A region in the 3' UTR of MnSOD RNA enhances translation of a heterologous RNA

Application of DNA microarray technology to gerontological studies

Gene expression patterns change dramatically in aging and age-related events. The DNA microarray is now recognized as a useful device in molecular biology and widely used to identify the molecular mechanisms of aging and the biological effects of drugs for therapeutic purpose in age-related diseases. Recently, numerous technological advantages have led to the evolution of DNA microarrays and microarray-based techniques, revealing the genomic modification and all transcriptional activity. Here, we show the step-by-step methods currently used in our lab to handling the oligonucleotide microarray and miRNA microarray. Moreover, we introduce the protocols of ribonucleoprotein [RNP] immunoprecipitation followed by microarray analysis (RIP-chip) which reveal the target mRNA of age-related RNA-binding proteins.

Molecular strategies to engineer transgenic rice seed compartments for large-scale production of plant-made pharmaceuticals

The use of plants as bioreactors for the large-scale production of recombinant proteins has emerged as an exciting area of research. The current shortages in protein therapeutics due to the capacity and economic bottlenecks faced with modern protein production platforms (microbial, yeast, mammalian) has driven considerable attention towards molecular pharming. Utilizing plants for the large-scale production of recombinant proteins is estimated to be 2-10% the cost of microbial platforms, and up to 1,000-fold more cost effective than mammalian platforms (Twyman et al. Trends Biotechnol 21:570-578, 2003; Sharma and Sharma, Biotechnol Adv 27:811-832, 2009). In order to achieve an economically feasible plant production host, protein expression and accumulation must be optimized. The seed, and more specifically the rice seed has emerged as an ideal candidate in molecular pharming due to its low protease activity, low water content, stable protein storage environment, relatively high biomass, and the molecular tools available for manipulation (Lau and Sun, Biotechnol Adv 27:1015-1022, 2009).

Clair DK. Regulation of superoxide dismutase genes: implications in disease

Numerous short-lived and highly reactive oxygen species (ROS) such as superoxide (O2(.-)), hydroxyl radical, and hydrogen peroxide are continuously generated in vivo. Depending upon concentration, location, and intracellular conditions, ROS can cause toxicity or act as signaling molecules. The cellular levels of ROS are controlled by antioxidant enzymes and small-molecule antioxidants. As major antioxidant enzymes, superoxide dismutases (SODs), including copper-zinc superoxide dismutase (Cu/ZnSOD), manganese superoxide dismutase, and extracellular superoxide dismutase, play a crucial role in scavenging O2(.-). This review focuses on the regulation of the sod genes coding for these enzymes, with an emphasis on the human genes. Current knowledge about sod structure and regulation is summarized and depicted as diagrams. Studies to date on genes coding for Cu/ZnSOD (sod1) are mostly focused on alterations in the coding region and their associations with amyotrophic lateral sclerosis. Evaluation of nucleotide sequences reveals that regulatory elements of the sod2 gene reside in both the noncoding and the coding region. Changes associated with sod2 lead to alterations in expression levels as well as protein function. We also discuss the structural basis for the changes in SOD expression associated with pathological conditions and where more work is needed to establish the relationship between SODs and diseases.

The 3'-untranslated region of rice glutelin GluB-1 affects accumulation of heterologous protein in transgenic rice

We compared the effect of the rice storage protein glutelin B-1 (GluB-1) terminator with the nopaline synthase (Nos) terminator on the accumulation of the modified house dust mite allergen mDer f 2 driven by the maize ubiquitin promoter in transgenic rice. Accumulation of mDer f 2 in transgenic seed and leaf using the GluB-1 terminator was greater than when using the Nos terminator construct. The mDer f 2 mRNA containing the GluB-1 3'UTR was processed and polyadenylated at the same sites as the native GluB-1 mRNA in the seeds but diverged in leaves of the transgenic plants. In contrast, the poly(A) sites of mDer f 2 containing Nos 3'UTR were more divergent in both seed and leaf. These results suggest that GluB-1 3'UTR functions as a faithful terminator and that termination at the specific sites may play an important role in mRNA stability and/or translatability, resulting in higher levels of protein accumulation.

The transcriptional landscape of the yeast genome defined by RNA sequencing

The identification of untranslated regions, introns, and coding regions within an organism remains challenging. We developed a quantitative sequencing-based method called RNA-Seq for mapping transcribed regions, in which complementary DNA fragments are subjected to high-throughput sequencing and mapped to the genome. We applied RNA-Seq to generate a high-resolution transcriptome map of the yeast genome and demonstrated that most (74.5%) of the nonrepetitive sequence of the yeast genome is transcribed. We confirmed many known and predicted introns and demonstrated that others are not actively used. Alternative initiation codons and upstream open reading frames also were identified for many yeast genes. We also found unexpected 3'-end heterogeneity and the presence of many overlapping genes. These results indicate that the yeast transcriptome is more complex than previously appreciated.

Plant SET domain-containing proteins: structure, function and regulation

Modification of the histone proteins that form the core around which chromosomal DNA is looped has profound epigenetic effects on the accessibility of the associated DNA for transcription, replication and repair. The SET domain is now recognized as generally having methyltransferase activity targeted to specific lysine residues of histone H3 or H4. There is considerable sequence conservation within the SET domain and within its flanking regions. Previous reviews have shown that SET proteins from Arabidopsis and maize fall into five classes according to their sequence and domain architectures. These classes generally reflect specificity for a particular substrate. SET proteins from rice were found to fall into similar groupings, strengthening the merit of the approach taken. Two additional classes, VI and VII, were established that include proteins with truncated/interrupted SET domains. Diverse mechanisms are involved in shaping the function and regulation of SET proteins. These include protein-protein interactions through both intra- and inter-molecular associations that are important in plant developmental processes, such as flowering time control and embryogenesis. Alternative splicing that can result in the generation of two to several different transcript isoforms is now known to be widespread. An exciting and tantalizing question is whether, or how, this alternative splicing affects gene function. For example, it is conceivable that one isoform may debilitate methyltransferase function whereas the other may enhance it, providing an opportunity for differential regulation. The review concludes with the speculation that modulation of SET protein function is mediated by antisense or sense-antisense RNA.

An exploration of 3'-end processing signals and their tissue distribution in Oryza sativa

The 3' untranslated regions deeply affect many properties of eukaryotic mRNA. In plants, the polyadenine control signals contained in these regions seem to be more variable than of mammals. Three cDNA libraries derived from the leaf, endosperm and stem tissues of rice were sequenced from the 3'-end. Of the 9911 transcripts analyzed, 5723 unique transcripts were identified from the leaf sequences, 2934 from the endosperm and 1254 from the stem. The information entropy and two statistical methods were used to compile a list of rice poly(A) control signals. Based on their distribution, these signals can be roughly grouped into far-upstream element (FUE), near-upstream element (NUE), T-rich region (TRE) and downstream element (DE). The distribution of rice conserved regions is similar to the previous model from Arabidopsis and yeast, with a few differences in word constructions. Interestingly, we also found the word distributions were diverse in the cleavage site of downstream sequences of different rice tissues. The signal bias in downstream sequences may lead mRNA to be differently cleaved in different rice tissues.

Computational analysis of 3'-ends of ESTs shows four classes of alternative polyadenylation in human, mouse, and rat

Alternative initiation, splicing, and polyadenylation are key mechanisms used by many organisms to generate diversity among mature mRNA transcripts originating from the same transcription unit. While previous computational analyses of alternative polyadenylation have focused on polyadenylation activities within or downstream of the normal 3'-terminal exons, we present the results of the first genome-wide analysis of patterns of alternative polyadenylation in the human, mouse, and rat genomes occurring over the entire transcribed regions of mRNAs using 3'-ESTs with poly(A) tails aligned to genomic sequences. Four distinct classes of patterns of alternative polyadenylation result from this analysis: tandem poly(A) sites, composite exons, hidden exons, and truncated exons. We estimate that at least 49% (human), 31% (mouse), and 28% (rat) of polyadenylated transcription units have alternative polyadenylation. A portion of these alternative polyadenylation events result in new protein isoforms.

Epigenetic regulation of the binding activity of translation inhibitory proteins that bind the 3' untranslated region of beta-F1-ATPase mRNA by adenine nucleotides and the redox state

Here, we describe the binding affinities and the regulation of the binding activities of the fetal liver proteins that interact with the 3' untranslated region of beta-F1-ATPase mRNA (beta-mRNA). These proteins (3'beta FBPs), which are involved in the repression of beta-mRNA translation during fetal development, have poly(A)-binding activity. Reducing agents do not affect the RNA-binding activity of 3'beta FBPs. In contrast, oxidizing and alkylating reagents abolished the binding activity of 3'beta FBPs to its target RNA element, an effect that is partially prevented by the presence of reducing agents. Interestingly, the availability of adenine nucleotides regulates in a concentration-dependent manner the binding activities of 3'beta FBPs. The results suggest that epigenetic changes that occur at the time of birth affecting both the redox and energy state of the liver play a relevant role in the regulation of the binding activities of 3'beta FBPs and therefore in the translation of beta-mRNA.

Analysis of the transcriptional complexity of Arabidopsis thaliana by massively parallel signature sequencing

Large-scale sequencing of short mRNA-derived tags can establish the qualitative and quantitative characteristics of a complex transcriptome. We sequenced 12,304,362 tags from five diverse libraries of Arabidopsis thaliana using massively parallel signature sequencing (MPSS). A total of 48,572 distinct signatures, each representing a different transcript, were expressed at significant levels. These signatures were compared to the annotation of the A. thaliana genomic sequence; in the five libraries, this comparison yielded between 17,353 and 18,361 genes with sense expression, and between 5,487 and 8,729 genes with antisense expression. An additional 6,691 MPSS signatures mapped to unannotated regions of the genome. Expression was demonstrated for 1,168 genes for which expression data were previously unknown. Alternative polyadenylation was observed for more than 25% of A. thaliana genes transcribed in these libraries. The MPSS expression data suggest that the A. thaliana transcriptome is complex and contains many as-yet uncharacterized variants of normal coding transcripts.

Regulation of the human high affinity IgE receptor beta-chain gene expression via an intronic element

The high affinity IgE receptor, FcepsilonRI, is a key regulatory molecule in the allergic reaction. By screening for cis-acting elements over the entire region of the human FcepsilonRI beta-chain gene, a sequence located in the fourth intron was revealed to serve as a repressor element. This element was recognized by a transcription factor, myeloid zinc finger protein 1 (MZF-1). Introduction of MZF-1 antisense inhibited the suppressive effect of the element on the beta-chain promoter and increased the mRNA for the beta-chain in KU812 cells, indicating that MZF-1 repressed human FcepsilonRI beta-chain gene expression via the element in the fourth intron. Furthermore, it was suggested that a cofactor binding with MZF-1, whose expression level was different among the cell types, was required for transcriptional repression by MZF-1.

Use of transcriptome data to unravel the fine structure of genes involved in sepsis

The sequence of the human genome is providing researchers with the scaffold upon which genes are built. The definition of the boundaries of the genes themselves and of their complex architecture requires a mapping of the transcriptome to the genome. A methodology was developed for generating a detailed transcriptome map and for reconstituting transcripts by using the genome as a template. As a demonstration of the potential of this method, the structure of the human Toll-like receptor (TLR) genes was reevaluated. For all TLR genes for which a genomic sequence was available (i.e., all except TLR10), novel features of the gene structure were discovered. These features include multiple alternative polyadenylation sites, additional exons or splice variants, and overlaps with other genes. These findings have implications for the analysis of TLR gene expression and for the diversity of the proteins encoded by these genes.

Poly(A)-binding protein positively affects YB-1 mRNA translation through specific interaction with YB-1 mRNA

The major protein of cytoplasmic mRNPs from rabbit reticulocytes, YB-1, is a member of an ancient family of proteins containing a common structural feature, cold-shock domain. In eukaryotes, this family is represented by multifunctional mRNA/Y-box DNA-binding proteins that control gene expression at different stages. To address possible post-transcriptional regulation of YB-1 gene expression, we examined effects of exogenous 5'- and 3'-untranslatable region-containing fragments of YB-1 mRNA on its translation and stability in a cell-free system. The addition of the 3' mRNA fragment as well as its subfragment I shut off protein synthesis at the initiation stage without affecting mRNA stability. UV cross-linking revealed four proteins (69, 50, 46, and 44 kDa) that specifically interacted with the 3' mRNA fragment; the inhibitory subfragment I bound two of them, 69- and 50-kDa proteins. We have identified these proteins as PABP (poly(A)-binding protein) (69 kDa) and YB-1 (50 kDa) and demonstrated that titrating out of PABP by poly(A) strongly and specifically inhibits YB-1 mRNA cap(+)poly(A)(-) translation in a cell-free system. Thus, PABP is capable of positively affecting YB-1 mRNA translation in a poly(A) tail-independent manner.

PKA-dependent binding of mRNA to the mitochondrial AKAP121 protein

Protein kinase A (PKA) anchoring proteins (AKAPs) tether PKA to various subcellular locations. AKAP121, which tethers PKAII to the outer mitochondrial membrane, includes a K homology (KH) RNA-binding motif. Purified AKAP121 KH domain binds the 3' untranslated regions (3'UTRs) of transcripts encoding the Fo-f subunit of mitochondrial ATP synthase and manganese superoxide dismutase (MnSOD). Binding requires a structural motif in the 3'UTR and is stimulated by PKA phosphorylation of the domain or a mutation that mimics this phosphorylation. AKAP121 expressed in HeLa cells promotes the translocation of MnSOD mRNA from cytosol to mitochondria and an increase in mitochondrial MnSOD. Both reactions are stimulated by cAMP. Thus, by focusing translation at the mitochondrial membrane, AKAP121 may facilitate import of mitochondrial proteins in response to cAMP stimulation.

Antioxidant enzyme expression in health and disease: effects of exercise and hypertension

Antioxidant enzymes (superoxide dismutases, catalase and glutathione peroxidase) are components of an organism's mechanisms for combating oxidative stress which is generated in normal metabolism and which may also be a reaction in response to external stimuli. This review identifies the general significance of antioxidant enzymes in health and disease, and some of the diseases that are now believed to have oxidative stress as a component. A discussion is then presented of the molecular mechanisms by which antioxidant enzyme expression is controlled at the transcriptional and post-transcriptional levels. The final sections of the review highlight the effects of exercise and hypertension on antioxidant enzyme expression in a number of different tissues, and the possibilities for future studies in these areas are discussed.

Superoxide dismutase multigene family: a comparison of the CuZn-SOD (SOD1), Mn-SOD (SOD2), and EC-SOD (SOD3) gene structures, evolution, and expression

Superoxide dismutases are an ubiquitous family of enzymes that function to efficiently catalyze the dismutation of superoxide anions. Three unique and highly compartmentalized mammalian superoxide dismutases have been biochemically and molecularly characterized to date. SOD1, or CuZn-SOD (EC 1.15.1.1), was the first enzyme to be characterized and is a copper and zinc-containing homodimer that is found almost exclusively in intracellular cytoplasmic spaces. SOD2, or Mn-SOD (EC 1.15.1.1), exists as a tetramer and is initially synthesized containing a leader peptide, which targets this manganese-containing enzyme exclusively to the mitochondrial spaces. SOD3, or EC-SOD (EC 1.15.1.1), is the most recently characterized SOD, exists as a copper and zinc-containing tetramer, and is synthesized containing a signal peptide that directs this enzyme exclusively to extracellular spaces. What role(s) these SODs play in both normal and disease states is only slowly beginning to be understood. A molecular understanding of each of these genes has proven useful toward the deciphering of their biological roles. For example, a variety of single amino acid mutations in SOD1 have been linked to familial amyotrophic lateral sclerosis. Knocking out the SOD2 gene in mice results in a lethal cardiomyopathy. A single amino acid mutation in human SOD3 is associated with 10 to 30-fold increases in serum SOD3 levels. As more information is obtained, further insights will be gained.

Long-range heterogeneity at the 3' ends of human mRNAs

The publication of a draft of the human genome and of large collections of transcribed sequences has made it possible to study the complex relationship between the transcriptome and the genome. In the work presented here, we have focused on mapping mRNA 3' ends onto the genome by use of the raw data generated by the expressed sequence tag (EST) sequencing projects. We find that at least half of the human genes encode multiple transcripts whose polyadenylation is driven by multiple signals. The corresponding transcript 3' ends are spread over distances in the kilobase range. This finding has profound implications for our understanding of gene expression regulation and of the diversity of human transcripts, for the design of cDNA microarray probes, and for the interpretation of gene expression profiling experiments.

Different regulatory mechanisms modulate the expression of a dinoflagellate iron-superoxide dismutase

Regulation of antioxidant enzymes is critical to control the levels of reactive oxygen species in cell compartments highly susceptible to oxidative stress. In this work, we studied the regulation of a chloroplastic iron superoxide dismutase (Fe-SOD) from Lingulodinium polyedrum (formerly Gonyaulax polyedra) under different physiological conditions. A cDNA-encoding Fe-SOD was isolated from this dinoflagellate, showing high sequence similarity to cyanobacterial, algal, and plant Fe-SODs. Under standard growth conditions, on a 12:12-h light-dark cycle, Lingulodinium polyedrum Fe-SOD exhibited a daily rhythm of activity and cellular abundance with the maximum occurring during the middle of the light phase. Northern analyses showed that this rhythmicity is not related to changes in Fe-SOD mRNA levels, indicative of translational regulation. By contrast, conditions of metal-induced oxidative stress resulted in higher levels of Fe-SOD transcripts, suggesting that transcriptional control is responsible for increased protein and activity levels. Daily (circadian) and metal-induced up-regulation of Fe-SOD expression in L. polyedrum are thus mediated by different regulatory pathways, allowing biochemically distinct changes appropriate to oxidative challenges.