Publications by authors named "Lipeng Feng"

13 Publications

  • Page 1 of 1

The pentapeptide-repeat protein, MfpA, interacts with mycobacterial DNA gyrase as a DNA T-segment mimic.

Proc Natl Acad Sci U S A 2021 Mar;118(11)

Department of Biological Chemistry, John Innes Centre, NR4 7UH Norwich, United Kingdom;

DNA gyrase, a type II topoisomerase, introduces negative supercoils into DNA using ATP hydrolysis. The highly effective gyrase-targeted drugs, fluoroquinolones (FQs), interrupt gyrase by stabilizing a DNA-cleavage complex, a transient intermediate in the supercoiling cycle, leading to double-stranded DNA breaks. MfpA, a pentapeptide-repeat protein in mycobacteria, protects gyrase from FQs, but its molecular mechanism remains unknown. Here, we show that MfpA (MsMfpA) inhibits negative supercoiling by gyrase (Msgyrase) in the absence of FQs, while in their presence, MsMfpA decreases FQ-induced DNA cleavage, protecting the enzyme from these drugs. MsMfpA stimulates the ATPase activity of Msgyrase by directly interacting with the ATPase domain (MsGyrB47), which was confirmed through X-ray crystallography of the MsMfpA-MsGyrB47 complex, and mutational analysis, demonstrating that MsMfpA mimics a T (transported) DNA segment. These data reveal the molecular mechanism whereby MfpA modulates the activity of gyrase and may provide a general molecular basis for the action of other pentapeptide-repeat proteins.
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http://dx.doi.org/10.1073/pnas.2016705118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7980463PMC
March 2021

Realization of linear-mapping between polarization Poincaré sphere and orbital Poincaré sphere based on stress birefringence in the few-mode fiber.

Opt Express 2019 Nov;27(24):35537-35547

Based on the spatial profiles and polarization states evolution process of the first-order modes resulted from stress-induced birefringence in the few-mode fiber (FMF), we analyze the mapping relationship between the input polarization states represented on polarization PS and the output spatial profiles represented on the orbital PS of the FMF with respect to the magnitude and orientation of birefringence. When the input mode lobe orientation and the phase differences between the four eigenmodes of FMF induced by the stress birefringence satisfy a given condition, the mapping relationship between the input polarization PS and the output orbital PS is linear. Thus, the arbitrary points on the orbit PS can be generated at the output of stressed FMF by controlling the polarization state of the input modes. Then we experimentally verify that, an electrical single-mode polarization controller, a mode converter for converting fundamental mode to higher-order mode, a polarization controller mounting a coil of two-mode fiber and a polarizer can be employed to generate arbitrary first-order spatial modes on the orbital PS by controlling the input single-mode polarization states. The positions on the orbital PS of the generated first-order modes, which are obtained by calculating the three normalized Stokes parameters of output modes, agree well with the simulation ones. The correlation coefficients between the theoretical mode profiles and the experimental ones are higher than 80%. Since the spatial profile evolutions depend on the variations of the input polarization states, a potential advantage of this method is high-speed switching among desired first-order modes by using the commercial devices switching the state of polarization.
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http://dx.doi.org/10.1364/OE.27.035537DOI Listing
November 2019

Generation of LP/LP modes with tunable mode lobe orientation controlled by polarization states.

Opt Express 2019 Apr;27(9):13150-13159

We propose and experimentally demonstrate a novel scheme to generate LP/LP modes with tunable mode lobe orientation (MLO). Wherein, the MLOs have an excellent linear relationship with the linearly-polarized states of input fundamental modes. The proposed scheme is composed of a polarization controller (PC), a mode converter, a mode and polarization controller (PMC) which is twined with the few mode fiber (FMF) and a polarizer. Experimental results show that the deviations of MLOs between generated LP/LP modes and simulated ones are less than 3.5 and 8 degrees over C band. Since polarization control up to nanosecond scale is available with GaAs or lithium based electro-optic modulator, the proposed scheme could enable nanosecond time scale MLO control, which would be immensely useful for optical trapping, fiber sensors and optical communications.
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http://dx.doi.org/10.1364/OE.27.013150DOI Listing
April 2019

All-fiber polarization-division multiplexing to mode-division multiplexing conversion for hybrid optical networks.

Appl Opt 2018 Dec;57(36):10528-10533

This paper proposes and experimentally demonstrates an all-fiber conversion method that transfers the polarization-division multiplexing (PDM) signals to the mode-division multiplexing (MDM) signals. The conversion scheme is based on a mode converter and a polarization-mode controller. The input X-polarized/Y-polarized fundamental modes are converted to the first-order linear-polarized LP11A/LP11B modes with crosstalk of -10  dB/-18  dB and insertion losses of 3.04 dB/3.1 dB at 1550 nm, respectively. Using the proposed converter, 11.2 GBaud/s polarization-division-multiplexed quadrature-phase-shift keying (PDM-QPSK) and 16 quadrature-amplitude-modulation (PDM-16QAM) signals are successfully converted to 11.2 GBaud/s MDM-QPSK and MDM-16QAM signals.
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http://dx.doi.org/10.1364/AO.57.010528DOI Listing
December 2018

All-fiber orbital angular momentum mode multiplexer based on a mode-selective photonic lantern and a mode polarization controller.

Opt Lett 2018 Oct;43(19):4779-4782

We demonstrate for the first time, to the best of our knowledge, an all-fiber orbital angular momentum (OAM) multiplexer that multiplexes both OAM modes of -l and +l up to the second order by using a mode-selective photonic lantern and a mode polarization controller. The experimentally obtained mode profiles are close to the theoretical results, and the mode purities are higher than 89% for all the OAM modes at 1550 nm. The losses for all mode generations are less than 3.8 dB in the C-band.
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http://dx.doi.org/10.1364/OL.43.004779DOI Listing
October 2018

Continuously tunable orbital angular momentum generation controlled by input linear polarization.

Opt Lett 2018 May;43(9):2130-2133

In this Letter, we theoretically and experimentally demonstrate a new method to generate tunable orbital angular momentum (OAM) by continuously changing the angle of linear polarization of the input light. We use the Fourier series of left- and right-hand projections to prove that the average OAM smoothly varied from l=-1 to l=1 with the angle of LP of input light changing from 0 to π, which is fulfilled by an electrical polarization controller.
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http://dx.doi.org/10.1364/OL.43.002130DOI Listing
May 2018

Association of ω with the C-Terminal Region of the β' Subunit Is Essential for Assembly of RNA Polymerase in Mycobacterium tuberculosis.

J Bacteriol 2018 06 24;200(12). Epub 2018 May 24.

CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China

The ω subunit is the smallest subunit of bacterial RNA polymerase (RNAP). Although homologs of ω are essential in both eukaryotes and archaea, this subunit has been known to be dispensable for RNAP in and in other bacteria. In this study, we characterized an indispensable role of the ω subunit in Unlike the well-studied RNAP, the RNAP core enzyme cannot be functionally assembled in the absence of the ω subunit. Importantly, substitution of ω with ω subunits from or cannot restore the assembly of RNAP. Furthermore, by replacing different regions in ω with the corresponding regions from ω, we found a nonconserved loop region in ω essential for its function in RNAP assembly. From RNAP structures, we noticed that the location of the C-terminal region of the β' subunit (β'CTD) in RNAP but not in or RNAP is close to the ω loop region. Deletion of this β'CTD in RNAP destabilized the binding of ω on RNAP and compromised core assembly, suggesting that these two regions may function together to play a role in ω-dependent RNAP assembly in Sequence alignment of the ω loop and the β'CTD regions suggests that the essential role of ω is probably restricted to mycobacteria. Together, our study characterized an essential role of ω and highlighted the importance of the ω loop region in RNAP assembly. DNA-dependent RNA polymerase (RNAP), which consists of a multisubunit core enzyme (αββ'ω) and a dissociable σ subunit, is the only enzyme in charge of transcription in bacteria. As the smallest subunit, the roles of ω remain the least well studied. In and some other bacteria, the ω subunit is known to be nonessential for RNAP. In this study, we revealed an essential role of the ω subunit for RNAP assembly in the human pathogen , and a mycobacterium-specific ω loop that plays a role in this function was also characterized. Our study provides fresh insights for further characterizing the roles of bacterial ω subunit.
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http://dx.doi.org/10.1128/JB.00159-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5971482PMC
June 2018

PhoPR Positively Regulates Expression in Response to Low pH in Pathogenic Mycobacteria.

J Bacteriol 2018 04 26;200(8). Epub 2018 Mar 26.

CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China

During infection, colonizes macrophages or necrotic granulomas, in which low pH is one of the major challenges. The PhoPR two-component regulatory system and the cytosolic redox sensor WhiB3 both play important roles in the response to low pH by However, whether close association exists between PhoPR and WhiB3 remains unclear. In this study, the positive regulation of by PhoPR in mycobacteria was characterized. We observed that the expression patterns of the gene under acidic conditions are different among mycobacterial species, suggesting that the regulation of differs among mycobacteria. A sequence analysis of the promoters () from and two closely related species, namely, and , showed that the regions from and contain a new type of PhoP box that is absent in the Direct binding of PhoP to from and but not that from was validated by protein-DNA binding assays. The direct activation of by PhoPR under acidic conditions was further verified by reverse transcription-quantitative PCR (qRT-PCR) analysis in Moreover, mutating the residues important for the phosphorylation pathway of PhoPR in abolished the activation of expression by PhoPR under acidic conditions, suggesting that low pH triggers the phosphorylation of PhoPR, which in turn activates the transcription of Since the PhoP box was only identified in of pathogenic mycobacteria, we suggest that the PhoPR- regulatory pathway may have evolved to facilitate mycobacterial infection. The low pH in macrophages is an important barrier for infection by microbes. The PhoPR two-component regulatory system is required for the response to low pH and plays a role in redox homeostasis in WhiB3, a cytosolic redox-sensing transcriptional regulator, is also involved in these processes. However, there is no direct evidence to demonstrate the regulation of WhiB3 by PhoPR. In this study, we found that PhoPR directly activates expression in response to low pH. An atypical PhoP box in the promoters has been identified and is only found in pathogenic mycobacteria, which suggests that the PhoPR- regulatory pathway may facilitate mycobacterial infection. This study provides novel information for further characterization of the PhoPR regulon.
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http://dx.doi.org/10.1128/JB.00766-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5869482PMC
April 2018

Mycobacterial WhiB6 Differentially Regulates ESX-1 and the Dos Regulon to Modulate Granuloma Formation and Virulence in Zebrafish.

Cell Rep 2016 08 18;16(9):2512-24. Epub 2016 Aug 18.

Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China. Electronic address:

During the course of infection, Mycobacterium tuberculosis (Mtb) is exposed to diverse redox stresses that trigger metabolic and physiological changes. How these stressors are sensed and relayed to the Mtb transcriptional apparatus remains unclear. Here, we provide evidence that WhiB6 differentially regulates the ESX-1 and DosR regulons through its Fe-S cluster. When challenged with NO, WhiB6 continually activates expression of the DosR regulons but regulates ESX-1 expression through initial activation followed by gradual inhibition. Comparative transcriptomic analysis of the holo- and reduced apo-WhiB6 complemented strains confirms these results and also reveals that WhiB6 controls aerobic and anaerobic metabolism, cell division, and virulence. Using the Mycobacterium marinum zebrafish infection model, we find that holo- and apo-WhiB6 modulate levels of mycobacterial infection, granuloma formation, and dissemination. These findings provide fresh insight into the role of WhiB6 in mycobacterial infection, dissemination, and disease development.
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http://dx.doi.org/10.1016/j.celrep.2016.07.080DOI Listing
August 2016

σ(E) -dependent activation of RbpA controls transcription of the furA-katG operon in response to oxidative stress in mycobacteria.

Mol Microbiol 2016 10 11;102(1):107-20. Epub 2016 Jul 11.

Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.

Mycobacterium tuberculosis adopts various strategies to cope with oxidative stress during infection. Transcriptional regulators, including σ factors, make important contributions to this stress response, but how these proteins cooperate with each other is largely unknown. In this study, the role of RbpA and its cooperation with σ factors in response to oxidative stress are investigated. Knock down expression of rbpA in Mycobacterium smegmatis attenuated bacterial survival in the presence of H2 O2 . Additionally, transcription of the rbpA gene was induced by H2 O2 in a σ(E) -dependent manner. After induction, RbpA interacts with the principal sigma factor, σ(A) , to control the transcription of furA-katG operon, which encodes an H2 O2 scavenging enzyme. Moreover, this regulation is responsible for the role of σ(E) in oxidative response because bacterial survival was attenuated and transcription of the furA-katG operon was down-regulated with H2 O2 treatment in sigE deletion mutant (ΔsigE), and over-expression of RbpA in ΔsigE strain restored all of these phenotypes. Taken together, our study first illustrated a mechanism for σ(E) in response to oxidative stress through regulation of rbpA transcription. This study was also the first to demonstrate that RbpA is required for the full response to oxidative stress by cooperating with the principal σ(A) .
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http://dx.doi.org/10.1111/mmi.13449DOI Listing
October 2016

Genome-wide characterization of monomeric transcriptional regulators in Mycobacterium tuberculosis.

Microbiology (Reading) 2016 05 16;162(5):889-897. Epub 2016 Feb 16.

Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology,Chinese Academy of Sciences, Wuhan, PRChina.

Gene transcription catalysed by RNA polymerase is regulated by transcriptional regulators, which play central roles in the control of gene transcription in both eukaryotes and prokaryotes. In regulating gene transcription, many regulators form dimers that bind to DNA with repeated motifs. However, some regulators function as monomers, but their mechanisms of gene expression control are largely uncharacterized. Here we systematically characterized monomeric versus dimeric regulators in the tuberculosis causative agent Mycobacterium tuberculosis. Of the >160 transcriptional regulators annotated in M. tuberculosis, 154 transcriptional regulators were tested, 22 % probably act as monomers and most are annotated as hypothetical regulators. Notably, all members of the WhiB-like protein family are classified as monomers. To further investigate mechanisms of monomeric regulators, we analysed the actions of these WhiB proteins and found that the majority interact with the principal sigma factor σA, which is also a monomeric protein within the RNA polymerase holoenzyme. Taken together, our study for the first time globally classified monomeric regulators in M. tuberculosis and suggested a mechanism for monomeric regulators in controlling gene transcription through interacting with monomeric sigma factors.
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http://dx.doi.org/10.1099/mic.0.000257DOI Listing
May 2016

LcrQ blocks the role of LcrF in regulating the Ysc-Yop type III secretion genes in Yersinia pseudotuberculosis.

PLoS One 2014 21;9(3):e92243. Epub 2014 Mar 21.

Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.

Pathogenic Yersinia species employ the Ysc-Yop type III secretion system (T3SS) encoded by a highly conserved pYV virulence plasmid to export the virulence effectors into host cells. The Ysc-Yop T3SS is tightly regulated by multiple contributing proteins that function at different levels. However, systematic transcriptional regulation analysis of Ysc-Yop T3SS is lacking and the detailed mechanism under this regulation process is still elusive. Aimed at systematically characterizing transcriptional regulations of all T3SS genes in Y. pseudotuberculosis, we amplified 97 non-coding fragments from the pYV plasmid and analyzed transcriptional responses of the T3SS genes under different growth conditions. Transcriptions of T3SS genes were induced at 37°C and genes encoding T3SS effectors were highly induced by further depletion of Ca2+. The temperature induced gene transcription process is mediated by modules encoded on the chromosome, while the Ca2+ depletion-induced process is controlled by the positive regulatory protein LcrF as well as the negative regulatory protein LcrQ. In this process, LcrQ shares the same targets with LcrF and the effect of LcrQ is dependent on the presence of LcrF. Furthermore, over-expression of LcrF showed the same phenotype as that of the lcrQ mutant strain and intracellular amount balance of LcrQ and LcrF is important in T3SS regulation. When the expression level of LcrF exceeds LcrQ, expression of the Ysc-Yop T3SS genes is activated and vice versa. Together, these data support a model in which LcrQ blocks the activation role of LcrF in regulating the transcription of T3SS genes in Yersinia.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0092243PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3962397PMC
January 2015

Ribosomal binding site switching: an effective strategy for high-throughput cloning constructions.

PLoS One 2012 21;7(11):e50142. Epub 2012 Nov 21.

Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.

Direct cloning of PCR fragments by TA cloning or blunt end ligation are two simple methods which would greatly benefit high-throughput (HTP) cloning constructions if the efficiency can be improved. In this study, we have developed a ribosomal binding site (RBS) switching strategy for direct cloning of PCR fragments. RBS is an A/G rich region upstream of the translational start codon and is essential for gene expression. Change from A/G to T/C in the RBS blocks its activity and thereby abolishes gene expression. Based on this property, we introduced an inactive RBS upstream of a selectable marker gene, and designed a fragment insertion site within this inactive RBS. Forward and reverse insertions of specifically tailed fragments will respectively form an active and inactive RBS, thus all background from vector self-ligation and fragment reverse insertions will be eliminated due to the non-expression of the marker gene. The effectiveness of our strategy for TA cloning and blunt end ligation are confirmed. Application of this strategy to gene over-expression, a bacterial two-hybrid system, a bacterial one-hybrid system, and promoter bank construction are also verified. The advantages of this simple procedure, together with its low cost and high efficiency, makes our strategy extremely useful in HTP cloning constructions.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0050142PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3503710PMC
May 2013