Identification of a Novel Human Gene Containing the Tetratricopeptide Repeat Domain from the Down Syndrome Region of Chromosome 21

The Down syndrome (DS) region on chromosome 21, which is responsiblefor the DS main features, has been defined by analysis of DSpatients with partial trisomy 21. Within the DS region, we constructeda 1.6-Mb P1 contig map previously. To isolate gene fragmentsfrom the 1.6-Mb region, we performed direct cDNA library screeningand exon trapping using the P1 clones and a human fetal braincDNA library, and obtained 67 cDNA fragments and 52 possibleexons. Among them, 23 cDNA fragments and 4 exons were interpretedto be derived from a single gene by localization on P1 clonesand by Northern analysis. To obtain the full-length cDNA sequence,longer cDNA clones were further screened from another humancDNA library which was enriched with longer cDNA species. Theseclones were sequenced and assembled to a sequence of 9045 bp.This transcribed sequence encodes a novel 2025 amino-acid proteincontaining tetratricopeptide repeat (TPR) motifs and thereforethe gene was designated as TPRD (a gene containing the TPR motifson the Down syndrome region). The TPR domain has been foundin a certain protein phosphatase and in other proteins involvedin the regulation of RNA synthesis or mitosis. The TPRD gene,the novel gene which was proved to be in the 1.6-Mb region andto have the interesting features described above, is a candidatefor genes responsible for the DS phenotypes.     

Molecular Cloning and Characterization of a cDNA for the r{beta} Subunit of a G Protein from Rice

We isolated a cDNA for the rß subunit of a heterotrimericG protein from rice (Oryza sativa L. cv. Nipponbare). The aminoacid sequence deduced from the cDNA was 76% and 94% homologusto the sequences of the rß subunits from Arabidopsisand maize (AGrß1 and ZGrß1), respectively. (Received July 28, 1995; Accepted December 25, 1995)     

Isolation and Characterization of cDNA Clones with Enhanced Expression in Tobacco Plants Expressing the Rice Homeobox Gene, OSH1

We have used subtractive hybridization to isolate cDNA cloneswhose expression were up-regulated in transgenic tobacco ectopicallyexpressing the rice homeobox gene, OSH1. Thirty-nine distinctcDNA clones, which we term HRGs (Homeobox Regulated Genes),were identified. Some of them were specifically expressed intransformants, indicating that their expression was possiblyregulated by transgene. (Received January 9, 1997; Accepted March 8, 1997)     

Development of {beta}-amylase activity and polymorphism in wheat seedling shoot tissues8

Increasing ß-amylase activity in wheat (Triticum aestlvum,var. Star) seedling shoot tissues was consistently accompaniedby the development of a characteristic polymorphism of the enzyme,as shown by electrophoresis employing amylopectin-containingpolyacrylamide gels. Very young shoot tissue contained one principalform of the enzyme (ß1), whereas two other major forms(ß2, ß3) appeared complementary to thisupon further growth. In vitro incubation experiments indicatedthat the polymorphism arose via a probably proteolytic conversionof ß1 into ß2 and ß3. The conversioninvolved neither an activation of ß-amylase nor asignificant modification of ß-amylase component plvalues. The electrophoretic ß-amylase patterns ofsubcellular leaf compartments suggested that ß1 issynthesized in the cytoplasm of leaf mesophyfi cells and thatthe other forms arise upon transfer of this ‘primary’form into the vacuole. The development of shoot ß-amylaseactivity did not require light, but appeared to be under thenegative control of the chloroplast and was stimulated by mineralnutrients. No clear relationship between ß-amylaseactivity and starch metabolism was evident, since the leaf activitywas largely absent from mesophyll protoplasts, could not beunequivocally demonstrated in the mesophyll chioroplasts, anddeveloped regardless of whether the tissues contained significantamounts of starch or not. Key words: Wheat, leaves, ß-amylase, polymorphism, compartmentation     

{beta}-Amylase Activity as an Index for Germination Potential in Rice

Seeds of different vigour also differ in their germination ability.In rice (Oryza sativa), this difference was correlated withthe level of incorporation of ³⁵S-methionine into 25-60% ammoniumsulphate precipitable material that was rich in amylase proteins.This protein fraction, from dry seeds, contained no -amylaseactivity. In contrast, ß-amylase activity was presentin all seed stocks capable of 99% germination, although thelevel was lower in seeds that grew slowly when germinated. Inlow viability low vigour stock (i.e. extensively deterioratedseeds) ß-amylase activity was absent. Alpha-amylaseactivity in all stocks was detected only after 24 h from thestart of imbibition. These results indicate that ß-amylaseactivity is reliable indicator of the germination ability ofrice seed stocks and of their vigour during germination.Copyright1995, 1999 Academic Press Rice (Oryza sativa L.,), germination, ß-amylase, -amylase, seed vigour     

The Isolation and Characterization of a Cytochrome b6f Complex from the Cyanobacterium Spirulina sp.

A cytochrome b₆f complex was isolated and purified from Spirulinasp. The complex was solubilized with n-heptyl ß-D-thioglucosideand chromatographed on a DEAE-Toyopearl 650M column. The purifiedcomplex contained a small amount of chlorophyll and carotenoid.At least four polypeptides were present in the complex: cytochromef (29 kDa), cytochrome b₆(23 kDa), iron-sulfur protein (ISP,23 kDa), and a 17 kDa polypeptide. Each polypeptide was separatedfrom the complex treated with 2-mercaptoethanol or urea. Theabsorption spectra of cytochrome b₆ and cytochrome f were similarto those of Anabaena and spinach as expected. The complex wasactive in supporting ubiquinol-cytochrome c oxidoreductase activity.Fifty percent inhibition of the activity was accomplished by1 µM dibromothymoquinone (DBMIB). The K_m values for ubiquinol-2and cytochrome c (horse heart) were 5.7 µM and 7.4 µM,respectively. (Received August 15, 1988; Accepted November 14, 1988)     

Computational analysis of RNA editing sites in plant mitochondrial genomes reveals similar information content and a sporadic distribution of editing sites

A computational analysis of RNA editing sites was performedon protein-coding sequences of plant mitochondrial genomes fromArabidopsis thaliana, Beta vulgaris, Brassica napus, and Oryzasativa. The distribution of nucleotides around edited and uneditedcytidines was compared in 41 nucleotide segments and included1481 edited cytidines and 21,390 unedited cytidines in the 4genomes. The distribution of nucleotides was examined in 1,2, and 3 nucleotide windows by comparison of nucleotide frequencyratios and relative entropy. The relative entropy analyses indicatethat information is encoded in the nucleotide sequences in the5 prime flank (–18 to –14, –13 to –10,–6 to –4, –2/–1) and the immediate 3prime flanking nucleotide (+1), and these regions may be importantin editing site recognition. The relative entropy was largewhen 2 or 3 nucleotide windows were analyzed, suggesting thatseveral contiguous nucleotides may be involved in editing siterecognition. RNA editing sites were frequently preceded by 2pyrimidines or AU and followed by a guanidine (HYCG) in themonocot and dicot mitochondrial genomes, and rarely precededby 2 purines. Analysis of chloroplast editing sites from a dicot,Nicotiana tabacum, and a monocot, Zea mays, revealed a similardistribution of nucleotides around editing sites (HYCA). Thesimilarity of this motif around editing sites in monocots anddicots in both mitochondria and chloroplasts suggests that amechanistic basis for this motif exists that is common in thesedifferent organelle and phylogenetic systems. The preferredsequence distribution around RNA editing sites may have an importantimpact on the acquisition of editing sites in evolution becausethe immediate sequence context of a cytidine residue may rendera cytidine editable or uneditable, and consequently determinewhether a T to C mutation at a specific position may be correctedby RNA editing. The distribution of editing sites in many protein-codingsequences is shown to be non-random with editing sites clusteredin groups separated by regions with no editing sites. The sporadicdistribution of editing sites could result from a mechanismof editing site loss by gene conversion utilizing edited sequenceinformation, possibly through an edited cDNA intermediate.     

A novel {beta}-galactosidase gene isolated from the bacterium Xanthomonas manihotis exhibits strong homology to several eukaryotic {beta}-galactosidases

The gene encoding a ß-galactosidase from Xanthomonasmanihotis was cloned into Escherichia coli. The gene resideson a 2.4 kb DNA fragment which was isolated from a partial Sau3Alibrary in the cloning vector pUC19 using 5-bromo-4-chloro-3-indolyl-ß-D-galactopyranoside(X-gal) as the selection. The enzyme produced by the clone hasa specificity for ß1-3->ß1-4-linked galactose.The nucleotide sequence of the gene was determined. The deducedprotein sequence contained 597 amino acids yielding a monomericmolecular mass of 66 kDa. The cloned ß-galactosidaseshowed no similarity to any known prokaryotic ß-galactosidase.However, extensive similarity was observed with eukaryotic ß-galactosidasesfrom animals, plants and fungi. The strongest similarity waswith the ß-galactosidases found hi the human and mouselysosomes (42 and 41% identity, respectively). Alignment ofthe X.manihotis and eukaryotic ß-galactosidase sequencesrevealed seven highly conserved domains common to each protein.Additionally, Domain 1 in X.manihotis showed similarity to regionswithin catalytic domains from seven xylanases and cellulasesbelonging to family 10 of glucosyl hydrolases. A region spanningDomain 2 showed similarity to the catalytic domain of endo ß1-3glucanases from tobacco and barley. cellulase ß-galactosidase G_M$$$gangliosidosis Morquio B syndrome Xanthomonas     

Identification, Purification and Properties of the Precursor of Conglutin {beta}, The 7S Storage Globulin of Lupinus albus L. Seeds

Lupinus albus L. developing cotyledons 35 d after floweringcontained a major polypeptide of-average M_r 64000, immunologicallyrelated to conglutin ß, the 7S storage globulin ofthis seed. This polypeptide decreased during seed maturation,without completely disappearing in the mature seed. This dropwas accompanied by the formation of polypeptide fragments typicalof the mature conglutin ß. The 64000 polypeptide hasbeen identified as the precursor polypeptide of conglutin ß. Undenatured conglutin ß precursor, purified by ionexchange chromatography and size exclusion chromatography, showedsurface and association properties identical to the mature conglutinß molecule. The precursor oligomer, of M_r 190000,consisted of an association of three 64000 subunits. They stronglyreacted with concanavalin A indicating the presence of covalentlylinked carbohydrate. Tryptic treatment of the undenatured conglutin ß precursorled to the accumulation of a relatively stable 59000 polypeptidewhich was cleaved later on and produced three large polypeptidefragments differing from the mature conglutin ß polypeptides. Key words: Conglutin ß, precursor, developing seeds, Lupinus albus L.     

Comparative mapping of HKT genes in wheat, barley, and rice, key determinants of Na+ transport, and salt tolerance

Salt tolerance of plants depends on HKT transporters (High-affinityK⁺ Transporter), which mediate Na⁺-specific transport or Na⁺-K⁺co-transport. Gene sequences closely related to rice HKT geneswere isolated from hexaploid bread wheat (Triticum aestivum)or barley (Hordeum vulgare) for genomic DNA southern hybridizationanalysis. HKT gene sequences were mapped on chromosomal armsof wheat and barley using wheat chromosome substitution linesand barley–wheat chromosome addition lines. In addition,HKT gene members in the wild diploid wheat ancestors, T. monococcum(A^m genome), T. urartu (A^u genome), and Ae. tauschii (D^t genome)were investigated. Variation in copy number for individual HKTgene members was observed between the barley, wheat, and ricegenomes, and between the different wheat genomes. HKT2;1/2-like,HKT2;3/4-like, HKT1;1/2-like, HKT1;3-like, HKT1;4-like, andHKT1;5-like genes were mapped to the wheat–barley chromosomegroups 7, 7, 2, 6, 2, and 4, respectively. Chromosomal regionscontaining HKT genes were syntenic between wheat and rice exceptfor the chromosome regions containing the HKT1;5-like gene.Potential roles of HKT genes in Na⁺ transport in rice, wheat,and barley are discussed. Determination of the chromosome locationsof HKT genes provides a framework for future physiological andgenetic studies investigating the relationships between HKTgenes and salt tolerance in wheat and barley. Key words: Barley, comparative mapping, HKT, rice, salt tolerance, sodium transport, wheat     

Characterization of a 47-Kilodalton Chlorophyll-Binding Polypeptide (CP-47) Isolated from a Photosystem II Core Complex

The purified photosystem II core complex from spinach with aparticle size of about 480 kDa and containing five constituentpolypeptides was further resolved by octyl-rß-D-glucopyranosidetreatment followed by separation by high-performance liquidchromatography using a gel-permeation column. Of the four clearlyseparated, chlorophyll-containing fractions, one with a particlesize of 170–180 kDa was composed entirely of a single,47-kDa polypeptide. This chlorophyll a-polypeptide containsrß-carotene and pheophytin a, but no plastoquinone.The number of chlorophyll a associated with this polypeptidein situ was estimated to be 6–7 and an oligomeric structureof this polypeptide in vivo was proposed on the basis of itschlorophyll/protein ratio and the isolated particle size. Thecomplex exhibited F-695 emission, but was photochemically inactive.The amino acid composition of the apoprotein was also determined. (Received March 12, 1984; Accepted June 7, 1984)     

The mechanism selecting the guide strand from small RNA duplexes is different among argonaute proteins

Double-stranded RNA induces RNA silencing and is cleaved into21–24 nt small RNA duplexes by Dicer enzyme. A strandof Dicer-generated small RNA duplex (called the guide strand)is then selected by a thermodynamic mechanism to associate withArgonaute (AGO) protein. This AGO–small RNA complex functionsto cleave mRNA, repress translation or modify chromatin structurein a sequence-specific manner. Although a model plant, Arabidopsisthaliana, contains 10 AGO genes, their roles and molecular mechanismsremain obscure. In this study, we analyzed the roles of ArabidopsisAGO2 and AGO5. Interestingly, the 5' nucleotide of small RNAsthat associated with AGO2 was mainly adenine (85.7%) and thatwith AGO5 was mainly cytosine (83.5%). Small RNAs that wereabundantly cloned from the AGO2 immunoprecipitation fraction(miR163-LL, which is derived from the Lower Left of mature miR163in pre-miR163, and miR390) and from the AGO5 immunoprecipitationfraction (miR163-UL, which is derived from the Upper Left ofmature miR163 in pre-miR163, and miR390^*) are derived from thesingle small RNA duplexes, miR163-LL/miR163-UL and miR390/miR390^*.Each strand of the miR163-LL/miR163-UL duplex is selectivelysorted to associate with AGO2 or AGO5 in a 5' nucleotide-dependentmanner rather than in a thermodynamic stability-dependent manner.Furthermore, we showed that both AGO2 and AGO5 have the abilityto bind cucumber mosaic virus-derived small RNAs. These resultsclearly indicate that the mechanism selecting the guide strandis different among AGO proteins and that multiple AGO genesare involved in anti-virus defense in plants.     

Levels of {beta}-Glucan and Lignin in Elongating Internodes of Deepwater Rice

Partial submergence or treatment with either ethylene or gibberellicacid (GA₃ induces rapid growth in deepwater rice (Oryza sativaL.). We correlated the synthesis of two cell wall componentswith two phases of internodal elongation, namely (13,14)-ß-glucanformation with cell elongation and lignification with differentiationof the secondary cell wall and cessation of growth. The contentof ß-glucan was highest in the zone of cell elongationin internodes of air-grown plants and plants that were inducedto grow rapidly by submergence. In the intercalary meristemand in the differentiation zone of the internode, ß-glucanlevels were ca. 70% lower than in the zone of cell elongation.The outer cell layers, enriched in epidermis, contained moreß-glucan in submerged, rapidly growing internodesthan in air-grown, control internodes. The ß-glucancontent of the inner, parenchymal tissue was unaffected or slightlylowered by submergence. The epidermis appears to be the growth-limitingstructure of rapidly growing rice internodes. We hypothesizethat elevated levels of ß-glucan contribute to elongationgrowth by increasing the extensibility of the cell wall. Lignificationwas monitored by measuring the content of lignin and the activitiesof two enzymes of the lignin biosynthetic pathway, coniferylalcohol dehydrogenase (CAD) and phenylalanine ammonia-lyase(PAL), in growing and non-growing regions of the internode.Using submerged whole plants and GA₃-treated excised stem segments,we showed that lignin content and CAD activity were up to sixfoldlower in newly formed internodal tissue of rapidly growing ricethan in slowly growing tissue. No differences were observedin parts of the internode that had been formed prior to inductionof growth. PAL activity was reduced throughout the internodeof submerged plants. We conclude that lignification is one ofthe processes that is suppressed to permit rapid growth. ¹ This work was supported by the National Science Foundationthrough grants No. DCB-8718873 and DCB-9103747 and by the Departmentof Energy through grant No. DE-FGO2-90ER20021. M.S. was therecipient of a fellowship from the Max Kade Foundation.     

Effects of Fluorogibberellins on Plant Growth and Gibberellin 3r{beta}-Hydroxylases

3rß-Fluorogibberellin A₉ (3rß-fluoro-GA₉),3rßfluoro-GA₂₀, 3rß-fluorodeoxygibberellinC (3rß-fluoro-DGC) and 13-fluoro-GA₉ were prepared,and their effects on plant growth and gibberellin (GA) 3rß-hydroxyIaseswere examined. 3rß-Fluoro-GA₉ and 3rß-fluoro-GA₂₀promoted the growth of dwarf rice (Oryza sativa L. cv. Tan-ginbozu)seedlings to three times higher than the control seedlings ata dosage of 3 µ plant^–1, and 3rßfluoro-DGCto twice higher at the same dosage. 3rßg-Fluoro-GA₉was active in cucumber (Cucumis sativus L.) hypocotyl assay,its activity being about one-thirtieth as much as that of GA₄.3rß-Fluoro-GAs were active per se in promoting theshoot elongation of rice. 3rß-Fluoro-DGC inhibitedthe 3rß-hydroxylation of [³H₂]GA₉ to [³H]GA₄ by GArß-hydroxylase from bean (Phaseolus vulgaris L.),but 3rß-fluoro-GA₉ and 3rß-fluoro-GA₂₀ didnot show any effects on the enzyme activity. These 3rß-fluoro-GAsalso showed no or only a weak inhibitory effect on the rß-hydroxylasefrom pumpkin (Cucurbita maxima L.). 13-Fluoro-GA₉ promoted growthof rice and cucumber seedlings, and inhibited the 3rß-hydroxylasesfrom both bean and cucumber. 13-Fluoro-GA₉was converted into13-fluoro-GA₄ and 2,3-didehydro-13-fluoro-GA₉, in a cell-freesystem from bean, and conversion of 13-fluoro-GA₉ into 13-fluoro-GA₄was also observed in a cell-free system from pumpkin. Theseresults suggest that 13-fluoro-GA₉ is one of the substratesof GA 3rß-hydroxy-lases, and that 13-fluoro-GA₉ isactive as a result of the conversion to 13-fluoro-GA₄ in riceand cucumber seedlings. (Received October 27, 1997; Accepted March 13, 1998)     

Tapetum-Specific Expression of the Gene for an Endo-{beta}-1,3-glucanase Causes Male Sterility in Transgenic Tobacco

A cDNA for a pathogenesis-related endo-ß-1,3-glucanaseisolated from soybean, was fused to an anther tapetum-specificpromoter (Osg6B promoter) isolated from rice and the resultingchimeric gene was introduced into tobacco. The Osg6B promoterbecame active in the anther tapetum during formation of tetradsand the tapetal glucanase activity in the transgenic plantscaused in a significant reduction in the number of fertile pollengrains. Most of the pollen grains were aberrant in shape, lackedgerminal apertures and aggregate of the pollen grains. Granulesof ß-1,3-glucan, which have not previously been reported,were often observed to adhere to the surface of the pollen grains.Further observations revealed that the callose wall was almostabsent in the pollen tetrads of transgenic plants. In wild-typeplants, by contrast, the tetrads were surrounded by callosethat was degraded soon after the tetrad stage to release freemicrospores. Thus, the introduced gene for endo-ß-1,3-endoglucanaseunder the control of the Osg6B promoter caused digestion ofthe callose wall at the beginning of the tetrad stage, a timethat was just a little earlier than the time at which endogenousglucanase activity normal appears. These results demonstratethat premature dissolution of the callose wall in pollen tetradscauses male sterility and suggest that the time at which tapetallyproduced glucanase is activate is critical for the normal developmentof microspores. (Received September 29, 1994; Accepted January 30, 1995)     

Effects of Deoxygibberellin C (DGC) and 16-Deoxo-DGC on Gibberellin 3{beta}-Hydroxylase and Plant Growth

Deoxygibberellin C (DGC), a C/D ring-rearranged isomer of GA₂₀,was shown to inhibit the conversion of [2,3-³H₂]GA₉ to [2-³H]GA₄by gibberellin 3ß-hydroxylase from immature seedsof Phaseolus vulgahs. Deoxygibberellin C inhibited the promotionof growth by exogenously applied GA₂₀ of rice (Oryza sativaL.) seedlings. Evidence is also presented that DGC is a competitiveinhibitor of the 3ß-hydroxylase from P. vulgaris.However, DGC only weakly inhibited the conversion catalyzedby the 3ß-hydroxylase from Cucurbita maxima at highconcentrations, and it did not inhibit the promotion of growthby exogenously applied GA₉ of cucumber (Cucumis sativus) seedlings.These results suggest that the 3ß-hydroxylases fromP. vulgaris and C. maxima have different structural requirementswith respect to their substrates. 16-Deoxo-DGC also inhibitedcatalysis of the same conversion by 3ß-hydroxylasefrom P. vulgaris, and it slightly inhibited the conversion catalyzedby the enzyme from C. maxima. Application of 16-deoxo-DGC causedthe promotion of the growth of seedlings of both rice and cucumber. ³ Present address: Genetic Engineering Center, Korea Instituteof Science and Technology, Daejeon 305–606, Korea ⁴ Present address: Department of Agricultural Chemistry, UtsunomiyaUniversity, Utsunomiya-shi, Tochigi, 321 Japan (Received September 25, 1990; Accepted December 17, 1990)     

cDNA Sequences of Three Kinds of {beta}-tubulins from Rice

Complete nucleotide sequences of three kinds of rice ß-tubulincDNA clones (pTUB22, R1623 and R2242) were determined. Southernhybridization indicated that these ß-tubulins consistof one gene family. Using RFLP mapping, these three ß-tubulincDNAs were mapped to different chromosomes indicating at leastthree loci for the ß-tubulin gene. The deduced aminoacid sequences of these cDNAs showed a high similarity to otherplant ß-tubulins. The asparagine residue located atthe 100th amino acid from the Nterminus of plant ß-tubulinswas also conserved with these three ß-tubulins. Thisasparagine is thought to be responsible for the sensitivityagainst rhizoxin, the toxin of the pathogen of rice seedlingblight, Rhizopus sp. a soil-borne microorganism. Expressionof the three ß-tubulin genes was analyzed by Northernblotting and all three clones were expressed in root, the possibletarget tissue of rhizoxin. These results suggest that theseclones are candidates of ß-tubulins targeted by rhizoxin.