The nonsense-mediated mRNA decay (NMD) pathway is a well-known eukaryotic surveillance mechanism that eliminates aberrant mRNAs that contain a premature termination codon (PTC). The UP-Frameshift ...(UPF) proteins, UPF1, UPF2, and UPF3, are essential for normal NMD function. Several NMD substrates have been identified, but detailed information on NMD substrates is lacking. Here, we noticed that, in Arabidopsis, most of the mRNA-like nonprotein-coding RNAs (ncRNAs) have the features of an NMD substrate. We examined the expression profiles of 2 Arabidopsis mutants, upf1-1 and upf3-1, using a whole-genome tiling array. The results showed that expression of not only protein-coding transcripts but also many mRNA-like ncRNAs (mlncRNAs), including natural antisense transcript RNAs (nat-RNAs) transcribed from the opposite strands of the coding strands, were up-regulated in both mutants. The percentage of the up-regulated mlncRNAs to all expressed mlncRNAs was much higher than that of the up-regulated protein-coding transcripts to all expressed protein- coding transcripts. This finding demonstrates that one of the most important roles of NMD is the genome-wide suppression of the aberrant mlncRNAs including nat-RNAs.
The physical interaction of the human growth factor receptor‐bound protein 14 (hGrb14) and the insulin receptor (IR) represses insulin signaling. With respect to the recruiting mechanism of hGrb14 to ...IR respond to insulin stimulus, our previous reports have suggested that phosphorylation of Ser358, Ser362, and Ser366 in hGrb14 by glycogen synthase kinase‐3 repressed hGrb14–IR complex formation. In this study, we investigated phosphatase‐mediated dephosphorylation of the hGrb14 phosphoserine residues. An in vitro phosphatase assay with hGrb14‐derived synthetic phosphopeptides suggested that protein phosphatase 1 (PP1) is involved in the dephosphorylation of Ser358 and Ser362. Furthermore, coimmunoprecipitation experiments suggested that insulin‐induced hGrb14–IR complex formation was repressed by the substitution of Ser358 or Ser362 with glutamic acid. These findings suggested that phosphate groups on Ser358 and Ser362 in hGrb14 are dephosphorylated by PP1, and the dephosphorylation facilitates hGrb14–IR complex formation.
The physical interaction of human growth factor receptor‐bound protein 14 (hGrb14) with intracellular domain of insulin receptor (IR) suppresses insulin signaling. The present study demonstrated that the phosphate groups on hGrb14 Ser358 and Ser362 can be dephosphorylated by protein phosphatase 1 (PP1), and absence of negative charges on the serine residues facilitated forming of hGrb14‐IR complex. These results suggested that hGrb14‐IR complex formation could be modulated by phosphorylation status of the serine residues.
Large-scale cDNA sequencing projects and tiling array studies have revealed the presence of many unannotated genes. For protein coding genes, small coding sequences may not be identified by gene ...finders because of the conservative nature of prediction algorithms. In this study, we identified small open reading frames (sORFs) with high coding potential by a simple gene finding method (Coding Index, CI) based on the nucleotide composition bias found in most coding sequences. Applying this method to 18 Arabidopsis thaliana and 84 yeast sORF genes with evidence of expression at the protein level gives 100% accurate prediction. In the A. thaliana genome, we identified 7159 sORFs that are likely coding sequences (coding sORFs) with the CI measure at the 1% false-positive rate. To determine if these coding sORFs are parts of functional genes, we evaluated each coding sORF for evidence of transcription or evolutionary conservation. At the 5% false-positive rate, we found that 2996 coding sORFs are likely expressed in at least one experimental condition of the A. thaliana tiling array data. In addition, the evolutionary conservation of each A. thaliana sORF was examined within A. thaliana or between A. thaliana and five plants with complete or partial genome sequences. In 3997 coding sORFs with readily identifiable homologous sequences, 2376 are subject to purifying selection at the 1% false-positive rate. After eliminating coding sORFs with similarity to known transposable elements and those that are likely missing exons of known genes, the remaining 3241 coding sORFs with either evidence of transcription or purifying selection likely belong to novel coding genes in the A. thaliana genome.
BACKGROUND: Iron (Fe) is essential micronutrient for plants and its deficiency as well as toxicity is a serious agricultural problem. The mechanisms of Fe deficiency are reasonably understood, ...however our knowledge about plants response to excess Fe is limited. Moreover, the regulation of small open reading frames (sORFs) in response to abiotic stress has not been reported in rice. Understanding the regulation of rice transcriptome in response to Fe deficiency and excess could provide bases for developing strategies to breed plants tolerant to Fe deficiency as well as excess Fe. RESULTS: We used a novel rice 110 K microarray harbouring ~48,620 sORFs to understand the transcriptomic changes that occur in response to Fe deficiency and excess. In roots, 36 genes were upregulated by excess Fe, of which three were sORFs. In contrast, 1509 genes were upregulated by Fe deficiency, of which 90 (6%) were sORFs. Co-expression analysis revealed that the expression of some sORFs was positively correlated with the genes upregulated by Fe deficiency. In shoots, 50 (19%) of the genes upregulated by Fe deficiency and 1076 out of 2480 (43%) genes upregulated by excess Fe were sORFs. These results suggest that excess Fe may significantly alter metabolism, particularly in shoots. CONCLUSION: These data not only reveal the genes regulated by excess Fe, but also suggest that sORFs might play an important role in the response of plants to Fe deficiency and excess.
Among human T cell leukemia virus type 1 (HTLV-1)-infected individuals, there is an association between HTLV-1 tax subgroups (subgroup-A or subgroup-B) and the risk of HAM/TSP in the Japanese ...population. To investigate the role of HTLV-1 subgroups in viral pathogenesis, we studied the functional difference in the subgroup-specific viral transcriptional regulators Tax and HBZ using microarray analysis, reporter gene assays, and evaluation of viral-host protein-protein interaction.
(1) Transcriptional changes in Jurkat Tet-On human T-cells that express each subgroup of Tax or HBZ protein under the control of an inducible promoter revealed different target gene profiles; (2) the number of differentially regulated genes induced by HBZ was 2-3 times higher than that induced by Tax; (3) Tax and HBZ induced the expression of different classes of non-coding RNAs (ncRNAs); (4) the chemokine CXCL10, which has been proposed as a prognostic biomarker for HAM/TSP, was more efficiently induced by subgroup-A Tax (Tax-A) than subgroup-B Tax (Tax-B), in vitro as well as in unmanipulated (ex vivo) PBMCs obtained from HAM/TSP patients; (5) reporter gene assays indicated that although transient Tax expression in an HTLV-1-negative human T-cell line activated the CXCL10 gene promoter through the NF-κB pathway, there was no difference in the ability of each subgroup of Tax to activate the CXCL10 promoter; however, (6) chromatin immunoprecipitation assays showed that the ternary complex containing Tax-A is more efficiently recruited onto the promoter region of CXCL10, which contains two NF-κB binding sites, than that containing Tax-B.
Our results indicate that different HTLV-1 subgroups are characterized by different patterns of host gene expression. Differential expression of pathogenesis-related genes by subgroup-specific Tax or HBZ may be associated with the onset of HAM/TSP.
Porcine reproductive and respiratory syndrome viruses (PRRSV) are divided into North American and European types, which show about 40% difference in their amino acid sequences. The divergence time of ...these two types has been estimated to be about 1980 from epidemiological data. This suggested that PRRSV have evolved at a higher evolutionary rate (order of 10(-2)/site/year) compared with other RNA viruses of 10(-3) to 10(-5)/site/year. Here, to test the evolutionary history of PRRSV speculated by the epidemiological background, we estimated the divergence time and evolutionary rate of PRRSV with molecular evolutionary analysis. Estimated divergence time (1972-1988) corresponded well to that estimated by the epidemiological data, and the evolutionary rate (4.71-9.8) x 10(-2) of PRRSV was indeed the highest among RNA viruses so far reported. Furthermore, we inferred important sites for the adaptation in order to examine how PRRSV have adapted to swine since they emerged. The adaptive sites were located not only in the epitopes related to immunity but also in the transmembrane regions including a signal peptide. In particular, the adaptive sites in the transmembrane regions were considered to affect compatibility to the host cell membrane. We conclude that PRRSV were transmitted from another host species to swine in about 1980 and have adapted to swine by altering the transmembrane regions.
Since plants cannot move to avoid stress, they have sophisticated acclimation mechanisms against a variety of abiotic stresses. The phytohormone abscisic acid (ABA) plays essential roles in abiotic ...stress tolerances in land plants. Therefore, it is interesting to address the evolutionary origins of ABA metabolism and its signaling pathways in land plants. Here, we focused on 48 ABA-related
Arabidopsis thaliana
genes with 11 protein functions, and generated 11 orthologous clusters of ABA-related genes from
A. thaliana
,
Arabidopsis lyrata
,
Populus trichocarpa
,
Oryza sativa
,
Selaginella moellendorffii
, and
Physcomitrella patens
. Phylogenetic analyses suggested that the common ancestor of these six species possessed most of the key protein functions of ABA-related genes. In two species (
A. thaliana
and
O. sativa
), duplicate genes related to ABA signaling pathways contribute to the expression variation in different organs or stress responses. In particular, there is significant expansion of gene families related to ABA in evolutionary periods associated with morphological divergence. Taken together, these results suggest that expansion of the gene families related to ABA signaling pathways may have contributed to the sophisticated stress tolerance mechanisms of higher land plants.
Excess soluble iron in acidic soil is an unfavorable environment that can reduce rice production. To better understand the tolerance mechanism and identify genetic loci associated with iron toxicity ...(FT) tolerance in a highly diverse indica Thai rice population, a genome-wide association study (GWAS) was performed using genotyping by sequencing and six phenotypic data (leaf bronzing score (LBS), chlorophyll content, shoot height, root length, shoot biomass, and root dry weight) under both normal and FT conditions. LBS showed a high negative correlation with the ratio of chlorophyll content and shoot biomass, indicating the FT-tolerant accessions can regulate cellular homeostasis when encountering stress. Sixteen significant single nucleotide polymorphisms (SNPs) were identified by association mapping. Validation of candidate SNP using other FT-tolerant accessions revealed that SNP:2_21262165 might be associated with tolerance to FT; therefore, it could be used for SNP marker development. Among the candidate genes controlling FT tolerance,
encodes an innate immune responsive protein that links to cellular redox homeostasis via interacting with abiotic stress-responsive Hsp90. Future research may apply the knowledge obtained from this study in the molecular breeding program to develop FT-tolerant rice varieties.
Selective ubiquitination of proteins is directed by diverse families of ubiquitin-protein ligases (or E3s) in plants. One important type uses Cullin-3 as a scaffold to assemble multisubunit E3 ...complexes containing one of a multitude of bric-a-brac/tramtrack/broad complex (BTB) proteins that function as substrate recognition factors. We previously described the 80-member BTB gene superfamily in Arabidopsis thaliana. Here, we describe the complete BTB superfamily in rice (Oryza sativa spp japonica cv Nipponbare) that contains 149 BTB domain--encoding genes and 43 putative pseudogenes. Amino acid sequence comparisons of the rice and Arabidopsis superfamilies revealed a near equal repertoire of putative substrate recognition module types. However, phylogenetic comparisons detected numerous gene duplication and/or loss events since the rice and Arabidopsis BTB lineages split, suggesting possible functional specialization within individual BTB families. In particular, a major expansion and diversification of a subset of BTB proteins containing Meprin and TRAF homology (MATH) substrate recognition sites was evident in rice and other monocots that likely occurred following the monocot/dicot split. The MATH domain of a subset appears to have evolved significantly faster than those in a smaller core subset that predates flowering plants, suggesting that the substrate recognition module in many monocot MATH-BTB E3s are diversifying to ubiquitinate a set of substrates that are themselves rapidly changing. Intriguing possibilities include pathogen proteins attempting to avoid inactivation by the monocot host.
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