Zhang H.,CAS Institute of Biophysics |
Li D.,BGI Shenzhen |
Li D.,Shenzhen Key Laboratory of Unknown Pathogen Identification |
Zhao L.,Chinese National Institute for Communicable Disease Control and Prevention |
And 30 more authors.
Nature Genetics | Year: 2013
The worldwide emergence of multidrug-resistant (MDR) and extensively drug-resistant (XDR) tuberculosis threatens to make this disease incurable. Drug resistance mechanisms are only partially understood, and whether the current understanding of the genetic basis of drug resistance in M. Tuberculosis is sufficiently comprehensive remains unclear. Here we sequenced and analyzed 161 isolates with a range of drug resistance profiles, discovering 72 new genes, 28 intergenic regions (IGRs), 11 nonsynonymous SNPs and 10 IGR SNPs with strong, consistent associations with drug resistance. On the basis of our examination of the dN/dS ratios of nonsynonymous to synonymous SNPs among the isolates, we suggest that the drug resistance-Associated genes identified here likely contain essentially all the nonsynonymous SNPs that have arisen as a result of drug pressure in these isolates and should thus represent a near-complete set of drug resistance-Associated genes for these isolates and antibiotics. Our work indicates that the genetic basis of drug resistance is more complex than previously anticipated and provides a strong foundation for elucidating unknown drug resistance mechanisms. © 2013 Nature America, Inc. All rights reserved.
PubMed | CAS Institute of Biophysics, Shanghai JiaoTong University, CAS Wuhan Institute of Virology, U.S. Center for Disease Control and Prevention and 2 more.
Type: Journal Article | Journal: Cell reports | Year: 2014
Poor understanding of the basic biology of Mycobacterium tuberculosis (MTB), the etiological agent of tuberculosis, hampers development of much-needed drugs, vaccines, and diagnostic tests. Better experimental tools are needed to expedite investigations of this pathogen at the systems level. Here, we present a functional MTB proteome microarray covering most of the proteome and an ORFome library. We demonstrate the broad applicability of the microarray by investigating global protein-protein interactions, small-molecule-protein binding, and serum biomarker discovery, identifying 59 PknG-interacting proteins, 30 bis-(3-5)-cyclic dimeric guanosine monophosphate (c-di-GMP) binding proteins, and 14 MTB proteins that together differentiate between tuberculosis (TB) patients with active disease and recovered individuals. Results suggest that the MTB rhamnose pathway is likely regulated by both the serine/threonine kinase PknG and c-di-GMP. This resource has the potential to generate a greater understanding of key biological processes in the pathogenesis of tuberculosis, possibly leading to more effective therapies for the treatment of this ancient disease.
PubMed | Baoan Chronic Diseases Prevention and Cure Hospital, Chinese Medicine Hospital of Huangpu District, GuangDong Provincial Hospital of Chinese Medicine, The Second Peoples Hospital of Zhongshan City and 7 more.
Type: | Journal: Tuberculosis (Edinburgh, Scotland) | Year: 2016
Tuberculosis (TB) continues to be one of the most serious infectious diseases in the world, however, no effective biomarkers can be used for rapid screening of latent tuberculosis infection (LTBI) and active TB. In this study, serum cytokines were screened and tested as potential biomarker for TB diagnosis.Cytokine array was used to track the cytokine profile and its dynamic change after TB infection. The different expressions of cytokines were confirmed by ELISA assay. ROC curve analyses were used to evaluate the efficacy of a cytokine or cytokine combination for diagnosis.Eotaxin-2, ICAM-1, MCSF, IL-12p70, and IL-11 were significantly higher in the LTBI individuals. I-309, MIG, Eotaxin-2, IL-8, ICAM-1, IL-6sR, and Eotaxin were significantly higher in active TB patients. ROC curve analyses gave AUCs of 0.843, 0.898, and 0.888 for I-309, MIG, and IL-8, respectively, and 0.894 for the combination panel in active TB diagnosis. IFN-/IL-4 and IL-2/TNF- ratios exhibit dynamic changes in the healthy control and LTBI to different stages of active TB.Serum cytokines, including I-309 and MIG, IL-8, Extoxin-2, ICAM-1 and combinations of cytokines, including IFN-/IL-4 and IL-2/TNF-, can be used as serum biomarkers for LTBI and active TB screening, thus indicating prospective clinical applications.
Wang J.,Sun Yat Sen University |
Yang K.,Sun Yat Sen University |
Zhou L.,Center for Tuberculosis Control of Guangdong Province |
Wu M.,Sun Yat Sen University |
And 9 more authors.
PLoS Pathogens | Year: 2013
Mycobacterium tuberculosis is a hard-to-eradicate intracellular pathogen that infects one-third of the global population. It can live within macrophages owning to its ability to arrest phagolysosome biogenesis. Autophagy has recently been identified as an effective way to control the intracellular mycobacteria by enhancing phagosome maturation. In the present study, we demonstrate a novel role of miR-155 in regulating the autophagy-mediated anti-mycobacterial response. Both in vivo and in vitro studies showed that miR-155 expression was significantly enhanced after mycobacterial infection. Forced expression of miR-155 accelerated the autophagic response in macrophages, thus promoting the maturation of mycobacterial phagosomes and decreasing the survival rate of intracellular mycobacteria, while transfection with miR-155 inhibitor increased mycobacterial survival. However, macrophage-mediated mycobacterial phagocytosis was not affected after miR-155 overexpression or inhibition. Furthermore, blocking autophagy with specific inhibitor 3-methyladenine or silencing of autophagy related gene 7 (Atg7) reduced the ability of miR-155 to promote autophagy and mycobacterial elimination. More importantly, our study demonstrated that miR-155 bound to the 3′-untranslated region of Ras homologue enriched in brain (Rheb), a negative regulator of autophagy, accelerated the process of autophagy and sequential killing of intracellular mycobacteria by suppressing Rheb expression. Our results reveal a novel role of miR-155 in regulating autophagy-mediated mycobacterial elimination by targeting Rheb, and provide potential targets for clinical treatment. © 2013 Wang et al.
PubMed | Baoan Chronic Diseases Prevention and Cure Hospital, Guangdong Polytechnic, Guangdong Provincial Hospital of Chinese Medicine, South China University of Technology and 2 more.
Type: | Journal: Materials science & engineering. C, Materials for biological applications | Year: 2015
To overcome the undesirable side effects and reduce the cytotoxicity of isoniazid (INH) and rifampin (RMP) in the digestive tract, a poly(methacrylic acid) (PMAA) nanogel was developed as a carrier of INH and RMP. This PMAA/INH/RMP nanogel was prepared as a treatment for intestinal tuberculosis caused by multidrug-resistant Mycobacterium tuberculosis (MTB). The morphology, size, and in vitro release properties were evaluated in a simulated gastrointestinal medium, and long-term antibacterial performance, cytotoxicity, stability, and activity of this novel PMAA/INH/RMP nanogel against multidrug-resistant MTB in the intestine were investigated. Our results indicate that the PMAA/INH/RMP nanogel exhibited extended antibacterial activity by virtue of its long-term release of INH and RMP in the simulated gastrointestinal medium. Further, this PMAA/INH/RMP nanogel exhibited lower cytotoxicity than did INH or RMP alone, suggesting that this PMAA/INH/RMP nanogel could be a more useful dosage form than separate doses of INH and RMP for intestinal MTB. The novel aspects of this study include the cytotoxicity study and the three-phase release profile study, which might be useful for other researchers in this field.
PubMed | Wenzhou University, Sun Yat Sen University and Center for Tuberculosis Control of Guangdong Province
Type: Journal Article | Journal: The Journal of infection | Year: 2015
To explore the role of myeloid-related protein 8/14 in mycobacterial infection.The mRNA and protein expression levels of MRP8 or MRP14 were measured by real-time PCR and flow cytometry, respectively. Role of MRP8/14 was tested by overexpression or RNA interference assays. Flow cytometry and colony forming unit were used to test the phagocytosis and the survival of intracellular Mycobacterium bovis BCG (BCG), respectively. Autophagy mediated by MRP8/14 was detected by Western blot and immunofluorescence. The colocalization of BCG phagosomes with autophagosomes or lysosomes was by detected by confocal microscopy. ROS production was detected by flow cytometry.MRP8/14 expressions were up-regulated in human monocytic THP1 cells and primary macrophages after mycobacterial challenge. Silencing of MRP8/14 suppressed bacterial killing, but had no influence on the phagocytosis of BCG. Importantly, silencing MRP8/14 decreased autophagy and BCG phagosome maturation in THP1-derived macrophages, thereby increasing the BCG survival. Additionally, we demonstrated that MRP8/14 promoted autophagy in a ROS-dependent manner.The present study revealed a novel role of MRP8/14 in the autophagy-mediated elimination of intracellular BCG by promoting ROS generation, which may provide a promising therapeutic target for tuberculosis and other intracellular bacterial infectious diseases.
PubMed | CAS Institute of Biophysics, Shandong University and Center for Tuberculosis Control of Guangdong Province
Type: Journal Article | Journal: Acta crystallographica. Section F, Structural biology communications | Year: 2014
7-Keto-8-aminopelargonic acid synthase (KAPA synthase; BioF) is an essential enzyme for mycobacterial growth that catalyses the first committed step in the biotin-synthesis pathway. It is a pyridoxal 5-phosphate (PLP)-dependent enzyme and is a potential drug target. Here, the cloning, expression, purification and crystallization of KAPA synthase from Mycobacterium smegmatis (MsBioF) and the characterization of MsBioF crystals using X-ray diffraction are described. The crystals diffracted to 2.3 resolution and belonged to the monoclinic space group P21, with unit-cell parameters a = 70.88, b = 91.68, c = 109.84, = 97.8. According to the molecular weight of MsBioF, the unit-cell parameters and the self-rotation function map, four molecules are present in each asymmetric unit with a VM value of 2.06(3)Da(-1) and a solvent content of 40.20%.
PubMed | CAS Wuhan Institute of Virology, CAS Institute of Biophysics and Center for Tuberculosis Control of Guangdong Province
Type: Journal Article | Journal: FEMS microbiology letters | Year: 2015
Lysine acetylation is an important post-translational modification and is known to regulate many eukaryotic cellular processes. Little, however, is known about acetylated proteins in prokaryotes. Here, using immunoblotting, mass spectrometry and mutagenesis studies, we investigate the acetylation dynamics of the DNA repair protein Ku and its relationship with the deacetylase protein Sir2 and the non-homologous end joining (NHEJ) pathway in Mycobacterium smegmatis. We report that acetylation of Ku increases with growth, while NHEJ activity decreases, providing support for the hypothesis that acetylation of Ku may be involved in the DNA damage response in bacteria. Ku has multiple lysine sites. Our results indicate that K29 is an important acetylation site and that deficiency of Sir2 or mutation of K29 affects the quantity of Ku and its acetylation dynamics. Our findings expand knowledge of acetylation targets in prokaryotes and indicate a new direction for further research on bacterial DNA repair mechanisms.
PubMed | CAS Institute of Biophysics and Center for Tuberculosis Control of Guangdong Province
Type: Journal Article | Journal: Acta crystallographica. Section F, Structural biology communications | Year: 2015
Rv0880 from the pathogen Mycobacterium tuberculosis is classified as a MarR family protein in the Pfam database. It consists of 143 amino acids and has an isoelectric point of 10.9. Crystals of Rv0880 belonged to space group P1, with unit-cell parameters a = 54.97, b = 69.60, c = 70.32 , = 103.71, = 111.06, = 105.83. The structure of the MarR family transcription regulator Rv0880 was solved at a resolution of 2.0 with an R(cryst) and R(free) of 21.2 and 24.9%, respectively. The dimeric structure resembles that of other MarR proteins, with each subunit comprising a winged helix-turn-helix domain connected to an -helical dimerization domain.
PubMed | Chinese Medicine Hospital of Huangpu District and Center for Tuberculosis Control of Guangdong Province
Type: Journal Article | Journal: Zhonghua jie he he hu xi za zhi = Zhonghua jiehe he huxi zazhi = Chinese journal of tuberculosis and respiratory diseases | Year: 2015
To study the dynamic changes of tuberculosis related cytokines among patients during the different courses of treatment, and to analyze their influences on the development and prognoses of tuberculosis.All patients with active tuberculosis were enrolled from Guangzhou, Shenzhen and Foshan TB control institutes. There were a total of 68 cases, 36 males and 32 females, aged 19 to 50 years [ average (309) years]. All the TB patients received standard chemotherapy regimen of anti-tuberculosis, and were divided into 2 groups: one completed treatment group (cured or clinically cured 38 cases) and 1 uncompleted treatment group (treatment failure or need to extend treatment, 30 cases). Peripheral blood serum at 0, 2, 6 month during the treatment from 68 tuberculosis patients were collected, and the concentration of IFN-,IL-4,IL-17,TGF-,TNF- and IL-10 were detected by ELISA tests.The concentration of IFN-, TGF- and IL-4 in all enrolled patients showed significant decrease (from 23.2 ng/L to 22.3 ng/L, from 169.1 ng/L to 123.2 ng/L; 65.0 ng/L to 31.9 ng/L) (t=2.67, 2.35 and 3.41, P<0.05) along with the extension of treatment. IL-10 increased significantly (12.9 ng/L) in the uncompleted treatment group but declined significantly (5.38 ng/L) (P<0.05) in the completed treatment group at the end of 6 month. Meanwhile, IL-4 decreased significantly (P<0.05) in the completed treatment group but no significant changes were observed in the uncompleted treatment group. Th1/Th2 (IFN-/IL-4) raised gradually in the completed treatment group (0 month <2 month <6 month, t=6.32, 6.03 and 5.85, P<0.05), while it was only at 6 month in the uncompleted treatment group (0 month <6 month, t=3.7, P<0.05). And the ratio of Th1/Th2 in the completed treatment group was significantly higher than that in the uncompleted group treatment (P<0.05).It suggests that the changes of Th1 cytokines (IFN-, TGF-) and the Th1/Th2 balance play an important role in the pathogenesis, development and prognosis of TB. The suppression of IFN-, TGF- or Th1/Th2 balance may be an important factor influencing the prognosis of TB.