Journal of Microbiology

Volume 54(4); April 2016

Review

MINIREVIEW] Hydroxylation of methane through component interactions in soluble methane monooxygenases: Seung Jae Lee; J. Microbiol. 2016;54(4):277-282. Published online April 1, 2016; DOI: https://doi.org/10.1007/s12275-016-5642-6

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Methane hydroxylation through methane monooxygenases (MMOs) is a key aspect due to their control of the carbon cycle in the ecology system and recent applications of methane gas in the field of bioenergy and bioremediation. Methanotropic bacteria perform a specific microbial conversion from methane, one of the most stable carbon compounds, to methanol through elaborate mechanisms. MMOs express particulate methane monooxygenase (pMMO) in most strains and soluble methane monooxygenase (sMMO) under copper-limited conditions. The mechanisms of MMO have been widely studied from sMMO belonging to the bacterial multicomponent monooxygenase (BMM) superfamily. This enzyme has diiron active sites where different types of hydrocarbons are oxidized through orchestrated hydroxylase, regulatory and reductase components for precise control of hydrocarbons, oxygen, protons, and electrons. Recent advances in biophysical studies, including structural and enzymatic achievements for sMMO, have explained component interactions, substrate pathways, and intermediates of sMMO. In this account, oxidation of methane in sMMO is discussed with recent progress that is critical for understanding the microbial applications of C-H activation in one-carbon substrates.

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Complete genome sequences of Methylococcus capsulatus (Norfolk) and Methylocaldum szegediense (Norfolk) isolated from a landfill methane biofilter
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Patrik Török, Dóra Lakk-Bogáth, Duenpen Unjaroen, Wesley R. Browne, József Kaizer
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Crucial Role of the Chaperonin GroES/EL for Heterologous Production of the Soluble Methane Monooxygenase from Methylomonas methanica MC09
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A growing family of O2 activating dinuclear iron enzymes with key catalytic diiron(III)-peroxo intermediates: Biological systems and chemical models
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Research Support, Non-U.S. Gov'ts

Hymenobacter sedentarius sp. nov., isolated from a soil: Jae-Jin Lee , Myung-Suk Kang , Eun Sun Joo , Hee-Young Jung , Myung Kyum Kim; J. Microbiol. 2016;54(4):283-289. Published online April 1, 2016; DOI: https://doi.org/10.1007/s12275-016-5386-3

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Abstract

A novel Gram-negative and red-pinkish bacterium designated DG5BT was isolated from a dry soil. Cells were rods that were catalase- and oxidase-positive, and non-motile. The strain was found to grow at temperatures from 10 to 30°C (optimum 25°C) and pH 6.0–8.0, (optimum pH 7) on R2A broth. 16S rRNA gene sequence (1,452 bp) analysis of this strain identified it as a member of the genus Hymenobacter that belongs to the class Cytophagia. The highest gene sequence similarities were with Hymenobacter arizonensis OR362-8T (98.3%), Hymenobacter humi DG31AT (97.6%), and Hymenobacter glaciei VUG-A130T (96.6%). Strain DG5BT exhibited <70% DNA-DNA relatedness with H. arizonensis (34.7 ± 7.0%; reciprocally, 29.7 ± 1.2%) and H. humi (39.4 ± 4.3%; reciprocally, 39.5 ± 3.3%) as a different genomic species, and its genomic DNA G+C content was 59.8%. Strain DG5BT had the following chemotaxonomic characteristics: the major fatty acids are iso-C15:0, anteiso-C15:0, C16:1 ω5c, and summed feature 3 (C16:1 ω7c / C16:1 ω6c); polar lipid profile contained phosphatidylethanolamine (PE), unknown aminophospholipid (APL), unknown glycolipids (GL), unknown phospholipids (PL), and unknown polar lipids (L); the major quinone is MK- 7. The absorbance peak of pigment is at 481.0 nm. Strain DG5BT showed low-level resistance to gamma-ray irradiation. Phenotypic, chemotaxonomic, and genotypic properties indicated that isolate DG5BT represents a novel species within the genus Hymenobacter for which the name Hymenobacter sedentarius sp. nov. is proposed. The type strain is DG5BT (=KCTC 32524T =JCM 19636T).

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Yerin Park, Hyun-Ju Noh, Chung Yeon Hwang, Seung Chul Shin, Soon Gyu Hong, Young Keun Jin, Hyoungseok Lee, Yung Mi Lee
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Complete genome sequence of Hymenobacter sedentarius DG5BT, a bacterium resistant to gamma radiation
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Species identity of Phellinus linteus (sanghuang) extensively used as a medicinal mushroom in Korea: Jae-Gu Han , Min-Woo Hyun , Chang Sun Kim , Jong Won Jo , Jae-Han Cho , Kang-Hyo Lee , Won-Sik Kong , Sang-Kuk Han , Junsang Oh , Gi-Ho Sung; J. Microbiol. 2016;54(4):290-295. Published online April 1, 2016; DOI: https://doi.org/10.1007/s12275-016-5520-2

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Abstract

Sanghuang is a medicinal mushroom that has gained particular attention in Korea. It has been extensively studied for the past few decades as a natural immune booster and cancer suppressor. Although the scientific name, Phellinus linteus, has been commonly used to refer to the sanghuang mushroom, the species identity of sanghuang has been called into question due to the ambiguity of its circumscription and the inadequacy of morphological distinctions within allied species. Because the species concept of sanghuang has been elucidated by recent molecular phylogenetic studies, it has become necessary to clarify the taxonomic positions of sanghuang strains extensively utilized in Korea. We conducted a phylogenetic analysis of 74 strains belonging to the P. linteus-baumii complex based on ITS nrDNA sequences. Parental stains of sanghuang varieties formally registered in the Korea Seed & Variety Service, including ASI 26046 (Corea sanghuang), 26114 (Boolro), and 26115 (HK 1-ho) were grouped with Sanghuangporus sanghuang instead of P. linteus in the inferred phylogeny.

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The first complete mitochondrial genome of Phellinus pomaceus var. prunastri (Pers.) Pat. 1926 (Hymenochaetales: Hymenochaetaceae) and phylogenetic analysis
Wei Gao, Shuyi Chen, Qiang Li
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Preparation, characterization and cytotoxic activity of selenium nanoparticles stabilized with a heteropolysaccharide isolated from Sanghuangporus vaninii residue
Wenqi Chu, Peng Liu, Zhong Zhang, Di Wu, Wen Li, Wanchao Chen, Zhengpeng Li, Weike Wang, Yan Yang
Carbohydrate Polymers.2024; 343: 122468. CrossRef
Comparative genomic analysis of Sanghuangporus sanghuang with other Hymenochaetaceae species
Xinyue Wang, Jiansheng Wei, Zhenwen Liu, Yi Wang, Xiaolong Yuan, Dong Wang, Junmei Niu, Yan Yang, Jing Zhou
Brazilian Journal of Microbiology.2024; 55(1): 87. CrossRef
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In vitro and in vivo inhibitory effects of the Sanghuang mushroom extracts against Candida albicans
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Sanghuangporus sanghuang extract extended the lifespan and healthspan of Caenorhabditis elegans via DAF-16/SIR-2.1
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Uncultured bacterial diversity in a seawater recirculating aquaculture system revealed by 16S rRNA gene amplicon sequencing: Da-Eun Lee , Jinhwan Lee , Young-Mog Kim , Jeong-In Myeong , Kyoung-Ho Kim; J. Microbiol. 2016;54(4):296-304. Published online April 1, 2016; DOI: https://doi.org/10.1007/s12275-016-5571-4

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Abstract

Bacterial diversity in a seawater recirculating aquaculture system (RAS) was investigated using 16S rRNA amplicon sequencing to understand the roles of bacterial communities in the system. The RAS was operated at nine different combinations of temperature (15°C, 20°C, and 25°C) and salinity (20‰, 25‰, and 32.5‰). Samples were collected from five or six RAS tanks (biofilters) for each condition. Fifty samples were analyzed. Proteobacteria and Bacteroidetes were most common (sum of both phyla: 67.2% to 99.4%) and were inversely proportional to each other. Bacteria that were present at an average of ≥ 1% included Actinobacteria (2.9%) Planctomycetes (2.0%), Nitrospirae (1.5%), and Acidobacteria (1.0%); they were preferentially present in packed bed biofilters, mesh biofilters, and maturation biofilters. The three biofilters showed higher diversity than other RAS tanks (aerated biofilters, floating bed biofilters, and fish tanks) from phylum to operational taxonomic unit (OTU) level. Samples were clustered into several groups based on the bacterial communities. Major taxonomic groups related to family Rhodobacteraceae and Flavobacteriaceae were distributed widely in the samples. Several taxonomic groups like [Saprospiraceae], Cytophagaceae, Octadecabacter, and Marivita showed a cluster-oriented distribution. Phaeobacter and Sediminicola-related reads were detected frequently and abundantly at low temperature. Nitrifying bacteria were detected frequently and abundantly in the three biofilters. Phylogenetic analysis of the nitrifying bacteria showed several similar OTUs were observed widely through the biofilters. The diverse bacterial communities and the minor taxonomic groups, except for Proteobacteria and Bacteroidetes, seemed to play important roles and seemed necessary for nitrifying activity in the RAS, especially in packed bed biofilters, mesh biofilters, and maturation biofilters.

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Effects of blue light on pigment biosynthesis of Monascus: Di Chen , Chunmao Xue , Mianhua Chen , Shufen Wu , Zhenjing Li , Changlu Wang; J. Microbiol. 2016;54(4):305-310. Published online April 1, 2016; DOI: https://doi.org/10.1007/s12275-016-6011-1

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Abstract

The influence of different illumination levels of blue light on the growth and intracellular pigment yields of Monascus strain M9 was investigated. Compared with darkness, constant exposure to blue light of 100 lux reduced the yields of six pigments, namely, rubropunctatamine (RUM), monascorubramine (MOM), rubropunctatin (RUN), monascorubrin (MON), monascin (MS), and ankaflavin (AK). However, exposure to varying levels of blue light had different effects on pigment production. Exposure to 100 lux of blue light once for 30 min/day and to 100 lux of blue light once and twice for 15 min/day could enhance RUM, MOM, MS, and AK production and reduce RUN and MON compared with non-exposure. Exposure to 100 lux twice for 30 min/day and to 200 lux once for 45 min/day decreased the RUM, MOM, MS, and AK yields and increased the RUN and MON. Meanwhile, the expression levels of pigment biosynthetic genes were analyzed by real-time quantitative PCR. Results indicated that gene MpPKS5, mppR1, mppA, mppB, mmpC, mppD , MpFasA, MpFasB, and mppF were positively correlated with the yields of RUN and MON, whereas mppE and mppR2 were associated with RUM, MOM, MS, and AK production.

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Effects of blue light on pigment and citrinin production in Monascus ruber M7 via MrcreD, encoding an arrestin-like protein
Xiaodi Wang, Jingyi Wei, Fufang Tang, Fusheng Chen
International Journal of Biological Macromolecules.2025; 288: 138604. CrossRef
Disruption of UDP-galactopyranose mutase expression: A novel strategy for regulation of galactomannan biosynthesis and monascus pigments secretion in Monascus purpureus M9
Xufeng Wang, Li Li, Chengfang Ding, Zhenjing Li, Wentao Ding, Huanhuan Liu, Nifei Wang, Changlu Wang, Qingbin Guo
International Journal of Biological Macromolecules.2024; 259: 129369. CrossRef
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Role of histone H3K4 methyltransferase in regulating Monascus pigments production by red light‐coupled magnetic field
Jialan Zhang, Yufeng Chen, Shaojin Wang, Yingbao Liu, Li Li, Mengxiang Gao
Photochemistry and Photobiology.2024; 100(1): 75. CrossRef
Regulation of the pigment production by changing Cell morphology and gene expression of Monascus ruber in high-sugar synergistic high-salt stress fermentation
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Journal of Applied Microbiology.2023;[Epub] CrossRef
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Quantitative Proteomics Analysis by Sequential Window Acquisition of All Theoretical Mass Spectra–Mass Spectrometry Reveals Inhibition Mechanism of Pigments and Citrinin Production of Monascus Response to High Ammonium Chloride Concentration
Bo Zhou, Yifan Ma, Yuan Tian, Jingbo Li, Haiyan Zhong
Journal of Agricultural and Food Chemistry.2020; 68(3): 808. CrossRef
The Effect of Blue Light on the Production of Citrinin in Monascus purpureus M9 by Regulating the mraox Gene through lncRNA AOANCR
Hua Yang, Xufeng Wang, Zhenjing Li, Qingbin Guo, Mingguan Yang, Di Chen, Changlu Wang
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Gong Chen, Qi Bei, Tao Huang, Zhenqiang Wu
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Ruijie Gao, Zhecun Xu, Huaxiang Deng, Zhengbing Guan, Xiangru Liao, Ye Zhao, Xiaohui Zheng, Yujie Cai
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Sugarcane bagasse hydrolysate as a potential feedstock for red pigment production by Monascus ruber
Ruly Terán Hilares, Rebeca Andrade de Souza, Paulo Franco Marcelino, Silvio Silvério da Silva, Giuliano Dragone, Solange I. Mussatto, Júlio César Santos
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The regulation mechanisms of soluble starch and glycerol for production of azaphilone pigments in Monascus purpureus FAFU618 as revealed by comparative proteomic and transcriptional analyses
Zi-Rui Huang, Wen-Bin Zhou, Xue-Ling Yang, Ai-Jun Tong, Jia-Li Hong, Wei-Ling Guo, Tian-Tian Li, Rui-Bo Jia, Yu-Yang Pan, Jun Lin, Xu-Cong Lv, Bin Liu
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Tao Huang, Meihua Wang, Kan Shi, Gong Chen, Xiaofei Tian, Zhenqiang Wu
AMB Express.2017;[Epub] CrossRef
The molecular mechanisms of Monascus purpureus M9 responses to blue light based on the transcriptome analysis
Di Chen, Mianhua Chen, Shufen Wu, Zhenjing Li, Hua Yang, Changlu Wang
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Xiaowei Zhang, Wenqing Liu, Xiying Chen, Junhui Cai, Changlu Wang, Weiwei He
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Rising temperature stimulates the biosynthesis of water-soluble fluorescent yellow pigments and gene expression in Monascus ruber CGMCC10910
Tao Huang, Hailing Tan, Gong Chen, Lu Wang, Zhenqiang Wu
AMB Express.2017;[Epub] CrossRef

Structural insight for substrate tolerance to 2-deoxyribose-5-phosphate aldolase from the pathogen Streptococcus suis: Thinh-Phat Cao , Joong-Su Kim , Mi-Hee Woo , Jin Myung Choi , Youngsoo Jun , Kun Ho Lee , Sung Haeng Lee; J. Microbiol. 2016;54(4):311-321. Published online April 1, 2016; DOI: https://doi.org/10.1007/s12275-016-6029-4

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Abstract

2-deoxyribose-5-phosphate aldolase (DERA) is a class I aldolase that catalyzes aldol condensation of two aldehydes in the active site, which is particularly germane in drug manufacture. Structural and biochemical studies have shown that the active site of DERA is typically loosely packed and displays broader substrate specificity despite sharing conserved folding architecture with other aldolases. The most distinctive structural feature of DERA compared to other aldolases is short and flexible C-terminal region. This region is also responsible for substrate recognition. Therefore, substrate tolerance may be related to the C-terminal structural features of DERA. Here, we determined the crystal structures of full length and C-terminal truncated DERA from Streptococcus suis (SsDERA). In common, both contained the typical (α/β)8 TIM-barrel fold of class I aldolases. Surprisingly, C-terminal truncation
result
ing in missing the last α9 and β8 secondary elements, allowed DERA to maintain activity comparable to the fulllength enzyme. Specifically, Arg186 and Ser205 residues at the C-terminus appeared mutually supplemental or less indispensible for substrate phosphate moiety recognition. Our results suggest that DERA might adopt a shorter C-terminal region than conventional aldolases during evolution pathway, resulting in a broader range of substrate tolerance through active site flexibility.

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Yating Li, Tong Xu, Yanqin Tu, Tong Li, Yifeng Wei, Yan Zhou, Ning-Yi Zhou
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Synthetic Activity of Recombinant Whole Cell Biocatalysts Containing 2‐Deoxy‐D‐ribose‐5‐phosphate Aldolase from Pectobacterium atrosepticum
Romina Fernández Varela, Ana Laura Valino, Eman Abdelraheem, Rosario Médici, Melisa Sayé, Claudio A. Pereira, Peter‐Leon Hagedoorn, Ulf Hanefeld, Adolfo Iribarren, Elizabeth Lewkowicz
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Rational engineering of 2-deoxyribose-5-phosphate aldolases for the biosynthesis of (R)-1,3-butanediol
Taeho Kim, Peter J. Stogios, Anna N. Khusnutdinova, Kayla Nemr, Tatiana Skarina, Robert Flick, Jeong Chan Joo, Radhakrishnan Mahadevan, Alexei Savchenko, Alexander F. Yakunin
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Marianne Schulte, Dušan Petrović, Philipp Neudecker, Rudolf Hartmann, Jörg Pietruszka, Sabine Willbold, Dieter Willbold, Vineet Panwalkar
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Marianne Schulte, Matthias Stoldt, Philipp Neudecker, Jӧrg Pietruszka, Dieter Willbold, Vineet Panwalkar
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Antibacterial effects of N-acetylcysteine against endodontic pathogens: Ji-Hoi Moon , Young-Suk Choi , Hyeon-Woo Lee , Jung Sun Heo , Seok Woo Chang , Jin-Yong Lee; J. Microbiol. 2016;54(4):322-329. Published online April 1, 2016; DOI: https://doi.org/10.1007/s12275-016-5534-9

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Abstract

The success of endodontic treatment depends on the eradication of microorganisms from the root canal system and the prevention of reinfection. The purpose of this investigation was to evaluate the antibacterial and antibiofilm efficacy of N-acetylcysteine (NAC), an antioxidant mucolytic agent, as an intracanal medicament against selected endodontic pathogens. Minimum inhibitory concentrations (MICs) of NAC for Actinomyces naeslundii, Lactobacillus salivarius, Streptococcus mutans, and Enterococcus faecalis were determined using the broth microdilution method. NAC showed antibacterial activity, with MIC values of 0.78–1.56 mg/ml. The effect of NAC on biofilm formation of each bacterium and a multispecies culture consisting of the four bacterial species was assessed by crystal violet staining. NAC significantly inhibited biofilm formation by all the monospecies and multispecies bacteria at minimum concentrations of 0.78–3.13 mg/ml. The efficacy of NAC for biofilm disruption was evaluated by scanning electron microscopy and ATP-bioluminescence quantification using mature multispecies biofilms. Preformed mature multispecies biofilms on saliva-coated hydroxyapatite disks were disrupted within 10 min by treatment with NAC at concentrations of 25 mg/ml or higher. After 24 h of treatment, the viability of mature biofilms was reduced by > 99% compared with the control. Moreover, the biofilm disrupting activity of NAC was significantly higher than that of saturated calcium hydroxide or 2% chlorhexidine solution. Within the limitations of this in vitro study, we conclude that NAC has excellent antibacterial and antibiofilm efficacy against endodontic pathogens and may be used as an alternative intracanal medicament in root canal therapies.

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A small hairpin RNA targeting myeloid cell leukemia-1 enhances apoptosis in host macrophages infected with Mycobacterium tuberculosis: Fei-yu Wang , Yu-qing Zhang , Xin-min Wang , Chan Wang , Xiao-fang Wang , Jiang-dong Wu , Fang Wu , Wan-jiang Zhang , Le Zhang; J. Microbiol. 2016;54(4):330-337. Published online April 1, 2016; DOI: https://doi.org/10.1007/s12275-016-5627-5

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Abstract

Myeloid cell leukemia-1 (Mcl-1) plays an important role in various cell survival pathways. Some studies indicated that the expression of Mcl-1 was upregulated in host cells during infection with the virulent Mycobacterium tuberculosis strain, H37Rv. The present study was designed to investigate the effect of inhibiting Mcl-1 expression both in vivo and in vitro on apoptosis of host macrophages infected with M. tuberculosis using a small hairpin (sh)RNA. Mcl-1 expression was detected by the real time-polymerase chain reaction, western blotting, and immunohistochemistry. Flow cytometry and transmission electron microscopy were used to measure host macrophage apoptosis. We found elevated Mcl-1 levels in host macrophages infected with M. tuberculosis H37Rv. The expression of Mcl-1 was downregulated efficiently in H37Rv-infected host macrophages using shRNA. Knockdown of Mcl-1 enhanced the extent of apoptosis in H37Rv-infected host macrophages significantly. The increased apoptosis correlated with a decrease in M. tuberculosis colony forming units recovered from H37Rv-infected cells that were treated with Mcl-1-shRNA. Reducing Mcl-1 accumulation by shRNA also reduced accumulation of the anti-apoptotic gene, Bcl-2, and increased expression of the pro-apoptotic gene, Bax, in H37Rv-infected host macrophages. Our results showed that specific knockdown of Mcl-1 expression increased apoptosis of host macrophages significantly and decreased the intracellular survival of a virulent strain of M. tuberculosis. These data indicate that interference with Mcl-1 expression may provide a new avenue for tuberculosis therapy.

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