Kyushu University Academic Staff Educational and Research Activities Database
List of Papers
Takashi Nakashima Last modified date:2023.11.27

Assistant Professor / molecular biochemistry / Department of Bioscience and Biotechnology / Faculty of Agriculture


Papers
1. Alaa Elgaabari, Nana Imatomi, Hirochika Kido, Miyumi Seki, Sakiho Tanaka, Yuji Matsuyoshi, Takashi Nakashima, Shoko Sawano, Wataru Mizunoya, Takahiro Suzuki, Mako Nakamura, Judy E Anderson, Ryuichi Tatsumi, A pilot study on nitration/dysfunction of NK1 segment of myogenic stem cell activator HGF., Biochemistry and biophysics reports, 10.1016/j.bbrep.2022.101295, 31, 101295-101295, 2022.09.
2. Xuchun Qiu, Koki Mukai, Yohei Shimasaki, Min Wu, Chen Chen, Yijiang Lu, Hirofumi Ichinose, Takashi Nakashima, Yoko Kato-Unoki, Yuji Oshima, Diurnal variations in expression of photosynthesis-related proteins in the harmful Raphidophyceae Chattonella marina var. antiqua, Journal of Experimental Marine Biology and Ecology, 10.1016/j.jembe.2020.151361, 527, 2020.06, Many biological features of Chattonella species display diurnal oscillations, but little is known about the corresponding cellular responses at the proteome level. In the present study, we hypothesized that the abundance of certain proteins would periodically fluctuate to suit the diurnal changes of biological processes in Chattonella cells. To test this hypothesis, we undertook proteomic analysis over 7 time points covering a 24-h period in C. marina var. antiqua cells at early stationary phase (12:00, 17:00, 20:00, 24:00 on day 8, and 05:00, 08:00, 12:00 on the following day). The protein profiles of C. marina var. antiqua cells collected from the diurnal cycle shared a majority of common protein spots. However, the expression of 16 out of 124 detected spots exhibited significant differences between light and dark periods and/or over the 7 time points of the diurnal cycle. The proteins of OEE, Cyt c553, and AtpB showed significantly higher expression levels in the light period, and generally were maximally expressed during the period of 12:00–17:00. The proteins of GAPDH and RPL12 generally showed higher expression levels in the dark period, and were maximally expressed during the period of 20:00–24:00. These findings support our hypothesis, and suggest that the periodic expressions of these proteins may be critical either for optimal cell utilization of resources or to maintain proper cell function throughout diurnal cycles..
3. 高緒柱,大嶋浩介,上田敏史,中島 崇, 木村 誠, A three-dimensional model of RNase P in the hyperthermophilic archaeon Pyrococcus horikoshii OT3, JOURNAL OF BIOCHEMISTRY, 10.1016/j.bbrc.2017.09.085, 493, 2, 1063-1068, 2017.11.
4. Xuchun Qiu, Kokl Mukai, Yohei Shimasaki, Michito Tsuyama, Tadashi Matsubara, Takashi Nakashima, Hirofumi Ichinose, Yu Nakajima, Ibuneo Honjo, Yuji Oshima, Variations in the expression of photosynthesis-related proteins in field Chattonella marina cells during a harmful algal bloom, Journal of the Faculty of Agriculture, Kyushu University, 62, 2, 373-380, 2017.09, Time series variations in protein expression profiles in field Chattonella marina cells were investigated during a HAB occurred in the inner part of Ariake Sea, Japan (5-14 September, 2012). This study aimed to gather information on the molecular mechanisms underlying the physiological responses in field C. marina population during HAB. Proteomic analysis showed that the abundance of -37% protein spots (40 out of 108 detected from 2-DE gel images) significantly varied with the sampling date. Significant decreases in the abundances of proteins involved in photosystem II (LHCP 4), electron transfer chain (Cyt c553), Calvin cycle (GAPDH), and chloroplast antioxidant system (2-Cys Prx) were observed as the bloom progressed, suggesting the efficiencies of those photosynthetic pathways declined during the bloom. In addition, the abundances of the above proteins showed significant positive correlations with the Fv/Fm ratio and growth rate of C. marina and with DIN concentrations (except LHCP 4). Our findings suggested that declined expressions of those photosynthesis-related proteins presented some molecular foundation of the decreases in Fv/Fm ratio and growth rate of C. marina during the bloom, and also provided insight into mechanistic links between the external/internal factors and physiological responses of C. marina that may ultimately dictate the ecology of the bloom..
5. 中島 崇, 木村 誠, Functional characterization of archaeal homologs of human nuclear RNase P proteins Rpp21 and Rpp29 provides insights into the molecular basis of their cooperativity in catalysis, JOURNAL OF BIOCHEMISTRY, 10.1016/j.bbrc.2016.10.142, 482, 1, 68-74, 2017.01.
6. 中島 崇, 木村 誠, Structural basis for recognition of a kink-turn motif by an archaeal homologue of human RNase P protein Rpp38, JOURNAL OF BIOCHEMISTRY, 10.1016/j.bbrc.2016.04.118, 474, 3, 541-546, 2016.06.
7. Takashi Nakashima, Yoshimitsu Kakuta, makoto kimura, Ueda T, Suematsu K, On archaeal homologs of the human RNase P proteins Pop5 and Rpp30 in the hyperthermophilic archaeon Thermococcus kodakarensis., Biosci Biotechnol Biochem. , 23, 1-8, 2015.02.
8. Takashi Nakashima, makoto kimura, Yoshimitsu Kakuta, Imai T, Ueda T, Hazeyama K, Furutani T, Enhancement of RNA annealing and strand displacement found in archaeal ribonuclease P proteins is conserved in Escherichia coli protein C5 and yeast protein Rpr2., Biosci Biotechnol Biochem. , 78, 10, 1700-1702, 2014.10.
9. Takashi Nakashima, Yoshimitsu Kakuta, makoto kimura, Takahiro Nakamura, Imai T, Maeda T, Pentatricopeptide repeat motifs in the processing enzyme PRORP1 in Arabidopsis thaliana play a crucial role in recognition of nucleotide bases at TψC loop in precursor tRNAs., Biochem Biophys Res Commun. , 450, 4, 1541-1546, 2014.08.
10. Takashi Nakashima, makoto kimura, Yoshimitsu Kakuta, Hino M, Zhang J, Takagi H, Miyoshi T, Uchiumi T, Characterization of putative toxin/antitoxin systems in Vibrio parahaemolyticus., J Appl Microbiol. , 117, 1, 185-195, 2014.07.
11. Toshihumi Ueda, Hiroshi Yamaguchi, Mitsuru Miyanoshita, Takashi Nakashima, Yoshimitsu Kakuta, makoto kimura, Characterization of the peripheral structures of archaeal RNase P RNA from Pyrococcus horikoshii OT3.
, J Biochem. , 155, 1, 25-33, 2014.01.
12. Takashi Nakashima, makoto kimura, Yoshimitsu Kakuta, Characterization of the peripheral structures of archaeal RNase P RNA from Pyrococcus horikoshii OT3., J Biochem, 2014.01.
13. Takashi Nakashima, M. IshiHara, T. Ueda, Etsuko Nishimoto, Yoshimitsu Kakuta, makoto kimura, Extra-structural elements in the RNA recognition motif in archaeal Pop5 play a crucial role in the activation of RNase P RNA from Pyrococcus horikoshii OT3.

, Biochem Biophys Res Commun. , 440, 4, 594-598, 2013.11.
14. Zwieb C, Nakao Y, Nakashima T, Takagi H, Goda S, Andersen ES, Kakuta Y, Kimura M., Structural modeling of RNase P RNA of the hyperthermophilic archaeon Pyrococcus horikoshii OT3., Biochem Biophys Res Commun., 414, 3, 517-522, 2011.10, Ribonuclease P (RNase P) is a ubiquitous trans-acting ribozyme that processes the 5' leader sequence of precursor tRNA (pre-tRNA). The RNase P RNA (PhopRNA) of the hyperthermophilic archaeon Pyrococcus horikoshii OT3 is central to the catalytic process and binds five proteins (PhoPop5, PhoRpp21, PhoRpp29, PhoRpp30, and PhoRpp38) which contribute to the enzymatic activity of the holoenzyme. Despite significant progress in determining the crystal structure of the proteins, the structure of PhopRNA remains elusive. Comparative analysis of the RNase P RNA sequences and existing crystallographic structural information of the bacterial RNase P RNAs were combined to generate a phylogenetically supported three-dimensional (3-D) model of the PhopRNA. The model structure shows an essentially flat disk with 16 tightly packed helices and a conserved face suitable for the binding of pre-tRNA. Moreover, the structure in solution was investigated by enzymatic probing and small-angle X-ray scattering (SAXS) analysis. The low resolution model derived from SAXS and the comparative 3-D model have similar overall shapes. The 3-D model provides a framework for a better understanding of structure-function relationships of this multifaceted primordial ribozyme..
15. Hara T, Terada A, Yamaguchi H, Nakashima T, Kakuta Y, Kimura M., The contribution of peripheral stem-loops to the catalytic activity of archaeal RNase P RNA from Pyrococcus horikoshii OT3., Biosci Biotechnol Biochem. , 75, 4, 816-819, 2011.04.
16. Hayashi T, Takamatsu N, Nakashima T, Arita T. , Immunological Characterization of Honey Proteins and Identification of MRJP 1 as an IgE-Binding Protein.

, Biocsi. Biotechnol. Biochem., 75(3), 556-560, 2011.03.
17. M.Shinohara, J.X. Guo, M. Mori, T. Nakashima, H. Takagi, E. Nishimoto, S. Yamashita, K. Tsumoto, Y. Kakuta, and M. Kimura, The sturctural mechanism of the inhibition of archaeal RelE toxin by iots cognate RelB antitoxin., Biochem. Biophys. Res. Commun., 2010.09.
18. Kosaka S, Hada K, Nakashima T, Kimura M. , Structural changes in ribonuclease P RNA in the hyperthermophilic archaeon Pyrococcus horikoshii OT3 induced on interaction with proteins., Biosci Biotechnol Biochem., 74(2):394-396., 2010.02.
19. Kikutake C, Shinohara M, Takagi H, Nakashima T, Kimura M., The C-terminal portion of an archaeal toxin, aRelE, plays a crucial role in protein synthesis inhibition., Biosci Biotechnol Biochem. , 73(12):2766-2778., 2009.12.
20. Vu NT, Shimada H, Kakuta Y, Nakashima T, Ida H, Omori T, Nishi A, Satoh H, Kimura M., Biochemical and crystallographic characterization of the starch branching enzyme I (BEI) from Oryza sativa L., Biosci Biotechnol Biochem. 2008 Nov;72(11):2858-66. Epub 2008 Nov 7., 72(11):2858-66. , 2008.11.
21. Hada K, Nakashima T, Osawa T, Shimada H, Kakuta Y, Kimura M. , Crystal structure and functional analysis of an archaeal chromatin protein Alba
from the hyperthermophilic archaeon Pyrococcus horikoshii OT3.
, Biosci Biotechnol Biochem, 72(3),749-58. (2008)
, 2008.03.
22. Zhang X, Nakashima T, Kakuta Y, Yao M, Tanaka I, Kimura M. , Crystal structure of an archaeal Ski2p-like protein from Pyrococcus horikoshii OT3.
, Protein Science, 17(1),136-45. (2008)
, 2008.01.
23. Shin Kawano, Yoshimitsu Kakuta, Takashi Nakashim. Makoto Kimura, Crystal structures of the Nicotiana glutinosa ribonuclease NT in complex with nucleoside monophosphates., Journal of Biochemistry, 140(3),375-381, 2006.09.
24. T. Nomura, K. Nakano, Y. Maki, T. Naganuma, T. Nakashima, I. Tanaka, M. Kimura, A. Hachimori, and T. Uchiumi, In vitro reconstitution of the GTPase-associated center of the archaebacterial ribosome: the functional features observed in a hybrid form with Escherichia coli 50S subunits., Biochemical Journal, 396(3),565-571, 2006.06.
25. T. Nakashima, M. Yao, S. Kawamura, K. Iwasaki, M. Kimura and I. Tanaka, Ribosomal protein L5 has a highly twisted concave surface and flexible arms responsible for rRNA binding, RNA, 10.1017/S1355838201002345, 7, 5, 692-701, 7, 692-701, 2001.05.
26. Shin Kawano, Takashi Nakashima, Yoshimitsu Kakuta, Isao Tanaka, Makoto Kimura , Crystal structure of protein Ph1481p in complex with protein Ph1877p of archaeal RNase P from Pyrococcus horikoshii OT3: implication of dimer formation of the holoenzyme, Journal of Moleculer Biology, 357(2),583-591, 2006.01.
27. T. Nakashima, M. Kimura, A. Nakagawa and I. Tanaka, Crystallization and preliminary X-ray crystallographic study of a 23S rRNA binding domain of the ribosomal protein L2 from Bacillus stearothermophilus, Journal of Structural Biology, 10.1006/jsbi.1998.4053, 124, 1, 99-101, 124, 99-101, 1998.12.