- 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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 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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Citations
Citations to this article as recorded by  - cAMP-independent Crp homolog adds to the multi-layer regulatory network in Porphyromonas gingivalis
Michał Śmiga, Ewa Roszkiewicz, Paulina Ślęzak, Michał Tracz, Teresa Olczak
Frontiers in Cellular and Infection Microbiology.2025;[Epub] CrossRef - 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
- Oxygen-mediated growth enhancement of an obligate anaerobic archaeon Thermococcus onnurineus NA1
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Seong Hyuk Lee , Hwan Youn , Sung Gyun Kang , Hyun Sook Lee
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J. Microbiol. 2019;57(2):138-142. Published online January 31, 2019
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DOI: https://doi.org/10.1007/s12275-019-8592-y
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72
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3
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2
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Abstract
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Thermococcus onnurineus NA1, an obligate anaerobic hyperthermophilic
archaeon, showed variable oxygen (O2) sensitivity
depending on the types of substrate employed as an
energy source. Unexpectedly, the culture with yeast extract
as a sole energy source showed enhanced growth by 2-fold
in the presence of O2. Genome-wide transcriptome analysis
revealed the upregulation of several antioxidant-related genes
encoding thioredoxin peroxidase (TON_0862), rubrerythrin
(TON_0864), rubrerythrin-related protein (TON_0873),
NAD(P)H rubredoxin oxidoreductase (TON_0865), or thioredoxin
reductase (TON_1603), which can couple the detoxification
of reactive oxygen species with the regeneration
of NAD(P)+ from NAD(P)H. We present a plausible mechanism
by which O2 serves to maintain the intracellular redox
balance. This study demonstrates an unusual strategy of an
obligate anaerobe underlying O2-mediated growth enhancement
despite not having heme-based or cytochrome-type
proteins.
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Citations
Citations to this article as recorded by - How low can they go? Aerobic respiration by microorganisms under apparent anoxia
Jasmine S Berg, Soeren Ahmerkamp, Petra Pjevac, Bela Hausmann, Jana Milucka, Marcel M M Kuypers
FEMS Microbiology Reviews.2022;[Epub] CrossRef - Reductive evolution and unique predatory mode in the CPR bacterium Vampirococcus lugosii
David Moreira, Yvan Zivanovic, Ana I. López-Archilla, Miguel Iniesto, Purificación López-García
Nature Communications.2021;[Epub] CrossRef
- Gly184 of the Escherichia coli cAMP receptor protein provides optimal context for both DNA binding and RNA polymerase interaction
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Matt N. Hicks , Sanjiva Gunasekara , Jose Serate , Jin Park , Pegah Mosharaf , Yue Zhou , Jin-Won Lee , Hwan Youn
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J. Microbiol. 2017;55(10):816-822. Published online September 28, 2017
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DOI: https://doi.org/10.1007/s12275-017-7266-x
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75
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Abstract
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The Escherichia coli cAMP receptor protein (CRP) utilizes the
helix-turn-helix motif for DNA binding. The CRP’s recognition
helix, termed F-helix, includes a stretch of six amino
acids (Arg180, Glu181, Thr182, Val183, Gly184, and Arg185)
for direct DNA contacts. Arg180, Glu181 and Arg185 are
known as important residues for DNA binding and specificity,
but little has been studied for the other residues. Here
we show that Gly184 is another F-helix residue critical for
the transcriptional activation function of CRP. First, glycine
was repeatedly selected at CRP position 184 for its unique
ability to provide wild type-level transcriptional activation
activity. To dissect the glycine requirement, wild type CRP
and mutants G184A, G184F, G184S, and G184Y were purified
and their in vitro DNA-binding activity was measured.
G184A and G184F displayed reduced DNA binding, which
may explain their low transcriptional activation activity. However,
G184S and G184Y displayed apparently normal DNA
affinity. Therefore, an additional factor is needed to account
for the diminished transcriptional activation function in
G184S and G184Y, and the best explanation is perturbations
in their interaction with RNA polymerase. The fact that glycine
is the smallest amino acid could not fully warrant its suitability,
as shown in this study. We hypothesize that Gly184
fulfills the dual functions of DNA binding and RNA polymerase
interaction by conferring conformational flexibility
to the F-helix.
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Citations
Citations to this article as recorded by -
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 - cAMP Activation of the cAMP Receptor Protein, a Model Bacterial Transcription Factor
Hwan Youn, Marcus Carranza
Journal of Microbiology.2023; 61(3): 277. CrossRef
- The inability of Bacillus licheniformis perR mutant to grow is mainly due to the lack of PerR-mediated fur repression
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Jung-Hoon Kim , Yoon-Mo Yang , Chang-Jun Ji , Su-Hyun Ryu , Young-Bin Won , Shin-Yeong Ju , Yumi Kwon , Yeh-Eun Lee , Hwan Youn , Jin-Won Lee
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J. Microbiol. 2017;55(6):457-463. Published online April 22, 2017
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DOI: https://doi.org/10.1007/s12275-017-7051-x
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84
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Abstract
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PerR, a member of Fur family protein, is a metal-dependent H2O2 sensing transcription factor that regulates genes in-volved in peroxide stress response. Industrially important bac-terium Bacillus licheniformis contains three PerR-like pro-teins (PerRBL, PerR2, and PerR3) compared to its close rela-tive Bacillus subtilis. Interestingly, unlike other bacteria in-cluding B. subtilis, no authentic perRBL null mutant could be established for B. licheniformis. Thus, we constructed a con-ditional perRBL mutant using a xylose-inducible promoter, and investigated the genes under the control of PerRBL. PerRBL regulon genes include katA, mrgA, ahpC, pfeT, hemA, fur, and perR as observed for PerRBS. However, there is some variation in the expression levels of fur and hemA genes be-tween B. subtilis and B. licheniformis in the derepressed state. Furthermore, katA, mrgA, and ahpC are strongly induced, whereas the others are only weakly or not induced by H2O2 treatment. In contrast to the B. subtilis perR null mutant which frequently gives rise to large colony phenotype mainly due to the loss of katA, the suppressors of B. licheniformis perR mutant, which can form colonies on LB agar, were all cata-lase-positive. Instead, many of the suppressors showed in-creased levels of siderophore production, suggesting that the suppressor mutation is linked to the fur gene. Consistent with this, perR fur double mutant could grow on LB agar without Fe supplementation, whereas perR katA double mutant could only grow on LB agar with Fe supplementation. Taken toge-ther, our data suggest that in B. licheniformis, despite the si-milarity in PerRBL and PerRBS regulon genes, perR is an essen-tial gene required for growth and that the inability of perR null mutant to grow is mainly due to elevated expression of Fur.
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Citations
Citations to this article as recorded by -
Characterization of the dual regulation by a c-di-GMP riboswitch Bc1 with a long expression platform from
Bacillus thuringiensis
Lu Liu, Dehua Luo, Yongji Zhang, Dingqi Liu, Kang Yin, Qing Tang, Shan-Ho Chou, Jin He, Beile Gao
Microbiology Spectrum.2024;[Epub] CrossRef - Meddling with Metal Sensors: Fur-Family Proteins as Signaling Hubs
Caroline H. Steingard, John D. Helmann, Tina M. Henkin
Journal of Bacteriology.2023;[Epub] CrossRef - Divergent Effects of Peptidoglycan Carboxypeptidase DacA on Intrinsic β-Lactam and Vancomycin Resistance
Si Hyoung Park, Umji Choi, Su-Hyun Ryu, Han Byeol Lee, Jin-Won Lee, Chang-Ro Lee, Krisztina M. Papp-Wallace
Microbiology Spectrum.2022;[Epub] CrossRef - Microbial Redox Regulator-Enabled Pulldown for Rapid Analysis of Plasma Low-Molecular-Weight Biothiols
Jin Oh Lee, Yoon-Mo Yang, Jae-Hoon Choi, Tae-Wuk Kim, Jin-Won Lee, Young-Pil Kim
Analytical Chemistry.2019; 91(15): 10064. CrossRef - Redox Sensing by Fe2+in Bacterial Fur Family Metalloregulators
Azul Pinochet-Barros, John D. Helmann
Antioxidants & Redox Signaling.2018; 29(18): 1858. CrossRef
- Sequence Analysis and Functional Expression of the Structural and Regulatory Genes for Pyruvate Dehydrogenase Complex from Streptomyces seoulensis
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Hwan Youn , Jangyul Kwak , Dong-Won Kim , Chang-Jin Lee , Yang-In Yim , Jin-Won Lee , In-Kwon Kim , Jeong-Il Yu , Hyung-Soon Yim , Sa-Ouk Kang
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J. Microbiol. 2002;40(1):43-50.
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Abstract
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A cluster of genes encoding the pyruvate dehydrogenase complex (PDC) of Streptomyces seoulensis, a Gram-positive bacterium, was cloned and sequenced. The genes of S. seoulensis consist of four open reading frames. The first gene, lpd, which encodes a lipoamide dehydrogenase, is followed by pdhB encoding a dihydrolipoamide acetyltransferase (E2p), pdhR, a regulatory gene, and pdhA encoding a pyruvate dehydrogenase component (E1p). E1p had an unusual homodimeric subunit, which has been known only in Gram-negative bacteria. S. seoulensis E2p contains two lipoyl domains like those of humans and Streptococcus faecalis. The pdhR gene appears to be clustered with the structural genes of S. seoulensis PDC. The PdhR-overexpressed S. seoulensis showed growth retardation and the decrease of E1p, indicating that PdhR regulates the function of PDC by repressing the expression of E1p. A strain of Streptomyces lividans overexpressing S. seoulensis PdhR showed a significant decrease in the level of actinorhodin, implying a regulatory role for Streptomyces PDC in antibiotic biosynthesis.
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