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Article ; Online: An oxidative metabolic pathway of 4-deoxy-L-erythro-5-hexoseulose uronic acid (DEHU) from alginate in an alginate-assimilating bacterium

Ryuji Nishiyama / Takao Ojima / Yuki Ohnishi / Yasuhiro Kumaki / Tomoyasu Aizawa / Akira Inoue

Communications Biology, Vol 4, Iss 1, Pp 1-

2021 Volume 13

Abstract: Nishiyama et al. report the biochemical pathway for the conversion of DEHU to α-ketoglutarate in the alginate-assimilating marine bacterium Flavobacterium sp. strain UMI-01. They show that a parallel oxidative pathway besides the reductive route is ... ...

Abstract	Nishiyama et al. report the biochemical pathway for the conversion of DEHU to α-ketoglutarate in the alginate-assimilating marine bacterium Flavobacterium sp. strain UMI-01. They show that a parallel oxidative pathway besides the reductive route is possible, and provide evidence that this pathway might be conserved in other alginate-degrading bacteria.
Keywords	Biology (General) ; QH301-705.5
Language	English
Publishing date	2021-11-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Decrease of α-defensin impairs intestinal metabolite homeostasis via dysbiosis in mouse chronic social defeat stress model

Kosuke Suzuki / Kiminori Nakamura / Yu Shimizu / Yuki Yokoi / Shuya Ohira / Mizu Hagiwara / Yi Wang / Yuchi Song / Tomoyasu Aizawa / Tokiyoshi Ayabe

Scientific Reports, Vol 11, Iss 1, Pp 1-

2021 Volume 15

Abstract: Abstract Psychological stress has been reported to relate to dysbiosis, imbalance of the intestinal microbiota composition, and contribute to the onset and exacerbation of depression, though, underlying mechanisms of psychological stress-related ... ...

Abstract	Abstract Psychological stress has been reported to relate to dysbiosis, imbalance of the intestinal microbiota composition, and contribute to the onset and exacerbation of depression, though, underlying mechanisms of psychological stress-related dysbiosis have been unknown. It has been previously established that α-defensins, which are effector peptides of innate enteric immunity produced by Paneth cells in the small intestine, play an important role in regulation of the intestinal microbiota. However, the relationship between disruption of intestinal ecosystem and α-defensin under psychological stress is yet to be determined. Here we show using chronic social defeat stress (CSDS), a mouse depression model that (1) the exposure to CSDS significantly reduces α-defensin secretion by Paneth cells and (2) induces dysbiosis and significant composition changes in the intestinal metabolites. Furthermore, (3) they are recovered by administration of α-defensin. These results indicate that α-defensin plays an important role in maintaining homeostasis of the intestinal ecosystem under psychological stress, providing novel insights into the onset mechanism of stress-induced depression, and may further contribute to discovery of treatment targets for depression.
Keywords	Medicine ; R ; Science ; Q
Subject code	150
Language	English
Publishing date	2021-05-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Response surface method for polyhydroxybutyrate (PHB) bioplastic accumulation in Bacillus drentensis BP17 using pineapple peel.

Watsana Penkhrue / Dieter Jendrossek / Chartchai Khanongnuch / Wasu Pathom-Aree / Tomoyasu Aizawa / Rachel L Behrens / S Lumyong

PLoS ONE, Vol 15, Iss 3, p e

2020 Volume 0230443

Abstract: Polyhydroxybutyrate (PHB) is a biodegradable biopolymer which is useful for various applications including packing, medical and coating materials. An endospore-forming bacterium (strain BP17) was isolated from composted soil and evaluated for PHB ... ...

Abstract	Polyhydroxybutyrate (PHB) is a biodegradable biopolymer which is useful for various applications including packing, medical and coating materials. An endospore-forming bacterium (strain BP17) was isolated from composted soil and evaluated for PHB production. Strain BP17, taxonomically identified as Bacillus drentensis, showed enhanced PHB accumulation and was selected for further studies. To achieve maximum PHB production, the culture conditions for B. drentensis BP17 were optimized through response surface methodology (RSM) employing central composite rotatable design (CCRD). The final optimum fermentation conditions included: pineapple peel solution, 11.5% (v/v); tryptic soy broth (TSB), 60 g/L; pH, 6.0; inoculum size, 10% (v/v) and temperature, 28°C for 36 h. This optimization yielded 5.55 g/L of PHB compared to the non-optimized condition (0.17 g/L). PHB accumulated by B. drentensis BP17 had a polydispersity value of 1.59 and an average molecular weight of 1.15x105 Da. Thermal analyses revealed that PHB existed as a thermally stable semi-crystalline polymer, exhibiting a thermal degradation temperature of 228°C, a melting temperature of 172°C and an apparent melting enthalpy of fusion of 83.69 J/g. It is evident that B. drentensis strain BP17 is a promising bacterium candidate for PHB production using agricultural waste, such as pineapple peel as a low-cost alternative carbon source for PHB production.
Keywords	Medicine ; R ; Science ; Q
Subject code	670 ; 660
Language	English
Publishing date	2020-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Implications for the impairment of the rapid channel closing of Proteomonas sulcata anion channelrhodopsin 1 at high Cl− concentrations

Takashi Tsukamoto / Chihiro Kikuchi / Hiromu Suzuki / Tomoyasu Aizawa / Takashi Kikukawa / Makoto Demura

Scientific Reports, Vol 8, Iss 1, Pp 1-

2018 Volume 11

Abstract: Abstract Natural anion channelrhodopsins (ACRs) have recently received increased attention because of their effectiveness in optogenetic manipulation for neuronal silencing. In this study, we focused on Proteomonas sulcata ACR1 (PsuACR1), which has rapid ...

Abstract	Abstract Natural anion channelrhodopsins (ACRs) have recently received increased attention because of their effectiveness in optogenetic manipulation for neuronal silencing. In this study, we focused on Proteomonas sulcata ACR1 (PsuACR1), which has rapid channel closing kinetics and a rapid recovery to the initial state of its anion channel function that is useful for rapid optogenetic control. To reveal the anion concentration dependency of the channel function, we investigated the photochemical properties of PsuACR1 using spectroscopic techniques. Recombinant PsuACR1 exhibited a Cl− dependent spectral red-shift from 531 nm at 0.1 mM to 535 nm at 1000 mM, suggesting that it binds Cl− in the initial state with a K d of 5.5 mM. Flash-photolysis experiments revealed that the photocycle was significantly changed at high Cl− concentrations, which led not only to suppression of the accumulation of the M-intermediate involved in the Cl− non-conducting state but also to a drastic change in the equilibrium state of the other photo-intermediates. Because of this, the Cl− conducting state is protracted by one order of magnitude, which implies an impairment of the rapid channel closing of PsuACR1 in the presence of high concentrations of Cl−.
Keywords	Medicine ; R ; Science ; Q
Subject code	541
Language	English
Publishing date	2018-09-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Functional importance of the oligomer formation of the cyanobacterial H+ pump Gloeobacter rhodopsin

Azusa Iizuka / Kousuke Kajimoto / Tomotsumi Fujisawa / Takashi Tsukamoto / Tomoyasu Aizawa / Naoki Kamo / Kwang-Hwan Jung / Masashi Unno / Makoto Demura / Takashi Kikukawa

Scientific Reports, Vol 9, Iss 1, Pp 1-

2019 Volume 12

Abstract: Abstract Many microbial rhodopsins self-oligomerize, but the functional consequences of oligomerization have not been well clarified. We examined the effects of oligomerization of a H+ pump, Gloeobacter rhodopsin (GR), by using nanodisc containing ... ...

Abstract	Abstract Many microbial rhodopsins self-oligomerize, but the functional consequences of oligomerization have not been well clarified. We examined the effects of oligomerization of a H+ pump, Gloeobacter rhodopsin (GR), by using nanodisc containing trimeric and monomeric GR. The monomerization did not appear to affect the unphotolyzed GR. However, we found a significant impact on the photoreaction: The monomeric GR showed faint M intermediate formation and negligible H+ transfer reactions. These changes reflected the elevated pKa of the Asp121 residue, whose deprotonation is a prerequisite for the functional photoreaction. Here, we focused on His87, which is a neighboring residue of Asp121 and conserved among eubacterial H+ pumps but replaced by Met in an archaeal H+ pump. We found that the H87M mutation removes the “monomerization effects”: Even in the monomeric state, H87M contained the deprotonated Asp121 and showed both M formation and distinct H+ transfer reactions. Thus, for wild-type GR, monomerization probably strengthens the Asp121-His87 interaction and thereby elevates the pKa of Asp121 residue. This strong interaction might occur due to the loosened protein structure and/or the disruption of the interprotomer interaction of His87. Thus, the trimeric assembly of GR enables light-induced H+ transfer reactions through adjusting the positions of key residues.
Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2019-07-01T00:00:00Z
Publisher	Nature Publishing Group
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Role of S-palmitoylation on IFITM5 for the interaction with FKBP11 in osteoblast cells.

Takashi Tsukamoto / Xianglan Li / Hiromi Morita / Takashi Minowa / Tomoyasu Aizawa / Nobutaka Hanagata / Makoto Demura

PLoS ONE, Vol 8, Iss 9, p e

2013 Volume 75831

Abstract: Recently, one of the interferon-induced transmembrane (IFITM) family proteins, IFITM3, has become an important target for the activity against influenza A (H1N1) virus infection. In this protein, a post-translational modification by fatty acids ... ...

Abstract	Recently, one of the interferon-induced transmembrane (IFITM) family proteins, IFITM3, has become an important target for the activity against influenza A (H1N1) virus infection. In this protein, a post-translational modification by fatty acids covalently attached to cysteine, termed S-palmitoylation, plays a crucial role for the antiviral activity. IFITM3 possesses three cysteine residues for the S-palmitoylation in the first transmembrane (TM1) domain and in the cytoplasmic (CP) loop. Because these cysteines are well conserved in the mammalian IFITM family proteins, the S-palmitoylation on these cysteines is significant for their functions. IFITM5 is another IFITM family protein and interacts with the FK506-binding protein 11 (FKBP11) to form a higher-order complex in osteoblast cells, which induces the expression of immunologically relevant genes. In this study, we investigated the role played by S-palmitoylation of IFITM5 in its interaction with FKBP11 in the cells, because this interaction is a key process for the gene expression. Our investigations using an established reporter, 17-octadecynoic acid (17-ODYA), and an inhibitor for the S-palmitoylation, 2-bromopalmitic acid (2BP), revealed that IFITM5 was S-palmitoylated in addition to IFITM3. Specifically, we found that cysteine residues in the TM1 domain and in the CP loop were S-palmitoylated in IFITM5. Then, we revealed by immunoprecipitation and western blot analyses that the interaction of IFITM5 with FKBP11 was inhibited in the presence of 2BP. The mutant lacking the S-palmitoylation site in the TM1 domain lost the interaction with FKBP11. These results indicate that the S-palmitoylation on IFITM5 promotes the interaction with FKBP11. Finally, we investigated bone nodule formation in osteoblast cells in the presence of 2BP, because IFITM5 was originally identified as a bone formation factor. The experiment resulted in a morphological aberration of the bone nodule. This also indicated that the S-palmitoylation contributes to bone formation.
Keywords	Medicine ; R ; Science ; Q
Subject code	570
Language	English
Publishing date	2013-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Probing the Cl−-pumping photocycle of pharaonis halorhodopsin: Examinations with bacterioruberin, an intrinsic dye, and membrane potential-induced modulation of the photocycle

Kikukawa, Takashi / Chikara Kusakabe / Asami Kokubo / Takashi Tsukamoto / Masakatsu Kamiya / Tomoyasu Aizawa / Kunio Ihara / Naoki Kamo / Makoto Demura

Biochimica et biophysica acta. 2015 Aug., v. 1847, no. 8

2015

Abstract: Halorhodopsin (HR) functions as a light-driven inward Cl− pump. The Cl− transfer process of HR from Natronomonas pharaonis (NpHR) was examined utilizing a mutant strain, KM-1, which expresses large amount of NpHR in a complex with the carotenoid ... ...

Abstract	Halorhodopsin (HR) functions as a light-driven inward Cl− pump. The Cl− transfer process of HR from Natronomonas pharaonis (NpHR) was examined utilizing a mutant strain, KM-1, which expresses large amount of NpHR in a complex with the carotenoid bacterioruberin (Brub). When Cl− was added to unphotolyzed Cl−-free NpHR–Brub complex, Brub caused the absorption spectral change in response to the Cl− binding to NpHR through the altered electrostatic environment and/or distortion of its own configuration. During the Cl−-puming photocycle, on the other hand, oppositely directed spectral change of Brub appeared during the O intermediate formation and remained until the decay of the last intermediate NpHR′. These results indicate that Cl− is released into the cytoplasmic medium during the N to O transition, and that the subsequent NpHR′ still maintains an altered protein conformation while another Cl− already binds in the vicinity of the Schiff base. Using the cell envelope vesicles, the effect of the interior negative membrane potential on the photocycle was examined. The prominent effect appeared in the shift of the N–O quasi-equilibrium toward N, supporting Cl− release during the N to O transition. The membrane potential had a much larger effect on the Cl− transfer in the cytoplasmic half channel compared to that in the extracellular half channel. This result may reflect the differences in dielectric constants and/or lengths of the pathways for Cl− transfers during N to O and O to NpHR′ transitions.
Keywords	absorption ; carotenoids ; chlorides ; membrane potential ; mutants ; protein conformation ; schiff bases
Language	English
Dates of publication	2015-08
Size	p. 748-758.
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	282711-6
ISSN	0005-2728 ; 0304-4173
ISSN	0005-2728 ; 0304-4173
DOI	10.1016/j.bbabio.2015.05.002
Database	NAL-Catalogue (AGRICOLA)

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Article: Photochemical characterization of actinorhodopsin and its functional existence in the natural host

Nakamura, Shintaro / Takashi Kikukawa / Jun Tamogami / Masakatsu Kamiya / Tomoyasu Aizawa / Martin W. Hahn / Kunio Ihara / Naoki Kamo / Makoto Demura

Biochimica et biophysica acta. 2016 Dec., v. 1857, no. 12

2016

Abstract: Actinorhodopsin (ActR) is a light-driven outward H+ pump. Although the genes of ActRs are widely spread among freshwater bacterioplankton, there are no prior data on their functional expression in native cell membranes. Here, we demonstrate ActR ... ...

Abstract	Actinorhodopsin (ActR) is a light-driven outward H+ pump. Although the genes of ActRs are widely spread among freshwater bacterioplankton, there are no prior data on their functional expression in native cell membranes. Here, we demonstrate ActR phototrophy in the native actinobacterium. Genome analysis showed that Candidatus Rhodoluna planktonica, a freshwater actinobacterium, encodes one microbial rhodopsin (RpActR) belonging to the ActR family. Reflecting the functional expression of RpActR, illumination induced the acidification of the actinobacterial cell suspension and then elevated the ATP content inside the cells. The photochemistry of RpActR was also examined using heterologously expressed RpActR in Escherichia coli membranes. The purified RpActR showed λmax at 534nm and underwent a photocycle characterized by the very fast formation of M intermediate. The subsequent intermediate, named P620, could be assigned to the O intermediate in other H+ pumps. In contrast to conventional O, the accumulation of P620 remains prominent, even at high pH. Flash-induced absorbance changes suggested that there exists only one kind of photocycle at any pH. However, above pH7, RpActR shows heterogeneity in the H+ transfer sequences: one first captures H+ and then releases it during the formation and decay of P620, while the other first releases H+ prior to H+ uptake during P620 formation.
Keywords	Actinobacteria ; Escherichia coli ; absorbance ; acidification ; adenosine triphosphate ; bacterioplankton ; cell membranes ; freshwater ; genes ; lighting ; pH ; photochemistry ; proton pump ; protons ; rhodopsin ; sequence analysis
Language	English
Dates of publication	2016-12
Size	p. 1900-1908.
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	282711-6
ISSN	0005-2728 ; 0304-4173
ISSN	0005-2728 ; 0304-4173
DOI	10.1016/j.bbabio.2016.09.006
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: In vivo fluorescence correlation spectroscopy analyses of FMBP‐1, a silkworm transcription factor

Motosuke Tsutsumi / Hideki Muto / Shohei Myoba / Mai Kimoto / Akira Kitamura / Masakatsu Kamiya / Takashi Kikukawa / Shigeharu Takiya / Makoto Demura / Keiichi Kawano / Masataka Kinjo / Tomoyasu Aizawa

FEBS Open Bio, Vol 6, Iss 2, Pp 106-

2016 Volume 125

Abstract: Fibroin modulator‐binding protein 1 (FMBP‐1) is a silkworm transcription factor that has a unique DNA‐binding domain called the one score and three amino acid peptide repeat (STPR). Here we used fluorescence correlation spectroscopy (FCS) to analyze the ... ...

Abstract	Fibroin modulator‐binding protein 1 (FMBP‐1) is a silkworm transcription factor that has a unique DNA‐binding domain called the one score and three amino acid peptide repeat (STPR). Here we used fluorescence correlation spectroscopy (FCS) to analyze the diffusion properties of an enhanced green fluorescent protein‐tagged FMBP‐1 protein (EGFP‐FMBP‐1) expressed in posterior silk gland (PSG) cells of Bombyx mori at the same developmental stage as natural FMBP‐1 expression. EGFP‐FMBP‐1 clearly localized to cell nuclei. From the FCS analyses, we identified an immobile DNA‐bound component and three discernible diffusion components. We also used FCS to observe the movements of wild‐type and mutant EGFP‐FMBP‐1 proteins in HeLa cells, a simpler experimental system. Based on previous in vitro observation, we also introduced a single amino acid substitution in order to suppress stable FMBP‐1‐DNA binding; specifically, we replaced the ninth Arg in the third repeat within the STPR domain with Ala. This mutation completely disrupted the slowest diffusion component as well as the immobile component. The diffusion properties of other FMBP‐1 mutants (e.g. mutants with N‐terminal or C‐terminal truncations) were also analyzed. Based on our observations, we suggest that the four identifiable movements might correspond to four distinct FMBP‐1 states: (a) diffusion of free protein, (b) and (c) two types of transient interactions between FMBP‐1 and chromosomal DNA, and (d) stable binding of FMBP‐1 to chromosomal DNA.
Keywords	DNA‐binding protein ; fluorescence correlation spectroscopy ; one score and three peptide repeat domain ; silkworm ; transcription factor ; Biology (General) ; QH301-705.5
Subject code	612
Language	English
Publishing date	2016-02-01T00:00:00Z
Publisher	Wiley
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Interaction between tachyplesin I, an antimicrobial peptide derived from horseshoe crab, and lipopolysaccharide

Kushibiki, Takahiro / Keiichi Kawano / Makoto Demura / Masakatsu Kamiya / Mineyuki Mizuguchi / Shun-ichiro Kawabata / Takashi Kikukawa / Tomoyasu Aizawa / Yasuhiro Kumaki

BBA - Proteins and Proteomics. 2014 Mar., v. 1844

2014

Abstract: Lipopolysaccharide (LPS) is a major constituent of the outer membrane of Gram-negative bacteria and is the very first site of interactions with antimicrobial peptides (AMPs). In order to gain better insight into the interaction between LPS and AMPs, we ... ...

Abstract	Lipopolysaccharide (LPS) is a major constituent of the outer membrane of Gram-negative bacteria and is the very first site of interactions with antimicrobial peptides (AMPs). In order to gain better insight into the interaction between LPS and AMPs, we determined the structure of tachyplesin I (TP I), an antimicrobial peptide derived from horseshoe crab, in its bound state with LPS and proposed the complex structure of TP I and LPS using a docking program.CD and NMR measurements revealed that binding to LPS slightly extends the two Î²-strands of TP I and stabilizes the whole structure of TP I. The fluorescence wavelength of an intrinsic tryptophan of TP I and fluorescence quenching in the presence or absence of LPS indicated that a tryptophan residue is incorporated into the hydrophobic environment of LPS. Finally, we succeeded in proposing a structural model for the complex of TP I and LPS by using a docking program. The calculated model structure suggested that the cationic residues of TP I interact with phosphate groups and saccharides of LPS, whereas hydrophobic residues interact with the acyl chains of LPS.
Keywords	antimicrobial peptides ; fluorescence ; Gram-negative bacteria ; hydrophobicity ; lipopolysaccharides ; Merostomata ; models ; nuclear magnetic resonance spectroscopy ; phosphates ; tryptophan ; wavelengths
Language	English
Dates of publication	2014-03
Size	p. 527-534.
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	2918798-9
ISSN	1878-1454 ; 1570-9639
ISSN (online)	1878-1454
ISSN	1570-9639
DOI	10.1016/j.bbapap.2013.12.017
Database	NAL-Catalogue (AGRICOLA)

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