Biomedical subjects

Naoko Shimada

Publications and source records attributed to Naoko Shimada.

8 recordsLinked to original sources

PubMed2006

Identification and characterization of L-arabonate dehydratase, L-2-keto-3-deoxyarabonate dehydratase, and L-arabinolactonase involved in an alternative pathway of L-arabinose metabolism. Novel evolutionary insight into sugar metabolism.

Azospirillum brasiliense possesses an alternative pathway of L-arabinose metabolism, different from the known bacterial and fungal pathways. In the preceding articles, we identified and characterized L-arabinose-1-dehydrogenase and alpha-ketoglutaric semialdehyde dehydrogenase, which catalyzes the first and final reaction steps in this pathway, respectively (Watanabe, S., Kodaki, T., and Makino, K. (2006) J. Biol. Chem. 281, 2612-2623 and Watanabe, S., Kodaki, T., and Makino, K. (2006) J. Biol. Chem. 281, 28876-28888). We here report the remaining three enzymes, L-arabonate dehydratase, L-2-keto-3-deoxyarabonate (L-KDA) dehydratase, and L-arabinolactonase. N-terminal amino acid sequences of L-arabonate dehydratase and L-KDA dehydratase purified from A. brasiliense cells corresponded to those of AraC and AraD genes, which form a single transcriptional unit together with the L-arabinose-1-dehydrogenase gene. Furthermore, the L-arabinolactonase gene (AraB) was also identified as a component of the gene cluster. Genetic characterization of the alternative L-arabinose pathway suggested a significant evolutional relationship with the known sugar metabolic pathways, including the Entner-Doudoroff (ED) pathway and the several modified versions. L-arabonate dehydratase belongs to the ILVD/EDD family and spectrophotometric and electron paramagnetic resonance analysis revealed it to contain a [4Fe-4S](2+) cluster. Site-directed mutagenesis identified three cysteine ligands essential for cluster coordination. L-KDA dehydratase was sequentially similar to DHDPS/NAL family proteins. D-2-Keto-3-deoxygluconate aldolase, a member of the DHDPS/NAL family, catalyzes the equivalent reaction to L-KDA aldolase involved in another alternative L-arabinose pathway, probably associating a unique evolutional event between the two alternative L-arabinose pathways by mutation(s) of a common ancestral enzyme. Site-directed mutagenesis revealed a unique catalytic amino acid residue in L-KDA dehydratase, which may be a candidate for such a natural mutation.

Amino Acid Sequence↗

PubMed2006

Activation of the chicken Ig-beta locus by the collaboration of scattered regulatory regions through changes in chromatin structure.

A total of 10 B-lymphocyte-specific DNase I hypersensitive sites located in the chicken Ig-beta locus were divided into four regions and combinations of deletions of these regions were carried out. A decrease in transcription of the Ig-beta gene to <3% was demonstrated in cells with deletions in all four regions. The Ig-beta chromatin was resistant to DNase I digestion in these cells. Thus, the collaboration is shown to convert the Ig-beta chromatin from the condensed state to a relaxed state. H3 and H4 acetylation decreased to <8% but H3K4 hypermethylation was observed at the Ig-beta promoter and exon 3. The collaboration of four regions had virtually no effect on CG hypomethylation in the region upstream the transcriptional start site. Accordingly, neither the DNase I general sensitive state in the Ig-beta chromatin nor hyperacetylation of H3 and H4 histones in the promoter proximal region causes H3K4 di-methylation or CG hypomethylation in the promoter. From these analyses, a chromatin situation was found in which both an active state, such as enhanced H3K4 methylation, or CG hypomethylation, and an inactive state, such as DNase I resistance in the Ig-beta chromatin or hypoacetylation of H3 and H4 histones in the Ig-beta locus, coexist.

Acetylation↗

PubMed2006

Changes in gravitational force cause changes in gene expression in the lens of developing zebrafish.

Gravity has been a constant physical factor during the evolution and development of life on Earth. We have been studying effects of simulated microgravity on gene expression in transgenic zebrafish embryos expressing gfp under the influence of gene-specific promoters. In this study, we assessed the effect of microgravity on the expression of the heat shock protein 70 (hsp70) gene in lens during development using transgenic zebrafish embryos expressing gfp under the control of hsp70 promoter/enhancer. Hsp70:gfp expression was up-regulated (45%) compared with controls during the developmental period that included the lens differentiation stage. This increase was lens specific, because the entire embryo showed only a 4% increase in gfp expression. Northern blot and in situ hybridization analysis indicated that the hsp70:gfp expression recapitulated endogenous hsp70 mRNA expression. Hypergravity exposure also increased hsp70 expression during the same period. In situ hybridization analysis for two lens-specific crystallin genes revealed that neither micro- nor hypergravity affected the expression level of betaB1-crystallin, a non-hsp gene used as a marker for lens differentiation. However, hypergravity changed the expression level of alphaA-crystallin, a member of the small hsp gene family. Terminal deoxynucleotidyl transferase-mediated deoxyuridinetriphosphate nick end-labeling (TUNEL) assay analysis showed that altered-gravity (Deltag) decreased apoptosis in lens during the same period and the decrease correlated with the up-regulation of hsp70 expression, suggesting that elimination of nuclei from differentiating lens fiber cells was suppressed probably through hsp70 up-regulation. These results support the idea that Deltag influences hsp70 expression and differentiation in lens-specific and developmental period specific manners and that hsp family genes play a specific role in the response to Deltag.

Animals↗

PubMed2005

Changes in gravitational force affect gene expression in developing organ systems at different developmental times.

BACKGROUND: Little is known about the affect of microgravity on gene expression, particularly in vivo during embryonic development. Using transgenic zebrafish that express the gfp gene under the influence of a beta-actin promoter, we examined the affect of simulated-microgravity on GFP expression in the heart, notochord, eye, somites, and rohon beard neurons. We exposed transgenic zebrafish to simulated-microgravity for different durations at a variety of developmental times in an attempt to determine periods of susceptibility for the different developing organ systems. RESULTS: The developing heart had a period of maximum susceptibility between 32 and 56 hours after fertilization when there was an approximately 30% increase in gene expression. The notochord, eye, somites, and rohon beard neurons all showed periods of susceptibility occurring between 24 and 72 hours after fertilization. In addition, the notochord showed a second period of susceptibility between 8 and 32 hours after fertilization. Interestingly, all organs appeared to be recovering by 80 hours after fertilization despite continued exposure to simulated-microgravity. CONCLUSION: These results support the idea that exposure to microgravity can cause changes in gene expression in a variety of developing organ systems in live embryos and that there are periods of maximum susceptibility to the effects.

Animals↗

PubMed2004

Novel metalloprotease-disintegrin, meltrin epsilon (ADAM35), expressed in epithelial tissues during chick embryogenesis.

Members of the ADAM (a disintegrin and metalloprotease) family are involved in fertilization, morphogenesis, and pathogenesis. Their metalloprotease domains mediate limited proteolysis, including ectodomain shedding of membrane-anchored growth factors and intercellular-signaling proteins, and their disintegrin domains play regulatory roles in cell adhesion and migration. In screening for cDNAs encoding chicken ADAM proteins expressed during muscle development, we identified Meltrin epsilon as a novel member of this family. To elucidate its functions, we investigated its expression during development by using antibodies raised against its protease domain. In the somites, Meltrin epsilon protein was specifically expressed in the myotomal cells, which delaminate from the dermomyotome to form epithelial sheets. It was also found in the surface ectoderm, lens placodes, otic vesicles, and the gut epithelia. Basolateral localization of Meltrin epsilon in these epithelial cells suggests its unique roles in the organization of the epithelial tissues and development of the sensory organs and the gut.

Amino Acid Sequence↗

PubMed2003

Equarin, a novel soluble molecule expressed with polarity at chick embryonic lens equator, is involved in eye formation.

The lens plays an important role in eye development. To investigate the molecular mechanisms involved, we used signal sequence trap screens with a chicken lens cDNA library and identified a novel secreted molecule, equarin. Equarin encodes consensus repeat domains conserved in human SRPX and mouse Urb. In the embryonic eye, equarin transcript is detected exclusively in the lens, and persists in the lens equatorial region in a high-dorsal-to-low-ventral gradient. In vitro analysis of equarin protein indicated that after translation, it is modified, cleaved, and secreted to extracellular locations. Microinjection of equarin mRNA into Xenopus embryos induced abnormal eye development. These data suggest that equarin is involved in eye formation.

Alternative Splicing↗

PubMed2003

Cooperative action between L-Maf and Sox2 on delta-crystallin gene expression during chick lens development.

Lens development is regulated by a variety of transcription factors with distinct properties. The lens-specific transcription factor, L-Maf, is essential for lens formation and induces lens-specific markers, such as the crystallin genes. In this study, we analyzed the mechanism by which L-Maf regulates delta-crystallin expression. Misexpression of L-Maf in the head ectoderm of lens placode-forming embryos by in ovo electroporation induced delta-crystallin only in the region surrounding the lens. To define this restricted expression, we misexpressed L-Maf together with other transcription factors implicated in delta-crystallin expression. Sox2 plus L-Maf expanded the delta-crystallin-inducible domain to the entire head ectoderm and simultaneously increased the quantity of delta-crystallin mRNA expressed. In contrast, co-expression of L-Maf with other factors such as Pax6, Six3 and Prox1 had little or no effect on delta-crystallin. We also observed that L-Maf and Sox2 cooperatively enhanced the transactivation of a reporter gene bearing the delta-crystallin enhancer in ovo, implying that L-Maf and Sox2 can induce delta-crystallin through the same enhancer. In conclusion, we report here that L-Maf and Sox2 cooperatively regulate the expression of delta-crystallin during chick lens development.

Animals↗

PubMed2003

RaxL regulates chick ganglion cell development.

RaxL is a paired-like homeobox gene involved in vertebrate eye morphogenesis. We examined RaxL protein expression patterns during chick retinal development in combination with ganglion cell markers including the RA4 antigen, cBrn-3, Islet-1 and neuronal type III beta-tubulin. Double-immunostaining demonstrated that downregulation of RaxL protein correlates with upregulation of ganglion cell markers in the ganglion cell layer (GCL). To explore this correlation in vivo, we performed gain- and loss-of-function experiments by electroporating retroviral vectors encoding wild-type and dominant-negative-RaxL into the optic vesicles of stage 10 chick embryos. Infection with virus expressing RaxL led to a 35% decrease in Islet-1-positive ganglion cells at E5.0 and a complete loss of ganglion cells at E15, with no effect on displaced amacrine cells in the GCL. When dominant-negative RaxL was expressed, the total number of cells in the GCL increased by approximately 40% at E5.0 but was reduced to 40% at E15, due to ectopic apoptosis in the GCL from E9 to E15. These results suggest that RaxL gives an inhibitory effect on ganglion cell development and that the loss of RaxL expression is required for maintenance of ganglion cells.

Animals↗