Journal of Microbiology

Journal Articles

Whole genome and RNA sequencing of oral commensal bacterium Streptococcus anginosus subsp. anginosus with vancomycin tolerance: Kyu Hwan Kwack , Jae-Hyung Lee , Ji-Hoi Moon; J. Microbiol. 2022;60(2):167-176. Published online January 7, 2022; DOI: https://doi.org/10.1007/s12275-022-1425-4

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“Antibiotic tolerance” promotes the rapid subsequent evolution of “antibiotic resistance,” however, it is often overlooked because it is difficult to distinguish between tolerant and susceptible organisms. A commensal bacterium S. anginosus subsp. anginosus strain KHUD_S1, isolated from dental biofilm was found to exhibit a high MBC/MIC ratio of 32 against vancomycin. We observed KHUD_S1 cells exposed to vancomycin did not grow but maintained viability. Transmission electron microscope showed KHUD_S1 cells possessed a dense, thick capsule and maintained the cell wall integrity upon vancomycin exposure. To infer the underlying mechanisms of the vancomycin tolerance in KHUD_S1, we performed whole genome sequencing and RNA sequencing. The KHUD_S1 genome carried three genes encoding branching enzymes that can affect peptidoglycan structure through interpeptide bridge formation. Global gene expression profiling revealed that the vancomycin-induced downregulation of carbohydrate and inorganic ion transport/metabolism as well as translation is less prominent in KHUD_S1 than in the vancomycin susceptible strain KHUD_S3. Based on the transcriptional levels of genes related to peptidoglycan synthesis, KHUD_S1 was determined to have a 3D peptidoglycan architecture distinct from KHUD_S3. It was found that, under vancomycin exposure, the peptidoglycan was remodeled through changes in the interpeptide bridge and transpeptidation reactions. Collectively, these features of S. anginosus KHUD_S1, including a dense capsule and differential gene expression in peptidoglycan synthesis, may contribute to vancomycin tolerance. Our results showing the occurrence of vancomycin tolerance amongst oral commensal bacteria highlight the need for considering future strategies for screening of antibiotic tolerance as an effort to reduce antibiotic resistance.

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Development of a Novel Multi‐Epitope Vaccine Against Streptococcus anginosus Infection via Reverse Vaccinology Approach
Linglan Xu, Nan Xie, Yiqing Liu, Hongmei Tang, Tian Li, Jiaofeng Peng, Ranhui Li
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Gut resistome profiling reveals high diversity and fluctuations in pancreatic cancer cohorts
Xudong Liu, Kexin Li, Yun Yang, Dingyan Cao, Xinjie Xu, Zilong He, Wenming Wu
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Ruby Dixon, Siobhon Egan, Sheree Hughes, Brendan Chapman
Forensic Science International.2023; 348: 111711. CrossRef

Identification of a novel phospholipase D gene and effects of carbon sources on its expression in Bacillus cereus ZY12: Yu Zhao , Yinfeng Xu , Fang Yu , Chunzhi Zhang; J. Microbiol. 2018;56(4):264-271. Published online April 2, 2018; DOI: https://doi.org/10.1007/s12275-018-7529-1

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In the present study, a new strain, Bacillus cereus ZY12, producing phospholipase D (PLD) was identified. The expression of PLD in this strain was found to be induced by its substrate, phosphatidylcholine (PC), and completely silenced by other carbon sources, such as glucose, fructose, and maltose, which are generally used in microbial growth cultures, thus presenting a unique expression pattern different from other PLD-producing microorganisms. This study is the first to report on the ability of B. cereus to produce PLD, and successfully clone its PLD-coding gene and identify its function, extending the knowledge on PLD distribution and evolution in microorganisms.

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Efficient Extracellular Production of Phospholipase D in Escherichia coli via Genetic and Process Engineering Modification
Huan Liu, Yang Yang, Tianyi Wang, Yuchen Ning, Li Deng, Fang Wang
Synthetic Biology and Engineering.2025; 3(2): 10006. CrossRef
A New Phospholipase D-Producing Bacillus cereus: Taxonomy, Mutagenesis, Fermentation Optimization and Enzyme Characterization
Ying He, Ao Huang, Yun Liu
Applied Biochemistry and Biotechnology.2025; 197(8): 5042. CrossRef
Structural insights into PA3488-mediated inactivation of Pseudomonas aeruginosa PldA
Xiaoyun Yang, Zongqiang Li, Liang Zhao, Zhun She, Zengqiang Gao, Sen-Fang Sui, Yuhui Dong, Yanhua Li
Nature Communications.2022;[Epub] CrossRef
Construction of a Super-Folder Fluorescent Protein-Guided Secretory Expression System for the Production of Phospholipase D in Bacillus subtilis
Haiyang Zhang, Xuehan Li, Qi Liu, Jianan Sun, Francesco Secundo, Xiangzhao Mao
Journal of Agricultural and Food Chemistry.2021; 69(24): 6842. CrossRef
Microbial phospholipase D: Identification, modification and application
Zhenxia Zhang, Ming Chen, Wei Xu, Wenli Zhang, Tao Zhang, Cuie Guang, Wanmeng Mu
Trends in Food Science & Technology.2020; 96: 145. CrossRef

Research Support, U.S. Gov't, Non-P.H.S.

Multiple cellular roles of Neurospora crassa plc-1, splA2, and cpe-1 in regulation of cytosolic free calcium, carotenoid accumulation, stress responses, and acquisition of thermotolerance§: Ananya Barman , Ranjan Tamuli; J. Microbiol. 2015;53(4):226-235. Published online January 31, 2015; DOI: https://doi.org/10.1007/s12275-015-4465-1

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Phospholipase C1 (PLC1), secretory phospholipase A2 (sPLA2) and Ca2+/H+ exchanger proteins regulate calcium signaling and homeostasis in eukaryotes. In this study, we investigate functions for phospholipase C1 (plc-1), sPLA2 (splA2) and a Ca2+/H+ exchanger (cpe-1) in the filamentous fungus Neurospora crassa. The Δplc-1, ΔsplA2, and Δcpe-1 mutants exhibited a growth defect on medium supplemented with the divalent ionophore A23187, suggesting that these genes might play a role in regulation of cytosolic free Ca2+ concentration ([Ca2+]c) in N. crassa. The strains lacking plc-1, splA2, and cpe-1 possessed higher carotenoid content than wild type at 8°C, 22°C, and 30°C, and showed increased ultraviolet (UV)- survival under conditions that induced carotenoid accumulation. Moreover, Δplc-1, ΔsplA2, and Δcpe-1 mutants showed reduced survival rate under hydrogen peroxide-induced oxidative stress and induced thermotolerance after exposure to heat shock temperatures. Thus, this study revealed multiple cellular roles for plc-1, splA2, and cpe-1 genes in regulation of [Ca2+]c, carotenoid accumulation, survival under stress conditions, and acquisition of thermotolerance induced by heat shock.

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PacC mediates spatial regulation of the phospholipid metabolism in the apple fruit-Penicillium expansum interaction
Yatong Zhu, Yuanyuan Zong, Di Gong, Xuexue Wang, William Oyom, Yang Bi, Dov Prusky
Postharvest Biology and Technology.2024; 208: 112666. CrossRef
Methods for the detection of intracellular calcium in filamentous fungi
Megha Rasaily, Serena Ngiimei D, Rahul Kumar Thaosen, Surabhi Gupta, Sangeeta Deka, Ranjan Tamuli
MethodsX.2024; 12: 102570. CrossRef
Thiourea Application Increases Seed and Oil Yields in Camelina Under Heat Stress by Modulating the Plant Water Relations and Antioxidant Defense System
Muhammad Ahmad, Ejaz Ahmad Waraich, Usman Zulfiqar, Aman Ullah, Muhammad Farooq
Journal of Soil Science and Plant Nutrition.2023; 23(1): 290. CrossRef
Trichosporon asahii PLA2 Gene Enhances Drug Resistance to Azoles by Improving Drug Efflux and Biofilm Formation
Xiaoping Ma, Hong Liu, Zhen Liu, Ya Wang, Zhijun Zhong, Guangneng Peng, Yu Gu
International Journal of Molecular Sciences.2023; 24(10): 8855. CrossRef
Interaction of calcium responsive proteins and transcriptional factors with the PHO regulon in yeasts and fungi
Juan F. Martín
Frontiers in Cell and Developmental Biology.2023;[Epub] CrossRef
The cell functions of phospholipase C-1, Ca2+/H+ exchanger-1, and secretory phospholipase A2 in tolerance to stress conditions and cellulose degradation in Neurospora crassa
Darshana Baruah, Ranjan Tamuli
Archives of Microbiology.2023;[Epub] CrossRef
Multiple calcium signaling genes play a role in the circadian period of Neurospora crassa
Darshana Baruah, Christy Noche K Marak, Avishek Roy, Dibakar Gohain, Ajeet Kumar, Pallavi Das, Katherine A Borkovich, Ranjan Tamuli
FEMS Microbiology Letters.2023;[Epub] CrossRef
Phospholipase C: Diverse functions in plant biotic stress resistance and fungal pathogenicity
Yuanpeng Fang, Junmei Jiang, Haixia Ding, Xiangyang Li, Xin Xie
Molecular Plant Pathology.2023; 24(9): 1192. CrossRef
A secretory phospholipase A2 of a fungal pathogen contributes to lipid droplet homeostasis, assimilation of insect‐derived lipids, and repression of host immune responses
Juan Deng, Zhuoyue Lu, Huifang Wang, Ning Li, Guimei Song, Qiankuan Zhu, Jingxin Sun, Yongjun Zhang
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Phospholipase C (AoPLC2) regulates mycelial development, trap morphogenesis, and pathogenicity of the nematode-trapping fungus Arthrobotrys oligospora
Meihua Xie, Ni Ma, Na Bai, Meichen Zhu, Ke-Qin Zhang, Jinkui Yang
Journal of Applied Microbiology.2022; 132(3): 2144. CrossRef
Disrupting a phospholipase A 2 gene increasing lipid accumulation in the oleaginous yeast Yarrowia lipolytica
J.X. Li, J. Xu, J.C. Ruan, H.M. Meng, H. Su, X.F. Han, M. Lu, F.L. Li, S.A. Wang
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Flexible online in-droplet cell/synthetic particle concentration utilizing alternating current electrothermal-flow field-effect transistor
Haizhen Sun, Yukun Ren, Ye Tao, Tianyi Jiang, Hongyuan Jiang
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Calcium signaling is involved in diverse cellular processes in fungi
Avishek Roy, Ajeet Kumar, Darshana Baruah, Ranjan Tamuli
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Dominant mutants of the calcineurin catalytic subunit (CNA-1) showed developmental defects, increased sensitivity to stress conditions, and CNA-1 interacts with CaM and CRZ-1 in Neurospora crassa
Ajeet Kumar, Avishek Roy, Mandar V. Deshmukh, Ranjan Tamuli
Archives of Microbiology.2020; 202(4): 921. CrossRef
Calcineurin responsive zinc‐finger‐1 binds to a unique promoter sequence to upregulate neuronal calcium sensor‐1, whose interaction with MID‐1 increases tolerance to calcium stress in Neurospora crassa
Dibakar Gohain, Ranjan Tamuli
Molecular Microbiology.2019; 111(6): 1510. CrossRef
The NcZrg-17 gene of Neurospora crassa encodes a cation diffusion facilitator transporter required for vegetative development, tolerance to endoplasmic reticulum stress and cellulose degradation under low zinc conditions
Anand Tiwari, Serena Daniel Ngiilmei, Ranjan Tamuli
Current Genetics.2018; 64(4): 811. CrossRef
Phospholipases play multiple cellular roles including growth, stress tolerance, sexual development, and virulence in fungi
Ananya Barman, Dibakar Gohain, Utpal Bora, Ranjan Tamuli
Microbiological Research.2018; 209: 55. CrossRef
The pleiotropic vegetative and sexual development phenotypes of Neurospora crassa arise from double mutants of the calcium signaling genes plc-1, splA2, and cpe-1
Ananya Barman, Ranjan Tamuli
Current Genetics.2017; 63(5): 861. CrossRef
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H.F. Shen, B. Zhao, J.J. Xu, W. Liang, W.M. Huang, H.H. Li
South African Journal of Botany.2017; 112: 338. CrossRef
Phenotypic abnormalities of fr , sp , and och-1 single mutants are suppressed by loss of putative GPI-phospholipase A2 in Neurospora crassa
Masayuki Kamei, Yuko Tsukagoshi, Shinpei Banno, Akihiko Ichiishi, Fumiyasu Fukumori, Makoto Fujimura
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Calcineurin Subunits A and B Interact to Regulate Growth and Asexual and Sexual Development in Neurospora crassa
Ranjan Tamuli, Rekha Deka, Katherine A. Borkovich, Stefanie Pöggeler
PLOS ONE.2016; 11(3): e0151867. CrossRef

Research Support, Non-U.S. Gov'ts

NOTE] The Activity of Phosphoinositide-Specific Phospholipase C Is Required for Vegetative Growth and Cell Wall Regeneration in Coprinopsis cinerea: Young Taek Oh , Chun-Seob Ahn , Kyung-Jin Lee , Jeong-Geun Kim , Hyeon-Su Ro , Jae Won Kim , Chang-Won Lee; J. Microbiol. 2012;50(4):689-692. Published online August 25, 2012; DOI: https://doi.org/10.1007/s12275-012-2004-x

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Three isotypes of phosphoinositide-specific phospholipase C designated CcPLC1, CcPLC2, and CcPLC3 were identified in Coprinopsis cinerea, through a search of the genome sequence database. The functional role of the PI-PLCs were studied by using U73122, which specifically inhibits the activity of PI-PLC. The specificity of the inhibitor effect was confirmed by using an inactive structural analog U73433. The inhibition of PI-PLCs activity resulted in severely retarded germination of basidiospores and oidia, reduced hyphal growth, knobbly hyphal tips with many irregular side branches, and aberrant (branch-like structure) clamp cells. Furthermore, U73122 definitely inhibited cell wall formation. Here we report that PI-PLCs play important roles in various aspects of C. cinerea biology.

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Phospholipase C: Diverse functions in plant biotic stress resistance and fungal pathogenicity
Yuanpeng Fang, Junmei Jiang, Haixia Ding, Xiangyang Li, Xin Xie
Molecular Plant Pathology.2023; 24(9): 1192. CrossRef
The PH Domain and C-Terminal polyD Motif of Phafin2 Exhibit a Unique Concurrence in Animals
Mahmudul Hasan, Daniel Capelluto
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Yi Huang, Yongcai Li, Dongmei Li, Yang Bi, Dov B. Prusky, Yupeng Dong, Tiaolan Wang, Miao Zhang, Xuemei Zhang, Yongxiang Liu
Frontiers in Microbiology.2020;[Epub] CrossRef
Phospholipases play multiple cellular roles including growth, stress tolerance, sexual development, and virulence in fungi
Ananya Barman, Dibakar Gohain, Utpal Bora, Ranjan Tamuli
Microbiological Research.2018; 209: 55. CrossRef
VdPLP, A Patatin-Like Phospholipase in Verticillium dahliae, Is Involved in Cell Wall Integrity and Required for Pathogenicity
Xiliang Qi, Xiaokang Li, Huiming Guo, Ning Guo, Hongmei Cheng
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Effects of Phospholipase C on Fusarium graminearum Growth and Development
Qili Zhu, Benguo Zhou, Zhengliang Gao, Yuancun Liang
Current Microbiology.2015; 71(6): 632. CrossRef
The phenotype of a phospholipase C (plc-1) mutant in a filamentous fungus, Neurospora crassa
Roger R. Lew, Rachel E. Giblon, Miranda S.H. Lorenti
Fungal Genetics and Biology.2015; 82: 158. CrossRef

Biochemical Characteristics of Immune-Associated Phospholipase A2 and Its Inhibition by an Entomopathogenic Bacterium, Xenorhabdus nematophila: Sony Shrestha , Yonggyun Kim; J. Microbiol. 2009;47(6):774-782. Published online February 4, 2010; DOI: https://doi.org/10.1007/s12275-009-0145-3

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An entomopathogenic bacterium, Xenorhabdus nematophila, induces an immunosuppression of target insects by inhibiting phospholipase A2 (PLA2) activity. Recently, an immune-associated PLA2 gene was identified from the red flour beetle, Tribolium castaneum. This study cloned this PLA2 gene in a bacterial expression vector to produce a recombinant enzyme. The recombinant T. castaneum PLA2 (TcPLA2) exhibited its characteristic enzyme activity with substrate concentration, pH, and ambient temperature. Its biochemical characteristics matched to a secretory type of PLA2 (sPLA2) because its activity was inhibited by dithiothreitol (a reducing agent of disulfide bond) and bromophenacyl bromide (a specific sPLA2 inhibitor) but not by methylarachidonyl fluorophosphonate (a specific cytosolic type of PLA2). The X. nematophila culture broth contained PLA2 inhibitory factor(s), which was most abundant in the media obtained at a stationary bacterial growth phase. The PLA2 inhibitory factor(s) was heat-resistant and extracted in both aqueous and organic fractions. Effect of a PLA2-inhibitory fraction on the immunosuppression of T. castaneum was equally comparable with that resulted from inhibition of the TcPLA2 gene expression by RNA interference.

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Molecular Cloning of the Phospholipase D Gene from Streptomyces sp. YU100 and Its Expression in Escherichia coli: Ji-Seon Lee , Munkhtsetseg Bat-Ochir , Atanas V. Demirev , Doo Hyun Nam; J. Microbiol. 2009;47(1):116-122. Published online February 20, 2009; DOI: https://doi.org/10.1007/s12275-008-0161-8

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The gene for phospholipase D (PLD) of Streptomyces sp. YU100 was cloned from λ phage library and heterologously expressed in Escherichia coli. Using an amplified gene fragment based on the consensus sequences of streptomycetes PLDs, λ phage library of Streptomyces sp. YU100 chromosomal DNA was screened. The sequencing result of BamHI-digested 3.8 kb fragment in a positive phage clone revealed the presence of an open reading frame of a full sequence of PLD gene encoding a 540-amino acid protein including 33-amino acid signal peptide. The deduced amino acid sequence showed a high homology with other Streptomyces PLDs, having the highly conserved ‘HKD’ motifs. The PLD gene excluding signal peptide sequence was amplified and subcloned into a pET-32b(+) expression vector in E. coli BL21(DE3). The recombinant PLD was purified by nickel affinity chromatography and compared the enzyme activity with wild-type PLD. The results imply that the recombinant PLD produced by E. coli had the nearly same enzyme activity as PLD from Streptomyces sp. YU100.

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A New Phospholipase D-Producing Bacillus cereus: Taxonomy, Mutagenesis, Fermentation Optimization and Enzyme Characterization
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Construction of a Super-Folder Fluorescent Protein-Guided Secretory Expression System for the Production of Phospholipase D in Bacillus subtilis
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Phosphate and Carbon Source Regulation of Alkaline Phosphatase and Phospholipase in Vibrio vulnificus: Wan-Seok Oh , Young-Sun Im , Kyu-Young Yeon , Young-Jun Yoon , Jung-Wan Kim; J. Microbiol. 2007;45(4):311-317.; DOI: https://doi.org/2567 [pii]

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Abstract PDF: In this study, the effects of phosphate concentration and carbon source on the patterns of alkaline phosphatase (APase) and phospholipase (PLase) expression in Vibrio vulnificus ATCC 29307 were assessed under various conditions. The activities of these enzymes were repressed by excess phosphate (4 mM) in the culture medium, but this repression was reversed upon the onset of phosphate starvation in low phosphate defined medium (LPDM) containing 0.2 mM of phosphate at approximately the end of the exponential growth phase. The expressions of the two enzymes were also influenced by different carbon sources, including glucose, fructose, maltose, glycerol, and sodium acetate at different levels. The APase activity was derepressed most profoundly in LPDM containing fructose as a sole carbon source. However, the repression/derepression of the enzyme by phosphate was not observed in media containing glycerol or sodium acetate. In LPDM-glycerol or sodium acetate, the growth rate was quite low. The highest levels of PLase activity were detected in LPDMsodium acetate, followed by LPDM-fructose. PLase was not fully repressed by high phosphate concentrations when sodium acetate was utilized as the sole carbon source. These results showed that multiple regulatory systems, including the phosphate regulon, may perform a function in the expression of both or either APase and PLC, in the broader context of the survival of V. vulnificus.

Isolation and Characterization of Fatty Acid Derivatives from an Actinomycetes and Examination of the Effects on Activities of Phospholipase C and Protein Kinase C: Ko, Hack Ryong , Kim, Bo Yeon , Lee, Hyun Sun , Kang, Dae Ook , Ryu, Sung Ho , Suh, Pann Ghill , Mheen, Tae Ick , Ahnm Jong Seog; J. Microbiol. 1998;36(4):316-321.

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Abstract PDF: In our screening to search inhibitors of phosphoinositide(PI)-specific phospholipase C (PI-PLC), two inhibitors, MT965-A and-B were isolated from a culture broth of an actinomycetes. MT965-A and-B were identified as fatty acid deribatives, 14-methylpentadecanoic acid and 16-methyllinoleic acid methyl ester, respectively, based on the spectral data including NMR and MS. Both inhibitors directly inhibited not only in vitro PLCγ1 activity but also the platelet-derived growth factor(PDGF)-induced inositol phosphates(IPt) formation in NIH 3T3γ1 cells ocerexpressing PLCγ1. However, the inhibitors enhanced in vitro protein kinase C (PKC) activity. On examination of the effects of various fatty acids(FAs) on activities of PLC, PKC, and PDGF-induced IPt formation, the unsaturated FAs(UFAs) showed the same activities like the inhibitors, but the saturated FAs(SFAs) did not show similar activities. It was inferred that the chain length, degree of unsaturation, methyl esterification, branching with a methyl group, and cis-configuration were important for their activity.

Bioluminescent Assay of Phospholipase C Using A Luminescent Marine Mutant Bacterium Vibrio harveyi M-17: Ki Woong Cho , SangJun Mo , Hyi-Seung Lee , Jung-Rae Rho , Jongheon Shin; J. Microbiol. 2000;38(3):150-155.

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Abstract PDF: A bioluminescent assay method for detecting the activity of phospholipase C (PLC; phosphatidyl choline cholinephosphohydrolase, EC 3.1.4.3) was developed using bioluminescent marine bacteria. Phospholipase C from Bacillus cereus and sn-1,2-dimyristoyl phosphatidyl choline (DMPC) as a substrate were used in the demonstration, and the produced sn-1,2-dimyristoyl glycerol was further hydrolyzed with lipase from Candida cylidracea. The hydrolyzed myristic acid was quantified using a dark mutant of Vibrio harveyi (designated as M-17). The in vivo light intensity of which was stimulated specifically up to one thousand fold in the presence of myristic acid. The rates of the hydrolysis of the DMPC substrate by the phospholipase measured by the luminescence method were linear with time and the amount of enzyme added. Activity measurement conditions (at 25 C, pH 6.5, 10 min fixed time assay) were established to detect as little as 0.1 mUnit of phospholipase C and 5 nM of myristic acid production.

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