Journal Article
- Unexpected Requirement of Small Amino Acids at Position 183 for DNA Binding in the Escherichia coli cAMP Receptor Protein
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Marcus Carranza, Amanda Rea, Daisy Pacheco, Christian Montiel, Jin Park, Hwan Youn
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J. Microbiol. 2024;62(10):871-882. Published online September 6, 2024
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DOI: https://doi.org/10.1007/s12275-024-00169-2
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Abstract
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The Escherichia coli cAMP receptor protein (CRP) relies on the F-helix, the recognition helix of the helix-turn-helix motif, for DNA binding. The importance of the CRP F-helix in DNA binding is well-established, yet there is little information on the roles of its non-base-contacting residues. Here, we show that a CRP F-helix position occupied by a non-base-contacting residue Val183 bears an unexpected importance in DNA binding. Codon randomization and successive in vivo screening selected six amino acids (alanine, cysteine, glycine, serine, threonine, and valine) at CRP position 183 to be compatible with DNA binding.
These amino acids are quite different in their amino acid properties (polar, non-polar, hydrophobicity), but one commonality is that they are all relatively small. Larger amino acid substitutions such as histidine, methionine, and tyrosine were made site-directedly and showed to have no detectable DNA binding, further supporting the requirement of small amino acids at CRP position 183.
Bioinformatics analysis revealed that small amino acids (92.15% valine and 7.75% alanine) exclusively occupy the position analogous to CRP Val183 in 1,007 core CRP homologs, consistent with our mutant data. However, in extended CRP homologs comprising 3700 proteins, larger amino acids could also occupy the position analogous to CRP Val183 albeit with low occurrence. Another bioinformatics analysis suggested that large amino acids could be tolerated by compensatory small-sized amino acids at their neighboring positions. A full understanding of the unexpected requirement of small amino acids at CRP position 183 for DNA binding entails the verification of the hypothesized compensatory change(s) in CRP.
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- SPD_0410 negatively regulates capsule polysaccharide synthesis and virulence in Streptococcus pneumoniae D39
Ye Tao, Li Lei, Shuhui Wang, Xuemei Zhang, Yibing Yin, Yuqiang Zheng
Frontiers in Microbiology.2025;[Epub] CrossRef
Review
- cAMP Activation of the cAMP Receptor Protein, a Model Bacterial Transcription Factor
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Hwan Youn , Marcus Carranza
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J. Microbiol. 2023;61(3):277-287. Published online March 9, 2023
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DOI: https://doi.org/10.1007/s12275-023-00028-6
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72
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Abstract
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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
- Enhancement of the solubility of recombinant proteins by fusion with a short-disordered peptide
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Jun Ren , Suhee Hwang , Junhao Shen , Hyeongwoo Kim , Hyunjoo Kim , Jieun Kim , Soyoung Ahn , Min-gyun Kim , Seung Ho Lee , Dokyun Na
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J. Microbiol. 2022;60(9):960-967. Published online July 14, 2022
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DOI: https://doi.org/10.1007/s12275-022-2122-z
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Abstract
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In protein biotechnology, large soluble fusion partners are
widely utilized for increased yield and solubility of recombinant
proteins. However, the production of additional large
fusion partners poses an additional burden to the host, leading
to a decreased protein yield. In this study, we identified
two highly disordered short peptides that were able to increase
the solubility of an artificially engineered aggregationprone
protein, GFP-GFIL4, from 0.6% to 61% (D3-DP00592)
and 46% (D4-DP01038) selected from DisProt database. For
further confirmation, the peptides were applied to two insoluble
E. coli proteins (YagA and YdiU). The peptides also
enhanced solubility from 52% to 90% (YagA) and from 27%
to 93% (YdiU). Their ability to solubilize recombinant proteins
was comparable with strong solubilizing tags, maltosebinding
protein (40 kDa) and TrxA (12 kDa), but much smaller
(< 7 kDa) in size. For practical application, the two peptides
were fused with a restriction enzyme, I-SceI, and they increased
I-SceI solubility from 24% up to 75%. The highly disordered
peptides did not affect the activity of I-SceI while I-SceI fused
with MBP or TrxA displayed no restriction activity. Despite
the small size, the highly disordered peptides were able to
solubilize recombinant proteins as efficiently as conventional
fusion tags and did not interfere with the function of recombinant
proteins. Consequently, the identified two highly disordered
peptides would have practical utility in protein biotechnology
and industry.
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Citations
Citations to this article as recorded by

- A review on computational models for predicting protein solubility
Teerapat Pimtawong, Jun Ren, Jingyu Lee, Hyang-Mi Lee, Dokyun Na
Journal of Microbiology.2025; 63(1): e:2408001. CrossRef - Synthetic intrinsically disordered protein fusion tags that enhance protein solubility
Nicholas C. Tang, Jonathan C. Su, Yulia Shmidov, Garrett Kelly, Sonal Deshpande, Parul Sirohi, Nikhil Peterson, Ashutosh Chilkoti
Nature Communications.2024;[Epub] CrossRef - Biosynthesis of Indigo Dyes and Their Application in Green Chemical and Visual Biosensing for Heavy Metals
Yan Guo, Shun-Yu Hu, Can Wu, Chao-Xian Gao, Chang-Ye Hui
ACS Omega.2024; 9(31): 33868. CrossRef - Functional small peptides for enhanced protein delivery, solubility, and secretion in microbial biotechnology
Hyang-Mi Lee, Thi Duc Thai, Wonseop Lim, Jun Ren, Dokyun Na
Journal of Biotechnology.2023; 375: 40. CrossRef - Directed Evolution of Soluble α-1,2-Fucosyltransferase Using Kanamycin Resistance Protein as a Phenotypic Reporter for Efficient Production of 2'-Fucosyllactose
Jonghyeok Shin, Seungjoo Kim, Wonbeom Park, Kyoung Chan Jin, Sun-Ki Kim, Dae-Hyuk Kweon
Journal of Microbiology and Biotechnology.2022; 32(11): 1471. CrossRef - Effects of spray drying, freeze drying, and vacuum drying on physicochemical and nutritional properties of protein peptide powder from salted duck egg white
Tianyin Du, Jicheng Xu, Shengnan Zhu, Xinjun Yao, Jun Guo, Weiqiao Lv
Frontiers in Nutrition.2022;[Epub] CrossRef
- [PROTOCOL] High-throughput cultivation based on dilution-to-extinction with catalase supplementation and a case study of cultivating acI bacteria from Lake Soyang
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Suhyun Kim , Miri S. Park , Jaeho Song , Ilnam Kang , Jang-Cheon Cho
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J. Microbiol. 2020;58(11):893-905. Published online October 30, 2020
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DOI: https://doi.org/10.1007/s12275-020-0452-2
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Abstract
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Multi-omics approaches, including metagenomics and single-
cell amplified genomics, have revolutionized our understanding
of the hidden diversity and function of microbes
in nature. Even in the omics age, cultivation is an essential
discipline in microbial ecology since microbial cultures are
necessary to assess the validity of an in silico prediction about
the microbial metabolism and to isolate viruses infecting bacteria
and archaea. However, the ecophysiological characteristics
of predominant freshwater bacterial lineages remain
largely unknown due to the scarcity of cultured representatives.
In an ongoing effort to cultivate the uncultured majority
of freshwater bacteria, the most abundant freshwater
Actinobacteria acI clade has recently been cultivated from
Lake Soyang through catalase-supplemented high-throughput
cultivation based on dilution-to-extinction. This method
involves physical isolation of target microbes from mixed populations,
culture media simulating natural habitats, and removal
of toxic compounds. In this protocol, we describe detailed
procedures for isolating freshwater oligotrophic microbes,
as well as the essence of the dilution-to-extinction culturing.
As a case study employing the catalase-supplemented
dilution-to-extinction protocol, we also report a cultivation
trial using a water sample collected from Lake Soyang. Of the
480 cultivation wells inoculated with a single lake-water sample,
75 new acI strains belonging to 8 acI tribes (acI-A1, A2,
A4, A5, A6, A7, B1, B4, C1, and C2) were cultivated, and each
representative strain per subclade could be revived from glycerol
stocks. These cultivation results demonstrate that the
protocol described in this study is efficient in isolating freshwater
bacterioplankton harboring streamlined genomes.
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Citations
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- Frontiers of lake microbial ecology opened up by new technologies.
Yusuke OKAZAKI
Japanese Journal of Limnology (Rikusuigaku Zasshi).2024; 85(1): 1. CrossRef - Sequencing-guided re-estimation and promotion of cultivability for environmental bacteria
Minjia Zheng, Linran Wen, Cailing He, Xinlan Chen, Laiting Si, Hao Li, Yiting Liang, Wei Zheng, Feng Guo
Nature Communications.2024;[Epub] CrossRef - Adaptive genetic traits in pelagic freshwater microbes
Maria‐Cecilia Chiriac, Markus Haber, Michaela M. Salcher
Environmental Microbiology.2023; 25(3): 606. CrossRef - Expanding success in the isolation of abundant marine bacteria after reduction in grazing and viral pressure and increase in nutrient availability
Xavier Rey-Velasco, Ona Deulofeu-Capo, Isabel Sanz-Sáez, Clara Cardelús, Isabel Ferrera, Josep M. Gasol, Olga Sánchez, Vincent J. Denef
Microbiology Spectrum.2023;[Epub] CrossRef - Two-Dimensional Cell Separation: a High-Throughput Approach to Enhance the Culturability of Bacterial Cells from Environmental Samples
Krishna K. Yadav, Yogesh Nimonkar, Bhagyashri J. Poddar, Lochana Kovale, Isita Sagar, Yogesh Shouche, Hemant J. Purohit, Anshuman A. Khardenavis, Stefan J. Green, Om Prakash, Kristen M. DeAngelis
Microbiology Spectrum.2022;[Epub] CrossRef - Marine microbial bioprospecting: Exploitation of marine biodiversity towards biotechnological applications—a review
Hoda Hosseini, Hareb M. Al‐Jabri, Navid R. Moheimani, Simil A. Siddiqui, Imen Saadaoui
Journal of Basic Microbiology.2022; 62(9): 1030. CrossRef - Prokaryotes of renowned Karlovy Vary (Carlsbad) thermal springs: phylogenetic and cultivation analysis
Tereza Smrhova, Kunal Jani, Petr Pajer, Gabriela Kapinusova, Tomas Vylita, Jachym Suman, Michal Strejcek, Ondrej Uhlik
Environmental Microbiome.2022;[Epub] CrossRef - Description of Vagococcus coleopterorum sp. nov., isolated from the intestine of the diving beetle, Cybister lewisianus, and Vagococcus hydrophili sp. nov., isolated from the intestine of the dark diving beetle, Hydrophilus acuminatus, and emended descrip
Dong-Wook Hyun, Euon Jung Tak, Pil Soo Kim, Jin-Woo Bae
Journal of Microbiology.2021; 59(2): 132. CrossRef - Metaviromics coupled with phage-host identification to open the viral ‘black box’
Kira Moon, Jang-Cheon Cho
Journal of Microbiology.2021; 59(3): 311. CrossRef - Heme auxotrophy in abundant aquatic microbial lineages
Suhyun Kim, Ilnam Kang, Jin-Won Lee, Che Ok Jeon, Stephen J. Giovannoni, Jang-Cheon Cho
Proceedings of the National Academy of Sciences.2021;[Epub] CrossRef - Recent trend, biases and limitations of cultivation-based diversity studies of microbes
Om Prakash, Mrinalini Parmar, Manali Vaijanapurkar, Vinay Rale, Yogesh S Shouche
FEMS Microbiology Letters.2021;[Epub] CrossRef - Cultivation of Dominant Freshwater Bacterioplankton Lineages Using a High-Throughput Dilution-to-Extinction Culturing Approach Over a 1-Year Period
Suhyun Kim, Md. Rashedul Islam, Ilnam Kang, Jang-Cheon Cho
Frontiers in Microbiology.2021;[Epub] CrossRef
- Development of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) thermal inactivation method with preservation of diagnostic sensitivity
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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
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J. Microbiol. 2020;58(10):886-891. Published online September 29, 2020
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DOI: https://doi.org/10.1007/s12275-020-0335-6
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23
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Abstract
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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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Heliyon.2024; 10(3): e25377. CrossRef - Validating the inactivation of viral pathogens with a focus on SARS-CoV-2 to safely transfer samples from high-containment laboratories
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Science of The Total Environment.2023; 856: 158966. CrossRef - Sputum handling for rheology
Lydia Esteban Enjuto, Matthieu Robert de Saint Vincent, Max Maurin, Bruno Degano, Hugues Bodiguel
Scientific Reports.2023;[Epub] CrossRef - A novel strategy to avoid sensitivity loss in pooled testing for SARS-CoV-2 surveillance: validation using nasopharyngeal swab and saliva samples
Georgia G. Millward, Shane M. Popelka, Anthony G. Gutierrez, William J. Kowallis, Robert L. von Tersch, Subrahmanyam V. Yerramilli
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Analytica Chimica Acta.2023; 1257: 341167. CrossRef - Methods of Inactivation of Highly Pathogenic Viruses for Molecular, Serology or Vaccine Development Purposes
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- Partial characteristics of hemolytic factors secreted from airborne Aspergillus and Penicillium, and an enhancement of hemolysis by Aspergillus micronesiensis CAMP-like factor via Staphylococcus aureus-sphingomyelinase
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Sumonrat Kaveemongkonrat , Kwanjit Duangsonk , Jos Houbraken , Phimchat Suwannaphong , Nongnuch Vanittanakom Vanittanakom , Malee Mekaprateep
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J. Microbiol. 2019;57(12):1086-1094. Published online November 4, 2019
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DOI: https://doi.org/10.1007/s12275-019-9133-4
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Abstract
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One of the advantages for initial survival of inhaled fungal
spores in the respiratory tract is the ability for iron acquisition
via hemolytic factor-production. To examine the ability
of indoor Aspergillus and Penicillium affecting hemolysis,
the secreted factors during the growth of thirteen strains from
eight species were characterized in vitro for their hemolytic
activity (HA) and CAMP-like reaction. The hemolytic index
of HA on human blood agar of Aspergillus micronesiensis,
Aspergillus wentii, Aspergillus westerdijkiae, Penicillium citrinum,
Penicillium copticola, Penicillium paxilli, Penicillium
steckii, and Penicillium sumatrense were 1.72 ± 0.34, 1.61 ±
0.41, 1.69 ± 0.16, 1.58 ± 0.46, 3.10 ± 0.51, 1.22 ± 0.19, 2.55 ±
0.22, and 1.90 ± 0.14, respectively. The secreted factors of
an Aspergillus wentii showed high HA when grown in undernourished
broth at 25°C at an exponential phase and were
heat sensitive. Its secreted proteins have an estimated relative
molecular weight over 50 kDa. Whereas, the factors of
Penicillium steckii were secreted in a similar condition at a
late exponential phase but showed low HA and heat tolerance.
In a CAMP-like test with sheep blood, the synergistic hemolytic
reactions between most tested mold strains and Staphylococcus
aureus were identified. Moreover, the enhancement
of α-hemolysis of Staphylococcus aureus could occur through
the interaction of Staphylococcus aureus-sphingomyelinase
and CAMP-like factors secreted from Aspergillus micronesiensis.
Further studies on the characterization of purified hemolytic-
and CAMP-like-factors secreted from Aspergillus
wentii and Aspergillus micronesiensis may lead to more understanding
of their involvement of hemolysis
-
Citations
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- Green Synthesis of Endolichenic Fungi Functionalized Silver Nanoparticles: The Role in Antimicrobial, Anti-Cancer, and Mosquitocidal Activities
Yugal Kishore Mohanta, Debasis Nayak, Awdhesh Kumar Mishra, Ishani Chakrabartty, Manjit Kumar Ray, Tapan Kumar Mohanta, Kumananda Tayung, Rajapandian Rajaganesh, Murugan Vasanthakumaran, Saravanan Muthupandian, Kadarkarai Murugan, Gouridutta Sharma, Hans-
International Journal of Molecular Sciences.2022; 23(18): 10626. CrossRef - Group B Streptococcus CAMP Factor Does Not Contribute to Interactions with the Vaginal Epithelium and Is Dispensable for Vaginal Colonization in Mice
Mallory B. Ballard, Vicki Mercado-Evans, Madelynn G. Marunde, Hephzibah Nwanosike, Jacob Zulk, Kathryn A. Patras, Mariola J. Edelmann
Microbiology Spectrum.2021;[Epub] CrossRef
- Arthrobacter dokdonellae sp. nov., isolated from a plant of the genus Campanula
-
Hyeon-Woo Koh , Myung-Suk Kang , Ki-Eun Lee , Eun-Young Lee , Hongik Kim , Soo-Je Park
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J. Microbiol. 2019;57(9):732-737. Published online May 11, 2019
-
DOI: https://doi.org/10.1007/s12275-019-8540-x
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5
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4
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Abstract
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A Gram-stain-positive, oxidase- and catalase-positive, motile,
aerobic, and rod-shaped bacterial strain, designated as
DCT-5T, was isolated from a native plant belonging to the genus
Campanula at Dokdo island, Republic of Korea. Growth
of the strain DCT-5T was observed at 15–37°C (optimum
30°C) on R2A broth, pH 6.0–8.0 (optimum 7.0), and 0–5%
(w/v) NaCl concentration (optimum 0%). The 16S rRNA gene
sequence analysis revealed that strain DCT-5T was most closely
related to Arthrobacter silviterrae KIS14-16T, Arthrobacter
livingstonensis LI2T, Arthrobacter stackebrandtii CCM
2783T, Arthrobacter cryoconiti Cr6-08T, Arthrobacter ramosus
CCM 1646T, and Arthrobacter psychrochitiniphilus GP3T with
pairwise sequence similarities of 98.76%, 97.47%, 97.25%,
97.11%, 97.11%, and 97.00%, respectively. The DNA G+C
content of strain DCT-5T was 64.7 mol%, and its DNA–DNA
relatedness values with A. silviterrae KIS14-16T, A. livingstonensis
LI2T, A. stackebrandtii CCM 2783T, A. psychrochitiniphilus
GP3T, A. ramosus CCM 1646T, and A. cryoconiti
Cr6-08T were 32.57 ± 2.02%, 28.75 ± 0.88%, 31.93 ± 1.15%,
34.73 ± 1.86%, 29.12 ± 1.56%, and 27.23 ± 0.88%, respectively.
The major quinone was MK-9(H2) and major fatty acids were
anteiso-C15:0, anteiso-C17:0, iso-C15:0, and iso-C16:0. The polar
lipids were diphosphatidylglycerol (DPG), phosphatidylglycerol
(PG), phosphatidylinositol (PI), unidentified glycolipid
(GL), two unidentified aminophospholipids (APLs), and three
unidentified lipids (Ls). The peptidoglycan type was A3α.
On the basis of phenotypic, phylogenetic, genotypic, and chemotaxonomic
characteristics, strain DCT-5T represents a
novel species of the genus Arthrobacter, for which the name
Arthrobacter dokdonellae sp. nov. is proposed. The type strain
is DCT-5T (= KCTC 49189T = LMG 31284T).
-
Citations
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- Biodegradation of dimethachlon by Arthrobacter sp. K5: Mechanistic insights and ecological implications
Zhenyu Qian, Yingpei Wang, Peicheng Lu, Minghui Wu, Haipeng Xie, Xiangyi Kong, Xiaoyan Wu, Shunli Hu
Journal of Environmental Chemical Engineering.2024; 12(6): 114473. CrossRef - Microbial adaptation to different environmental conditions: molecular perspective of evolved genetic and cellular systems
Atif Khurshid Wani, Nahid Akhtar, Farooq Sher, Acacio Aparecido Navarrete, Juliana Heloisa Pinê Américo-Pinheiro
Archives of Microbiology.2022;[Epub] CrossRef -
Arthrobacter sunyaminii sp. nov. and Arthrobacter jiangjiafuii sp. nov., new members in the genus Arthrobacter
Gui Zhang, Jing Yang, Dong Jin, Xin-He Lai, Shan Lu, Zhihong Ren, Tian Qin, Liyun Liu, Ji Pu, Yue Liu, Lin Ye, Juan Zhou, Xianglian Lv, Yuanmeihui Tao, Jianguo Xu
International Journal of Systematic and Evolutionary Microbiology
.2022;[Epub] CrossRef - Genotype to ecotype in niche environments: adaptation of Arthrobacter to carbon availability and environmental conditions
Sara Gushgari-Doyle, Lauren M Lui, Torben N Nielsen, Xiaoqin Wu, Ria G Malana, Andrew J Hendrickson, Heloise Carion, Farris L Poole, Michael W W Adams, Adam P Arkin, Romy Chakraborty
ISME Communications.2022;[Epub] CrossRef
- Role of putative virulence traits of Campylobacter jejuni in regulating differential host immune responses
-
Ankita Singh , Amirul Islam Mallick
-
J. Microbiol. 2019;57(4):298-309. Published online February 22, 2019
-
DOI: https://doi.org/10.1007/s12275-019-8165-0
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45
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13
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10
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Abstract
-
Among the major enteric pathogens, Campylobacter jejuni is
considered an important source of diarrheal illness in humans.
In contrast to the acute gastroenteritis in humans, C. jejuni
exhibits prolonged cecal colonization at a high level with little
or no pathology in chickens. Although several known virulence
determinants of C. jejuni have been found to be associated
with a higher degree of pathogenesis in humans, to date, little
is known about their functions in the persistent colonization
of chickens. The present study was undertaken to assess the
role of C. jejuni in imparting differential host immune responses
in human and chicken cells. Based on the abundance
of major genes encoding virulence factors (GEVFs), we used
a particular isolate that harbors the cadF, flaA, peb1, racR,
ciaB, cdtB, and hcp genes. This study showed that hypervirulent
C. jejuni isolate that encodes a functional type VI secretion
system (T6SS) has a greater ability to invade and create
characteristic “attaching and effacing” lesions in human
INT407 compared to primary chicken embryo intestinal cells
(CEICs). Furthermore, we demonstrated that the higher bacterial
invasion in human INT407 triggered higher levels of
expression of major proinflammatory cytokines, such as IL-
1β and IL-6, and significant downregulation of IL-17A gene
expression (P ≤ 0.05). The findings of the present study suggest
that the enhanced ability of C. jejuni to invade human
cells is tightly regulated by proinflammatory cytokines in the
gut and possibly holds the keys to the observed differences
in pathogenesis between human and chicken cells.
-
Citations
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- Targeted Bioimaging of Microencapsulated Recombinant LAB Vector Expressing Fluorescent Reporter Protein: A Non-invasive Approach for Microbial Tracking
Prakash Biswas, Afruja Khan, Amirul Islam Mallick
ACS Biomaterials Science & Engineering.2024; 10(8): 5210. CrossRef - Identification and functional characterization of putative ligand binding domain(s) of JlpA protein of Campylobacter jejuni
Chandan Gorain, Subhadeep Gupta, S.S. Mahafujul Alam, Mehboob Hoque, Andrey V. Karlyshev, Amirul Islam Mallick
International Journal of Biological Macromolecules.2024; 264: 130388. CrossRef - Heterogeneity and Compositional Diversities of Campylobacter jejuni Outer Membrane Vesicles (OMVs) Drive Multiple Cellular Uptake Processes
Afruja Khan, Avijit Sardar, Pradip K. Tarafdar, Amirul I. Mallick
ACS Infectious Diseases.2023; 9(11): 2325. CrossRef - Multimodal Biofilm Inactivation Using a Photocatalytic Bismuth Perovskite–TiO2–Ru(II)polypyridyl-Based Multisite Heterojunction
Noufal Kandoth, Sonu Pratap Chaudhary, Subhadeep Gupta, Kumari Raksha, Atin Chatterjee, Shresth Gupta, Safakath Karuthedath, Catherine S. P. De Castro, Frédéric Laquai, Sumit Kumar Pramanik, Sayan Bhattacharyya, Amirul Islam Mallick, Amitava Das
ACS Nano.2023; 17(11): 10393. CrossRef - In Silico and In Vitro Analysis of Helicobacter pullorum Type Six Secretory Protein Hcp and Its Role in Bacterial Invasion and Pathogenesis
Kashaf Javed, Farzana Gul, Rashda Abbasi, Sidra Batool, Zobia Noreen, Habib Bokhari, Sundus Javed
Current Microbiology.2022;[Epub] CrossRef - Gut Microbe-Derived Outer Membrane Vesicles: A Potential Platform to Control Cecal Load of Campylobacter jejuni
Ankita Singh, Afruja Khan, Tamal Ghosh, Samiran Mondal, Amirul I. Mallick
ACS Infectious Diseases.2021; 7(5): 1186. CrossRef - Mucosal delivery of live Lactococcus lactis expressing functionally active JlpA antigen induces potent local immune response and prevent enteric colonization of Campylobacter jejuni in chickens
Chandan Gorain, Ankita Singh, Sudipta Bhattacharyya, Anirban Kundu, Aritraa Lahiri, Subhadeep Gupta, Amirul I. Mallick
Vaccine.2020; 38(7): 1630. CrossRef - Immunopathological properties of the Campylobacter jejuni flagellins and the adhesin CadF as assessed in a clinical murine infection model
Anna-Maria Schmidt, Ulrike Escher, Soraya Mousavi, Nicole Tegtmeyer, Manja Boehm, Steffen Backert, Stefan Bereswill, Markus M. Heimesaat
Gut Pathogens.2019;[Epub] CrossRef - A One Health approach to prevention, treatment, and control of campylobacteriosis
Francesca Schiaffino, James Platts-Mills, Margaret N. Kosek
Current Opinion in Infectious Diseases.2019; 32(5): 453. CrossRef - Immunogenicity and protective efficacy of mucosal delivery of recombinant hcp of Campylobacter jejuni Type VI secretion system (T6SS) in chickens
Ankita Singh, Khairun Nisaa, Sudipta Bhattacharyya, Amirul Islam Mallick
Molecular Immunology.2019; 111: 182. CrossRef
- Paraburkholderia dokdonella sp. nov., isolated from a plant from the genus Campanula
-
Man-Young Jung , Myung-Suk Kang , Ki-Eun Lee , Eun-Young Lee , Soo-Je Park
-
J. Microbiol. 2019;57(2):107-112. Published online November 19, 2018
-
DOI: https://doi.org/10.1007/s12275-019-8500-5
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48
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1
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8
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8
Crossref
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Abstract
-
The novel Gram-stain-negative, rod-shaped, aerobic bacterial
strain DCR-13T was isolated from a native plant belonging
to the genus Campanula on Dokdo, an island in the
Republic of Korea. Comparative analysis of the 16S rRNA
gene sequence indicated that this strain is closely related to
Paraburkholderia peleae PP52-1T (98.43% 16S rRNA gene sequence
similarity), Paraburkholderia oxyphila NBRC 105797T
(98.42%), Paraburkholderia sacchari IPT 101T (98.28%), Paraburkholderia
mimosarum NBRC 106338T (97.80%), Paraburkholderia
denitrificans KIS30-44T (97.46%), and Paraburkholderia
paradise WAT (97.45%). This analysis of the 16S
rRNA gene sequence also suggested that DCR-13T and the
six closely related strains formed a clade within the genus
Paraburkholderia, but that DCR-13T was clearly separated
from the established species. DCR-13T had ubiquinone 8 as
its predominant respiratory quinone, and its genomic DNA
G + C content was 63.9 mol%. The isolated strain grew at a
pH of 6.0–8.0 (with an optimal pH of 6.5), 0–4% w/v NaCl
(with an optimal level of 0%), and a temperature of 18–42°C
(with an optimal temperature of 30°C). The predominant
fatty acids were C16:0, summed feature 8 (C18:1 ω7c/C18:1 ω6c),
C17:0 cyclo, C19:0 cyclo ω8c, summed feature 3 (C16:1 ω6c/C16:1
ω7c) and summed feature 2 (C12:0 aldehyde), and the major
polar lipids were phosphatidylglycerol and phosphatidylethanolamine.
On the basis of polyphasic evidence, it is proposed
that strain DCR-13T (= KCTC 62811T = LMG 30889T)
represents the type strain of a novel species, Paraburkholderia
dokdonella sp. nov.
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Citations
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- Genome-based taxonomy of Burkholderia sensu lato: Distinguishing closely related species
Evelise Bach, Camila Gazolla Volpiano, Fernando Hayashi Sant’Anna, Luciane Maria Pereira Passaglia
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Munusamy Madhaiyan, Shankar Sriram, Nedounsejian Kiruba, Venkatakrishnan Sivaraj Saravanan
Current Microbiology.2022;[Epub] CrossRef - Engineering of a newly isolated Bacillus tequilensis BL01 for poly-γ-glutamic acid production from citric acid
Dexin Wang, Xiaoping Fu, Dasen Zhou, Jiaqi Gao, Wenqin Bai
Microbial Cell Factories.2022;[Epub] CrossRef - The Hidden Genomic Diversity, Specialized Metabolite Capacity, and Revised Taxonomy of Burkholderia Sensu Lato
Alex J. Mullins, Eshwar Mahenthiralingam
Frontiers in Microbiology.2021;[Epub] CrossRef - The history and distribution of nodulating Paraburkholderia, a potential inoculum for Fynbos forage species
Chrizelle W. Beukes, Stephanus N. Venter, Emma T. Steenkamp
Grass and Forage Science.2021; 76(1): 10. CrossRef - International Committee on Systematics of Prokaryotes Subcommittee on the Taxonomy of Rhizobia and Agrobacteria Minutes of the closed meeting by videoconference, 17 July 2019
Philippe de Lajudie, J. Peter W. Young
International Journal of Systematic and Evolutionary Microbiology
.2020; 70(5): 3563. CrossRef - Spontaneous formation and mechanism of anaerobic ammonium oxidation (anammox) bacteria in swine wastewater treatment system
Zhenzhong Pan, Ruizhi Dai, Jingsong Liao, Jih-Gaw Lin, Yiguo Hong, Jiayin Ling, Yanbin Xu, Yuxin Li, Jiaen Peng
International Biodeterioration & Biodegradation.2020; 154: 105058. CrossRef - A newly isolated Bacillus siamensis SB1001 for mass production of poly-γ-glutamic acid
Dexin Wang, Jin-Su Hwang, Dong-Ho Kim, Sungbeom Lee, Dae-Hyuk Kim, Min-Ho Joe
Process Biochemistry.2020; 92: 164. CrossRef
- Paenibacillus seodonensis sp. nov., isolated from a plant of the genus Campanula
-
Myung-Suk Kang , Ki-Eun Lee , Eun-Young Lee , Soo-Je Park
-
J. Microbiol. 2018;56(12):874-879. Published online October 25, 2018
-
DOI: https://doi.org/10.1007/s12275-018-8455-y
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59
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1
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1
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-
Abstract
-
Strain DCT-19T, representing a Gram-stain-positive, rodshaped,
aerobic bacterium, was isolated from a native plant
belonging to the genus Campanula on Dokdo, the Republic of
Korea. Comparative analysis of the 16S rRNA gene sequence
showed that this strain was closely related to Paenibacillus
amylolyticus NRRL NRS-290T (98.6%, 16S rRNA gene sequence
similarity), Paenibacillus tundrae A10bT (98.1%), and
Paenibacillus xylanexedens NRRL B-51090T (97.6%). DNADNA
hybridization indicated that this strain had relatively
low levels of DNA-DNA relatedness with P. amylolyticus
NRRL NRS-290T (30.0%), P. xylanexedens NRRL B-51090T
(29.0%), and P. tundrae A10bT (24.5%). Additionally, the genomic
DNA G + C content of DCT-19T was 44.8%. The isolated
strain grew at pH 6.0–8.0 (optimum, pH 7.0), 0–4%
(w/v) NaCl (optimum, 0%), and a temperature of 15–45°C
(optimum 25–30°C). The sole respiratory quinone in the strain
was menaquinone-7, and the predominant fatty acids were
C15:0 anteiso, C16:0 iso, and C16:0. In addition, the major polar
lipids were diphosphatidylglycerol and phosphatidylethanolamine.
Based on its phenotypic properties, genotypic distinctiveness,
and chemotaxonomic features, strain DCT-19T
is proposed as a novel species in the genus Paenibacillus, for
which the name Paenibacillus seodonensis sp. nov. is proposed
(=KCTC 43009T =LMG 30888T). The type strain of
Paenibacillus seodonensis is DCT-19T.
-
Citations
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- Molecular Evidence of Crosstalk Between Bacterial Endophytes and Plant Transcriptome in Brassica juncea
Garima Sharma, Pooja Gokhale Sinha, Vartika Mathur
Journal of Plant Growth Regulation.2024; 43(12): 4397. CrossRef
- De novo transcriptome assembly and characterization of the 10-hydroxycamptothecin-producing Xylaria sp. M71 following salicylic acid treatment
-
Xiaowei Ding , Kaihui Liu , Yonggui Zhang , Feihu Liu
-
J. Microbiol. 2017;55(11):871-876. Published online October 27, 2017
-
DOI: https://doi.org/10.1007/s12275-017-7173-1
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46
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6
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Abstract
-
In the present study, we identified genes that are putatively
involved in the production of fungal 10-hydroxycamptothecin
via transcriptome sequencing and characterization of the
Xylaria sp. M71 treated with salicylic acid (SA). A total of
60,664,200 raw reads were assembled into 26,044 unigenes.
BLAST assigned 8,767 (33.7%) and 10,840 (41.6%) unigenes
to 40 Gene Ontology (GO) annotations and 108 Kyoto Encyclopedia
of Genes and Genomes (KEGG) pathways, respectively.
A total of 3,713 unigenes comprising 1,504 upregulated
and 2,209 downregulated unigenes were found to be differentially
expressed between SA-induced and control fungi.
Based on the camptothecin biosynthesis pathway in plants,
13 functional genes of Xylaria sp. M71 were mapped to the
mevalonate (MVA) pathway, suggesting that the fungal 10-hydroxycamptothecin
is produced via the MVA pathway. In
summary, analysis of the Xylaria sp. M71 transcriptome allowed
the identification of unigenes that are putatively involved
in 10-hydroxycamptothecin biosynthesis in fungi.
-
Citations
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- The hidden treasures in endophytic fungi: a comprehensive review on the diversity of fungal bioactive metabolites, usual analytical methodologies, and applications
Jefferson Brendon Almeida dos Reis, Adriana Sturion Lorenzi, Danilo Batista Pinho, Patrícia Cardoso Cortelo, Helson Mario Martins do Vale
Archives of Microbiology.2024;[Epub] CrossRef - Genomic and transcriptomic analysis of camptothecin producing novel fungal endophyte: Alternaria burnsii NCIM 1409
Shakunthala Natarajan, Boas Pucker, Smita Srivastava
Scientific Reports.2023;[Epub] CrossRef - Plant probiotics – Endophytes pivotal to plant health
Shiv Shanker Pandey, Rahul Jain, Priyanka Bhardwaj, Ankita Thakur, Manju Kumari, Shashi Bhushan, Sanjay Kumar
Microbiological Research.2022; 263: 127148. CrossRef - Using Next-Generation Sequencing Technology to Explore Genetic Pathways in Endophytic Fungi in the Syntheses of Plant Bioactive Metabolites
Monika Bielecka, Bartosz Pencakowski, Rosario Nicoletti
Agriculture.2022; 12(2): 187. CrossRef - Microbial endophytes: application towards sustainable agriculture and food security
Vagish Dwibedi, Santosh Kumar Rath, Mahavir Joshi, Rajinder Kaur, Gurleen Kaur, Davinder Singh, Gursharan Kaur, SukhminderJit Kaur
Applied Microbiology and Biotechnology.2022; 106(17): 5359. CrossRef - How and why do endophytes produce plant secondary metabolites?
Sachin Naik, Ramanan Uma Shaanker, Gudasalamani Ravikanth, Selvadurai Dayanandan
Symbiosis.2019; 78(3): 193. CrossRef
- Epidemiological relationships of Campylobacter jejuni strains isolated from humans and chickens in South Korea
-
Jae-Young Oh , Yong-Kuk Kwon , Bai Wei , Hyung-Kwan Jang , Suk-Kyung Lim , Cheon-Hyeon Kim , Suk-Chan Jung , Min-Su Kang
-
J. Microbiol. 2017;55(1):13-20. Published online December 30, 2016
-
DOI: https://doi.org/10.1007/s12275-017-6308-8
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51
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30
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-
Abstract
-
Thirty-nine human isolates of Campylobacter jejuni obtained
from a national university hospital during 2007–2010 and
38 chicken isolates of C. jejuni were collected from poultry
farms during 2009–2010 in South Korea were used in this
study. Campylobacter genomic species and virulence-associated
genes were identified by PCR. Pulsed-field gel electrophoresis
(PFGE) and multilocus sequence typing (MLST)
were performed to compare their genetic relationships. All
isolates were highly resistant to ciprofloxacin, nalidixic acid,
and tetracycline. Of all isolates tested, over 94% contained
seven virulence associated genes (flaA, cadF, racR, dnaJ, cdtA,
cdtB, and cdtC). All isolates were classified into 39 types by
PFGE clustering with 90% similarity. Some chicken isolates
were incorporated into some PFGE types of human isolates.
MLST analysis for the 39 human isolates and 38 chicken isolates
result
ed in 14 and 23 sequence types (STs), respectively,
of which 10 STs were new. STs overlapped in both chicken
and human isolates included ST-21, ST-48, ST-50, ST-51,
and ST-354, of which ST-21 was the predominant ST in both
human and chicken isolates. Through combined analysis of
PFGE types and STs, three chicken isolates were clonally related
to the three human isolates associated with food poisoning
(VII-ST-48, XXII-ST-354, and XXVIII-ST-51). They
were derived from geographically same or distinct districts.
Remarkably, clonal spread of food poisoning pathogens between
animals and humans was confirmed by population
genetic analysis. Consequently, contamination of campylobacters
with quinolone resistance and potential virulence genes in poultry production and consumption may increase
the risk of infections in humans.
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Animals.2021; 12(1): 83. CrossRef - Antimicrobial Resistance Profiles, Virulence Genes, and Genetic Diversity of Thermophilic Campylobacter Species Isolated From a Layer Poultry Farm in Korea
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Reviews
- MINIREVIEW] Clinical relevance of infections with zoonotic and human oral species of Campylobacter
-
Soomin Lee , Jeeyeon Lee , Jimyeong Ha , Yukyung Choi , Sejeong Kim , Heeyoung Lee , Yohan Yoon , Kyoung-Hee Choi
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J. Microbiol. 2016;54(7):459-467. Published online June 28, 2016
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DOI: https://doi.org/10.1007/s12275-016-6254-x
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Abstract
-
Genus Campylobacter has been recognized as a causative bacterial
agent of animal and human diseases. Human Campylobacter
infections have caused more concern. Campylobacters
can be classified into two groups in terms of their original host:
zoonotic and human oral species. The major zoonotic species
are Campylobacter jejuni and Campylobacter coli, which
mostly reside in the intestines of avian species and are transmitted
to humans via consumption of contaminated poultry
products, thus causing human gastroenteritis and other diseases
as sequelae. The other campylobacters, human oral species,
include C. concisus, C. showae, C. gracilis, C. ureolyticus,
C. curvus, and C. rectus. These species are isolated from the
oral cavity, natural colonization site, but have potential clinical
relevance in the periodontal region to varying extent. Two
species, C. jejuni and C. coli, are believed to be mainly associated
with intestinal diseases, but recent studies suggested
that oral Campylobacter species also play a significant role in
intestinal diseases. This review offers an outline of the two
Campylobacter groups (zoonotic and human oral), their virulence
traits, and the associated illnesses including gastroenteritis.
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- MINIREVIEW] The cAMP/protein kinase A signaling pathway in pathogenic basidiomycete fungi: Connections with iron homeostasis
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Jaehyuk Choi , Won Hee Jung , James W. Kronstad
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J. Microbiol. 2015;53(9):579-587. Published online August 1, 2015
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DOI: https://doi.org/10.1007/s12275-015-5247-5
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44
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43
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Abstract
-
A number of pathogenic species of basidiomycete fungi are
either life-threatening pathogens of humans or major economic
pests for crop production. Sensing the host is a key
aspect of pathogen proliferation during disease, and signal
transduction pathways are critically important for detecting
environmental conditions and facilitating adaptation. This
review focuses on the contributions of the cAMP/protein
kinase A (PKA) signaling pathway in Cryptococcus neoformans,
a species that causes meningitis in humans, and Ustilago
maydis, a model phytopathogen that causes a smut disease on
maize. Environmental sensing by the cAMP/PKA pathway
regulates the production of key virulence traits in C. neoformans
including the polysaccharide capsule and melanin.
For U. maydis, the pathway controls the dimorphic transition
from budding growth to the filamentous cell type required
for proliferation in plant tissue. We discuss recent advances
in identifying new components of the cAMP/PKA pathway
in these pathogens and highlight an emerging theme that
pathway signaling influences iron acquisition.
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- Expression of Escherichia coli DcuS-R Two-Component Regulatory System is Regulated by the Secondary Internal Promoter Which is Activated by CRP-cAMP
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Tomoya Oyamada , Katsushi Yokoyama , Michiko Morinaga , Masashi Suzuki , Kozo Makino
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J. Microbiol. 2007;45(3):234-240.
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DOI: https://doi.org/2537 [pii]
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Abstract
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The DcuS-R two-component system of Escherichia coli senses C4-dicarboxylates of the medium and regulates expression of the genes related to utilization of them. It is known that phospho-DcuR induces expression of genes such as the dcuB-fumB operon, the frdABCD operon, and the dctA gene. We analyzed promoters of the dcuS-R operon to elucidate the transcriptional regulation system. We found a novel internal promoter within the dcuS gene that is regulated by the transcriptional regulator, CRP-cAMP, in both aerobic and anaerobic conditions.