bims-polyam 2019-06-09 papers

bims-polyam

Biomed News

on Polyamines

Issue of 2019‒06‒09
seventeen papers selected by
Alexander Ivanov
Engelhardt Institute of Molecular Biology

Discovery and antitumor evaluation of novel inhibitors of spermine oxidase.
New coordination compounds of citric acid and polyamines with lanthanide ions - potential application in monitoring the treatment of cancer diseases.
MYC-driven small cell lung cancer is metabolically distinct and vulnerable to arginine depletion.
The C-terminal flexible region of branched-chain polyamine synthase facilitates substrate specificity and catalysis.
Spermidine strongly increases the fidelity of Escherichia coli CRISPR Cas1-Cas2 integrase.
Absolute requirement for polyamines for growth of Escherichia coli mutants (mnmE/G) defective in modification of the wobble anticodon of transfer-RNA.
A metabolic profile of polyamines in Parkinson's disease: a promising biomarker.
Amniculibacterium aquaticum gen. nov., sp. nov., a new member of the family Flavobacteriaceae isolated from a stream.
Polyamines modulate growth, antioxidant activity, and genomic DNA in heavy metal-stressed wheat plant.
Flavobacterium stagni sp. nov., isolated from a freshwater reservoir.
Molecular Targets for Malarial Chemotherapy: A Review.
Inhella crocodyli sp. nov., isolated from a crocodile pond.
Hymenobacter oligotrophus sp. nov., isolated from a contaminated agar plate.
Arginase II activity regulates cytosolic Ca2+ level in a p32-dependent manner that contributes to Ca2+-dependent vasoconstriction in native low-density lipoprotein-stimulated vascular smooth muscle cells.
Sphingobium terrigena sp. nov., isolated from gasoline-contaminated soil.
Chakrabartia godavariana gen. nov., sp. nov., a novel member of the family Sphingomonadaceae isolated from the Godavari River, India.
Disturbance of I1-imidazoline receptor signal transduction in cardiomyocytes of Spontaneously Hypertensive Rats.

J Enzyme Inhib Med Chem. 2019 Dec;34(1): 1140-1151

Discovery and antitumor evaluation of novel inhibitors of spermine oxidase.

Lidan Sun, Jianlin Yang, Yu Qin, Yanlin Wang, Hongyan Wu, You Zhou, Chunyu Cao.

  Increasing knowledge of the relationship between cancer and dysregulated polyamine catabolism suggests interfering with aberrant polyamine metabolism for anticancer therapy that will have considerable clinical promise. SMO (spermine oxidase) plays an essential role in regulating the polyamines homeostasis. Therefore, development of SMO inhibitors has increasingly attracted much attention. Previously, we successfully purified and characterised SMO. Here, we presented an in silico drug discovery pipeline by combining pharmacophore modelling and molecular docking for the virtual screening of SMO inhibitors. In vitro evaluation showed that N-(3-{[3-(dimethylamino)propyl]amino}propyl)-8-quinolinecarboxamide (SI-4650) inhibited SMO enzyme activity, increased substrate spermine content and reduced product spermidine content, indicating that SI-4650 can interfere with polyamine metabolism. Furthermore, SI-4650 treatment suppressed cell proliferation and migration. Mechanistically, SI-4650 caused cell cycle arrest, induced cell apoptosis, and promoted autophagy. These results demonstrated the properties of interfering with polyamine metabolism of SI-4650 as a SMO inhibitor and the potential for cancer treatment.

Keywords:  Quinolinecarboxamide; antitumor activity; spermine oxidase

DOI:  https://doi.org/10.1080/14756366.2019.1621863
J Inorg Biochem. 2019 May 17. pii: S0162-0134(19)30093-5. [Epub ahead of print]198 110715

New coordination compounds of citric acid and polyamines with lanthanide ions - potential application in monitoring the treatment of cancer diseases.

Michał Zabiszak, Martyna Nowak, Malwina Gabryel, Kazuma Ogawa, Małgorzata T Kaczmarek, Zbigniew Hnatejko, Renata Jastrzab.

  Non-covalent interaction in the binary systems of polyamines (putrescine, spermidine, spermine) with citric acid and complex formation in the binary as well as ternary systems of lanthanide(III) ions, citric acid and polyamine have been investigated. The studies were performed in aqueous solution. The overall stability constants of the complexes were determined using the potentiometric method with computer analysis of the data. Only mononuclear type of complexes were found in the ternary systems and polyamines were located in the outer as well as inner coordination sphere. Non-covalent interaction between biogenic amines and citric acid in the binary and ternary systems were confirmed on the basis of the equilibrium constants analysis and spectroscopic studies.

Keywords:  Biogenic amines; Citric acid; F-electron complexes; Non-covalent interactions; Potentiometric measurements; Spectroscopic studies

DOI:  https://doi.org/10.1016/j.jinorgbio.2019.110715
Clin Cancer Res. 2019 Jun 04. pii: clincanres.4140.2018. [Epub ahead of print]

MYC-driven small cell lung cancer is metabolically distinct and vulnerable to arginine depletion.

Milind D Chalishazar, Sarah J Wait, Fang Huang, Abbie S Ireland, Anandaroop Mukhopadhyay, Younjee Lee, Sophia Schuman, Matthew R Guthrie, Kristofer Berrett, Jeffery Vahrenkamp, Zeping Hu, Marek Kudla, Katarzyna Modzelewska, Guoying Wang, Nicholas T Ingolia, Jason Gertz, David Henry Lum, Sabina C Cosulich, John S Bomalaski, Ralph J DeBerardinis, Trudy G Oliver.

PURPOSE: Small cell lung cancer (SCLC) has been treated clinically as a homogeneous disease, but recent discoveries suggest that SCLC is heterogeneous. Whether metabolic differences exist among SCLC subtypes is largely unexplored. In this study, we aimed to determine whether metabolic vulnerabilities exist between SCLC subtypes that can be therapeutically exploited.EXPERIMENTAL DESIGN: We performed steady state metabolomics on tumors isolated from distinct GEMMs representing the MYC and MYCL-driven subtypes of SCLC. Using genetic and pharmacological approaches, we validated our findings in chemo-naive and resistant human SCLC cell lines, multiple GEMMs, four human cell line xenografts, and four newly-derived PDX models.
RESULTS: We discover that SCLC subtypes driven by different MYC family members have distinct metabolic profiles. MYC-driven SCLC preferentially depends on arginine-regulated pathways including polyamine biosynthesis and mTOR pathway activation. Chemo-resistant SCLC cells exhibit increased MYC expression and similar metabolic liabilities as chemo-naive MYC-driven cells. Arginine depletion with pegylated arginine deiminase (ADI-PEG 20) dramatically suppresses tumor growth and promotes survival of mice specifically with MYC-driven tumors, including in GEMMs, human cell line xenografts, and a PDX from a relapsed patient. Finally, ADI-PEG 20 is significantly more effective than the standard of care chemotherapy.
CONCLUSIONS: These data identify metabolic heterogeneity within SCLC and suggest arginine deprivation as a subtype-specific therapeutic vulnerability for MYC-driven SCLC.

DOI: https://doi.org/10.1158/1078-0432.CCR-18-4140
FEBS J. 2019 Jun 04.

The C-terminal flexible region of branched-chain polyamine synthase facilitates substrate specificity and catalysis.

Ryota Hidese, Masataka Toyoda, Ken-Ichi Yoshino, Wakao Fukuda, Gita Adhirani Wihardja, Seigo Kimura, Junso Fujita, Masaru Niitsu, Tairo Oshima, Tadayuki Imanaka, Eiichi Mizohata, Shinsuke Fujiwara.

  Branched-chain polyamine synthase (BpsA) catalyzes sequential aminopropyl transfer from the donor, decarboxylated S-adenosylmethionine (dcSAM), to the acceptor, linear-chain polyamine, resulting in the production of a quaternary-branched polyamine via tertiary branched polyamine intermediates. Here, we analyzed the catalytic properties and X-ray crystal structure of Tth-BpsA from Thermus thermophilus and compared them with those of Tk-BpsA from Thermococcus kodakarensis, which revealed differences in acceptor substrate specificity and C-terminal structure between these two enzymes. To investigate the role of the C-terminal flexible region in acceptor recognition, a region (LQDEEATTY) in Tth-BpsA was replaced with that in Tk-BpsA (YDDEESSTT) to create chimeric Tth-BpsA C9, which showed a severe reduction in catalytic efficiency toward N4 -aminopropylnorspermidine, but not toward N4 -aminopropylspermidine, mimicking Tk-BpsA substrate specificity. Tth-BpsA C9 Tyr346 and Thr354 contributed to discrimination between tertiary branched-chain polyamine substrates, suggesting that the C-terminal region of BpsA recognizes acceptor substrates. Liquid chromatography-tandem mass spectrometry analysis on a Tk-BpsA reaction mixture with dcSAM revealed two aminopropyl groups bound to two of five aspartate/glutamate residues (Glu339 , Asp342 , Asp343 , Glu344 , and Glu345 ) in the C-terminal flexible region. Mutating each of these five amino acid residues to asparagine/glutamine resulted in a slight decrease in activity. The quadruple mutant D342N/D343N/E344Q/E345Q exhibited a severe reduction in catalytic efficiency, suggesting that these aspartate/glutamate residues function to receive aminopropyl chains. In addition, the X-ray crystal structure of the Tk-BpsA ternary complex bound to N4 -bis(aminopropyl)spermidine revealed that Asp126 and Glu259 interacted with the aminopropyl moiety in N4 -aminopropylspermidine. This article is protected by copyright. All rights reserved.

Keywords:  Branched-chain polyamine; Thermophile; crystal structure; enzyme mechanism

DOI:  https://doi.org/10.1111/febs.14949
J Biol Chem. 2019 Jun 06. pii: jbc.RA119.007619. [Epub ahead of print]

Spermidine strongly increases the fidelity of Escherichia coli CRISPR Cas1-Cas2 integrase.

Pierre Plateau, Clara Moch, Sylvain Blanquet.

  Site-selective CRISPR array expansion at the origin of bacterial adaptive immunity relies on recognition of sequence-dependent DNA structures by the conserved Cas1-Cas2 integrase. Off-target integration of a new spacer sequence outside canonical CRISPR arrays has been described in vitro However, this nonspecific integration activity is rare in vivo Here, we designed gel assays to monitor fluorescently labeled protospacer insertion in a supercoiled 3-kb plasmid harboring a minimal CRISPR locus derived from the Escherichia coli type I-E system. This assay enabled us to distinguish and quantify target and off-target insertion events catalyzed by E. coli Cas1-Cas2 integrase. We show that addition of the ubiquitous polyamine spermidine or of another polyamine, spermine, significantly alters the ratio between target and off-target insertions. Notably, addition of 2 mM spermidine quenched the off-target spacer insertion rate by a factor of 20-fold, and, in the presence of integration host factor (IHF), spermidine also increased insertion at the CRISPR locus 1.5-fold. The observation made in our in vitro system that spermidine strongly decreases nonspecific activity of Cas1-Cas2 integrase outside the leader-proximal region of a CRISPR array suggests that this polyamine plays a potential role in the fidelity of the spacer integration also in vivo.

Keywords:  CRISPR/Cas; DNA-protein interaction; Integration Host Factor (IHF); genomic instability; integrase; polyamine

DOI:  https://doi.org/10.1074/jbc.RA119.007619
FEMS Microbiol Lett. 2019 Jun 04. pii: fnz110. [Epub ahead of print]

Absolute requirement for polyamines for growth of Escherichia coli mutants (mnmE/G) defective in modification of the wobble anticodon of transfer-RNA.

Christopher Keller, Manas Chattopadhyay, Herbert Tabor.

  The genes mnmE and mnmG are responsible for the modification of uridine 34, 'the wobble position' of many aminoacyl-tRNAs. Deletion of these genes affects the strength of the codon-anticodon interactions of the aminoacyl-tRNAs with the mRNAs and the ribosomes. However, deletion of these genes does not usually have a significant effect on the growth rate of the standard Escherichia coli strains. In contrast we have found that if the host E. coli strain is deficient in the synthesis of polyamines, deletion of the mnmE or mnmG gene results in complete inhibition of growth unless the medium contains polyamines. The finding of an absolute requirement for polyamines in our current work will be significant in studies on polyamine function, in studies on the function of the mnmE/G genes, and in studies on the role of aminoacyl-tRNAs in protein biosynthesis.

Keywords:  Gene mnmE; aminoacyl-tRNA; mRNA; polyamines; putrescine; spermidine

DOI:  https://doi.org/10.1093/femsle/fnz110
Ann Neurol. 2019 Jun 02.

A metabolic profile of polyamines in Parkinson's disease: a promising biomarker.

Shinji Saiki, Yukiko Sasazawa, Motoki Fujimaki, Koji Kamagata, Naoko Kaga, Hikari Taka, Yuanzhe Li, Sanae Souma, Taku Hatano, Yoko Imamichi, Norihiko Furuya, Akio Mori, Yutaka Oji, Shin-Ichi Ueno, Shuko Nojiri, Yoshiki Miura, Takashi Ueno, Manabu Funayama, Shigeki Aoki, Nobutaka Hattori.

  OBJECTIVE: Aging is the highest risk factor for Parkinson's disease (PD). Under physiological conditions, spermidine and spermine experimentally enhance longevity via autophagy induction. Accordingly, we evaluated the ability of each polyamine metabolite to act as age-related, diagnostic and severity-associated PD biomarkers.METHODS: Comprehensive metabolome analysis of plasma was performed in Cohort A (controls: 45, PD: 145), followed by analysis of seven polyamine metabolites in Cohort B (controls: 49, PD: 186, progressive supranuclear palsy: 19, Alzheimer's disease: 23). Furthermore, 20 patients with PD who were successively examined within Cohort B were studied using diffusion tensor imaging (DTI). Association of each polyamine metabolite with disease severity was assessed according to Hoehn and Yahr stage (H&Y) and Unified Parkinson's Disease Rating Scale motor section (UPDRS-III). Additionally, the autophagy induction ability of each polyamine metabolite was examined in vitro in various cell lines.
RESULTS: In Cohort A, N8-acetylspermidine and N-acetylputrescine levels were significantly and mildly elevated in PD, respectively. In Cohort B, spermine levels and spermine/spermidine ratio were significantly reduced in PD, concomitant with hyperacetylation. Furthermore, N1,N8-diacetylspermidine levels had the highest diagnostic value, and correlated with H&Y, UPDRS-III, and axonal degeneration quantified by DTI. The spermine/spermidine ratio in controls declined with age, but was consistently suppressed in PD. Among polyamine metabolites, spermine was the strongest autophagy inducer, especially in SH-SY5Y cells. No significant genetic variations in five genes encoding enzymes associated with spermine/spermidine metabolism, were detected compared with controls.
INTERPRETATION: Spermine synthesis and N1,N8-diacetylspermidine may respectively be useful diagnostic and severity-associated biomarkers for PD. This article is protected by copyright. All rights reserved.

Keywords:  N1,N8-diacetylspermidine; Parkinson's disease; autophagy; biomarker; spermine

DOI:  https://doi.org/10.1002/ana.25516
Arch Microbiol. 2019 Jun 04.

Amniculibacterium aquaticum gen. nov., sp. nov., a new member of the family Flavobacteriaceae isolated from a stream.

Wen-Ming Chen, Ya-Ping Guo, Ceshing Sheu, Shih-Yi Sheu.

  Strain KYPW7T, isolated from the Funglin Stream in Taiwan, was characterized using a polyphasic taxonomy approach. Cells of strain KYPW7T were Gram-stain-negative, aerobic, non-spore forming, non-motile rods and formed white colonies. Growth occurred at 15-30 °C (optimum 25 °C), at pH 6-8 (optimum pH 6.5) and with 0-1% NaCl (optimum 0%). Phylogenetic analyses based on 16S rRNA and coding sequences of 92 protein clusters showed that strain KYPW7T represents a novel genus in the family Flavobacteriaceae. The 16S rRNA gene sequence of strain KYPW7T was related to the species of the genera Chryseobacterium (91.8-96.0% sequence similarity), Bergeyella (95.1-95.8%), Cloacibacterium (94.5-95.7%), Daejeonia (95.6%) and Riemerella (94.0-95.0%). Strain KYPW7T showed less than 72% average nucleotide identity and less than 24% digital DNA-DNA hybridization identity compared to the type strains of related genera within the family Flavobacteriaceae. The predominant fatty acids were iso-C15:0 and iso-C17:0 3-OH. The major isoprenoid quinone was MK-6 and the DNA G + C content was 36.8 mol%. The polar lipids had phosphatidylethanolamine, three uncharacterized aminophospholipids and an uncharacterized phospholipid. The polyamines contained homospermidine, putrescine and spermidine. On the basis of the genotypic and phenotypic data, strain KYPW7T represents a novel species of a new genus in the family Flavobacteriaceae, for which the name Amniculibacterium aquaticum gen. nov., sp. nov. is proposed. The type strain is KYPW7T (= BCRC 81123T = LMG 30598T = KCTC 62512T).

Keywords:  Amniculibacterium aquaticum gen. nov., sp. nov.; Bacteroidetes; Flavobacteriaceae; Flavobacteriales; Flavobacteriia; Polyphasic taxonomy

DOI:  https://doi.org/10.1007/s00203-019-01688-y
Environ Sci Pollut Res Int. 2019 Jun 01.

Polyamines modulate growth, antioxidant activity, and genomic DNA in heavy metal-stressed wheat plant.

Hanan A A Taie, Mohamed A Seif El-Yazal, Safia M A Ahmed, Mostafa M Rady.

  A pot experiment was performed to assess the useful effects of seed soaking or seedling foliar spray using 0.25 mM spermine (Spm), 0.50 mM spermidine (Spd), or 1 mM putrescine (Put) on heavy metal tolerance in wheat plants irrigated with water contaminated by cadmium (2 mM Cd2+ in CdCl2) or lead (2 mM Pb2+ in PbCl2). Cd2+ or Pb2+ presence in the growth medium resulted in significant reductions in growth and yield characteristics and activities of leaf peroxidase (POD), glutathione reductase (GR), ascorbic acid oxidase (AAO), and polyphenol oxidase (PPO) of wheat plants. In contrast, significant increases were observed for Cd2+ content in roots, leaves and grains, superoxide dismutase (SOD) and catalase (CAT) activities, radical scavenging activity (DPPH), reducing power capacity, and fragmentation in DNA in comparison to controls (without Cd2+ or Pb2+ addition). However, treating the Cd2+- or Pb2+-stressed wheat plants with Spm, Spd, or Put, either by seed soaking or foliar spray, significantly improved growth and yield characteristics and activities of POD, GR, AAO, PPO, SOD, and CAT, DPPH, and reducing power capacity in wheat plants. In contrast, Cd2+ levels in roots, leaves, and yielded grains, and fragmentation in DNA were significantly reduced compared with the stressed (with Cd2+ or Pb2+) controls. Generally, seed soaking treatments were more effective than foliar spray treatments. More specifically, seed priming in Put was the best treatment under heavy metal stress. Results of this study recommend using polyamines, especially Put, as seed soaking to relieve the adverse effects of heavy metals in wheat plants.

Keywords:  Antioxidant activity; Antioxidant enzymes; Cadmium; Genomic DNA; Growth and productivity; Lead; Polyamines; Wheat

DOI:  https://doi.org/10.1007/s11356-019-05555-7
Int J Syst Evol Microbiol. 2019 Jun 03.

Flavobacterium stagni sp. nov., isolated from a freshwater reservoir.

Wen-Ming Chen, Ya-Ping Guo, Soon-Wo Kwon, Ceshing Sheu, Shih-Yi Sheu.

Strain WWJ-16T was isolated from a freshwater reservoir in Taiwan. Phylogenetic analyses based on 16S rRNA gene sequences and an up-to-date bacterial core gene set (92 protein clusters) indicated that strain WWJ-16T is affiliated with the species in the genus Flavobacterium. Strain WWJ-16T was most closely related to Flavobacterium fontis MIC3010T (97.9 % 16S rRNA gene sequence identity) and Flavobacterium squillarum CMJ-5T (97.6 %). Strain WWJ-16T showed 77.4 % average nucleotide identity and 20.6 % digital DNA-DNA hybridization identity with F. fontis MIC3010T. Cells of strain WWJ-16T were Gram-stain-negative, strictly aerobic, non-motile, rod-shaped and formed yellow colonies. Optimal growth occurred at 25 °C, pH 7 and in 0.5-1 % NaCl (w/v). Strain WWJ-16T contained iso-C15 : 1 G and iso-C15 : 0 as predominant fatty acids. The major hydroxyl fatty acids were iso-C15 : 0 3-OH, iso-C17 : 0 3-OH and iso-C16 : 0 3-OH. The polar lipid profile consisted of phosphatidylethanolamine, four uncharacterized aminophospholipids and four uncharacterized phospholipids. The major polyamine was homospermidine. The major isoprenoid quinone was MK-6. The genomic DNA G+C content of strain WWJ-16T was 39.4 mol%, as determined by genome sequencing. The genotypic and phenotypic characteristics indicate that strain WWJ-16T represents a novel species of the genus Flavobacterium, for which the name Flavobacterium stagni sp. nov. is proposed. The type strain is WWJ-16T (=BCRC 81125T =LMG 30600T=KCTC 62515T).

DOI: https://doi.org/10.1099/ijsem.0.003488
Curr Top Med Chem. 2019 Jun 02.

Molecular Targets for Malarial Chemotherapy: A Review.

Dharmendra Kumar Yadav, Surendra Kumar, Mahesh K Teli, Ravikant Yadav, Sandeep Chaudhary.

  The malaria parasite resistance to the existing drugs is a serious problem to currently used anti-malarials and, thus, highlights the urgent need to develop new and effective anti-malarial molecules. This could be achieved either by the identification of the new drugs for the validated targets or by further refining/improving the existing antimalarials; or by combining previously effective agents with new/existing drugs to have synergistic effect that counter parasite resistance; or by identifying novel targets for the malarial chemotherapy. In this review article, a comprehensive collection of some of the novel molecular targets has been enlisted for the antimalarial drugs. The targets which could be deliberated for developing new anti-malarial drugs could be: membrane biosynthesis, mitochondrial system, apicoplasts, parasite transporters, shikimate pathway, hematin crystals, parasite proteases, glycolysis, isoprenoid synthesis, cell cycle control/cycline dependent kinase, redox system, nucleic acid metabolism, methionine cycle and the polyamines, folate metabolism, the helicases, erythrocyte G-protein, and farnesyl transferases. Modern genomic tools approaches such as structural biology and combinatorial chemistry, novel targets could be identified followed by drug development for drug resistant strains provide wide ranges of novel targets in the development of new therapy. The new approaches and targets mentioned in the manuscript provide a basis for the development of new unique strategies for antimalarial therapy with limited off- target effects in the near future.

Keywords:  Cyclin-dependent kinases; Drug targets; Helicases; Parasite proteases; Plasmodium falciparum; anti-malaria; drug development

DOI:  https://doi.org/10.2174/1568026619666190603080000
Int J Syst Evol Microbiol. 2019 Jun 03.

Inhella crocodyli sp. nov., isolated from a crocodile pond.

Wen-Ming Chen, Yi-Ru Xie, Chiu-Chung Young, Shih-Yi Sheu.

Strain CCP-18T, isolated from a freshwater pond in Taiwan, was characterized by using a polyphasic taxonomy approach. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain CCP-18T belongs to the genus Inhella and has the highest levels of sequence similarity with respect to Inhella inkyongensis IMCC1713T (98.9 %) and Inhella fonticola TNR-25T (98.0 %). Cells were Gram-stain-negative, aerobic, motile, rod-shaped and formed white-coloured colonies. Optimal growth occurred at 25 °C, pH 6 and in the absence of NaCl. The major fatty acids of strain CCP-18T were summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, two unidentified aminophospholipids, an unidentified phospholipid, an unidentified aminolipid and an unidentified lipid. The predominant polyamine was putrescine. The major isoprenoid quinone was Q-8. The draft genome was approximately 3.76 Mb in size with a G+C content of 68.9 mol%. The DNA-DNA hybridization values for strain CCP-18Twith I.inkyongensis IMCC1713T and I.nhella fonticola TNR-25T were less than 40 %. Based on the phylogenetic and phenotypic data, strain CCP-18T should be classified within the genus Inhella as a representative of a novel species, named Inhella crocodyli sp. nov. The type strain is CCP-18T (=BCRC 81120T=LMG 30595T=KCTC 62511T).

DOI: https://doi.org/10.1099/ijsem.0.003496
Antonie Van Leeuwenhoek. 2019 Jun 04.

Hymenobacter oligotrophus sp. nov., isolated from a contaminated agar plate.

Yingchao Geng, Yumin Zhang, Jin Tian, Jia Liu, Kun Qin, Yao Huang, Ziyan Wei, Fang Peng.

  A taxonomic study of a Gram-stain negative, rod-shaped, motile, asporogenous, catalase- and oxidase-positive bacterium, sh-6T, forming pink-red colonies, isolated from a contaminated R2A plate in the laboratory was performed. Its optimum growth temperature was determined to be 28 °C in the absence of NaCl on R2A plates. On the basis of 16S rRNA gene sequence analysis, strain sh-6T belongs to the genus Hymenobacter and is closely related to Hymenobacter deserti ZLB-3T (95.05%), Hymenobacter paludis KBP-30T (94.96%), Hymenobacter coalescens WW84T (94.04%), Hymenobacter gummosus ANT-18T (93.38%), Hymenobacter ocellatus Myx2105T (93.70%), Hymenobacter jeollabukensis 1-3-3-8T (93.48%) and Hymenobacter koreensis GYR3077T (93.21%). Comparison of the genome of strain sh-6T and that of H. gummosus ANT-18T gave digital DNA-DNA hybridization and Average Nucleotide Identity values of 20.6% and 78.4%, respectively. The respiratory isoprenoid quinone and polyamine component were identified as MK-7 and sym-homospermidine, respectively. The major cellular fatty acids identified as iso-C15:0, summed feature 4 (iso-C17:1 I/anteiso B), iso-C16:0, iso-C17:0 3-OH and iso-C17:0. The major polar lipid of strain sh-6T determined to be phosphatidylethanolamine. The DNA G+C content was determined to be 60.5 mol%. On the basis of the evidence presented in this study, a novel species of the genus Hymenobacter, Hymenobacter oligotrophus sp. nov., is proposed, with the type strain sh-6T (= CCTCC AB 2016064T = KCTC 62345T).

Keywords:  Hymenobacter oligotrophus; Novel species; Phylogenetic analysis; Taxonomy

DOI:  https://doi.org/10.1007/s10482-019-01279-3
Exp Mol Med. 2019 Jun 03. 51(6): 60

Arginase II activity regulates cytosolic Ca2+ level in a p32-dependent manner that contributes to Ca2+-dependent vasoconstriction in native low-density lipoprotein-stimulated vascular smooth muscle cells.

Bon-Hyeock Koo, Dongeui Hong, Hyeon Don Hong, Hyun Kyo Lim, Kwang Lae Hoe, Moo-Ho Won, Young Myeong Kim, Dan E Berkowitz, Sungwoo Ryoo.

Although arginase II (ArgII) is abundant in mitochondria, Ca2+-accumulating organelles, the relationship between ArgII activity and Ca2+ translocation into mitochondria and the regulation of cytosolic Ca2+ signaling are completely unknown. We investigated the effects of ArgII activity on mitochondrial Ca2+ uptake through mitochondrial p32 protein (p32m) and on CaMKII-dependent vascular smooth muscle cell (VSMC) contraction. Native low-density lipoprotein stimulation induced an increase in [Ca2+]m as measured by CoCl2-quenched calcein-AM fluorescence, which was prevented by Arg inhibition in hAoSMCs and reduced in mAoSMCs from ArgII-/- mice. Conversely, [Ca2+]c analyzed with Fluo-4 AM was increased by Arg inhibition and ArgII gene knockout. The increased [Ca2+]c resulted in CaMKII and MLC 20 phosphorylation, which was associated with enhanced vasoconstriction activity to phenylephrine (PE) in the vascular tension assay. Cy5-tagged siRNA against mitochondrial p32 mRNA (sip32m) abolished mitochondrial Ca2+ uptake and induced activation of CaMKII. Spermine, a polyamine, induced mitochondrial Ca2+ uptake and dephosphorylation of CaMKII and was completely inhibited by sip32m incubation. In mAoSMCs from ApoE-null mice fed a high-cholesterol diet (ApoE-/- +HCD), Arg activity was increased, and spermine concentration was higher than that of wild-type mice. Furthermore, [Ca2+]m and p32m levels were elevated, and CaMKII phosphorylation was reduced in mAoSMCs from ApoE-/- +HCD. In vascular tension experiments, an attenuated response to vasoconstrictors in de-endothelialized aorta from ApoE-/- +HCD was recovered by incubation of sip32m. ArgII activity-dependent production of spermine augments Ca2+ transition from the cytosol to the mitochondria in a p32m-dependent manner and regulates CaMKII-dependent constriction in VSMCs.

DOI: https://doi.org/10.1038/s12276-019-0262-y
Int J Syst Evol Microbiol. 2019 Jun 06.

Sphingobium terrigena sp. nov., isolated from gasoline-contaminated soil.

Yu Jin Park, Kyung Hyun Kim, Dong Min Han, Dong Ho Lee, Che Ok Jeon.

A Gram-stain-negative, strictly aerobic bacterial strain, designated EO9T, was isolated from gasoline-contaminated soil in the Republic of Korea. Cells were non-motile short rods showing catalase- and oxidase-positive reactions. Growth was observed at 10-37 °C (optimum, 30 °C), at pH 6.0-9.0 (pH 6.5) and in the presence of 0-0.5 % (w/v) NaCl (0 %). Ubiquinone-10 (Q-10) and spermidine were identified as the predominant respiratory quinone and polyamine, respectively. Summed feature 8 (comprising C18:1ω7c/C18:1ω6c), summed feature 3 (comprising C16:1ω7c/C16:1ω6c), C16:0 and C14:0 2-OH were identified as major cellular fatty acids. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, sphingoglycolipid, phosphatidylglycerol and an unidentified phospholipid. The G+C content of the genomic DNA was 62.8 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain EO9T formed a tight phylogenetic lineage with Sphingobium xenophagum NBRC 107872T and Sphingobium hydrophobicum C1T within the genus Sphingobium. Strain EO9T was most closely related to S. xenophagum NBRC 107872T (97.2 %) and S. hydrophobicum C1T (97.2 %), but DNA-DNA relatedness levels between strain EO9T and the type strains of S. xenophagum and S. hydrophobicum were 37.1 and 36.8 % , respectively. Based on its phenotypic, chemotaxonomic and molecular features, strain EO9T clearly represents a novel species of the genus Sphingobium, for which the name Sphingobium terrigena sp. nov. is proposed. The type strain is EO9T (=KACC 19523T=JCM 32762T).

DOI: https://doi.org/10.1099/ijsem.0.003514
Int J Syst Evol Microbiol. 2019 Jun 05.

Chakrabartia godavariana gen. nov., sp. nov., a novel member of the family Sphingomonadaceae isolated from the Godavari River, India.

Kunal Jani, Guang-Da Feng, Hong-Hui Zhu, Om Prakash, Jayashree Bandal, Vinay Rale, Yogesh Shouche, Avinash Sharma.

A Gram-stain-negative, aerobic, yellow-pigmented, oxidase-positive and rod-shaped bacterium, designated PRB40T, was isolated from the Godavari River in India during the course of 'Kumbh Mela', the world's largest mass gathering event. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain PRB40T formed a lineage within the family Sphingomonadaceae and was distinct from the most closely related genera Sphingorhabdus, Novosphingobiumand Sphingomonas with sequence similarity values ≤95.2 %. Growth of strain PRB40T occurred at 10-40 °C (optimum 30 °C), at pH 6.0-9.0 (pH 7.0) and with 0-0.5 % (w/v) NaCl concentration (0 %). The major respiratory quinone was ubiquinone-10 (Q-10). It contained C17 : 1ω6c, C14 : 0 2-OH, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) as the major cellular fatty acids. The predominant polar lipids were phospholipid, phosphatidylethanolamine and sphingoglycolipid. It took sym-homospermidine as the major polyamine. The DNA G+C content based on its draft genome sequence was 63.7 mol%. The polyphasic taxonomic analyses indicated that strain PRB40T represents a novel species of a novel genus within the family Sphingomonadaceae, for which the name Chakrabartia godavariana gen. nov., sp. nov. is proposed. The type strain of Chakrabartia godavariana is PRB40T (=MCC 3406T=GDMCC 1.1197T=KCTC 52678T=LMG 29985T).

DOI: https://doi.org/10.1099/ijsem.0.003512
Arch Biochem Biophys. 2019 May 31. pii: S0003-9861(19)30267-X. [Epub ahead of print]

Disturbance of I1-imidazoline receptor signal transduction in cardiomyocytes of Spontaneously Hypertensive Rats.

Alexander V Maltsev, Edward V Evdokimovskii, Yury M Kokoz.

  Imidazoline receptor of the first type (I1R) in addition to the established inhibition of sympathetic neurons may mediate the direct control of myocellular functions. Earlier, we reveal that I1-mediated signaling in the normotensive rat cardiomyocytes suppresses the nitric oxide production by endothelial NO synthase, impairs sarco(endo)plasmic reticulum Ca2+-ATPase (SERCA) activity, and elevates intracellular calcium in the cytosol. Also, I1-agonists counteract β-adrenoceptor stimulation effects in respect to voltage-gated calcium currents. This study ascertains the I1R signal transduction in the normotensive Wistar and SHR cardiomyocytes. Reduction of Ca2+-currents by rilmenidine, a specific agonist of I1R, ensued from the phosphatidylcholine-specific phospholipase C-mediated activation of protein kinase C. There is a stimulation of serine/threonine phosphatase activity. In SHR cardiomyocytes, both the rilmenidine, and putative endogenous ligand, agmatine, almost twofold less effectively reduced L-type of Ca2+-currents. Average mRNA level of Nischarin, established functional component of I1R, is slightly decreased in SHR, whereas the protein levels are not significantly differed from normotensive rats. Disturbance of I1R signal transduction in SHR may aggravate the development of this cardiovascular pathology.

Keywords:  Adrenergic stress; Agmatine; L-type Ca(2+)-channel; PKC; Rilmenidine

DOI:  https://doi.org/10.1016/j.abb.2019.05.024