Takeshi Ishimizu

Primary structural features of rosaceous S-RNases associated with gametophytic self-incompatibility.

We isolated cDNA clones encoding five S-RNases (S1-,S3- , S5-, S6-, S7-RNases) from pistils of Pyrus pyrifolia (Japanese pear), a member of the Rosaceae. Their amino acid sequences were aligned with those of other rosaceous S-RNases sequenced so far. A total of 76 conserved amino acid residues were stretched throughout the sequence, but were absent from the 51–66 region which was designated the hypervariable (HV) region. The phylogenetic tree of rosaceous S-RNases showed that S-RNase polymorphism predated the divergence of Pyrus and Malus. Pairwise comparison of these S-RNases detected two highly homologous pairs, P. pyrifolia S1- and S4-RNases (90.0%) and P. pyrifolia S3- and S5-RNases (95.5%). The positions of amino acid substitutions between S1- and S4-RNases were spread over the entire region, but in the pair of S3- and S5-RNases, amino acid substitutions were found in the 21–90 region including the HV region. The substitutions in this restricted region appear to be sufficient to discriminate between S3 and S5 pollen and to trigger the self-incompatible reaction.

Rice Expression Atlas In Reproductive Development

Gene expression throughout the reproductive process in rice (Oryza sativa) beginning with primordia development through pollination/fertilization to zygote formation was analyzed. We analyzed 25 stages/organs of rice reproductive development including early microsporogenesis stages with 57,381 probe sets, and identified around 26,000 expressed probe sets in each stage. Fine dissection of 25 reproductive stages/organs combined with detailed microarray profiling revealed dramatic, coordinated and finely tuned changes in gene expression. A decrease in expressed genes in the pollen maturation process was observed in a similar way with Arabidopsis and maize. An almost equal number of ab initio predicted genes and cloned genes which appeared or disappeared coordinated with developmental stage progression. A large number of organ-/stage-specific genes were identified; notably 2,593 probe sets for developing anther, including 932 probe sets corresponding to ab initio predicted genes. Analysis of cell cycle-related genes revealed that several cyclin-dependent kinases (CDKs), cyclins and components of SCF E3 ubiquitin ligase complexes were expressed specifically in reproductive organs. Cell wall biosynthesis or degradation protein genes and transcription factor genes expressed specifically in reproductive stages were also newly identified. Rice genes homologous to reproduction-related genes in other plants showed expression profiles both consistent and inconsistent with their predicted functions. The rice reproductive expression atlas is likely to be the most extensive and most comprehensive data set available, indispensable for unraveling functions of many specific genes in plant reproductive processes that have not yet been thoroughly analyzed.

Various spatiotemporal expression profiles of anther-expressed genes in rice.

The male gametophyte and tapetum play different roles during anther development although they are differentiated from the same cell lineage, the L2 layer. Until now, it has not been possible to delineate their transcriptomes due to technical difficulties in separating the two cell types. In the present study, we characterized the separated transcriptomes of the rice microspore/pollen and tapetum using laser microdissection (LM)-mediated microarray. Spatiotemporal expression patterns of 28,141 anther-expressed genes were classified into 20 clusters, which contained 3,468 (12.3%) anther-enriched genes. In some clusters, synchronous gene expression in the microspore and tapetum at the same developmental stage was observed as a novel characteristic of the anther transcriptome. Noteworthy expression patterns are discussed in connection with gene ontology (GO) categories and gene annotations, which are related to important biological events in anther development, such as pollen maturation, pollen germination, pollen tube elongation and pollen wall formation.

Identification of regions in which positive selection may operate in S-RNase of Rosaceae: Implication for S-allele-specific recognition sites in S-RNase

A stylar S‐RNase is associated with gametophytic self‐incompatibility in the Rosaceae, Solanaceae, and Scrophulariaceae. This S‐RNase is responsible for S‐allele‐specific recognition in the self‐incompatible reaction, but how it functions in specific discrimination is not clear. Window analysis of the numbers of synonymous (dS ) and non‐synonymous (dN ) substitutions in rosaceous S‐RNases detected four regions with an excess of dN over dS in which positive selection may operate (PS regions). The topology of the secondary structure of the S‐RNases predicted by the PHD method is very similar to that of fungal RNase Rh whose tertiary structure is known. When the sequences of S‐RNases are aligned with the sequence of RNase Rh based on the predicted secondary structures, the four PS regions correspond to two surface sites on the tertiary structure of RNase Rh. These findings suggest that in S‐RNases the PS regions also form two sites and are candidates for the recognition sites for S‐allele‐specific discrimination.

UDP-Glucose Pyrophosphorylase is Rate Limiting in Vegetative and Reproductive Phases in Arabidopsis thaliana

UDP-glucose pyrophosphorylase (UGPase) is an important enzyme in the metabolism of UDP-glucose, a precursor for the synthesis of carbohydrate cell wall components, such as cellulose and callose. The Arabidopsis thaliana genome contains two putative genes encoding UGPase, AtUGP1 and AtUGP2. These genes are expressed in all organs. In order to determine the role of UGPase in vegetative and reproductive organs, we employed a reverse genetic approach using the T-DNA insertion mutants, atugp1 and atugp2. Despite a significant decrease in UGPase activity in both the atugp1 and atugp2 single mutants, no decrease in normal growth and reproduction was observed. In contrast, the atugp1/atugp2 double mutant displayed drastic growth defects and male sterility. At the reproductive phase, in the anthers of atugp1/atugp2, pollen mother cells developed normally, but callose deposition around microspores was absent. Genes coding for enzymes at the subsequent steps in the cellulose and callose synthesis pathway were also down-regulated in the double mutant. Taken together, these results demonstrate that the AtUGP1 and AtUGP2 genes are functionally redundant and UGPase activity is essential for both vegetative and reproductive phases in Arabidopsis. Importantly, male fertility was not restored in the double knockout mutant by an application of external sucrose, whereas vegetative growth was comparable in size with that of the wild type. In contrast, an application of external UDP-glucose recovered male fertility in the double mutant, suggesting that control of UGPase in carbohydrate metabolism is different in the vegetative phase as compared with the reproductive phase in A. thaliana.

Successive glycosyltransfer activity and enzymatic characterization of pectic polygalacturonate 4-α-galacturonosyltransferase solubilized from pollen tubes of Petunia axillaris using pyridylaminated oligogalacturonates as substrates

Polygalacturonate 4-α-galacturonosyltransferase (pectin synthase) was solubilized from pollen tubes of Petunia axillaris and characterized. To accomplish this, an assay method using fluorogenic pyridylaminated-oligogalacturonic acids (PA-OGAs) as acceptor substrates was developed. When the pollen tube enzyme was solubilized with 0.5% (v/v) Triton X-100 and was incubated with PA-OGA and UDP-galacturonic acid (UDP-GalUA), successive transfer activity of more than 10 GalUAs from UDP-GalUA to the nonreducing end of PA-OGA was observed by diethylaminoethyl high-performance liquid chromatography. This activity was time- and enzyme concentration-dependent. The optimum enzyme activity was observed at pH 7.0 and 30°C. Among the PA-OGAs investigated, those with a degree of polymerization of more than 10 were preferred as substrates. The crude pollen tube enzyme had an apparentK m value of 13 μm for the PA-OGA with a degree of polymerization 11 and 170 μm for UDP-GalUA. The characteristics of the P. axillarispollen tube enzyme and the usefulness of fluorogenic PA-OGAs for the assay of this enzyme are discussed.

Sequence comparison of the 5' flanking regions of Japanese pear (Pyrus pyrifolia) S-RNases associated with gametophytic self-incompatibility

Abstract Genomic clones of 2.8 kb, 4.3 kb and 6.5 kb for the S2-, S3- and S5-RNases of Japanese pear(Pyrus pyrifolia), respectively, were isolated and sequenced. Comparison of the 5’-flanking regions of these genes with the same region of the S4-RNase gene indicated that a highly similar region of approximately 200 bp exists in the regions just upstream of the putative TATA boxes of the four Japanese pear S-RNase genes. This suggests the presence of cis-regulatory element(s) in this region.

Enhanced solubilization of membrane proteins by alkylamines and polyamines

Around 25% of proteins in living organisms are membrane proteins that perform many critical functions such as synthesis of biomolecules and signal transduction. Membrane proteins are extracted from the lipid bilayer and solubilized with a detergent for biochemical characterization; however, their solubilization is an empirical technique and sometimes insufficient quantities of proteins are solubilized in aqueous buffer to allow characterization. We found that addition of alkylamines and polyamines to solubilization buffer containing a detergent enhanced solubilization of membrane proteins from microsomes. The solubilization of polygalacturonic acid synthase localized at the plant Golgi membrane was enhanced by up to 9.9‐fold upon addition of spermidine to the solubilization buffer. These additives also enhanced the solubilization of other plant membrane proteins localized in other organelles such as the endoplasmic reticulum and plasma membrane as well as that of an animal Golgi‐localized membrane protein. Thus, addition of alkylamines and polyamines to solubilization buffer is a generally applicable method for effective solubilization of membrane proteins. The mechanism of the enhancement of solubilization is discussed.

In vitro stabilization and minimum active component of polygalacturonic acid synthase involved in pectin biosynthesis.

Polygalacturonic acid (PGA) synthase successively transfers galacturonic acid to oligogalacturonic acid by an α1,4-linkage to synthesize PGA, the backbone of plant pectic homogalacturonan. PGA synthase has not been purified to date due to its instability in vitro. In this study, we found stable conditions in vitro and separated a minimum active component of the enzymes from pea and azuki bean epicotyls. The PGA synthase lost its activity in 500 mM of sodium chloride or potassium chloride, while it was relatively stable at low salt concentrations. Under low salt concentrations, three peaks bearing PGA synthase activity were separated, by gel filtration and sucrose density gradient centrifugation. The molecular masses of these enzymes solubilized with 3-[(3-cholamidopropyl)dimethyl-ammonio]propanesulfonic acid were estimated to be 21,000, 5,000, and 590 kDa. The two higher molecular mass PGA synthases converted to smaller PGA synthase proteins when treated with high salt concentrations, while retaining their activity, indicating that PGA synthase has a minimum active component for its activity.

Synthesis of β-mannosides using the transglycosylation activity of endo-β-mannosidase from Lilium longiflorum

Endo‐β‐mannosidase is an endoglycosidase that hydrolyzes only the Manβ1‐4GlcNAc linkage of the core region of N‐linked sugar chains. Recently, endo‐β‐mannosidase was purified to homogeneity from Lilium longiflorum (Lily) flowers, its corresponding gene was cloned and important catalytic amino acid residues were identified [Ishimizu T., Sasaki A., Okutani S., Maeda M., Yamagishi M. & Hase S. (2004) J. Biol. Chem.279, 38555–38562]. In the presence of Manβ1‐4GlcNAcβ1‐4GlcNAc‐peptides as a donor substrate and p‐nitrophenyl β‐N‐acetylglucosaminide as an acceptor substrate, the enzyme transferred mannose to the acceptor substrate by a β1‐4‐linkage regio‐specifically and stereo‐specifically to give Manβ1‐4GlcNAcβ1‐pNP as a transfer product. Further studies indicated that not only p‐nitrophenyl β‐N‐acetylglucosaminide but also p‐nitrophenyl β‐glucoside and p‐nitrophenyl β‐mannoside worked as acceptor substrates, however, p‐nitrophenyl β‐N‐acetylgalactosaminide did not work, indicating that the configuration of the hydroxyl group at the C4 position of an acceptor is important. Besides mannose, oligomannoses were also transferred. In the presence of (Man)nManα1‐6Manβ1‐4GlcNAcβ1‐4GlcNAc‐peptides (n = 0–2) and pyridylamino GlcNAcβ1‐4GlcNAc, the enzyme transferred (Man)nManα1‐6Man en bloc to the acceptor substrate to produce pyridylamino (Man)nManα1‐6Manβ1‐4GlcNAcβ1‐4GlcNAc (n =0–2). Thus, the lily endo‐β‐mannosidase is useful for the enzymatic preparation of oligosaccharides containing the mannosyl β1,4‐structure, chemical preparations of which have been frequently reported to be difficult.