Mannitol in six autotrophic stramenopiles and Micromonas

Mannitol plays a central role in brown algal physiology since it represents an important pathway used to store photoassimilate. Several specific enzymes are directly involved in the synthesis and recycling of mannitol, altogether forming the mannitol cycle. The recent analysis of algal genomes has allowed tracing back the origin of this cycle in brown seaweeds to a horizontal gene transfer from bacteria, and furthermore suggested a subsequent transfer to the green micro-alga Micromonas. Interestingly, genes of the mannitol cycle were not found in any of the currently sequenced diatoms, but were recently discovered in pelagophytes and dictyochophytes. In this study, we quantified the mannitol content in a number of ochrophytes (autotrophic stramenopiles) from different classes, as well as in Micromonas. Our results show that, in accordance with recent observations from EST libraries and genome analyses, this polyol is produced by most ochrophytes, as well as the green alga tested, although it was found at a wide range of concentrations. Thus, the mannitol cycle was probably acquired by a common ancestor of most ochrophytes, possibly after the separation from diatoms, and may play different physiological roles in different classes.Key words: algae, stramenopiles, mannitol cycle, primary metabolism, osmotic stress, evolutionBrown algae produce mannitol directly from the photoassimilate fructose-6-phosphate. Its metabolism occurs through the mannitol cycle, which involves four enzymatic reactions: (1) the reduction of fructose-6-phosphate (F6P) to mannitol-1-phosphate (M1P) via the activity of an M1P dehydrogenase (M1PDH); (2) the production of mannitol from M1P via an M1P phosphatase (M1Pase); (3) the oxidation of mannitol via the activity of a mannitol-2-dehydrogenase (M2DH) yielding fructose; and (4) the phosphorylation of fructose yielding F6P and involving a hexokinase (HK).^1,2 The first completed draft of a brown algal genome enabled the identification of candidate genes for each of these steps.³ As these genes were not found in the genomes of the diatoms Thalassiosira pseudonana and Phaeodactylum tricornutum, mannitol metabolism in stramenopiles was considered a trait typical for brown algae. The corresponding genes were thought to have been acquired horizontally from bacteria and subsequently transferred to some green algae.⁴ Recently, however, homologs of several genes of the cycle were also found in the genome of the pelagophyte Aureococcus anophagefferens⁵ and an EST library produced for the dictyochophyte Pseudochattonella farcimen (Dittami et al. personal communication). These observations prompted us to examine the presence of mannitol in a range of strains covering different classes of autotrophic stramenopiles (ochrophytes). In addition, because of the identification of genes encoding enzymes for the production of mannitol through the mannitol cycle in the green alga Micromonas, one strain of this genus was also included in our analysis.     

Genome-wide identification of the class III aminotransferase gene family in rice and expression analysis under abiotic stress

Aminotransferases are pyridoxal 5′-phosphate-dependent enzymes that play crucial roles in plant growth, development, and responses to abiotic stress. The class III aminotransferase family (ATIII family) is an important subfamily. However, no characterization of rice ATIII genes has been previously reported. Using available rice genome sequence information, we identified 12 japonica and 13 indica ATIII genes that were randomly localized on chromosomes 2, 3, 4, 5, 7, 8, and 11. Information provided by the Plant Genome Duplication Database revealed that four japonica and four indica ATIII genes are the results of segmental duplications, and two japonica and six indica genes resulted from tandem duplications. A phylogenetic analysis of the ATIII genes in japonica, indica and Arabidopsis enabled the classification of the genes into six different groups, and the characteristics were established before the monocot-dicot and japonica–indica split. An analysis of the Ka/Ks, divergence time and average indel length suggested the diverse selection styles of the duplicated gene pairs. Gene structure and motif analyses revealed that the ATIII gene family has experienced extensive divergence. Real-time PCR was performed to examine the expression pattern of the japonica ATIII genes in response to various abiotic stresses including drought, salt, and cold. The results suggested that most of the genes were differentially up- or down-regulated in rice seedlings in response to at least one stress factor, which indicates the key role of the rice ATIII gene family in responding to abiotic stresses. These results provide a basis for elucidating the roles of the ATIII genes and their further functional analysis under abiotic stresses.     

Molecular cloning,expression and antioxidant activity of a peroxiredoxin 2 homologue from Lampetra japonica

Peroxiredoxin (Prx) is a cellular antioxidant protein family that plays important roles in oxidative stress and immune cytotoxicity. In this study, we cloned a homologue of the Prx2 from the buccal gland of Lampetra japonica (L. japonica). L. japonica Prx2 (Lj-Prx2) contained two highly conserved motifs and shared more than 70% identity with the homologs from other vertebrate species. Phylogenetic analysis revealed that Lj-Prx2 is closely related to other available teleost Prx2. The real-time PCR results demonstrated that the Prx2 gene was widely expressed in adult lamprey. In addition, the expression of Prx2 gene was particularly up-regulated in red blood cells (RBCs) after the experimental animals were challenged with lipopolysaccharide (LPS) in vivo. Lj-Prx2 gene was subcloned into the pET23b vector and expressed in Escherichia coli BL21 (DE3). The recombinant L. japonica Prx2 (rLj-Prx2) was purified by using His Bind affinity chromatography. Polyclonal antibody to rLj-Prx2 was generated in New Zealand Rabbit. Western blot analysis showed that the Lj-Prx2 is present in the buccal gland secretion, suggesting the secretory feature of it. The function assays revealed that rLj-Prx2 has the capability to reduce the H₂O₂ when dithiothreitol (DTT) is used as a reducing equivalent and to protect DNA from oxidative damage. These findings suggested that Lj-Prx2 probably plays an essential role in antioxidant defense in RBCs to keep lamprey alive.     

A Series of Beta-Carboline Derivatives Inhibit the Kinase Activity of PLKs

Polo-like kinases play an essential role in the ordered execution of mitotic events and 4 mammalian PLK family members have been identified. Accumulating evidence indicates that PLK1 is an attractive target for anticancer drugs. In this paper, a series of beta-carboline derivatives were synthesized and three compounds, DH281, DH285 and DH287, were identified as potent new PLK inhibitors. We employed various biochemical and cellular approaches to determine the effects of these compounds on the activity of PLK1 and other mitotic kinases and on cell cycle progression. We found that these three compounds could selectively inhibit the kinase activity of purified PLK1, PLK2 and PLK3 in vitro. They show strong antitumor activity against a number of cancer cell lines with relatively low micromolar IC₅₀s, but are relatively less toxic to non-cancer cells (MRC5). Moreover, these compounds could induce obvious accumulation of HeLa cells in G₂/M and S phases and trigger apoptosis. Although MRC5 cells show clear S-phase arrest after treatment with these compounds, the G2/M arrest and apoptosis are less insignificant, indicating the distinct sensitivity between normal and cancer cells. We also found that HeLa cells treated with these drugs exhibit monopolar spindles and increased Wee1 protein levels, the characteristics of cells treated with PLK1 inhibitors. Together, these results demonstrate that DH281, DH285 and DH287 beta-carboline compounds are new PLK inhibitors with potential for cancer treatment.     

Polyol-specific long-chain dehydrogenases/reductases of mannitol metabolism in Aspergillus fumigatus: biochemical characterization and pH studies of mannitol 2-dehydrogenase and mannitol-1-phosphate 5-dehydrogenase

Functional genomics data suggests that the metabolism of mannitol in the human pathogen Aspergillus fumigatus involves the action of two polyol-specific long-chain dehydrogenases/reductases, mannitol-1-phosphate 5-dehydrogenase (M1PDH) and mannitol 2-dehydrogenase (M2DH). The gene encoding the putative M2DH was expressed in Escherichia coli, and the purified recombinant protein was characterized biochemically. The predicted enzymatic function of a NAD(+)-dependent M2DH was confirmed. The enzyme is a monomer of 58kDa in solution and does not require metals for activity. pH profiles for M2DH and the previously isolated M1PDH were recorded in the pH range 6.0-10.0 for the oxidative and reductive direction of the reactions under conditions where substrate was limiting (k(cat)/K) or saturating (k(cat)). The pH-dependence of logk(cat) was usually different from that of log(k(cat)/K), suggesting that more than one step of the enzymatic mechanism was affected by changes in pH. The greater complexity of the pH profiles of log(k(cat)/K) for the fungal enzymes as compared to the analogous pH profiles for M2DH from Pseudomonas fluorescens may reflect sequence changes in vicinity of the conserved catalytic lysine.     

Chromosomal regions associated with segregation distortion of molecular markers in F2 , backcross, doubled haploid, and recombinant inbred populations in rice (Oryza sativa L.)

Chromosomal regions associated with marker segregation distortion in rice were compared based on six molecular linkage maps. Mapping populations were derived from one interspecific backcross and five intersubspecific (indica?/?japonica) crosses, including two F₂ populations, two doubled haploid (DH) populations, and one recombinant inbred (RI) population. Mapping data for each population consisted of 129–629 markers. Segregation distortion was determined based on chi-square analysis (P?<?0.01) and was observed at 6.8–31.8% of the mapped marker loci. Marker loci associated with skewed allele frequencies were distributed on all 12 chromosomes. Distortion in eight chromosomal regions bracketed previously identified gametophyte (ga) or sterility genes (S). Distortion in three other chromosomal regions was found only in DH populations, where japonica alleles were over-represented, suggesting that loci in these regions may be associated with preferential regeneration of japonica genotypes during anther culture. Three additional clusters of skewed markers were observed in more than one population in regions where no gametophytic or sterility loci have previously been reported. A total of 17 segregation distortion loci may be postulated based on this study and their locations in the rice genome were estimated.     

Sph3 Is a Glycoside Hydrolase Required for the Biosynthesis of Galactosaminogalactan in Aspergillus fumigatus

Aspergillus fumigatus is the most virulent species within the Aspergillus genus and causes invasive infections with high mortality rates. The exopolysaccharide galactosaminogalactan (GAG) contributes to the virulence of A. fumigatus. A co-regulated five-gene cluster has been identified and proposed to encode the proteins required for GAG biosynthesis. One of these genes, sph3, is predicted to encode a protein belonging to the spherulin 4 family, a protein family with no known function. Construction of an sph3-deficient mutant demonstrated that the gene is necessary for GAG production. To determine the role of Sph3 in GAG biosynthesis, we determined the structure of Aspergillus clavatus Sph3 to 1.25 Å. The structure revealed a (β/α)₈ fold, with similarities to glycoside hydrolase families 18, 27, and 84. Recombinant Sph3 displayed hydrolytic activity against both purified and cell wall-associated GAG. Structural and sequence alignments identified three conserved acidic residues, Asp-166, Glu-167, and Glu-222, that are located within the putative active site groove. In vitro and in vivo mutagenesis analysis demonstrated that all three residues are important for activity. Variants of Asp-166 yielded the greatest decrease in activity suggesting a role in catalysis. This work shows that Sph3 is a glycoside hydrolase essential for GAG production and defines a new glycoside hydrolase family, GH135.     

Ethanol production from marine algal hydrolysates using Escherichia coli KO11

Algae biomass is a potential raw material for the production of biofuels and other chemicals. In this study, biomass of the marine algae, Ulva lactuca, Gelidium amansii,Laminaria japonica, and Sargassum fulvellum, was treated with acid and commercially available hydrolytic enzymes. The hydrolysates contained glucose, mannose, galactose, and mannitol, among other sugars, at different ratios. The Laminaria japonica hydrolysate contained up to 30.5% mannitol and 6.98% glucose in the hydrolysate solids. Ethanogenic recombinant Escherichia coli KO11 was able to utilize both mannitol and glucose and produced 0.4 g ethanol per g of carbohydrate when cultured in L. japonica hydrolysate supplemented with Luria-Bertani medium and hydrolytic enzymes. The strategy of acid hydrolysis followed by simultaneous enzyme treatment and inoculation with E. coli KO11 could be a viable strategy to produce ethanol from marine alga biomass.     

The isolation and characterization of simultaneous saccharification and fermentation microorganisms for Laminaria japonica utilization

Brown seaweed contains various carbohydrates, such as alginate, laminaran, and mannitol, therefore ethanol fermentation was attempted with Nuruk and a mixed culture that included Laminaria japonica. Nuruk is used to make Korean traditional alcohol. In the research, four microorganisms that produced ethanol and had the ability to achieve alginate degradation were obtained on the L. japonica medium. Nuruk 4 was found to produce a better result than the other tested microorganisms, and the optimal substrate for ethanol production was found to be mannitol (2.59 g/L at 96 h). Nuruk 4 was more than three times better compared with Candida tropicalis in regards to ethanol production. When alginate lyase activity occurred, it appeared as a clear zone around Nuruk 3. The maximal ethanol production yield conditions were comprised of Nuruk 3 and 4 on the anaerobic culture. In this case, 2.0 g/L of ethanol were efficiently produced under the same conditions.     

金银花丙酮酸激酶基因的克隆与表达特性分析

采用RT-PCR和RACE技术,首次从金银花中克隆丙酮酸激酶基因全长cDNA,命名为LjPkc(GenBank登录号JQ621946.1),LjPkc基因编码区序列全长为1 533bp,共编码510个氨基酸。基于基因序列亲缘关系分析结果显示,LjPkc基因与烟草Pkc基因亲缘关系最近,属于双子叶植物Pkc基因家族。蛋白质亚细胞定位分析认为LjPkc在线粒体或叶绿体中发挥作用。LjPkc蛋白质的三维空间结构预测结果显示,LjPkc蛋白主要由α-螺旋、不规则盘绕组成。定量PCR检测发现,LjPkc基因在金银花不同组织中广泛表达,但表达水平各有差异,黄花中表达量最高。该研究丰富了Pkc基因库资源,为揭示LjPkc基因在金银花糖代谢方面的生物学作用奠定了基础。     

Genome Sequence of Dyella japonica Strain A8, a Quorum-Quenching Bacterium That Degrades N-Acylhomoserine Lactones,Isolated from Malaysian Tropical Soil

Dyella japonica strain A8 is a Malaysian tropical soil bacterial strain which shows N-acylhomoserine lactone-degrading activity. Here, we present its draft genome sequence. A putative quorum-quenching gene was identified based on the genome sequence analysis of strain A8. To the best of our knowledge, this is the first genome announcement of a member from the genus of Dyella, and this is also the first work that reports the quorum-quenching activity of Dyella japonica.     

Characterization of Insulin-like Peptide (ILP) and Its Potential Role in Ovarian Development of the Cuttlefish Sepiella japonica

The insulin-like peptide (ILP) family is well known for regulating reproduction in invertebrates, while its role in mollusks remains largely unknown. In this study, we first isolated and characterized the ILP gene in the cuttlefish Sepiella japonica. The full-length SjILP cDNA obtained was 926 bp and encoded a precursor protein of 161 amino acids. The precursor protein consisted of a signal peptide, a B chain, a C-peptide, and an A chain. It possessed the typical features of ILP proteins, including two cleavage sites (KR) and eight conserved cysteines. To define the function of SjILP, the expression of SjILP in different tissues and ovarian development stages were analyzed using qRT-PCR. SjILP was mainly expressed in the ovary, and its gene expression correlated with ovarian development. Furthermore, silencing SjILP using RNA interference (RNAi) dramatically decreased the expression levels of four ovarian-development-related genes (vitellogenin1, vitellogenin2, cathepsin L1-like, and follistatin). These data suggest the critical role of SjILP in the regulation of ovarian development in S. japonica.     

Phylogenetic Genomewide Comparisons of the Pentatricopeptide Repeat Gene Family in indica and japonica Rice

More than 400 pentatricopeptide repeat (PPR) genes have been found in higher plants, but most of them have not been functionally analyzed and their origins are still obscure. In this study, we performed phylogenetic genomewide comparisons of the PPR gene family in indica and japonica rice to explore the expansion mechanisms of these genes in higher plants. The functions of PPR genes in plant CMS/Rf systems are also discussed. The results indicate that (1) unequal crossing over participated in the expansion of the newly evolved PPR genes in indica and japonica rice genomes, (2) CMS/Rf systems are different in monocots and dicots, (3) the BT-type CMS/Rf system exists in both indica and japonica rice, and (4) both the PPR gene family and the BT-type CMS/Rf system may have existed before the divergence of indica and japonica rice.     

Sequence and expression analysis of the Arabidopsis IQM family

Four major families have been found so far to possess the calmodulin binding IQ motif/s in plants: the IQD, the myosin, the CAMTA and the CNGC family. We have systematically identified and characterized a novel IQ motif-containing protein family, IQM, in Arabidopsis (Arabidopsis thaliana) using bioinformatics methods. IQM family contains six-member proteins (IQM1-6) which share sequence homology with a pea heavy metal-induced protein 6 and a ribosome-inactivating protein, trichosanthin, as well as IQ motif. IQM family can be divided into two groups, IQM3 and the other member proteins, based on sequence similarity and phylogenetic analysis of sequences. Though almost constitutive expression patterns were found in various plant organs of 6-week-old plants for IQM1 and 2, the other genes exhibited distinct organ-specific expression patterns. Light irradiation and treatment with heavy metals such as CdCl₂ or Pb(NO₃)₂ and high concentrations of mannitol or NaCl also changed expression of each IQM gene in a distinct manner in 7-day-old seedlings. However, treatment with various hormones, such as auxin, abscisic acid, gibberellin, methyl jasmonate and ethylene precursor, did not affect gene expression significantly. These results suggest that each IQM family gene plays a different role in plant development and responses to environmental cues.     

<Emphasis Type="Italic">Rf5</Emphasis> is able to partially restore fertility to Honglian-type cytoplasmic male sterile <Emphasis Type="Italic">japonica</Emphasis> rice (<Emphasis Type="Italic">Oryza sativa</Emphasis>) lines

Three-line japonica hybrids have been developed mainly on Chinsurah Boro II (BT)-type cytoplasmic male sterile (CMS) lines of Oryza sativa L., but the unstable sterility of some BT-type CMS lines, and the threat of genetic vulnerability when using a single cytoplasm source, have inhibited their use in rice cultivation. Previously, the sterility of Honglian (HL)-type japonica CMS lines derived from common red-awned wild rice (Oryza rufipogon) has been proven to be more stable than that of BT-type japonica CMS lines. Here, we genetically characterized HL-type japonica CMS lines and the restorer-of-fertility (Rf) gene for breeding HL-type japonica hybrids. HL-type japonica CMS lines displayed stained abortive pollen grains, unlike HL-type indica CMS lines. The BT-type japonica restorer lines, which contain Rf, had different capabilities to restore HL-LiuqianxinA (HL-LqxA), an HL-type japonica CMS line, and the restorers for the HL-type japonica CMS lines could be selected from the preexisting BT-type japonica restorers in rice production. A genetic analysis showed that the restoration of normal fertility to HL-LqxA was controlled by a major gene and was affected by minor effector genes and/or modifiers. The major Rf in SiR2982, a BT-type japonica restorer, was mapped to a ~100-kb physical region on chromosome 10, and was demonstrated to be Rf5 (Rf1a) by sequencing. Furthermore, Rf5 partially restored fertility and had a dosage effect on HL-type japonica CMS lines. These results will be helpful for the development of HL-type japonica hybrids.