific growth rates. Expression of two genes encoding ribosomal proteins, rpsC and rplL, was further evaluated with quantitative reverse transcription-PCR (qRT-PCR) in cells with doubling times ranging from 6.56 h to 89.28 h. Transcript abundance of rpsC correlated best (r(2) = 0.90) with specific growth rates. Therefore, expression patterns of rpsC were used to estimate specific growth rates of Geobacter species during an in situ uranium bioremediation field experiment in which acetate was added to the groundwater to promote dissimilatory metal reduction. Initially, increased availability of acetate in the groundwater resulted in higher expression of Geobacter rpsC, and the increase in the number of Geobacter cells estimated with fluorescent in situ hybridization compared well with specific growth rates estimated from levels of in situ rpsC expression. However, in later phases, cell number increases were substantially lower than predicted from rpsC transcript abundance. This change coincided with a bloom of protozoa and increased attachment of Geobacter species to solid phases. These results suggest that monitoring rpsC expression may better reflect the actual rate that Geobacter species are metabolizing and growing during in situ uranium bioremediation than changes in cell abundance.

Expression of 1alpha-HYD and 24-HYD in bovine kidney mediated by vitamin D3 supplementation.

In order to better understand vitamin D3 in cattle metabolism, we quantified 1alpha-HYD and 24-HYD gene expression. In the kidneys of 35 male Nellore cattle, these were divided into a control group and two treatment groups (2 x 10(6) international units of vitamin D3 administered for 2 or 8 consecutive days pre-slaughter). Vitamin D3 supplementation resulted in a significant increase in 1alpha-HYD gene expression; however, significantly increased 24-HYD gene expression was only detected in cattle that had 8 days of supplementation. The finding of upregulation of 24-HYD due to vitamin D supplementation is in line with the expected rise in 24,25-di-hydroxy-vitamin D3 synthesis observed when plasma vitamin D3 concentrations are high, stimulating excretion by the organism. On the other hand, upregulation of 1alpha-HYD was unexpected, since vitamin D3 supplementation has been reported to impact these two genes in opposite directions. We conclude that vitamin D3 metabolism in these animals is more complex than previously reported.

Linking chemistry and genetics in the growing cyanobactin natural products family.

Ribosomal peptide natural products are ubiquitous, yet relatively few tools exist to predict structures and clone new pathways. Cyanobactin ribosomal peptides are found in ~30% of all cyanobacteria, but the connection between gene sequence and structure was not defined, limiting the rapid identification of new compounds and pathways. Here, we report discovery of four orphan cyanobactin gene clusters by genome mining and an additional pathway by targeted cloning, which represented a tyrosine O-prenylating biosynthetic pathway. Genome mining enabled discovery of five cyanobactins, including peptide natural products from Spirulina supplements. A phylogenetic model defined four cyanobactin genotypes, which explain the synthesis of multiple cyanobactin structural classes and help direct pathway cloning and structure prediction efforts. These strategies were applied to DNA isolated from a mixed cyanobacterial bloom containing cyanobactins.

Critical selection of reliable reference genes for gene expression study in the HepaRG cell line.

The human HepaRG cell line has shown to be a valuable in vitro tool for repeated exposure to chemical compounds and to evaluate their potential toxic outcome. Seen the importance given by the actual EU legislation of cosmetics and chemical substances to the use of in vitro methods in human safety evaluation, one can expect that HepaRG cells will gain importance as human-relevant cell source. At the transcriptional level, RT-qPCR assays are often used to obtain quantitative results. The choice of internal control is important since it may affect the study outcome. Indeed, it is well-known that expression levels of traditional reference genes can vary across tissue types and across experimental settings within one specific tissue type. From a review of the scientific literature, it appears that, for HepaRG cells, S18 often is used as internal control, but without any evidence of its expression stability in this cell line. Therefore, we aimed to select the most optimal reference genes for gene expression studies in HepaRG cells and to check whether S18 is a suitable reference gene. Twelve candidate genes' expression stability level was analyzed by three algorithms (geNorm, BestKeeper, Normfinder), which identified the optimal single reference gene (TBP) and the most suitable set of reference genes (TBP, UBC, SDHA, RLP13, YHWAZ, HMBS, B2M and HPRT1) for HepaRG transcriptional profiling. This study provides a new set of reference genes that is suitable for testing whenever RT-qPCR data for HepaRG cells are generated. The most stable ones can then be selected for further normalization.

Ribosomal protein L3 mediated the transport of digoxin in Xenopus laevis oocyte.

Ribosomal protein L3 (RPL3) is known to be an indispensable and essential component for the peptidyltransferase center. In the present study, we found a novel function of RPL3 using a Xenopus laevis oocyte expression system. When expressed in X. oocytes, RPL3 mediated the high affinity transport of [(3)H]digoxin (K(m) = 213.3 ± 46.8 nM) in a time-, concentration-, and sodium-dependent manners. The maximum velocity of the transport of [(3)H]digoxin via RPL3 produced at physiological pH. However, we did not observe RPL3-mediated transport of several organic solutes such as [(14)C]androstenedione, [(3)H]dexamethasone, [(3)H]dehydroepiandrosterone sulfate, [(3)H]L-tryptophan, [(14)C]L-ascorbic acid, [(14)C]α-ketoglutarate, [(14)C]glutarate, [(3)H]methotrexate, [(3)H]bumetanide, [(3)H]probenecid, [(14)C]salicylic acid, [(14)C]theophylline and [(3)H]valproate. Our results suggest that RPL3 functions as a drug carrier protein and may be involved in the digoxin toxicity in the human body.

[Transcription factor YY1 participates in activation transcription of the human ribosomal protein L11 gene].

Ribosomal protein L11 plays important role in ribosome, being involved in several steps in protein synthesis and also activates p53-dependent cell cycle arrest. Changes in the rpL11 levels might be implicated in cell cycle control and carcinogenesis. Therefore, the mechanism of regulation of rpL11 expression has increasing importance. Article presents research results of interaction of promotor elements of gene HRPL11 with proteins of nuclear extracts of cells of a various cell origin. Use oligonucleotide competitors containing known transcription factor-binding sites, and also polyclonal antibodies has shown, that transcription factor YY1 participates in regulation of a transcription of gene HRPL11 in all investigated cellular lines. Our data obtained from comparison of protein binding profiles using nuclear extracts from rapidly growth cells, normal cell lines and serum deprivation repressed cell allows us to consider of transcription factor YY1 as activator of HRPL11 gene transcription.

Diallyl disulfide, a chemopreventive agent in garlic, induces multidrug resistance-associated protein 2 expression.

The organosulfur compounds (OSCs), present in garlic, are studied for their protective effect against human cancers. P-glycoprotein (P-gp) and multidrug resistance protein 2 (Mrp2) are two transporters involved in the defense of cells and in the development of multidrug resistance. Whereas OSCs increase glutathione S-transferase activity (GST), Mrp2 plays a role in the transport of glutathione (GSH)-conjugates. In this study, we have investigated the effect of two OSCs, diallyl disulfide (DADS) and S-allyl cysteine (SAC), on P-gp and Mrp2 expression in renal brush-border membranes. By Western blot analysis, our results show that DADS induces Mrp2 expression (by 7-fold), which correlates with the rise of GST activity and GSH levels. Surprisingly, a co-administration of OSC with cisplatin, an anticancer drug, significantly increased Mrp2 gene and protein expression (by 30-fold), suggesting that DADS could potentiate the effects of cisplatin. Interestingly, SAC and cisplatin in co-treatment decreased P-gp protein expression and mdr1b isoform mRNA levels. In addition, modulation of the mdr1b isoform and Mrp2 by cisplatin was completely abolished by a glutathione precursor, N-acetyl cysteine. These results indicate that OSCs present in a garlic-rich diet might alter chemotherapeutic treatments using P-gp or Mrp2 substrates.

Expression of ribosomal protein L4 (rpL4) during neurogenesis and 5-azacytidine (5AzC)-induced apoptotic process in the rat.

5-Azacytidine (5AzC) induces neuronal apoptosis in rat and mouse fetuses. 5AzC also induces apoptosis in undifferentiated PC12 cells, and ribosomal protein L4 (rpL4) mRNA expression increases prior to apoptosis. To clarify the roles of rpL4 during neurogenesis, we first examined the distribution of rpL4 mRNA in the developing rat brain by in situ hybridization and RT-PCR, and compared the results to the distribution of TUNEL- or PCNA-positive cells. rpL4 mRNA expression was strong in the ventricular zone (VZ), subventricular zone (SVZ), cortical plate (CP), cerebral cortex, granule cell layer (GCL), pyramidal cell layer (Py) and external granular layer (EGL) during embryonic and early postnatal days, and it was remarkably weakened thereafter. A lot of PCNA-positive cells were observed in VZ, SVZ, and EGL during embryonic and early postnatal days, and such distribution of PCNA-positive cells was almost identical to rpL4 mRNA distribution. Only few TUNEL-positive cells were observed in VZ, SVZ, cerebral cortex, EGL, and hippocampus during embryonic and early postnatal days, and the regions with TUNEL-positive cells were not identical to rpL4 mRNA distribution. Next, the changes of rpL4 mRNA expression in the brain of 5AzC-treated rat fetuses were examined by in situ hybridization and RT-PCR. Apoptotic cells appeared at 9 to 24 hours after treatment (HAT). However, the rpL4 mRNA expression was unchanged during the apoptotic process. From the results, it is suggested that rpL4 would have certain roles in cell proliferation and differentiation during neurogenesis, but have no roles in 5AzC-induced apoptosis in the fetal brain.

Expression analysis of human HL60 cells exposed to 60 Hz square- or sine-wave magnetic fields.

A total of 960 complementary DNA (cDNA) clones from an HL60 cell cDNA library were screened to discover genes that were differentially expressed in HL60 cells exposed to 60 Hz square-wave magnetic fields (MFs) compared to sham-exposed cells. Square-wave fields are rich in odd harmonic frequency content. We used a two-gel cDNA library screening method (BIGEL) to identify treatment-induced alterations in gene expression. Four cDNA clones were tentatively identified as differentially expressed after exposure to square-wave MFs at 2 mT for 24 h. BIGEL-identified genes (GenBank accession number) corresponding to these clones were: TI227H (D50525), EST Homo sapiens partial cDNA (Z17814), human ribosomal protein S13 (L01124), and AICAR transformylase mRNAs (D82348). The differences in mRNA levels were not confirmed in test compared to experimental cells by Northern analysis. In other experiments, we used concurrent exposure to 60 Hz sine- or square-wave MFs (0 or 2 mT, duration of 3 or 24 h, no postexposure delay). In addition to the four BIGEL genes, we also investigated MYC, HSP70, RAN and SOD1. In the case of MYC and HSP70, square-wave MFs appeared to exhibit more marked alterations when compared to sinusoidal waveforms, but the overall results indicated no effect of possible differential magnetic-field-induced expression of all eight genes. In contrast, alterations of mRNA levels were observed for seven genes after exposure to X irradiation, hyperthermia and TPA. These results are contrary to previously proposed similarities between the action of these agents and MF effects on gene transcription.

The carboxyl extensions of two rat ubiquitin fusion proteins are ribosomal proteins S27a and L40.

Two rat recombinant cDNAs were characterized; they encode fusion proteins that have at their NH2 terminus the conserved 76 amino acid ubiquitin and at their carboxyl terminus the extension ribosomal proteins S27a (80 amino acids and a molecular weight of 9,397) or L40 (52 amino acids and a molecular weight of 6,177). The fusion proteins are processed in a reticulocyte lysate to ubiquitin and either S27a or L40. Hybridization of cDNAs to digests of nuclear DNA suggests that there are 14 to 19 copies of the S27a, and 6 to 10 of the L40, genes. The mRNA for ubiquitin-S27a has about 700 nucleotides and ubiquitin-L40 about 650. Ribosomal proteins S27a and L40 contain zinc finger motifs of the C2-C2 variety. S27a and L40 are related to ribosomal proteins from other species.

The primary structures of rat ribosomal proteins L4 and L41.

The amino acid sequences of the rat 60S ribosomal subunit proteins L4 and L41 were deduced from the sequences of nucleotides in recombinant cDNAs. Ribosomal protein L4 has 421 amino acids; the molecular weight is 47,280. L41 is the smallest ribosomal protein; it has 25 amino acids and a molecular weight of 3,454. Hybridization of the cDNAs to digests of nuclear DNA suggests that there are 7 to 8 copies of the L4, and 9 to 12 of the L41, genes. The mRNA for L4 is about 1,500 nucleotides in length and that for L41 about 500 nucleotides. The 5' noncoding sequence of the L4 cDNA is exceptional in that it has, in addition to a short polypyrimidine sequence at the 5' end, a second stretch of 15 consecutive pyrimidines near the site of initiation of translation. The 3' noncoding sequence of the L41 mRNA is unusual in that it is at least 246 nucleotides long. Rat L4 and L41 are related to ribosomal proteins from other eukaryotes.

Primary structure and expression of a gene encoding the cytosolic ribosomal protein S4 from potato.

The primary structure of a cDNA clone encoding the S4 protein from the small subunit of 80S ribosomes from potato was determined. Cytosolic ribosomal protein S4 is hydrophilic and has a prevalence for positively charged residues. In potato it is 264 amino acids long and contains a putative nuclear targeting signal close to the N-terminus. Having 65-69% identical amino acids cytosolic ribosomal protein S4 from mammals, fungi and plants belongs to the highly conserved proteins. The S4 gene is transcribed in all potato tissues analysed and has a relatively high expression level in comparison to nuclear genes encoding mitochondrial proteins.

Human ribosomal protein L37 has motifs predicting serine/threonine phosphorylation and a zinc-finger domain.

Ribosomal protein L37 mRNA is overexpressed in colon cancer. The nucleotide sequences of human L37 from several tumor and normal, colon and liver cDNA sources were determined to be identical. L37 mRNA was approximately 375 nucleotides long encoding 97 amino acids with M(r) = 11,070, pI = 12.6, multiple potential serine/threonine phosphorylation sites and a zinc-finger domain. The human sequence is compared to other species.

A ribosomal protein S10 gene is found in the mitochondrial genome in Solanum tuberosum.

The S10 ribosomal protein gene (rps10), which has not been previously reported in any angiosperm mitochondrial genome, was identified by sequence analysis in the potato mitochondrial DNA. This gene is found downstream of a truncated non-functional apocytochrome b (cob) pseudogene, and is expressed as multiple transcripts ranging in size from 0.8 to 5.0 kb. Southern hybridization analysis indicates that rps10-homologous sequences are not present in the wheat mitochondrial genome. Sequence analysis of a single-copy region of the pea mitochondrial genome located upstream of cox1 [11] shows that a non-functional rps10 pseudogene is present in this species. These results suggest that the functional genes coding for wheat and pea mitochondrial RPS10 polypeptides have been translocated to the nucleus.

Isolation of a ubiquitin-ribosomal protein gene (ubi3) from potato and expression of its promoter in transgenic plants.

A genomic clone encoding the potato homolog of the yeast ubiquitin-ribosomal protein fusion gene ubi3 was isolated and characterized. Chimeric genes containing the ubi3 promoter (920 bp of 5' to the ubiquitin start codon) were constructed in which the reporter gene beta-glucuronidase (GUS) was either fused directly to the promoter, or introduced as a translational fusion to the ubiquitin-coding region. After introduction into the potato by Agrobacterium-mediated transformation, GUS activities were measured in leaves and in tubers of transgenic clones. GUS activity was 5- to 10-fold higher in clones expressing the ubiquitin-GUS translational fusion than in clones containing GUS fused directly to the ubi3 promoter. For both types of constructs, GUS activity was highest in meristematic leaves and declined during leaf expansion, then rose again to near the meristematic levels during senescence. GUS activity in tubers was similar to that in young leaves. In contrast to the native ubi3 genes, the chimeric ubi3-GUS transgenes were not activated in the tuber by wounding.

Nucleotide sequence and expression of the ribosomal protein L2 gene in pea chloroplasts.

We sequenced the nucleotides around the rpl2 gene, encoding the ribosomal protein L2, in pea (Pisum sativum cv. Alaska) chloroplasts and analyzed the expression of the rpl2 gene. During deetiolation, accumulation of the rpl2 transcript did not require de novo protein synthesis on chloroplastic ribosomes, in contrast to that of most chloroplast-encoded genes. This suggested that the mechanism involved in the expression of rpl2 differed from that of most chloroplast-encoded genes.

Sequence of an acidic ribosomal protein from the jellyfish Polyorchis penicillatus.

We have isolated a cDNA clone from the jellyfish Polyorchis penicillatus that encodes the homologue of the A1 acidic ribosomal protein previously characterized in human, brine shrimp, fruit fly, and yeast. The sequence of this protein is strongly conserved among the five eukaryotic species for which it has been determined. Conservation is greatest in the amino-terminal 51 amino acids and the carboxyl-terminal 25 amino acids. This suggests that these regions are necessary for interactions with other components of the protein synthetic machinery, while the central part of the protein has a less specific role to play. Comparison of the sequences obtained from the different species indicate that the metazoan lineages all appear to have arisen at approximately the same time and significantly later than the time of divergence of yeast from the common ancestor of the Metazoa.

The plastid rpoA gene encoding a protein homologous to the bacterial RNA polymerase alpha subunit is expressed in pea chloroplasts.

The gene rpoA, encoding a protein homologous to the alpha subunit of RNA polymerase from Escherichia coli has been located in pea chloroplast DNA downstream of the petD gene for subunit IV of the cytochrome b-f complex. Nucleotide sequence analysis has revealed that rpoA encodes a polypeptide of 334 amino acid residues with a molecular weight of 38916. Northern blot analysis has shown that rpoA is co-transcribed with the gene for ribosomal protein S11. A lacZ-rpoA gene-fusion has been constructed and expressed in E. coli. Antibodies raised against the fusion protein have been employed to demonstrate the synthesis of the rpoA gene product in isolated pea chloroplasts. Western blot analysis using these antibodies and antibodies against the RNA polymerase core enzyme from the cyanobacterium, Anabaena 7120, has revealed the presence of the gene product in a crude RNA polymerase preparation from pea chloroplasts.