Multiple Histone Deacetylases and the CREB-binding Protein Regulate Pre-mRNA 3′-End Processing

Trichostatin A (TSA), a specific inhibitor of histone deacetylases (HDACs), induces acetylation of various non-histone proteins such as p53 and alpha-tubulin. We purified several acetylated proteins by the affinity to an anti-acetylated lysine (AcLys) antibody from cells treated with TSA and identified them by mass spectrometry. Here we report on acetylation of CFIm25, a component of mammalian cleavage factor Im (CF Im), and poly(A) polymerase (PAP), a polyadenylating enzyme for the pre-mRNA 3'-end. The residues acetylated in these proteins were mapped onto the regions required for interaction with each other. Whereas CBP acetylated these proteins, HDAC1, HDAC3, HDAC10, SIRT1, and SIRT2 were involved in in vivo deacetylation. Acetylation of the CFIm25 occurred depending on the cleavage factor complex formation. Importantly, the interaction between PAP and CF Im complex was decreased by acetylation. We also demonstrated that acetylation of PAP inhibited the nuclear localization of PAP by inhibiting the binding to the importin alpha/beta complex. These results suggest that CBP and HDACs regulate the 3'-end processing machinery and modulate the localization of PAP through the acetylation and deacetylation cycle.

Detection of enzymatic activity of transfer RNA modification enzymes using radiolabeled tRNA substrates

The presence of modified ribonucleotides derived from adenosine, guanosine, cytidine, and uridine is a hallmark of almost all cellular RNA, and especially tRNA. The objective of this chapter is to describe a few simple methods that can be used to identify the presence or absence of a modified nucleotide in tRNA and to reveal the enzymatic activity of particular tRNA-modifying enzymes in vitro and in vivo. The procedures are based on analysis of prelabeled or postlabeled nucleotides (mainly with [(32)P] but also with [(35)S], [(14)C] or [(3)H]) generated after complete digestion with selected nucleases of modified tRNA isolated from cells or incubated in vitro with modifying enzyme(s). Nucleotides of the tRNA digests are separated by two-dimensional (2D) thin-layer chromatography on cellulose plates (TLC), which allows establishment of base composition and identification of the nearest neighbor nucleotide of a given modified nucleotide in the tRNA sequence. This chapter provides useful maps for identification of migration of approximately 70 modified nucleotides on TLC plates by use of two different chromatographic systems. The methods require only a few micrograms of purified tRNA and can be run at low cost in any laboratory.

Identification of modified residues in RNAs by reverse transcription-based methods

Naturally occurring modified residues derived from canonical RNA nucleotides are present in most cellular RNAs. Their detection in RNA represents a difficult task because of their great diversity and their irregular distribution within RNA molecules. Over the decades, multiple experimental techniques were developed for the identification and localization of RNA modifications. Most of them are quite laborious and require purification of individual RNA to a homogeneous state. An alternative to these techniques is the use of reverse transcription (RT)-based approaches. In these approaches, purification of RNA to homogeneity is not necessary, because the selection of the analyzed RNA species is done by specific annealing of oligonucleotide DNA primers. However, results from primer extension analysis are difficult to interpret because of the unpredictable nature of RT pauses. They depend not only on the properties of nucleotides but also on the RNA primary and secondary structure. In addition, the degradation of cellular RNA during extraction, even at a very low level, may complicate the analysis of the data. RT-based techniques for the identification of modified residues were considerably improved by the development of selected chemical reagents specifically reacting with a given modified nucleotide. The RT profile obtained after such chemical modifications generally allows unambiguous identification of the chemical nature of the modified residues and their exact location in the RNA sequence. Here, we provide experimental protocols for selective chemical modification and identification of several modified residues: pseudouridine, inosine, 5-methylcytosine, 2'-O-methylations, 7-methylguanosine, and dihydrouridine. Advice for an optimized use of these methods and for correct interpretation of the data is also given. We also provide some helpful information on the ability of other naturally occurring modified nucleotides to generate RT pauses.

Post-transcriptional regulation of the xynA expression by a novel mRNA binding protein, XaiF

XaiF, a novel 32kDa protein encoded by the ORF located in the immediate downstream of the xynA gene of Bacillus stearothermophilus No. 236, was identified to be the xylanase-specific trans-activator. In this study, the positive effect of XaiF was confirmed to be xylanase-specific, and the results from Northern blot and in vitro transcription assays showed that the XaiF increased the xynA transcripts at post-transcriptional step. Moreover, analysis of the mRNA decay rate led to the assertion that the XaiF functions to stabilize the xynA mRNA. Intriguingly, in vitro RNA-protein binding assay and analysis using gst-xynA 3'-UTR chimeric gene constructs demonstrated that the XaiF stabilizes xynA mRNA by direct binding onto the 3'-UTR of the mRNA.

hnRNP-U enhances the expression of specific genes by stabilizing mRNA

Heterogeneous nuclear ribonucleoproteins (hnRNPs) are thought to be involved in pre-mRNA processing. hnRNP-U, also termed scaffold attachment factor A (SAF-A), binds to pre-mRNA and nuclear matrix/scaffold attachment region DNA elements. However, its role in the regulation of gene expression is as yet poorly understood. In the present study, we show that hnRNP-U specifically enhances the expression of tumor necrosis factor alpha mRNA by increasing its stability, possibly through binding to the 3' untranslated region. We also show that hnRNP-U enhances the expression of several other genes as well, including GADD45A, HEXIM1, HOXA2, IER3, NHLH2, and ZFY, by binding to and stabilizing these mRNAs. These results suggest that hnRNP-U enhances the expression of specific genes by regulating mRNA stability.

RNAi interference of XPO1 and Sm genes and their effect on the spliced leader RNA in Trypanosoma brucei

In trypanosomes, trans-splicing is a major essential RNA-processing mechanism that involves the addition of a spliced leader sequence to all mRNAs from a small RNA species, known as the spliced leader RNA (SL RNA). SL RNA maturation is poorly understood and it is not clear where assembly with Sm proteins takes place. In this study, we followed the localization of the SL RNA during knockdown of Sm proteins and XPO1, which in metazoa functions in transport of mRNA and U snRNAs from the nucleus to the cytoplasm. We found that XPO1 has no role in SL RNA biogenesis in wild-type cells, or when the cells are depleted of Sm proteins. During Sm depletion, 'defective' SL RNA lacking cap modification at position +4 first accumulates in the nucleus, suggesting that Sm assembly on SL RNA most probably takes place in this compartment. Only after massive nuclear accumulation is the 'defective' SL RNA exported to the cytoplasm to form SL RNP-C, which may be a route to dispose of SL RNA when its normal biogenesis is blocked.

Evidence of post-transcriptional regulation in the maintenance of a partial muscle phenotype by electrogenic cells of S. macrurus

Electrocytes, the current-producing cells of electric organs (EOs) in electric fish, are unique in that they derive from striated muscle and they possess biochemical characteristics of both muscle and non-muscle cells. In the freshwater teleost Sternopygus macrurus, electrocytes are multinucleated cells that do not contract yet retain expression of some proteins common to skeletal muscle cells. Given the role that transcriptional regulation plays in the activation of the myogenic program in vertebrates, we examined the expression patterns of several genes associated with multiple functions of skeletal muscle in mature electrocytes of S. macrurus. Our expression analyses detected transcripts for alpha-actin, alpha-acetylcholine (ACh) receptor (alpha-AChR), desmin, muscle creatine kinase (MCK), myosin heavy chain (MHC) isoforms, titin, tropomyosin, and troponin-T genes in the EO. However, immunolabeling studies revealed that electrocytes do not contain MCK, MHCs, or tropomyosin or troponin-T proteins. These results underscore the contribution of gene regulatory mechanisms in the maintenance of the muscle-like phenotype of EO that may be transcriptional-independent. We also report the classification and frequency of distinct transcripts from a random selection of 420 clones from an EO cDNA library. This is the first characterization of expressed genes in an EO, and it is an important step toward identifying mechanisms that affect different muscle protein systems for the evolution of highly specialized noncontractile tissues. Evidence of post-transcriptional regulation in the maintenance of a partial muscle phenotype by electrogenic cells of S. macrurus.

Effects of RNA splicing and post-transcriptional regulation on HIV-1 growth: a quantitative and integrated perspective

Despite major advances over the last two decades in our understanding of RNA splicing and (post-) transcriptional regulation in human immunodeficiency virus type-1 (HIV-1), debate continues on the mechanisms and effects of Rev protein on HIV-1 growth. Moreover, arguments that HIV-1 has been optimised for growth have been largely based on speculation. Here, we begin systematically to address these issues by developing a detailed kinetic model for HIV-1 intracellular development. The model accounts for transcription, successive steps in RNA splicing, nuclear export of mRNAs, translation and shuttling of Rev and Tat, Tat-mediated transactivation of transcription, thresholds on Rev in its effects on nuclear export of mRNA, and inhibitory effects of Rev on splicing. Using the model, we found that inefficient splicing of HIV-1 mRNA was generally beneficial for HIV-1 growth, but that an excessive reduction in the splicing efficiency could be detrimental, suggesting that there exists a splicing efficiency that optimises HIV-1 growth. Further, we identified two key contributors to splicing efficiency, the intrinsic splicing rate and the extent of Rev-mediated splicing inhibition, and we showed how these should be balanced for HIV-1 to optimise its growth. Finally, we found that HIV-1 growth is relatively insensitive to different levels of the Rev export threshold, and we suggest that this mechanism evolved to delay viral growth, perhaps to enable evasion of host defensive responses. In summary, our model provides a quantitative and qualitative framework for probing how constituent mechanisms contribute to the complex, yet logical, process of HIV-1 growth.

Impact of nonsense-mediated mRNA decay on the global expression profile of budding yeast

Nonsense-mediated mRNA decay (NMD) is a eukaryotic mechanism of RNA surveillance that selectively eliminates aberrant transcripts coding for potentially deleterious proteins. NMD also functions in the normal repertoire of gene expression. In Saccharomyces cerevisiae, hundreds of endogenous RNA Polymerase II transcripts achieve steady-state levels that depend on NMD. For some, the decay rate is directly influenced by NMD (direct targets). For others, abundance is NMD-sensitive but without any effect on the decay rate (indirect targets). To distinguish between direct and indirect targets, total RNA from wild-type (Nmd⁺) and mutant (Nmd⁻) strains was probed with high-density arrays across a 1-h time window following transcription inhibition. Statistical models were developed to describe the kinetics of RNA decay. 45% ± 5% of RNAs targeted by NMD were predicted to be direct targets with altered decay rates in Nmd⁻ strains. Parallel experiments using conventional methods were conducted to empirically test predictions from the global experiment. The results show that the global assay reliably distinguished direct versus indirect targets. Different types of targets were investigated, including transcripts containing adjacent, disabled open reading frames, upstream open reading frames, and those prone to out-of-frame initiation of translation. Known targeting mechanisms fail to account for all of the direct targets of NMD, suggesting that additional targeting mechanisms remain to be elucidated. 30% of the protein-coding targets of NMD fell into two broadly defined functional themes: those affecting chromosome structure and behavior and those affecting cell surface dynamics. Overall, the results provide a preview for how expression profiles in multi-cellular eukaryotes might be impacted by NMD. Furthermore, the methods for analyzing decay rates on a global scale offer a blueprint for new ways to study mRNA decay pathways in any organism where cultured cell lines are available.

Genes determine the structure of proteins through transcription and translation in which an RNA copy of the gene is made (mRNA) and then translated to make the protein. Cellular protein levels reflect the relative rates of mRNA synthesis and degradation, which are subject to multiple layers of controls. Mechanisms also exist to ensure the quality of each mRNA. One quality control mechanism called nonsense-mediated mRNA decay (NMD) triggers the rapid degradation of mRNAs containing coding errors that would otherwise lead to the production of non-functional or potentially deleterious proteins. NMD occurs in yeasts, plants, flies, worms, mice, and humans. In humans, NMD affects the etiology of genetic disorders by affecting the expression of genes that carry disease-causing mutations. Besides quality assurance, NMD plays another role in gene expression by controlling the abundance of hundreds of normal mRNAs that are devoid of coding errors. In this paper, the authors used DNA arrays to monitor the relative decay rates of all mRNAs in budding yeast and found a subset where decay rates were dependent on NMD. Many of the corresponding proteins perform related functional roles affecting both the structure and behavior of chromosomes and the structure and integrity of the cell surface.

PGC-1alpha regulates the isoform mRNA ratio of the alternatively spliced thyroid hormone receptor alpha transcript

Transcripts derived from the thyroid hormone receptor alpha (TRalpha) gene are alternatively spliced resulting in a functional receptor TRalpha1 and a non-T3-binding variant TRalpha2 that can exert a dominant negative effect on the transactivation functions of other TRs. There is evidence that the ratio of TRalpha isoform transcripts can be modulated and here, we investigate whether the PPARgamma co-activator alpha (PGC-1alpha) has an effect on this splicing process. PGC-1alpha was discovered not only as a transcriptional co-activator, but also has certain motifs characteristic of splicing factors. We demonstrate that PGC-1alpha alters the ratio of endogenously expressed TRalpha isoform transcripts in HepG2 cells, by decreasing TRalpha1 mRNA levels twofold. This change in isoform ratio is accompanied by a decrease in 5'-deiodinase expression, whereas no differences were found in TRbeta1 expression. Deletion of the RNA-processing domain of PGC-1alpha abrogated the effect on the TRalpha splicing, whereas expression of only the RNA-processing domain favored TRalpha1 expression. PGC-1alpha showed a similar effect on the splicing of a TRalpha minigene containing only the last four exons and introns of the TRalpha gene. These data suggest that PGC-1alpha is involved in the RNA processing of TRalpha transcripts.

Both integrated and differential regulation of components of the IL-2/IL-2 receptor system

Interleukin-2 was discovered in 1976 as a T-cell growth factor. It was the first type I cytokine cloned and the first for which a receptor component was cloned. Its importance includes its multiple actions, therapeutic potential, and lessons for receptor biology, with three components differentially combining to form high, intermediate, and low-affinity receptors. IL-2Ralpha and IL-2Rbeta, respectively, are markers for double-negative thymocytes and regulatory T-cells versus memory cells. gamma(c), which is shared by six cytokines, is mutated in patients with X-linked severe-combined immunodeficiency. We now cover an under-reviewed area-the regulation of genes encoding IL-2 and IL-2R components, with an effort to integrate/explain this knowledge.

SERRATE is a novel nuclear regulator in primary microRNA processing in Arabidopsis

The Arabidopsis gene SERRATE (SE) controls leaf development, meristem activity, inflorescence architecture and developmental phase transition. It has been suggested that SE, which encodes a C(2)H(2) zinc finger protein, may change gene expression via chromatin modification. Recently, SE has also been shown to regulate specific microRNAs (miRNAs), miR165/166, and thus control shoot meristem function and leaf polarity. However, it remains unclear whether and how SE modulates specific miRNA processing. Here we show that the se mutant exhibits some similar developmental abnormalities as the hyponastic leaves1 (hyl1) mutant. Since HYL1 is a nuclear double-stranded RNA-binding protein acting in the DICER-LIKE1 (DCL1) complex to regulate the first step of primary miRNA transcript (pri-miRNA) processing, we hypothesized that SE could play a previously unrecognized and general role in miRNA processing. Genetic analysis supports that SE and HYL1 act in the same pathway to regulate plant development. Consistently, SE is critical for the accumulation of multiple miRNAs and the trans-acting small interfering RNA (ta-siRNA), but is not required for sense post-transcriptional gene silencing. We further demonstrate that SE is localized in the nucleus and interacts physically with HYL1. Finally, we provide evidence that SE and HYL1 probably act with DCL1 in processing pri-miRNAs before HEN1 in miRNA biogenesis. In plants and animals, miRNAs are known to be processed in a stepwise manner from pri-miRNA. Our data strongly suggest that SE plays an important and general role in pri-miRNA processing, and it would be interesting to determine whether animal SE homologues may play similar roles in vivo.

Posttranscriptional regulation of Git1p, the glycerophosphoinositol/glycerophosphocholine transporter of Saccharomyces cerevisiae

Glycerophosphoinositol (GroPIns) and glycerophosphocholine (GroPCho) are the products of phospholipase-B mediated deacylation of phosphatidylinositol and phosphatidylcholine, respectively. GroPIns and GroPCho are transported across the Saccharomyces cerevisiae plasma membrane into the cell via the transporter encoded by GIT1. Previous studies have shown that GIT1 expression is regulated by inorganic phosphate (P(i)) availability through the transcription factors Pho2p and Pho4p. We now report that posttranscriptional mechanisms also regulate Git1p activity in response to P(i) availability. Mutations that inhibit endocytosis and vacuolar proteolysis inhibit Git1p degradation, indicating that Git1p downregulation involves internalization and subsequent degradation in the vacuole. Similar to the effect seen with P(i), provision of cells with high levels of the Git1p substrates, GroPIns and GroPCho, posttranscriptionally downregulates Git1p activity. Unlike P(i), high levels of GroPCho and GroPIns do not repress GIT1 promoter-driven reporter gene activity. These results indicate that Git1p transport activity is regulated at multiple levels by P(i) availability. In addition, the results indicate that the Git1p substrates (and alternate phosphate sources) GroPIns and GroPCho behave distinctly from P(i) in their ability to affect GIT1 expression.

Mak16p is required for the maturation of 25S and 5.8S rRNAs in the yeast Saccharomyces cerevisiae

The nucleolar Mak16p protein of Saccharomyces cerevisiae has been implicated in 60S ribosome biogenesis. To learn more about the role of Mak16p in this process, ribosomal RNA processing was examined in a mak16-1 temperature-sensitive yeast strain. Steady-state levels of the 25S and 5.8S mature rRNA species dropped dramatically over a 4 h period in the mak16-1 yeast after a shift to the non-permissive temperature, while 18S and 5S rRNA levels decreased only moderately. Ribosomal RNA processing (rRNA) analyses showed that the most prominent defect at the non-permissive temperature was a dramatic decrease in 27SB precursor RNA levels, with no significant increase in the levels of any precursor. These data indicate an essential role for Mak16p in the stability of the 27SB precursor rRNA. Association of Mak16p with the 66S preribosomal complex does not appear to be sufficient for its function, because the mutant Mak16-1p protein was detected in sucrose density gradient fractions corresponding to the 66S pre-RNP complex.

Rethinking the microprocessor

MicroRNAs (miRNAs) are tiny regulators of gene expression that are processed from longer primary transcripts. In this issue, Han et al. (2006) report some of the structural features of the primary transcript that ensure that the Drosha-DGCR8 enzyme complex liberates precisely the correct precursor sequence, enabling production of a fully functional miRNA.

The tRNase Z family of proteins: physiological functions, substrate specificity and structural properties

tRNase Z is the endoribonuclease that generates the mature 3'-end of tRNA molecules by removal of the 3'-trailer elements of precursor tRNAs. This enzyme has been characterized from representatives of all three domains of life (Bacteria, Archaea and Eukarya), as well as from mitochondria and chloroplasts. tRNase Z enzymes come in two forms: short versions (280-360 amino acids in length), present in all three kingdoms, and long versions (750-930 amino acids), present only in eukaryotes. The recently solved crystal structure of the bacterial tRNase Z provides the structural basis for the understanding of central functional elements. The substrate is recognized by an exosite that protrudes from the main protein body and consists of a metallo-beta-lactamase domain. Cleavage of the precursor tRNA occurs at the binuclear zinc site located in the other subunit of the functional homodimer. The first gene of the tRNase Z family was cloned in 2002. Since then a comprehensive set of data has been acquired concerning this new enzyme, including detailed functional studies on purified recombinant enzymes, mutagenesis studies and finally the determination of the crystal structure of three bacterial enzymes. This review summarizes the current knowledge about these exciting enzymes.

Structural basis for non-catalytic and catalytic activities of ribonuclease III

Ribonuclease III (RNase III) represents a highly conserved family of double-stranded (ds) RNA-specific endoribonucleases, exemplified by bacterial RNase III and eukaryotic Rnt1p, Drosha and Dicer. Bacterial RNase III, containing an endonuclease domain followed by a dsRNA-binding domain, is the most extensively studied member of the family. It can affect RNA structure and gene expression in either of two ways: as a processing enzyme that cleaves dsRNA or as a binding protein that binds but does not cleave dsRNA. The available biochemical and structural data support the existence of two distinct forms of the RNase III-dsRNA complex which reflect the dual activities of the protein. The information revealed by the structures of bacterial RNase III provides insight into the mechanism of dsRNA processing by all members of the family.

Probing genuine strong interactions and post-translational modifications in the heterogeneous yeast exosome protein complex

The characterization of heterogeneous multicomponent protein complexes, which goes beyond identification of protein subunits, is a challenging task. Here we describe and apply a comprehensive method that combines a mild affinity purification procedure with a multiplexed mass spectrometry approach for the in-depth characterization of the exosome complex from Saccharomyces cerevisiae expressed at physiologically relevant levels. The exosome is an ensemble of primarily 3' --> 5' exoribonucleases and plays a major role in RNA metabolism. The complex has been reported to consist of 11 proteins in molecular mass ranging from 20 to 120 kDa. By using native macromolecular mass spectrometry we measured accurate masses (around 400 kDa) of several (sub)exosome complexes. Combination of these data with proteolytic peptide LC tandem mass spectrometry using a linear ion trap coupled to a FT-ICR mass spectrometer and intact protein LC mass spectrometry provided us with the identity of the different exosome components and (sub)complexes, including the subunit stoichiometry. We hypothesize that the observed complexes provide information about strongly and weakly interacting exosome-associated proteins. In our analysis we also identified for the first time phosphorylation sites in seven different exosome subunits. The phosphorylation site in the Rrp4 subunit is fully conserved in the human homologue of Rrp4, which is the only previously reported phosphorylation site in any of the human exosome proteins. The described multiplexed mass spectrometry-based procedure is generic and thus applicable to many different types of cellular molecular machineries even if they are expressed at endogenous levels.

A Mutation in At-nMat1a, Which Encodes a Nuclear Gene Having High Similarity to Group II Intron Maturase, Causes Impaired Splicing of Mitochondrial NAD4 Transcript and Altered Carbon Metabolism in Arabidopsisthaliana

To elucidate the mechanism of cellulose synthesis, we isolated a mutant of Arabidopsis (changed sensitivity to cellulose synthesis inhibitors 1, css1) that showed changed sensitivity to cellulose biosynthesis inhibitor. The analysis of phenotypes indicated that the css1 mutation influenced various fundamental metabolic pathways including amino acid metabolism, triacylglycerol degradation and polysaccharide synthesis (cellulose and starch) during the early stage of plant growth. Unexpectedly, the map-based cloning of the gene responsible for the css1 mutation identified a protein (At-nMat1a) that was assumed to be a splicing factor of the mitochondrial group II intron. In accordance with this result, this mutant exhibited improper splicing of the mitochondrial NAD4 transcript. We noticed that the phenotypes of the css1 mutant are similar to the responses to anoxia that hinders mitochondrial aerobic respiration. It seems that the defect in the function of mitochondria influences various aspects of fundamental cellular metabolism including cellulose synthesis. Our results suggested that sucrose synthase (SuSy), an enzyme involved in the biosynthesis of cellulose, plays key roles in the connection between mitochondria and cellulose synthesis. The isolation of the css1 mutant also provides a useful resource in the study of post-transcriptional gene regulation in mitochondria.

Modifications in Thermus thermophilus 23 S ribosomal RNA are centered in regions of RNA-RNA contact

Ribosomal RNA from all organisms contains post-transcriptionally modified nucleotides whose function is far from clear. To gain insight into the molecular interactions of modified nucleotides, we investigated the modification status of Thermus thermophilus 5 S and 23 S ribosomal RNA by mass spectrometry and chemical derivatization/primer extension. A total of eleven modified nucleotides was found in 23 S rRNA, of which eight were singly methylated nucleotides and three were pseudouridines. These modified nucleotides were mapped into the published three-dimensional ribosome structure. Seven of the modified nucleotides located to domain IV, and four modified nucleotides located to domain V of the 23 S rRNA. All posttranscriptionally modified nucleotides map in the center of the ribosome, and none of them are in contact with ribosomal proteins. All except one of the modified nucleotides were found in secondary structure elements of the 23 S ribosomal RNA that contact either 16 S ribosomal RNA or transfer RNA, with five of these nucleotides physically involved in intermolecular RNA-RNA bridges. These findings strongly suggest that the post-transcriptional modifications play a role in modulating intermolecular RNA-RNA contacts, which is the first suggestion on a specific function of endogenous ribosomal RNA modifications.

Two substrates are better than one: dual specificities for Dnmt2 methyltransferases

Dnmt2 enzymes have been widely conserved during evolution and contain all of the signature motifs of DNA (cytosine-5)-methyltransferases; however, the DNA methyltransferase activity of these proteins is comparatively weak and their biochemical and functional properties remain enigmatic. Recent evidence now shows that Dnmt2 has a novel tRNA methyltransferase activity, raising the possibility that the biological roles of these proteins might be broader than previously thought. This finding has important implications for understanding the evolutionary relationships among these enzymes.

Arabidopsis UPF1 RNA helicase for nonsense-mediated mRNA decay is involved in seed size control and is essential for growth

UPF1 RNA helicase plays a central role in nonsense-mediated mRNA decay (NMD), which specifically recognizes aberrant mRNAs containing premature termination codons and targets them for degradation. Although NMD factors are highly conserved among eukaryotes, little is known about the role of NMD in plant growth and development. The lba1 mutant of Arabidopsis thaliana with a Gly(851)-->Glu missense mutation in AtUPF1 yielded seeds that were on average 22% longer in the long axis and 35% heavier than the wild-type Col seeds. Expression of the wild-type AtUPF1 in this mutant reduced the seeds to a normal size. During early stages of seed development, globular to torpedo stages of the embryos were contained within seed sacs that were larger in lba1 than in Col. Furthermore, the distance between seeds in siliques was greater in lba1 than in Col, suggesting that the lba1 mutation may affect ovule development. Self-pollinated atupf1-3(+/-) plants heterozygous for AtUPF1 disrupted by T-DNA insertion developed atupf1-3(-/-) seeds with a size and shape similar to those of Col seeds. However, the atupf1-3(-/-) seedlings stopped growing after radicle emergence from the seed coat, and this seedling lethality was rescued by expressing the wild-type AtUPF1. These results suggest that the lba1 mutation in AtUPF1 maternally affects seed development and that AtUPF1 is essential for seedling growth.

Murine Spam1 mRNA: involvement of AU-rich elements in the 3'UTR and antisense RNA in its tight post-transcriptional regulation in spermatids

Sperm adhesion molecule1 (SPAM1), the best characterized hyaluronidase gene, is abundantly expressed in the testis. We attempted to overexpress mouse Spam1 via transgenesis using either the endogenous promoter in a BAC or a heterologous Protamine1 promoter for a Spam1 cDNA transgene. Although transgene-copy numbers ranged from 2 to 15 and transgenic transcripts were expressed, there was a general failure of overexpression of the RNA and protein in the testis of all seven founders. Also, three transgenic lines showed a modest downregulation or co-suppression of the RNA for Spam1 and Hyal5, present on the BAC. We provide evidence for the potential involvement of two co-ordinating post-transcriptional regulatory processes in the failure of overexpression: abundant endogenous antisense RNA and adenosine-uridine (AU)-rich element-mediated regulation of RNA turnover. We demonstrate that AU-rich elements (AREs) in the 3'UTR of mRNAs, well-known to interact with trans-acting proteins to target the RNA for (in)stability, are present in Spam1 RNA and specifically bind to six testicular cytoplasmic proteins. These AU-binding proteins (AUBPs) were virtually absent from the kidney where transcripts are rare, and were shown to interact with the cytoskeleton, which modulates mRNA turnover. In addition to a role in the RNAi pathway, antisense RNA can also modulate ARE-mediated regulation of mRNA by hybridizing to the AREs and specifically silencing their function. This potentially links the two processes in the regulation of Spam1 expression. We hypothesize that testicular Spam1 RNA is regulated post-transcriptionally by cis-acting ARE(s) in the 3'UTR which recognize AUBPs and which are modulated by antisense transcripts.

The 3' untranslated region of a soybean cytosolic glutamine synthetase (GS1) affects transcript stability and protein accumulation in transgenic alfalfa

Higher plants assimilate nitrogen in the form of ammonia through the concerted activity of glutamine synthetase (GS) and glutamate synthase (GOGAT). The GS enzyme is either located in the cytoplasm (GS1) or in the chloroplast (GS2). Glutamine synthetase 1 is regulated in different plants at the transcriptional level and there are some reports of regulation at the level of protein stability. Here we present data that clearly establish that GS1 in plants is also regulated at the level of transcript turnover and at the translational level. Using a Glycine max (soybean) GS1 transgene, with and without its 3' untranslated region (UTR), driven by the constitutive CaMV 35S promoter in Medicago sativa (alfalfa) and Nicotiana tabacum (tobacco), we show that the 3' UTR plays a major role in both transcript turnover and translation repression in both the leaves and the nodules. Our data suggest that the 3' UTR mediated turnover of the transcript is regulated by a nitrogen metabolite or carbon/nitrogen ratios. We also show that the 3' UTR of the gene for the soybean GS1 confers post-transcriptional regulation on a reporter gene. Our dissection of post-transcriptional and translational levels of regulation of GS in plants shows that the situation in plants strongly resembles that in other organisms where GS is regulated at almost all levels. Multistep regulation of GS shows the high priority given by organisms to regulating and ensuring optimal control of nitrogen substrates and preventing overproduction of glutamine and drainage of the glutamate pool.