Journal of Microbiology

Review

cAMP Activation of the cAMP Receptor Protein, a Model Bacterial Transcription Factor: Hwan Youn , Marcus Carranza; J. Microbiol. 2023;61(3):277-287. Published online March 9, 2023; DOI: https://doi.org/10.1007/s12275-023-00028-6

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The active and inactive structures of the Escherichia coli cAMP receptor protein (CRP), a model bacterial transcr!ption factor, are compared to generate a paradigm in the cAMP-induced activation of CRP. The resulting paradigm is shown to be consistent with numerous biochemical studies of CRP and CRP*, a group of CRP mutants displaying cAMP-free activity. The cAMP affinity of CRP is dictated by two factors: (i) the effectiveness of the cAMP pocket and (ii) the protein equilibrium of apo-CRP. How these two factors interplay in determining the cAMP affinity and cAMP specificity of CRP and CRP* mutants are discussed. Both the current understanding and knowledge gaps of CRP-DNA interactions are also described. This review ends with a list of several important CRP issues that need to be addressed in the future.

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Identification of a cellular role of hemolysin co-regulatory protein (Hcp) in Vibrio alginolyticus modulating substrate metabolism and biofilm formation by cAMP-CRP
Shuilong Wu, Yu Huang, Minhui Wu, Huapu Chen, Bei Wang, Kwaku Amoah, Jia Cai, Jichang Jian
International Journal of Biological Macromolecules.2024; 282: 136656. CrossRef
cAMP-independent DNA binding of the CRP family protein DdrI from Deinococcus radiodurans
Yudong Wang, Jing Hu, Xufan Gao, Yuchen Cao, Shumai Ye, Cheng Chen, Liangyan Wang, Hong Xu, Miao Guo, Dong Zhang, Ruhong Zhou, Yuejin Hua, Ye Zhao, Paul Babitzke
mBio.2024;[Epub] CrossRef
Unexpected Requirement of Small Amino Acids at Position 183 for DNA Binding in the Escherichia coli cAMP Receptor Protein
Marcus Carranza, Amanda Rea, Daisy Pacheco, Christian Montiel, Jin Park, Hwan Youn
Journal of Microbiology.2024; 62(10): 871. CrossRef
Bacterial Regulatory Mechanisms for the Control of Cellular Processes: Simple Organisms’ Complex Regulation
Jin-Won Lee
Journal of Microbiology.2023; 61(3): 273. CrossRef
Mechanisms and biotechnological applications of transcription factors
Hehe He, Mingfei Yang, Siyu Li, Gaoyang Zhang, Zhongyang Ding, Liang Zhang, Guiyang Shi, Youran Li
Synthetic and Systems Biotechnology.2023; 8(4): 565. CrossRef

Journal Articles

Eradication of drug-resistant Acinetobacter baumannii by cell-penetrating peptide fused endolysin: Jeonghyun Lim , Jaeyeon Jang , Heejoon Myung , Miryoung Song; J. Microbiol. 2022;60(8):859-866. Published online May 25, 2022; DOI: https://doi.org/10.1007/s12275-022-2107-y

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Abstract

Antimicrobial agents targeting peptidoglycan have shown successful results in eliminating bacteria with high selective toxicity. Bacteriophage encoded endolysin as an alternative antibiotics is a peptidoglycan degrading enzyme with a low rate of resistance. Here, the engineered endolysin was developed to defeat multiple drug-resistant (MDR) Acinetobacter baumannii. First, putative endolysin PA90 was predicted by genome analysis of isolated Pseudomonas phage PBPA. The His-tagged PA90 was purified from BL21(DE3) pLysS and tested for the enzymatic activity using Gram-negative pathogens known for having a high antibiotic resistance rate including A. baumannii. Since the measured activity of PA90 was low, probably due to the outer membrane, cell-penetrating peptide (CPP) DS4.3 was introduced at the N-terminus of PA90 to aid access to its substrate. This engineered endolysin, DS-PA90, completely killed A. baumannii at 0.25 μM, at which concentration PA90 could only eliminate less than one log in CFU/ml. Additionally, DS-PA90 has tolerance to NaCl, where the ~50% of activity could be maintained in the presence of 150 mM NaCl, and stable activity was also observed with changes in pH or temperature. Even MDR A. baumannii strains were highly susceptible to DS-PA90 treatment: five out of nine strains were entirely killed and four strains were reduced by 3–4 log in CFU/ml. Consequently, DS-PA90 could protect waxworm from A. baumannii-induced death by ~70% for ATCC 17978 or ~44% for MDR strain 1656-2 infection. Collectively, our data suggest that CPP-fused endolysin can be an effective antibacterial agent against Gramnegative pathogens regardless of antibiotics resistance mechanisms.

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Antimicrobial peptide thanatin fused endolysin PA90 (Tha-PA90) for the control of Acinetobacter baumannii infection in mouse model
Jeonghyun Lim, Heejoon Myung, Daejin Lim, Miryoung Song
Journal of Biomedical Science.2024;[Epub] CrossRef
Tissue damage alleviation and mucin inhibition by P5 in a respiratory infection mouse model with multidrug-resistant Acinetobacter baumannii
Jun Hee Oh, Jonggwan Park, Hee Kyoung Kang, Hee Joo Park, Yoonkyung Park
Biomedicine & Pharmacotherapy.2024; 181: 117724. CrossRef
Potential of antimicrobial peptide-fused endolysin LysC02 as therapeutics for infections and disinfectants for food contact surfaces to control Cronobacter sakazakii
Doyeon Kim, Jinwoo Kim, Minsik Kim
Food Control.2024; 157: 110190. CrossRef
Gram-negative endolysins: overcoming the outer membrane obstacle
Hazel M Sisson, Simon A Jackson, Robert D Fagerlund, Suzanne L Warring, Peter C Fineran
Current Opinion in Microbiology.2024; 78: 102433. CrossRef
LysJEP8: A promising novel endolysin for combating multidrug‐resistant Gram‐negative bacteria
Jose Vicente Carratalá, Neus Ferrer‐Miralles, Elena Garcia‐Fruitós, Anna Arís
Microbial Biotechnology.2024;[Epub] CrossRef
You get what you test for: The killing effect of phage lysins is highly dependent on buffer tonicity and ionic strength
Roberto Vázquez, Diana Gutiérrez, Zoë Dezutter, Bjorn Criel, Philippe de Groote, Yves Briers
Microbial Biotechnology.2024;[Epub] CrossRef
Endolysins: a new antimicrobial agent against antimicrobial resistance. Strategies and opportunities in overcoming the challenges of endolysins against Gram-negative bacteria
Fazal Mehmood Khan, Fazal Rasheed, Yunlan Yang, Bin Liu, Rui Zhang
Frontiers in Pharmacology.2024;[Epub] CrossRef
Characterization of Three Different Endolysins Effective against Gram-Negative Bacteria
Tae-Hwan Jeong, Hye-Won Hong, Min Soo Kim, Miryoung Song, Heejoon Myung
Viruses.2023; 15(3): 679. CrossRef
Design strategies for positively charged endolysins: Insights into Artilysin development
Jose Vicente Carratalá, Anna Arís, Elena Garcia-Fruitós, Neus Ferrer-Miralles
Biotechnology Advances.2023; 69: 108250. CrossRef

Transposon insertion site sequencing (TIS) of Pseudomonas aeruginosa: Hongbaek Cho; J. Microbiol. 2021;59(12):1067-1074. Published online December 4, 2021; DOI: https://doi.org/10.1007/s12275-021-1565-y

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Abstract

Transposon insertion site sequencing (TIS) is a technique that determines the insertion profile of a transposon mutant library by massive parallel sequencing of transposon-genomic DNA junctions. Because the transposon insertion profile reflects the abundance of each mutant in the library, it provides information to assess the fitness contribution of each genetic locus of a bacterial genome in a specific growth condition or strain background. Although introduced only about a dozen years ago, TIS has become an important tool in bacterial genetics that provides clues to study biological functions and regulatory mechanisms. Here, I describe a protocol for generating high density transposon insertion mutant libraries and preparing Illumina sequencing samples for mapping the transposon junctions of the transposon mutant libraries using Pseudomonas aeruginosa as an example.

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Optimizing phage-based mutant recovery and minimizing heat effect in the construction of transposon libraries in Staphylococcus aureus
Sally W. Yousief, Nader Abdelmalek, Bianca Paglietti
Scientific Reports.2024;[Epub] CrossRef
The biological essence of synthetic lethality: Bringing new opportunities for cancer therapy
Meiyi Ge, Jian Luo, Yi Wu, Guobo Shen, Xi Kuang
MedComm – Oncology.2024;[Epub] CrossRef
Optimization of Transposon Mutagenesis Methods in Pseudomonas antarctica
Sangha Kim, Changhan Lee
Microorganisms.2023; 11(1): 118. CrossRef
Construction of high-density transposon mutant library of Staphylococcus aureus using bacteriophage ϕ11
Wonsik Lee
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Development of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) thermal inactivation method with preservation of diagnostic sensitivity: Young-Il Kim , Mark Anthony B. Casel , Se-Mi Kim , Seong-Gyu Kim , Su-Jin Park , Eun-Ha Kim , Hye Won Jeong , Haryoung Poo , Young Ki Choi; J. Microbiol. 2020;58(10):886-891. Published online September 29, 2020; DOI: https://doi.org/10.1007/s12275-020-0335-6

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Abstract

Various treatments and agents had been reported to inactivate RNA viruses. Of these, thermal inactivation is generally considered an effective and cheap method of sample preparation for downstream assays. The purpose of this study is to establish a safe inactivation method for SARS-CoV-2 without compromising the amount of amplifiable viral genome necessary for clinical diagnoses. In this study, we demonstrate the infectivity and genomic stability of SARSCoV- 2 by thermal inactivation at both 56°C and 65°C. The
results
substantiate that viable SARS-CoV-2 is readily inactivated when incubated at 56°C for 30 min or at 65°C for 10 min. qRT-PCR of specimens heat-inactivated at 56°C for 30 min or 65°C for 15 min revealed similar genomic RNA stability compared with non-heat inactivated specimens. Further, we demonstrate that 30 min of thermal inactivation at 56°C could inactivate viable viruses from clinical COVID-19 specimens without attenuating the qRT-PCR diagnostic sensitivity. Heat treatment of clinical specimens from COVID-19 patients at 56°C for 30 min or 65°C for 15 min could be a useful
method
for the inactivation of a highly contagious agent, SARS-CoV-2. Use of this method would reduce the potential for secondary infections in BSL2 conditions during diagnostic procedures. Importantly, infectious virus can be inactivated in clinical specimens without compromising the sensitivity of the diagnostic RT-PCR assay.

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Georgenia faecalis sp. nov. isolated from the faeces of Tibetan antelope: Xiaoxia Wang , Jing Yang , Yuyuan Huang , Xiaomin Wu , Licheng Wang , Limei Han , Sha Li , Huan Li , Xiaoying Fu , Hai Chen , Xiong Zhu; J. Microbiol. 2020;58(9):734-740. Published online July 24, 2020; DOI: https://doi.org/10.1007/s12275-020-0060-1

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Abstract

Two aerobic, Gram-stain-positive, non-motile, non-sporulating coccoid strains, designated ZLJ0423T and ZLJ0321, were isolated from the faeces of Tibetan antelope (Pantholops hodgsonii). Their optimal temperature, NaCl concentration and pH for growth were 28°C, 0.5% (w/v) NaCl and pH 7.5, respectively. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strains ZLJ0423T and ZLJ0321 were very similar to each other (99.8%) and had a sequence similarity of 97.0% with Georgenia satyanarayanai NBRC 107612T and Georgenia subflava CGMCC 1.12782T. Phylogenomic analysis based on 688 core genes indicated that these strains formed a clade with G. satyanarayanai NBRC 107612T and Georgenia wutianyii Z294T. The predominant cellular fatty acids were anteiso-C15:0, anteiso-C15:1 A and C16:0. The major menaquinone was MK-8(H4). The cell-wall amino acids consisted of alanine, lysine, glycine and aspartic acid, with lysine as the diagnostic diamino acid. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannosides and two unidentified lipids formed the polar lipid profile. The DNA G + C content of both isolates was 73.9 mol%. The digital DNA–DNA hybridization value between strains ZLJ0423T and ZLJ0321 was 91.2%, but their values with closely related species and other available type strains of the genus Georgenia were lower than the 70% threshold. On the basis of polyphasic taxonomic data, strains ZLJ0423T and ZLJ0321 represent a novel species within the genus Georgenia, for which the name Georgenia faecalis sp. nov. is proposed. The type strain is ZLJ0423T (= CGMCC 1.13681T = JCM 33470T).

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Short-term high-temperature pretreated compost increases its application value by altering key bacteria phenotypes
Linpei Han, Lei Li, Yun Xu, Xinyi Xu, Wenjie Ye, Yuanji Kang, Feng Zhen, Xuya Peng
Waste Management.2024; 180: 135. CrossRef
Georgenia halotolerans sp. nov., a halotolerant actinobacterium isolated from Taklamakan desert soil
Shao-Wei Liu, Ke-Ke Luo, Fei-Na Li, Ben-Yin Zhang, De-Jun Zhang, Cheng-Hang Sun
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef

Carbohydrate-binding specificities of potential probiotic Lactobacillus strains in porcine jejunal (IPEC-J2) cells and porcine mucin: Valerie Diane Valeriano , Bernadette B. Bagon , Marilen P. Balolong , Dae-Kyung Kang; J. Microbiol. 2016;54(7):510-519. Published online June 28, 2016; DOI: https://doi.org/10.1007/s12275-016-6168-7

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Abstract

Bacterial lectins are carbohydrate-binding adhesins that recognize glycoreceptors in the gut mucus and epithelium of hosts. In this study, the contribution of lectin-like activities to adhesion of Lactobacillus mucosae LM1 and Lactobacillus johnsonii PF01, which were isolated from swine intestine, were compared to those of the commercial probiotic Lactobacillus rhamnosus GG. Both LM1 and PF01 strains have been reported to have good adhesion ability to crude intestinal mucus of pigs. To confirm this, we quantified their adhesion to porcine gastric mucin and intestinal porcine enterocytes isolated from the jejunum of piglets (IPEC-J2). In addition, we examined their carbohydrate-binding specificities by suspending bacterial cells in carbohydrate solutions prior to adhesion assays. We found that the selected carbohydrates affected the adherences of LM1 to IPEC-J2 cells and of LGG to mucin. In addition, compared to adhesion to IPEC-J2 cells, adhesion to mucin by both LM1 and LGG was characterized by enhanced specific recognition of glycoreceptor components such as galactose, mannose, and N-acetylglucosamine. Hydrophobic interactions might make a greater contribution to adhesion of PF01. A similar adhesin profile between a probiotic and a pathogen, suggest a correlation between shared pathogen–probiotic glycoreceptor recognition and the ability to exclude enteropathogens such as Escherichia coli K88 and Salmonella Typhimurium KCCM 40253. These findings extend our understanding of the mechanisms of the intestinal adhesion and pathogen-inhibition abilities of probiotic Lactobacillus strains.

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Effect of apple extracts and selective polyphenols on the adhesion of potential probiotic strains of Lactobacillus gasseri R and Lactobacillus casei FMP
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Use of Atomic Force Microscopy to Study the Multi-Modular Interaction of Bacterial Adhesins to Mucins
A. Gunning, Devon Kavanaugh, Elizabeth Thursby, Sabrina Etzold, Donald MacKenzie, Nathalie Juge
International Journal of Molecular Sciences.2016; 17(11): 1854. CrossRef

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

Development of a stringent ELISA protocol to evaluate anti-viral hemorrhagic septicemia virus-specific antibodies in olive flounder Paralichthys olivaceus with improved specificity: Hyoung Jun Kim , Jeong Su Park , Se Ryun Kwon; J. Microbiol. 2015;53(7):481-485. Published online June 27, 2015; DOI: https://doi.org/10.1007/s12275-015-5101-9

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Abstract

Olive flounder were vaccinated with polyinosinic:polycytidylic acid [Poly (I:C)] to prevent viral hemorrhagic septicemia (VHS). Vaccine efficacy was verified by detection of anti- VHS virus (VHSV) antibodies using enzyme-linked immunosorbent assay (ELISA). In the study, ELISA absorbance values of the negative control group [Poly (I:C)-MEM10] were saturated when an ELISA protocol, that includes pretreatment of the fish sera with 5% skim milk, was used. However, the saturated OD values in the negative control did not correlate with a specific immune response against VHSV, because the group showed low survival rate (only 10%) following the VHSV challenge. Also, OD values of Poly (I:C)- VHSV group were high, and the group showed high survival rate (97.5%) against VHSV challenge test. It was suggested that the high OD values were possibly due to the presence of anti-fetal bovine serum (FBS) cross-reactivity. To compensate this, we subtracted the absorbance of infectious hematopoietic necrosis (IHNV)-Ag plates from those of the VHSV-Ag plates. However, the average value for the Poly (I:C)-VHSV group (0.167) was lower than expected even though high survival rate. We used an advanced ELISA system to pre-treat fish sera with 5% skim milk and two novirhabdoviruses as capture antigens as well as 50% FBS. The corrected absorbance values for pre-treated fish sera from the negative control Poly (I:C)-MEM10 and experimental Poly (I:C)-VHSV groups averaged 0.033 and 0.579, respectively. The specific VHSV antibody response of the vaccinated group was assessed using fish sera pretreated with skim milk and FBS and by calculating the corrected absorbance values from ELISA with two novirhabdovirus capture antigens.

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Development of an indirect ELISA for detection of the adaptive immune response of black carp (Mylopharyngodon piceus)
Tongtong Wang, Shanshan Jin, Ruoxuan Lv, Yuting Meng, Guozhong Li, Yuxing Han, Qiusheng Zhang
Journal of Immunological Methods.2023; 521: 113550. CrossRef
Detection of Salmonid IgM Specific to the Piscine Orthoreovirus Outer Capsid Spike Protein Sigma 1 Using Lipid-Modified Antigens in a Bead-Based Antibody Detection Assay
Lena Hammerlund Teige, Subramani Kumar, Grethe M. Johansen, Øystein Wessel, Niccolò Vendramin, Morten Lund, Espen Rimstad, Preben Boysen, Maria K. Dahle
Frontiers in Immunology.2019;[Epub] CrossRef
Production of a monoclonal antibody against of muskellunge (Esox masquinongy) IgM heavy chain and its use in development of an indirect ELISA for titrating circulating antibodies against VHSV-IVB
Mohamed Faisal, Isaac F. Standish, Mary Ann Vogelbein, Elena V. Millard, Stephen L. Kaattari
Fish & Shellfish Immunology.2019; 88: 464. CrossRef
Phylogenetic analysis and duplex RT-PCR detection of viral hemorrhagic septicemia virus in olive flounder (Paralichthys olivaceus) from Korea
Jee Youn Hwang, Seongdo Lee, Thanthrige Thiunuwan Priyathilaka, Hyerim Yang, Hyukjae Kwon, Mun Gyeong Kwon, Seong Don Hwang, Myoung-Jin Kim, Jehee Lee
Aquaculture.2018; 484: 242. CrossRef
Herpesvirus Infection Induces both Specific and Heterologous Antiviral Antibodies in Carp
Julio M. Coll
Frontiers in Immunology.2018;[Epub] CrossRef
Validation of a serum neutralization test for detection of antibodies specific to cyprinid herpesvirus 3 in infected common and koi carp (Cyprinus carpio)
J Cabon, L Louboutin, J Castric, S Bergmann, G Bovo, M Matras, O Haenen, N J Olesen, T Morin
Journal of Fish Diseases.2017; 40(5): 687. CrossRef
The amino-terminal domain of ORF149 of koi herpesvirus is preferentially targeted by IgM from carp populations surviving infection
F. Torrent, A. Villena, P. A. Lee, W. Fuchs, S. M. Bergmann, J. M. Coll
Archives of Virology.2016; 161(10): 2653. CrossRef

Effect of promoter-upstream sequence on σ38-dependent stationary phase gene transcription: Hyung-Ju Lim , Kwangsoo Kim , Minsang Shin , Jae-Ho Jeong , Phil Youl Ryu , Hyon E. Choy; J. Microbiol. 2015;53(4):250-255. Published online April 8, 2015; DOI: https://doi.org/10.1007/s12275-015-4681-8

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Abstract

σ38 in Escherichia coli is required for expression of a subset of stationary phase genes. However, the promoter elements for σ38-dependent genes are virtually indistinguishable from that for σ70-dependent house-keeping genes. hdeABp is a σ38-dependent promoter and LEE5p is a σ70-dependent promoter, but both are repressed by H-NS, a bacterial histone- like protein, which acts at promoter upstream sequence. We swapped the promoter upstream sequences of the two promoters and found that the σ dependency was switched. This was further verified using lacUV5 core promoter. The
results
suggested that the determinant for σ38-dependent promoter lies in the promoter upstream sequence.

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Sequence-dependent model of genes with dual σ factor preference
Ines S.C. Baptista, Vinodh Kandavalli, Vatsala Chauhan, Mohamed N.M. Bahrudeen, Bilena L.B. Almeida, Cristina S.D. Palma, Suchintak Dash, Andre S. Ribeiro
Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms.2022; 1865(3): 194812. CrossRef
Function Enhancement of a Metabolic Module via Endogenous Promoter Replacement for Pseudomonas sp. JY-Q to Degrade Nicotine in Tobacco Waste Treatment
Jun Li, Fengmei Yi, Guoqing Chen, Fanda Pan, Yang Yang, Ming Shu, Zeyu Chen, Zeling Zhang, Xiaotong Mei, Weihong Zhong
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Recent advances in genetic engineering tools based on synthetic biology
Jun Ren, Jingyu Lee, Dokyun Na
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A Genome-Wide Identification of Genes Potentially Associated with Host Specificity of Brucella Species: Kyung Mo Kim , Kyu-Won Kim , Samsun Sung , Heebal Kim; J. Microbiol. 2011;49(5):768-775. Published online November 9, 2011; DOI: https://doi.org/10.1007/s12275-011-1084-3

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Abstract

Brucella species are facultative intracellular pathogenic α-Proteobacteria that can cause brucellosis in humans and domestic animals. The clinical and veterinary importance of the bacteria has led to well established studies on the molecular mechanisms of Brucella infection of host organisms. However, to date, no genome-wide study has scanned for genes related to the host specificity of Brucella spp. The majority of bacterial genes related to specific environmental adaptations such as host specificity are well-known to have evolved under positive selection pressure. We thus detected signals of positive selection for individual orthologous genes among Brucella genomes and identified genes related to host specificity. We first determined orthologous sets from seven completely sequenced Brucella genomes using the Reciprocal Best Hits (RBH). A maximum likelihood analysis based on the branch-site test was accomplished to examine the presence of positive selection signals, which was subsequently confirmed by phylogenetic analysis. Consequently, 12 out of 2,033 orthologous genes were positively selected by specific Brucella lineages, each of which belongs to a particular animal host. Extensive literature reviews revealed that half of these computationally identified genes are indeed involved in Brucella host specificity. We expect that this genome-wide approach based on positive selection may be reliably used to screen for genes related to environmental adaptation of a particular species and that it will provide a set of appropriate candidate genes.

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Clade-specific positive selection on a developmental gene: BRANCHLESS TRICHOME and the evolution of stellate trichomes in Physaria (Brassicaceae)
Abigail R. Mazie, David A. Baum
Molecular Phylogenetics and Evolution.2016; 100: 31. CrossRef
Identification of Recombination and Positively Selected Genes in Brucella
Udayakumar S. Vishnu, Jagadesan Sankarasubramanian, Jayavel Sridhar, Paramasamy Gunasekaran, Jeyaprakash Rajendhran
Indian Journal of Microbiology.2015; 55(4): 384. CrossRef
Comparison of Brucella canis genomes isolated from different countries shows multiple variable regions
Miryan Margot Sánchez-Jiménez, Juan Pablo Isaza, Juan F. Alzate, Martha Olivera-Angel
Genomics.2015; 106(1): 43. CrossRef
Complete Genome Sequence of Brucella canis Strain 118, a Strain Isolated from Canine
Guangjun Gao, Jing Li, Tiefeng Li, Zhengfang Zhang, Liping Wang, Xitong Yuan, Yufei Wang, Jie Xu, Yuehua Ke, Liuyu Huang, Dali Wang, Zeliang Chen, Xingran Xu
Journal of Bacteriology.2012; 194(23): 6680. CrossRef
Complete Genome Sequence of Brucella canis BCB018, a Strain Isolated from a Human Patient
Yufei Wang, Yuehua Ke, Qing Zhen, Xitong Yuan, Jie Xu, Yefeng Qiu, Zhoujia Wang, Tiefeng Li, Dali Wang, Liuyu Huang, Zeliang Chen
Journal of Bacteriology.2012; 194(23): 6697. CrossRef

Distinctive Endophytic Fungal Assemblage in Stems of Wild Rice (Oryza granulata) in China with Special Reference to Two Species of Muscodor (Xylariaceae): Zhi-lin Yuan , Zhen-zhu Su , Li-juan Mao , Yang-qing Peng , Guan-mei Yang , Fu-cheng Lin , Chu-long Zhang; J. Microbiol. 2011;49(1):15-23. Published online March 3, 2011; DOI: https://doi.org/10.1007/s12275-011-0213-3

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Abstract: Ecological niches in the rhizosphere and phyllosphere of grasses capable of sustaining endophytes have been extensively studied. In contrast, little information regarding the identity and functions of endophytic fungi in stems is available. In this study, we investigated the taxonomic affinities, diversity, and host specificities of culturable endophytes in stems of wild rice (Oryza granulata) in China. Seventy-four isolates were recovered. Low recovery rate (11.7%) indicated that there were relatively few sites for fungal infection. Identification using morphology, morphospecies sorting, and molecular techniques resulted in classification into 50 taxa, 36 of which were recovered only once. Nucleotide sequence similarity analysis indicated that 30% of the total taxa recovered were highly divergent from known species and thus may represent lineages new to science. Most of the taxa were classified as members of the classes Sordariomycetes or Dothideomycetes (mainly in Pleosporales). The presence of Arthrinium and Magnaporthaceae species, most often associated with poaceous plants, suggested a degree of host specificity. A polyphasic approach was employed to identify two Muscodor taxa based on (i) ITS and RPB2 phylogenies, (ii) volatile compounds produced, and (iii) an in vitro bioassay of antifungal activity. This to our knowledge is only the second report regarding the isolation of Muscodor spp. in China. Therefore, we hypothesize that wild plants represent a huge reservoir of unknown fungi. The prevalence, novelty, and species-specificity of unique isolates necessitate a reevaluation of their contribution to ecosystem function and fungal biodiversity.

Evaluation of the Sensitivity and Specificity of Primer Pairs and the Efficiency of RNA Extraction Procedures to Improve Noroviral Detection from Oysters by Nested Reverse Transcription-Polymerase Chain Reaction: Cheonghoon Lee , Sooryun Cheong , Hee-Jung Lee , Miye Kwon , Ilnam Kang , Eun-Gyoung Oh , Hong-Sik Yu , Soon-Bum Shin , Sang-Jong Kim; J. Microbiol. 2010;48(5):586-593. Published online November 3, 2010; DOI: https://doi.org/10.1007/s12275-010-0047-4

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Abstract: Noroviruses (NoV) are the key cause of acute epidemic gastroenteritis, and oysters harvested from NoVpolluted sea areas are considered as the significant vectors of viral transmission. To improve NoV detection from oyster using nested reverse transcription-polymerase chain reaction (RT-PCR), we evaluated the sensitivity and specificity of previously published primer pairs and the efficiency of different RNA extraction procedures. Among the primer pairs used for RT-PCR, the sensitivity of GIF1/GIR1-GIF2/GIR1 and GIIF1/GIIR1-GIIF2/GIIR1 was higher than that of other primer pairs used in nested RT-PCR for the detection of NoV genogroup I (NoV GI) and NoV GII from both NoV-positive stool suspension and NoVseeded oyster concentrates, respectively; the resulting products showed neither unspecific bands in the positive samples nor false-positive bands in the negative controls. The extraction of NoV RNA from oyster samples using a QIAamp? Viral RNA Mini kit with a QIAshredderTM Homogenizer pretreatment afforded more efficient recovery (mean recovery for NoV GI and GII, 6.4%) and the procedure was less time consuming (<30 min) than most other RNA extraction procedures. The results of RNA extraction procedure and primer pairs evaluated by nested RT-PCR assay in this study can be useful for monitoring NoV contamination in oysters, which is an indicator of possible public health risks.

Development of a Latex Agglutination Test for Norovirus Detection: Heetae Lee , YoungBin Park , Misoon Kim , Youngmee Jee , Doo-sung Cheon , Hae Sook Jeong , GwangPyo Ko; J. Microbiol. 2010;48(4):419-425. Published online August 20, 2010; DOI: https://doi.org/10.1007/s12275-010-0071-4

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Abstract: Norovirus (NoV) is the leading cause of acute gastroenteritis worldwide. Currently, reverse transcription polymerase chain reaction (RT-PCR) is used commonly to detect NoVs in both clinical and environmental samples. However, RT-PCR requires expensive equipment and cannot be performed on site. In this study, a latex agglutination test (LAT) using antibody-labeled latex beads for detecting NoVs was developed. Two kinds of polyclonal antibodies, one generated from synthetic peptides and the other from E. coli-expressed NoV capsid proteins, were used to develop the LAT. Each of these polyclonal antibodies was immobilized on the surface of latex beads and tested for the ability to detect NoVs. Under optimized conditions, our LAT detected GII.4 NoV at concentrations as low as 3.3×105 RT-PCR units/ml in stool samples. The detection limit for the LAT was approximately 1.7×103 RT-PCR units. Forty-eight stool samples were tested for NoVs using this LAT. In comparison with an RT-PCR assay, the sensitivity and specificity of the LAT were 35% and 100%, respectively. With further optimization, this LAT used with appropriate antibodies could be applied for convenient detection of NoVs in clinical diagnosis and food monitoring.

Cloning, Expression, and Characterization of Xylose Reductase with Higher Activity from Candida tropicalis: Feiwei Zhang , Dairong Qiao , Hui Xu , Chong Liao , Shilin Li , Yi Cao; J. Microbiol. 2009;47(3):351-357. Published online June 26, 2009; DOI: https://doi.org/10.1007/s12275-008-0225-9

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Abstract

Xylose reductase (XR) is a key enzyme in xylose metabolism because it catalyzes the reduction of xylose to xylitol. In order to study the characteristics of XR from Candida tropicalis SCTCC 300249, its XR gene(xyl1) was cloned and expressed in Escherichia coli BL21 (DE3). The fusion protein was purified effectively by Ni2+-chelating chromatography, and the kinetics of the recombinant XR was investigated. The Km values of the C. tropicalis XR for NADPH and NADH were 45.5 uM and 161.9 uM, respectively, which demonstrated that this XR had dual coenzyme specificity. Moreover, this XR showed the highest catalytic efficiency (kcat=1.44x04 min-1) for xylose among the characterized aldose reductases. Batch fermentation was performed with Saccharomyces serivisiae W303-1A:pYES2XR, and resulted in 7.63 g/L cell mass, 93.67 g/L xylitol, and 2.34 g/Lh xylitol productivity. This XR coupled with its dual coenzyme specificity, high activity, and catalytic efficiency proved its utility in in vitro xylitol production.

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Efficient production of ginsenoside Rh2 from xylose by remodeling metabolism in Saccharomyces cerevisiae
Wanze Zhang, Jiale Zhang, Xiaomeng Zhao, Zhanwei Zhang, Shifan He, Xueke Bian, Haibin Wang, Chuanbo Zhang, Wenyu Lu
Chemical Engineering Journal.2024; 494: 153120. CrossRef
Recent insights, applications and prospects of xylose reductase: a futuristic enzyme for xylitol production
Yogita Lugani, Munish Puri, Balwinder Singh Sooch
European Food Research and Technology.2021; 247(4): 921. CrossRef
Characterization of d-xylose reductase, XyrB, from Aspergillus niger
Agata Terebieniec, Tania Chroumpi, Adiphol Dilokpimol, Maria Victoria Aguilar-Pontes, Miia R. Mäkelä, Ronald P. de Vries
Biotechnology Reports.2021; 30: e00610. CrossRef
Combining Xylose Reductase from Spathaspora arborariae with Xylitol Dehydrogenase from Spathaspora passalidarum to Promote Xylose Consumption and Fermentation into Xylitol by Saccharomyces cerevisiae
Adriane Mouro, Angela A. dos Santos, Denis D. Agnolo, Gabriela F. Gubert, Elba P. S. Bon, Carlos A. Rosa, César Fonseca, Boris U. Stambuk
Fermentation.2020; 6(3): 72. CrossRef
Kinetics and Predicted Structure of a Novel Xylose Reductase from Chaetomium thermophilum
Julian Quehenberger, Tom Reichenbach, Niklas Baumann, Lukas Rettenbacher, Christina Divne, Oliver Spadiut
International Journal of Molecular Sciences.2019; 20(1): 185. CrossRef
Biosynthetic strategies to produce xylitol: an economical venture
Yirong Xu, Ping Chi, Muhammad Bilal, Hairong Cheng
Applied Microbiology and Biotechnology.2019; 103(13): 5143. CrossRef
A halotolerant aldose reductase from Debaryomyces nepalensis: gene isolation, overexpression and biochemical characterization
Bhaskar Paidimuddala, Gopala Krishna Aradhyam, Sathyanarayana N. Gummadi
RSC Advances.2017; 7(33): 20384. CrossRef
Inhibition of Debaryomyces nepalensis xylose reductase by lignocellulose derived by-products
Bhaskar Paidimuddala, Ashish Rathod, Sathyanarayana N. Gummadi
Biochemical Engineering Journal.2017; 121: 73. CrossRef
Bioprospecting and evolving alternative xylose and arabinose pathway enzymes for use in Saccharomyces cerevisiae
Sun-Mi Lee, Taylor Jellison, Hal S. Alper
Applied Microbiology and Biotechnology.2016; 100(5): 2487. CrossRef
The yeast Scheffersomyces amazonensis is an efficient xylitol producer
Raquel M. Cadete, Monaliza A. Melo-Cheab, Adriana L. Viana, Evelyn S. Oliveira, César Fonseca, Carlos A. Rosa
World Journal of Microbiology and Biotechnology.2016;[Epub] CrossRef
Identification and characterization of d-arabinose reductase and d-arabinose transporters from Pichia stipitis
Seiya Watanabe, Yuki Utsumi, Shigeki Sawayama, Yasuo Watanabe
Bioscience, Biotechnology, and Biochemistry.2016; 80(11): 2151. CrossRef
Sequence analysis of KmXYL1 genes and verification of thermotolerant enzymatic activities of xylose reductase from four Kluyveromyces marxianus strains
Jae-Bum Park, Jin-Seong Kim, Seung-Won Jang, Deok-Ho Kweon, Eock Kee Hong, Won Cheol Shin, Suk-Jin Ha
Biotechnology and Bioprocess Engineering.2016; 21(5): 581. CrossRef
Cloning, expression, and characterization of a novel xylose reductase from Rhizopus oryzae
Min Zhang, Shao‐tong Jiang, Zhi Zheng, Xing‐jiang Li, Shui‐zhong Luo, Xue‐feng Wu
Journal of Basic Microbiology.2015; 55(7): 907. CrossRef
Metabolic engineering strategies for improving xylitol production from hemicellulosic sugars
Buli Su, Mianbin Wu, Jianping Lin, Lirong Yang
Biotechnology Letters.2013; 35(11): 1781. CrossRef
Identification of a xylose reductase gene in the xylose metabolic pathway of Kluyveromyces marxianus NBRC1777
Biao Zhang, Ling Zhang, Dongmei Wang, Xiaolian Gao, Jiong Hong
Journal of Industrial Microbiology & Biotechnology.2011; 38(12): 2001. CrossRef
Purification and biochemical characterization of a moderately halotolerant NADPH dependent xylose reductase from Debaryomyces nepalensis NCYC 3413
Sawan Kumar, Sathyanarayana N. Gummadi
Bioresource Technology.2011; 102(20): 9710. CrossRef
Cosubstrate effect on xylose reductase and xylitol dehydrogenase activity levels, and its consequence on xylitol production by Candida tropicalis
Elena Tamburini, Ercolina Bianchini, Alessandro Bruni, Giuseppe Forlani
Enzyme and Microbial Technology.2010; 46(5): 352. CrossRef

Isoforms of Glucose 6-Phosphate Dehydrogenase in Deinococcus radiophilus: Ji Youn Sung , Young Nam Lee; J. Microbiol. 2007;45(4):318-325.; DOI: https://doi.org/2566 [pii]

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Abstract: Glucose 6-phosphate dehydrogenase (G6PDH, EC 1.1.1.49) in Deinococcus radiophilus, an extraordinarily UV-resistant bacterium, was investigated to gain insight into its resistance as it was shown to be involved in a scavenging system of superoxide (O2-1) and peroxide (O2-2) generated by UV and oxidative stresses. D. radiophilus possesses two G6PDH isoforms: G6PDH-1 and G6PDH-2, both showing dual coenzyme specificity for NAD and NADP. Both enzymes were detected throughout the growth phase; however, the substantial increase in G6PDH-1 observed at stationary phase or as the results of external oxidative stress indicates that this enzyme is inducible under stressful environmental conditions. The G6PDH-1 and G6PDH-2 were purified 122- and 44-fold (using NADP as cofactor), respectively. The purified G6PDH-1 and G6PDH-2 had the specific activity of 2,890 and 1,033 U/mg protein (using NADP as cofactor) and 3,078 and 1,076 U/mg protein (using NAD as cofactor), respectively. The isoforms also evidenced distinct structures; G6PDH-1 was a tetramer of 35 kDa subunits, whereas G6PDH-2 was a dimer of 60 kDa subunits. The pIs of G6PDH-1 and G6PDH-2 were 6.4 and 5.7, respectively. Both G6PDH-1 and G6PDH-2 were inhibited by both ATP and oleic acid, but G6PDH-1 was found to be more susceptible to oleic acid than G6PDH-2. The profound inhibition of both enzymes by β-naphthoquinone-4-sulfonic acid suggests the involvement of lysine at their active sites. Cu2+ was a potent inhibitor to G6PDH-2, but a lesser degree to G6PDH-1. Both G6PDH-1 and G6PDH-2 showed an optimum activity at pH 8.0 and 30°C.

Propagation of Bombyx mori Nucleopolyhedrovirus in Nonpermissive Insect Cell Lines: Soo-Dong Woo , Jong Yul Roh , Jae Young Choi , Byung Rae Jin; J. Microbiol. 2007;45(2):133-138.; DOI: https://doi.org/2522 [pii]

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Abstract: This study addresses the susceptibility of Spodoptera frugiperda (Sf9 and Sf21), Trichoplusia ni (Hi5), and S. exigua (Se301) cells to the Bombyx mori nucleopolyhedrovirus (BmNPV). Although these cells have classically been considered nonpermissive to BmNPV, the cytopathic effect, an increase in viral yield, and viral DNA synthesis by BmNPV were observed in Sf9, Sf21, and Hi5 cells, but not in Se301 cells. Very late gene expression by BmNPV in these cell lines was also detected via β-galactosidase expression under the control of the polyhedrin promoter. Sf9 cells were most susceptible to BmNPV in all respects, followed by Sf21 and Hi5 cells in decreasing order, while the Se301 cells evidenced no distinct viral replication. This particular difference in viral susceptibility in each of the cell lines can be utilized for our understanding of the mechanisms underlying the host specificity of NPVs.

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