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Asymmetric arginine dimethylation of heterogeneous nuclear ribonucleoprotein K by protein-arginine methyltransferase 1 inhibits its interaction with c-Src.

Arginine methylation is a post-translational modification found in many RNA-binding proteins. Heterogeneous nuclear ribonucleoprotein K (hnRNP K) from HeLa cells was shown, by mass spectrometry and Edman degradation, to contain asymmetric N(G),N(G)-dimethylarginine at five positions in its amino acid sequence (Arg256, Arg258, Arg268, Arg296, and Arg299). Whereas these five residues were quantitatively modified, Arg303 was asymmetrically dimethylated in <33% of hnRNP K and Arg287 was monomethylated in <10% of the protein. All other arginine residues were unmethylated. Protein-arginine methyltransferase 1 was identified as the only enzyme methylating hnRNP K in vitro and in vivo. An hnRNP K variant in which the five quantitatively modified arginine residues had been substituted was not methylated. Methylation of arginine residues by protein-arginine methyltransferase 1 did not influence the RNA-binding activity, the translation inhibitory function, or the cellular localization of hnRNP K but reduced the interaction of hnRNP K with the tyrosine kinase c-Src. This led to an inhibition of c-Src activation and hnRNP K phosphorylation. These findings support the role of arginine methylation in the regulation of protein-protein interactions.

Amino Acid Sequence↗

Sno/scaRNAbase: a curated database for small nucleolar RNAs and cajal body-specific RNAs.

Small nucleolar RNAs (snoRNAs) and Cajal body-specific RNAs (scaRNAs) are named for their subcellular localization within nucleoli and Cajal bodies (conserved subnuclear organelles present in the nucleoplasm), respectively. They have been found to play important roles in rRNA, tRNA, snRNAs, and even mRNA modification and processing. All snoRNAs fall in two categories, box C/D snoRNAs and box H/ACA snoRNAs, according to their distinct sequence and secondary structure features. Box C/D snoRNAs and box H/ACA snoRNAs mainly function in guiding 2'-O-ribose methylation and pseudouridilation, respectively. ScaRNAs possess both box C/D snoRNA and box H/ACA snoRNA sequence motif features, but guide snRNA modifications that are transcribed by RNA polymerase II. Here we present a Web-based sno/scaRNA database, called sno/scaRNAbase, to facilitate the sno/scaRNA research in terms of providing a more comprehensive knowledge base. Covering 1979 records derived from 85 organisms for the first time, sno/scaRNAbase is not only dedicated to filling gaps between existing organism-specific sno/scaRNA databases that are focused on different sno/scaRNA aspects, but also provides sno/scaRNA scientists with an opportunity to adopt a unified nomenclature for sno/scaRNAs. Derived from a systematic literature curation and annotation effort, the sno/scaRNAbase provides an easy-to-use gateway to important sno/scaRNA features such as sequence motifs, possible functions, homologues, secondary structures, genomics organization, sno/scaRNA gene's chromosome location, and more. Approximate searches, in addition to accurate and straightforward searches, make the database search more flexible. A BLAST search engine is implemented to enable blast of query sequences against all sno/scaRNAbase sequences. Thus our sno/scaRNAbase serves as a more uniform and friendly platform for sno/scaRNA research. The database is free available at http://gene.fudan.sh.cn/snoRNAbase.nsf.

Base Sequence↗

The use of new antiretroviral therapy in combination with chemotherapy.

With rapid scientific advances in HIV pathogenesis and antiretroviral therapy, the oncologist is faced with new challenges in the treatment of patients with HIV infection and malignancy. HIV infection, by causing immune dysregulation and cytokine production, may alter the natural history of certain neoplasms. Treatment of cancer with chemotherapy can also affect the course of HIV disease. The use of combination antiretroviral agents, particularly the protease inhibitors, can maximally suppress replication of HIV. Improved clinical outcome is associated with more profound decreases in plasma HIV RNA, although development of resistant strains may hinder sustained antiretroviral activity. Antiretroviral therapy should be continued during chemotherapy with the goal of achieving plasma HIV-RNA levels below 500 copies/mL. Modifications in the regimen should be done when intolerable toxicity occurs or if viral load is increased. Although information regarding the use of newer antiretroviral agents with chemotherapy is limited, the use of several reverse transcriptase inhibitors has been well tolerated in patients with AIDS-related malignancies such as Kaposi's sarcoma and lymphoma.

Anti-HIV Agents↗

The ClpXP and ClpAP proteases degrade proteins with carboxy-terminal peptide tails added by the SsrA-tagging system.

Interruption of translation in Escherichia coli can lead to the addition of an 11-residue carboxy-terminal peptide tail to the nascent chain. This modification is mediated by SsrA RNA (also called 10Sa RNA and tmRNA) and marks the tagged polypeptide for proteolysis. Degradation in vivo of lambda repressor amino-terminal domain variants bearing this carboxy-terminal SsrA peptide tag is shown here to depend on the cytoplasmic proteases ClpXP and ClpAP. Degradation in vitro of SsrA-tagged substrates was reproduced with purified components and required a substrate with a wild-type SsrA tail, the presence of both ClpP and either ClpA or ClpX, and ATP. Clp-dependent proteolysis accounts for most degradation of SsrA-tagged amino-domain substrates at 32 degrees C, but additional proteases contribute to the degradation of some of these SsrA-tagged substrates at 39 degrees C. The existence of multiple cytoplasmic proteases that function in SsrA quality-control surveillance suggests that the SsrA tag is designed to serve as a relatively promiscuous signal for proteolysis. Having diverse degradation systems able to recognize this tag may increase degradation capacity, permit degradation of a wide variety of different tagged proteins, or allow SsrA-tagged proteins to be degraded under different growth conditions.

Adenosine Triphosphatases↗

An adenosine at position 27 in the human immunodeficiency virus type 1 trans-activation response element is not critical for transcriptional or translational activation by Tat.

Tat protein binds to the trans-activation response (TAR) element of human immunodeficiency virus type 1 RNAs and activates gene expression at the level of transcription in mammalian cell lines and translation in Xenopus oocytes. Certain residues within TAR are important for Tat binding in vitro, including residue A-27, which appears to be able to be modified in a Tat-dependent manner in Xenopus oocytes (L. Sharmeen, B. Bass, N. Sonenberg, H. Weintraub, and M. Groudine, Proc. Natl. Acad. Sci. USA 88:8096-8100, 1991). Activation by Tat in oocytes occurs via a covalent modification of TAR-containing RNA. We have found that in both mammalian cells and Xenopus oocytes, conversion of A-27.U-38 or C-27.G-38 or C-27.G-38 reduces activation. However, conversion to G-27.U-38 or G-27.C-38 had little or no effect on activation, and in oocytes, these mutant RNAs were still covalently modified. These data exclude a specific role for the adenosine at residue 27 for Tat activation but suggest a requirement for a purine at this position.

Adenosine↗

Dicer-dependent turnover of intergenic transcripts from the human beta-globin gene cluster.

The widespread occurrence of intergenic transcription in eukaryotes is increasingly evident. Intergenic transcription in the beta-globin gene cluster has been described in murine and human cells, and models for a role in gene and chromatin activation have been proposed. In this study, we analyze intergenic transcription and the chromatin state throughout the human beta-globin gene cluster and find that the data are not consistent with such activation-linked models. Thus, intergenic transcript levels correlate with neither chromatin activation nor globin gene expression. Instead, we find that intergenic transcripts of the beta-globin gene cluster are specifically upregulated in Dicer-deficient cells. This is accompanied by a shift towards more activated chromatin as indicated by changes in histone tail modifications. Our results strongly implicate RNA interference (RNAi)-related mechanisms in regulating intergenic transcription in the human beta-globin gene cluster and further suggest that RNAi-dependent chromatin silencing in vertebrates is not restricted to the centromeres.

Centromere↗

Regulation of repair by the 26S proteasome.

Cellular processes such as transcription and DNA repair may be regulated through diverse mechanisms, including RNA synthesis, protein synthesis, posttranslational modification and protein degradation. The 26S proteasome, which is responsible for degrading a broad spectrum of proteins, has been shown to interact with several nucleotide excision repair proteins, including xeroderma pigmentosum B protein (XPB), Rad4, and Rad23. Rad4 and Rad23 form a complex that binds preferentially to UV-damaged DNA. The 26S proteasome may regulate repair by degrading DNA repair proteins after repair is completed or, alternatively, the proteasome may act as a molecular chaperone to promote disassembly of the repair complex. In either case, the interaction between the proteasome and nucleotide excision repair depends on proteins like Rad23 that bind ubiquitin-conjugated proteins and the proteasome. While the iteration between Rad4 and Rad23 is well established, it will be interesting to determine what other proteins are regulated in a Rad23-dependent manner.

Journal Article↗

Androgens modulate nitric oxide synthase messenger ribonucleic acid expression in neurons of the major pelvic ganglion in the rat.

Expression and androgen regulation of the gene for neuronal nitric oxide synthase (NOS I) were examined in neurons of the major pelvic ganglia in male rats. Some of these postganglionic neurons innervate the penis and produce nitric oxide, which is believed to play a major role in penile erection. Rats were either castrated or sham operated and implanted with SILASTIC brand capsules filled with powdered testosterone (T) or 5alpha-dihydrotestosterone (5alphaDHT) or left empty. After 4 days, the number of neurons intensely stained for NADPH-diaphorase as well as those giving a NOS I signal in in situ hybridization experiments increased in castrated rats treated with testosterone by 31% and 42%, respectively, relative to those in untreated castrated rats. This suggests that the increase in NADPH-diaphorase activity resulted from enzyme synthesis and was due to a modification of NOS I messenger RNA (mRNA) accumulation. After 7 days, Northern blot analysis showed that castration produced a decrease in the amount of NOS I mRNA relative to that of ribosomal RNA. This decrease was almost prevented by T treatment. No significant differences were observed by reverse transcriptase-PCR between 7-day and 28-day treatments. However, in 7-day castrated rats treated with 5alphaDHT, NOS I signals relative to those of hypoxanthine phosphoribosyltransferase, taken as reference, were significantly higher than those in castrated rats and resembled those in sham-castrated rats, suggesting that 5alphaDHT was probably more potent than testosterone in preventing the decrease in NOS I mRNA levels elicited by castration. These results show that NOS I can be positively regulated by androgens and are consistent with the suggestion that these steroids play a role in the physiological processes of penile erection.

Androgens↗

Advances in isolation and characterization of homogeneous cell populations using laser microdissection.

The isolation and characterization of homogeneous cell populations are of great importance for the analysis of gene expression, because normal tissues contain various types of cells, and the differences in the populations of isolated cells exert significant effects on gene expression analysis. Researchers have attempted to develop methods for the isolation of homogeneous cell populations, such as flow cytometry and mechanical dissection. However, the recent emergence of laser-assisted microdissection has revolutionized the isolation of single-cell populations from solid tissues. With the help of a cutting laser, laser microdissection can isolate tissues (cells) of interest without contamination from surrounding tissues with the microscopic visualization field. By combining laser microdissection and subsequent microarray technology, several studies have resulted in the identification of disease-related genes. In this review, we summarize the principle of laser microdissection and provide several successful examples of target-gene identification using the conventional method combining laser microdissection and microarray. Next, we discuss the practical drawbacks of the combinational method, such as the need for a large number of cells and the disturbance of the relative abundance of transcripts during RNA amplification. We introduce our modifications to combined laser microdissection and microarray for detection of disease-related genes; the technique is simple, yet practical and accurate. Finally, versatile applications of laser microdissection, not only to transcript expression analysis, but also to other genomics and proteomics analyses are, also presented.

Animals↗

The macrolide-bacterium interaction and its biological basis.

Erythromycin, the first antibacterial macrolide introduced into the clinical setting over 50 years ago, was used extensively not only for the treatment of respiratory tract infections in both adults and children, but also for bone and soft tissue infections, and specific sexually transmitted diseases. Macrolide antibiotics have undergone a dramatic chemical evolution over the past 50 years, culminating in the improved 14- and 16-membered macrolides, acylides and new ketolides. In all cases, improvements in antibacterial activity involved changes in the interplay between the chemical structure of the macrolide and the components of the bacterial cell that dictate ultimate antibacterial activity and efficacy. Target site modification by methylation of ribosomal RNA, the so-called Macrolide-Streptogramin-Lincosamide, (MLS0 resistance and active efflux are the two most common forms of resistance present in the clinic today; however, other resistance mechanisms are known. The first macrolide that bound to MLS-resistant ribosomes was reported in 1989, demonstrating that appropriate structural changes could regain access to the modified ribosome-binding site. In addition, macrolide analogs with reduced affinity for the active efflux pump were identified in 1990, demonstrating that features of pump recognition could be separated from ribosome binding site recognition. Progressive medicinal chemistry led to the synthesis and development of the more recent ketolide class, which combines attributes of both prototypes into one molecule, i.e. non-recognition by the efflux pump and regaining some access to the modified ribosome binding site. Ketolide also lack of induction of erm methylase as do 16-member macrolides.

Animals↗

Extracellular matrix and the regulation of lung development and repair.

During lung development the extracellular matrix regulates cellular growth, migration, and differentiation. Pulmonary cells reciprocate and regulate extracellular matrix formation by elaborating a variety of peptides that affect gene transcription, RNA processing, translation, and posttranslational modifications of proteins. This regulation involves prenatal events such as the branching of airways and postnatal events such as alveolar septal formation. Normal airway branching requires multiple extracellular matrix proteins, proteoglycans, and the expression of cellular receptors for these molecules. Alveolar septal formation exemplifies how cells regulate the production, export, and deposition of an important structural protein, elastin, which is essential for the development of normal gas exchange units. Repair after injury to the adult lung engages some of the same factors that regulate lung development. However, in this case, inflammatory cells that enter the lung after injury elaborate many of these regulatory peptides. The effects of these peptides on the resident cells, which produce extracellular matrix, are a major determinant of whether the repair restores normal pulmonary architecture or progresses to fibrosis and additional impairment of gas exchange.

Animals↗

Molecular detection of dengue viruses in field caught Aedes aegypti mosquitoes from northeastern Argentina.

Most molecular protocols for Dengue virus detection described so far are time consuming and cumbersome with mosquito samples. In order to count with a sensitive and specific molecular detection system for monitoring possible Dengue outbreaks and circulating viral serotypes in field-caught Aedes aegypti populations from Northeastern Argentina, a RT-PCR and RFLP assay was developed. The original RT-PCR assay proposed by Sudiro et al. for human serum was optimized for mosquito samples. Modifications were done at the RNA extraction-purification and at the thermal profile steps. The generic 230 bp amplicon was validated by RFLP assay and cycle sequencing. Results showed that, due to the generic characteristic of the primers used, certain mosquito genome regions could be co-amplified, making confirmation of the Dengue specific amplicon by RFLP assay a required step. Under these conditions, the proposed method can be employed as a Dengue viral generic screening procedure in Aedes aegypti mosquito samples, giving in our hands an estimated 99.52% of confirmed negatives (207/208 tested samples).

Aedes↗

[Simultaneous in situ detection of viral antigens and RNA in brain tissues from a patient with herpes simplex encephalitis by immunocytochemistry and in situ hybridization].

In order to elucidate the correlation between herpes simplex virus (HSV-1) and the central nervous system tissue, we performed the simultaneous detection of viral antigens and RNA in the brain tissue sections from a patient with herpes simplex virus (HSV) encephalitis using immunocytochemistry and in situ hybridization. In the present study the hybridization protocol reported by Brahic M et al. in 1984 were applied for the simultaneous detection of viral RNA and antigens with a few modification. The sections were first immunocytochemically stained to detect HSV-1 antigens by ABC method, and then hybridized with 3H-labelled HSV-1 cDNA probe for the detection of RNA after the acetylation of slides for the prevention of nonspecific bindings of isotope to slides. In the present study, viral antigens were immunocytochemically stained to brown-colored deposits located in the cytoplasm and nucleus whereas viral RNA were detected as the accumulation of many silver grains over the nuclei or cytoplasm. In this case the light microscopic findings in a part of temporal lobe showed multiple areas of necrosis mainly involving the gray matter and a few inflammatory changes such as perivascular cell cuffings. HSV-1 infected Vero cells as positive control demonstrated both antigens and RNA as shown in Fig.1 a. However, no hybridization signals and color deposits were observed in uninfected Vero cells.(ABSTRACT TRUNCATED AT 250 WORDS)

Antigens, Viral↗

Oncofetal fibronectins in oral carcinomas: correlation of two different types.

Different isoforms of fibronectin are derived from a single gene by alternative processing of the primary RNA transcript or by posttranslational modifications. We have previously demonstrated that an oncofetal fibronectin (FN) isoform derived by O-glycosylation is highly associated with malignancy in breast and oral tumors. Another oncofetal FN isoform containing the ED-B sequence is derived by alternative splicing, and FN containing ED-B has been found to be a stromal marker of malignancies in various tissues. Here we report a comparative study by immunohistology of the distribution of the ED-B-containing isoform and the oncofetal FN isoform derived by O-glycosylation, in oral squamous cell carcinomas, premalignant lesions, and normal oral mucosa. A selective expression of the ED-B-containing isoform was demonstrated in close relation to the invading carcinoma (38/38), whereas there was virtually no staining in submucosa underlying premalignant lesions (1/11) and normal epithelium (0/5). The ED-B-containing FN showed close co-distribution and staining pattern with the oncofetal isoform derived by O-glycosylation. These results demonstrate that accumulation of FN adjacent to oral carcinomas includes both the ED-B-containing isoform and the isoform derived by O-glycosylation. Although both the change in primary structure and glycosylation of FN create conformational and immunologically detectable changes, the functional consequences in association with invasive carcinoma are poorly understood at present. Diagnostic implications especially of borderline lesions as well as evaluation of tumor aggressiveness may, however, be important.

Aged↗

Regulation of RNA function by aminoacylation and editing?

The chemical modification of nucleic acids is a ubiquitous phenomenon. Aminoacylation of tRNAs by aminoacyl-tRNA synthetases (ARSs) is a reaction essentially devoted to protein synthesis but it is used also as an emergency mechanism to recycle stalled ribosomes, and it is required for genome replication in some RNA viruses. In several aminoacyl-tRNA synthetases a correction mechanism known as editing is present to prevent aminoacylation errors. Genome data reveal a growing number of open reading frames encoding ARS-like proteins. This strongly suggests the existence of a widespread and nonconventional machinery for aminoacylation and editing. Here we review the different biological functions of aminoacylation and editing; also we propose an evolutionary scenario for the origin of these two reactions, and hypothesize an extant role for RNA charging and editing outside the genetic code.

Amino Acyl-tRNA Synthetases↗

The brome mosaic virus RNA3 intergenic replication enhancer folds to mimic a tRNA TpsiC-stem loop and is modified in vivo.

The genome of brome mosaic virus (BMV), a positive-strand RNA virus in the alphavirus-like superfamily, consists of three capped, messenger-sense RNAs. RNA1 and RNA2 encode viral replication proteins 1a and 2a, respectively. RNA3 encodes the 3a movement protein and the coat protein, which are essential for systemic infection in plants but dispensable for RNA3 replication in plants and yeast. A subset of the 250-base intergenic region (IGR), the replication enhancer (RE), contains all cis-acting signals necessary for a crucial, early template selection step, the 1a-dependent recruitment of RNA3 into replication. One of these signals is a motif matching the conserved box B sequence of RNA polymerase III transcripts. Using chemical modification with CMCT, kethoxal, DMS, DEPC, and lead, we probed the structure of the IGR in short, defined transcripts and in full-length RNA3 in vitro, in yeast extracts, and in whole yeast cells. Our results reveal a stable, unbranched secondary structure that is not dependent on the surrounding ORF sequences or on host factors within the cell. Functional 5' and 3' deletions that defined the minimal RE in earlier deletion studies map to the end of a common helical segment. The box B motif is presented as a hairpin loop of 7 nt closed by G:C base pairs in perfect analogy to the TpsiC-stem loop in tRNA(Asp). An adjacent U-rich internal loop, a short helix, and another pyrimidine-rich loop were significantly protected from base modifications. This same arrangement is conserved between BMV and cucumoviruses CMV, TAV, and PSV. In the BMV box B loop sequence, uridines corresponding to tRNA positions T54 and psi55 were found to be modified in yeast and plants to 5mU and pseudouridine. Together with the aminoacylated viral 3'-end, this is thus the second RNA replication signal within BMV where the virus has evolved a tRNA structural mimicry to a degree that renders it a substrate for classical tRNA modification reactions in vivo.

Aldehydes↗

Radiochemical cross-linking between proteins and RNA within 70 S ribosomal particles from E. coli MRE600.

In the absence of oxygen, gamma-irradiation produces covalent links between some ribosomal proteins and 16 S RNA to 23 S RNA, within 70 S ribosomes from E. coli MRE600. Under optimal conditions minimizing the structural modifications induced by radiations, in situ formed cross-links appear specific and reflect close RNA-protein contacts. In view of these results, the spatial organization of the 30 S, 50 S subunit interfaces is discussed. In addition, the gamma-irradiation technique reveals that subunit association induces modifications of some protein--RNA interactions.

Bacterial Proteins↗

RNA editing of a miRNA precursor.

Micro RNAs comprise a large family of small, functional RNAs with important roles in the regulation of protein coding genes in animals and plants. Here we show that human and mouse miRNA22 precursor molecules are subject to posttranscriptional modification by A-to-I RNA editing in vivo. The observed editing events are predicted to have significant implications for the biogenesis and function of miRNA22 and might point toward a more general role for RNA editing in the regulation of miRNA gene expression.

Animals↗