Arabidopsis thaliana nucleosidase mutants provide new insights into nucleoside degradation

A central step in nucleoside and nucleobase salvage pathways is the hydrolysis of nucleosides to their respective nucleobases. In plants this is solely accomplished by nucleosidases (EC 3.2.2.x). To elucidate the importance of nucleosidases for nucleoside degradation, general metabolism, and plant growth, thorough phenotypic and biochemical analyses were performed using Arabidopsis thaliana T-DNA insertion mutants lacking expression of the previously identified genes annotated as uridine ribohydrolases (URH1 and URH2). Comprehensive functional analyses of single and double mutants demonstrated that both isoforms are unimportant for seedling establishment and plant growth, while one participates in uridine degradation. Rather unexpectedly, nucleoside and nucleotide profiling and nucleosidase activity screening of soluble crude extracts revealed a deficiency of xanthosine and inosine hydrolysis in the single mutants, with substantial accumulation of xanthosine in one of them. Mixing of the two mutant extracts, and by in vitro activity reconstitution using a mixture of recombinant URH1 and URH2 proteins, both restored activity, thus providing biochemical evidence that at least these two isoforms are needed for inosine and xanthosine hydrolysis. This mutant study demonstrates the utility of in vivo systems for the examination of metabolic activities, with the discovery of the new substrate xanthosine and elucidation of a mechanism for expanding the nucleosidase substrate spectrum.     

拟南芥基因组中新的microRNA预测及分析

MicroRNA（miRNA）是一类存在于动植物体内、长度为21～25nt的内源性小RNA,对生物体的转录后基因调控起着关键作用,但一些低丰度的miRNA和组织特异性miRNA往往很难发现。为了系统识别拟南芥基因组中新的非同源miRNA,首先基于已报道的拟南芥miRNA的特征,从全基因组范围中筛选出453条可能的miRNA前体;其次,为了进一步对上述miRNA前体进行筛选,利用人的miRNA前体数据构建了支持向量机模型GenomicSVM,该模型对人测试集的敏感性和特异性分别为86.3％和98．1％（30个人miRNA前体和1000个阴性miRNA前体）,对拟南芥测试集的正确率为93．6％（78个miRNA前体）;最后,利用GenomicSVM预测上述453条miRNA前体序列,得到了37条候选的新的拟南芥miRNA前体,为进一步的miRNA实验发现研究提供了指导。     

Global profiling of miRNAs and the hairpin precursors: insights into miRNA processing and novel miRNA discovery

MicroRNAs (miRNAs) constitute an important class of small regulatory RNAs that are derived from distinct hairpin precursors (pre-miRNAs). In contrast to mature miRNAs, which have been characterized in numerous genome-wide studies of different organisms, research on global profiling of pre-miRNAs is limited. Here, using massive parallel sequencing, we have performed global characterization of both mouse mature and precursor miRNAs. In total, 87 369 704 and 252 003 sequencing reads derived from 887 mature and 281 precursor miRNAs were obtained, respectively. Our analysis revealed new aspects of miRNA/pre-miRNA processing and modification, including eight Ago2-cleaved pre-miRNAs, eight new instances of miRNA editing and exclusively 5′ tailed mirtrons. Furthermore, based on the sequences of both mature and precursor miRNAs, we developed a miRNA discovery pipeline, miRGrep, which does not rely on the availability of genome reference sequences. In addition to 239 known mouse pre-miRNAs, miRGrep predicted 41 novel ones with high confidence. Similar as known ones, the mature miRNAs derived from most of these novel loci showed both reduced abundance following Dicer knockdown and the binding with Argonaute2. Evaluation on data sets obtained from Caenorhabditis elegans and Caenorhabditis sp.11 demonstrated that miRGrep could be widely used for miRNA discovery in metazoans, especially in those without genome reference sequences.     

Molecular Phenotyping by Proteomic Pattern Analysis in Arabidopsis thaliana

We are conducting a large scale functional analysis of plant genes utilizing the promoter trap lines and proteomic analyses as a part of the Crop functional genomics research program of Korea. Here, I describe the progresses we have made during last 2.5 years and a future plan.     

Further insights into the isoenzyme composition and activity of glutamate dehydrogenase in Arabidopsis thaliana

Following the discovery that in Arabidopsis, a third isoenzyme of NADH-dependent glutamate dehydrogenase (GDH) is expressed in the mitochondria of the root companion cells, we have re-examined the GDH isoenzyme composition. By analyzing the NADH-GDH isoenzyme composition of single, double and triple mutants deficient in the expression of the three genes encoding the enzyme, we have found that the α, β and γ polypeptides that comprise the enzyme can be assembled into a complex combination of heterohexamers in roots. Moreover, we observed that when one or two of the three root isoenzymes were missing from the mutants, the remaining isoenzymes compensated for this deficiency. The significance of such complexity is discussed in relation to the metabolic and signaling function of the NADH-GDH enzyme. Although it has been shown that a fourth gene encoding a NADPH-dependent enzyme is present in Arabidopsis, we were not able to detect corresponding enzyme activity, even in the triple mutant totally lacking NADH-GDH activity.     

Novel insights into cadherin processing by subtilisin-like convertases

Proprotein convertases (PCs) are known to activate many important molecules and their overexpression plays a significant role in tumor progression. Only little is known about the involvement of PCs in the processing of cadherin adhesion molecules, which are potent tumor suppressors. Here we show in a baculovirus overexpression system that the desmosomal cadherins Dsg1 and Dsg3 are substrates for the PC furin. Accordingly, inhibition of PCs in differentiating mouse keratinocytes by alpha 1-anti-trypsin Portland (alpha 1-PDX) negatively interfered with pro-epithelial (proE)-cadherin processing, but unexpectedly also resulted in a dramatic reduction of E-cadherin, Dsg1 and Dsg3 protein and Dsg1 mRNA. Because loss of intercellular adhesion is a rate-limiting step in the transition from benign to malignant tumors, these results have significant implications for the use of PC inhibitors as possible therapeutic tools.     

Dissecting the interactions of SERRATE with RNA and DICER-LIKE 1 in Arabidopsis microRNA precursor processing

Efficient and precise microRNA (miRNA) biogenesis in Arabidopsis is mediated by the RNaseIII-family enzyme DICER-LIKE 1 (DCL1), double-stranded RNA-binding protein HYPONASTIC LEAVES 1 and the zinc-finger (ZnF) domain-containing protein SERRATE (SE). In the present study, we examined primary miRNA precursor (pri-miRNA) processing by highly purified recombinant DCL1 and SE proteins and found that SE is integral to pri-miRNA processing by DCL1. SE stimulates DCL1 cleavage of the pri-miRNA in an ionic strength-dependent manner. SE uses its N-terminal domain to bind to RNA and requires both N-terminal and ZnF domains to bind to DCL1. However, when DCL1 is bound to RNA, the interaction with the ZnF domain of SE becomes indispensible and stimulates the activity of DCL1 without requiring SE binding to RNA. Our results suggest that the interactions among SE, DCL1 and RNA are a potential point for regulating pri-miRNA processing.     

The crystal structure of Arabidopsis thaliana allene oxide cyclase: insights into the oxylipin cyclization reaction

We describe the crystallization and structure elucidation of Arabidopsis thaliana allene oxide cyclase 2 (AOC2), a key enzyme in the biosynthesis of jasmonates. In a coupled reaction with allene oxide synthase, AOC2 releases the first cyclic and biologically active metabolite, 12-oxo-phytodienoic acid (OPDA). AOC2 (AT3G25770) folds into an eight-stranded antiparallel beta-barrel with a C-terminal partial helical extension. The protein forms a hydrophobic binding cavity with two distinct polar patches. AOC2 is trimeric in crystals, in vitro and in planta. Based on the observed folding pattern, we assigned AOC2 as a low molecular weight member of the lipocalin family with enzymatic activity in plants. We determined the binding position of the competitive inhibitor vernolic acid (a substrate analog) in the binding pocket. Based on models for bound substrate 12,13-epoxy-9,11,15-octadecatrienoic acid and product OPDA, we propose a reaction scheme that explains the influence of the C15 double bond on reactivity. Reaction is promoted by anchimeric assistance through a conserved Glu residue. The transition state with a pentadienyl carbocation and an oxyanion is stabilized by a strongly bound water molecule and favorable pi-pi interactions with aromatic residues in the cavity. Stereoselectivity results from steric restrictions to the necessary substrate isomerizations imposed by the protein.     

Expanding ecological and evolutionary insights from wild Arabidopsis thaliana accessions

The analytical power of Arabidopsis thaliana genomics has turned its local varieties (accessions) from divergent habitats into important genetic resources. Variant alleles harbored in those accessions are used to identify loci controlling important plant traits with enormous benefits for analytical as well as applied purposes. We argue here that the information derived from Arabidopsis accessions can be further expanded, if a systematic effort for recording the growth conditions of new Arabidopsis accessions is rapidly implemented. The modest and feasible changes in genetic sampling practice that we propose will dramatically increase the quality and quantity of data obtained from Arabidopsis accessions. The broader data set will no longer focus solely on the genetic mechanism within the plant, but will also address the plant''s interaction with its environment. We suggest (a) a modified sampling strategy involving sample size and the recording of additional growth conditions (Appendix) and (b) the establishment of a centralized and expandable database to cover all available information regarding the habitats of Arabidopsis accessions.Key words: adaptation, Arabidopsis, ecology, evolution, genetic resources, sampling strategyThe influence of the immediate abiotic and biotic environment on the evolution of developmental, physiological, reproductive, defense-related and a variety of ecological characteristics of plants is well documented,^1–3 but is rarely connected to the level of individual gene activities. This is partly because for most plants, the genetic dissection of adaptation processes at the individual, population and evolutionary levels is inherently difficult. The current and foreseeable wealth of molecular insights in the Arabidopsis model system could fill this void. With its very wide natural geographic distribution over large parts of Asia and Europe⁴ and it''s more recent (human-induced) colonization of habitats in America, Arabidopsis thaliana provides immediate opportunities for studying adaptation processes in great molecular and genetic detail. Therefore, it is not surprising that Arabidopsis has also been used as a model system for population genetics and ecological adaptation in recent years.^5–8 In a parallel dramatic development, increasing numbers of Arabidopsis accessions are currently being characterized in unprecedented molecular detail to be used as parental lines in QTL mapping studies. These two lines of research could most productively benefit from each other, if habitat information for each accession would become available.An example of a relevant question is: how are environmental variables correlated to phenotypic or gene expression profiles of Arabidopsis accessions? An expandable list of such variables to be recorded at the sampling site would include elevation, aspect (facing north, south, east or west), soil type and soil conditions, rainfall, temperature regime, wind direction and velocity, exposure to sun irradiation, level of shade, UV level, photoperiod, snow cover, local plant communities, herbivore diversity, frequency and pressure, fire history, evidence of various disturbances and apparent diseases. We know, for instance, that various characters, such as vascular structure, fiber length and density, cuticle thickness, stomata density and pigment composition, can be subject to selection even within small, locally restricted populations.^9–12 At a time when phenotypic and molecular profiles of Arabidopsis accession are being scrutinized with ever increasing precision, it would be an inexcusable loss, if the corresponding habitat data for those accessions were simply not recorded or retrievable. It seems evident that with a small, but well-coordinated additional effort, it could be possible to address a much wider array of questions and to direct the power of Arabidopsis genomics and genetics to the study of plant adaptations and evolution. Specifically, we propose that a standard list of environmental data should be provided with each accession of seeds, together with multiple deposited plants as well as electronic images of the exact site and general environment and a precise geographical position (GPS) of the sampling site (see appendix). Precise site documentation may enable re-sampling of populations to study their genetic changes over time.Detailed recording of accession habitats and the collection of multiple plants at each location would reciprocally benefit QTL mapping efforts. First, it would firmly establish that the parental lines of a mapping cross are true natural genotypes. This is important, because any exploitation of natural alleles in breeding and biotechnology should rely in the assumption that these alleles have passed the test of natural selection and are not spontaneous mutants or propagation contaminants. Secondly, emerging correlations between habitat conditions and phenotype can guide accession choices for the establishment of new mapping populations. Phenotyping of accessions for specific cell biological or biochemical traits can be labor intensive. To keep numbers manageable, habitat properties with predictive power would be highly desirable.In summary, we do not consider our suggestions of approximately 30 parameters (see the appendix) to be more than the beginning of a discussion. However, it seems to us that the need for organized habitat characterization and sampling is so urgent that this discussion should begin immediately.     

Molecular paleontology of transposable elements from Arabidopsis thaliana

We report results of a comprehensive computer-assisted analysis of new transposable elements (TEs) from Arabidopsis thaliana. Our analysis revealed several previously unknown pogo- and En/Spm-like families and two novel superfamilies of DNA transposons, Arnold and Harbinger. One of the En/Spm-like families (Atenspm) was found to be involved in generating satellite arrays in paracentromeric regions. Of the two superfamilies reported, Harbinger is distantly related to bacterial IS5-like insertion elements, and Arnold contains DNA transposons without terminal inverted repeats (TIRs), which were never reported in eukaryotes before. Furthermore, we report a large number of young and diverse copia-like autonomous and nonautonomous retroelements and discuss their potential evolutionary relationship with mammalian retroviruses. The A.thaliana genome harbors copia-like retroelements which encode a putative env-like protein reported previously in the SIRE-1 retrotransposon from soybean. Finally, we demonstrate a nonrandom chromosomal distribution of the most abundant A.thaliana TEs clustered in the first half of chromosome II, which includes the centromeric region. The families of TEs from A.thaliana are relatively young, extremely diverse and much smaller than those from mammalian genomes. We discuss the potential factors determining similarities and differences in the evolution of TEs in mammals and A. thaliana. This revised version was published online in July 2006 with corrections to the Cover Date.     

Molecular characterisation of RecQ homologues in Arabidopsis thaliana

Members of the RecQ family of DNA helicases are involved in processes linked to DNA replication, DNA recombination and gene silencing. RecQ homologues of various animals have been described recently. Here, for the first time for plants, we characterised cDNAs of all in all six different RecQ-like proteins that are expressed to different extents in Arabidopsis thaliana. Surprisingly, three of these proteins are small in size [AtRecQl1, AtRecQl2, AtRecQl3—606, 705 and 713 amino acids (aa), respectively], whereas the two bigger proteins result from a duplication event during plant evolution [AtRecQl4A and AtRecQl4B—1150 and 1182 aa, respectively]. Another homologue (AtRecQsim, 858 aa) most probably arose by insertion of an unrelated sequence within its helicase domain. The presence of these homologues demonstrates the conservation of RecQ family functions in higher eukaryotes. We also detected a small gene (AtWRNexo) encoding 285 aa which, being devoid of any RecQ-like helicase domain, reveals a striking homology to the exonuclease domain of human Werner protein, a prominent RecQ helicase of larger size. By means of the two-hybrid assay we were able to detect an interaction between AtWRNexo and AtRecQl2, indicating that activities that reside in a single protein chain in mammals might in plants be complemented in trans.     

Structure-function studies of a plant tyrosyl-DNA phosphodiesterase provide novel insights into DNA repair mechanisms of Arabidopsis thaliana

Our recent studies suggest that H2 (hydrogen) has a potential as a novel radioprotector without known toxic side effects. The present study was designed to examine the underlying radioprotective mechanism of H2 and its protective role on irradiated germ cells. Produced by the Fenton reaction and radiolysis of H2O, hydroxyl radicals (?OH) were identified as the free radical species that were reduced by H2. We used a H2 microelectrode to dynamically detect H2 concentration in vivo, and found H2 significantly reduced in situ fluorescence intensity of hydroxyphenyl fluorescein; however, as we treated the mice with H2 after irradiation, the decrease is not significant. We found that pre-treatment of H2 to IR (ionizing radiation) significantly suppressed the reaction of ?OH and the cellular macromolecules which caused lipid peroxidation, protein carbonyl and oxidatively damaged DNA. The radioprotective effect of H2 on male germ cells was supported by ameliorated apoptotic findings examined by morphological changes and TUNEL (terminal deoxynucleotidyltransferase-mediated dUTP nick-end labelling) in testicular tissue, and by preserved viability of stem spermatogonia examined for testicular histological parameters, daily sperm production and sperm quality; we used WR-2721 [S-2-(3-aminopropylamino)ethyl phosphorothioic acid] as a reference compound. Our results represent the first in vivo evidence in support of a radioprotective role of H2 by neutralizing ?OH in irradiated tissue with no side effects.