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Winkler KR, Mizrahi V, Warner DF, De Wet TJ. High-throughput functional genomics: A (myco)bacterial perspective. Mol Microbiol 2023; 120:141-158. [PMID: 37278255 PMCID: PMC10953053 DOI: 10.1111/mmi.15103] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 04/06/2023] [Accepted: 05/21/2023] [Indexed: 06/07/2023]
Abstract
Advances in sequencing technologies have enabled unprecedented insights into bacterial genome composition and dynamics. However, the disconnect between the rapid acquisition of genomic data and the (much slower) confirmation of inferred genetic function threatens to widen unless techniques for fast, high-throughput functional validation can be applied at scale. This applies equally to Mycobacterium tuberculosis, the leading infectious cause of death globally and a pathogen whose genome, despite being among the first to be sequenced two decades ago, still contains many genes of unknown function. Here, we summarize the evolution of bacterial high-throughput functional genomics, focusing primarily on transposon (Tn)-based mutagenesis and the construction of arrayed mutant libraries in diverse bacterial systems. We also consider the contributions of CRISPR interference as a transformative technique for probing bacterial gene function at scale. Throughout, we situate our analysis within the context of functional genomics of mycobacteria, focusing specifically on the potential to yield insights into M. tuberculosis pathogenicity and vulnerabilities for new drug and regimen development. Finally, we offer suggestions for future approaches that might be usefully applied in elucidating the complex cellular biology of this major human pathogen.
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Affiliation(s)
- Kristy R. Winkler
- Molecular Mycobacteriology Research Unit and DSI/NRF Centre of Excellence for Biomedical TB Research, Department of Pathology and Institute of Infectious Disease and Molecular MedicineUniversity of Cape TownRondeboschSouth Africa
| | - Valerie Mizrahi
- Molecular Mycobacteriology Research Unit and DSI/NRF Centre of Excellence for Biomedical TB Research, Department of Pathology and Institute of Infectious Disease and Molecular MedicineUniversity of Cape TownRondeboschSouth Africa
- Wellcome Centre for Infectious Diseases Research in AfricaUniversity of Cape TownRondeboschSouth Africa
| | - Digby F. Warner
- Molecular Mycobacteriology Research Unit and DSI/NRF Centre of Excellence for Biomedical TB Research, Department of Pathology and Institute of Infectious Disease and Molecular MedicineUniversity of Cape TownRondeboschSouth Africa
- Wellcome Centre for Infectious Diseases Research in AfricaUniversity of Cape TownRondeboschSouth Africa
| | - Timothy J. De Wet
- Molecular Mycobacteriology Research Unit and DSI/NRF Centre of Excellence for Biomedical TB Research, Department of Pathology and Institute of Infectious Disease and Molecular MedicineUniversity of Cape TownRondeboschSouth Africa
- Wellcome Centre for Infectious Diseases Research in AfricaUniversity of Cape TownRondeboschSouth Africa
- Department of Integrative Biomedical SciencesUniversity of Cape TownRondeboschSouth Africa
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2
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Badhwar P, Ahmad I, Sharma R, Taneja B. Structural investigation and gene deletion studies of mycobacterial oligoribonuclease reveal modulation of c-di-GMP-mediated phenotypes. Int J Biol Macromol 2022; 223:161-172. [PMID: 36356862 DOI: 10.1016/j.ijbiomac.2022.11.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 10/26/2022] [Accepted: 11/01/2022] [Indexed: 11/09/2022]
Abstract
Cyclic-di-GMP (c-di-GMP) is a ubiquitous bacterial second messenger required for normal physiology as well as survival under hypoxic and reductive stress conditions of mycobacterial cells. Complete degradation of c-di-GMP is necessary for signal termination and maintaining its homeostasis inside the cells. Homeostasis of c-di-GMP in mycobacteria is brought about by the bifunctional diguanylate cyclase (DGC) that synthesizes c-di-GMP from two molecules of GTP and also catalyses the asymmetric cleavage of c-di-GMP to linear pGpG through its phosphodiesterase activity. However, the mycobacterial enzyme for the last step of degradation from pGpG to GMP has not been characterized thus far. Here, we present the identification of oligoribonuclease (Orn) as the most likely phosphodiesterase to degrade pGpG to GMP through AlphaFold-empowered structural homology that exhibited in vitro phosphodiesterase activity on pGpG substrates. In order to understand the physiological role of Orn in mycobacteria, we created a deletion mutant of orn in M. smegmatis and analysed the phenotypes that are associated with c-di-GMP signaling. We find that orn plays important roles in vivo and is required not only for proper growth of M. smegmatis in normal and stress conditions but also for biofilm formation.
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Affiliation(s)
- Pooja Badhwar
- CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Iftekhar Ahmad
- CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Rakesh Sharma
- CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Bhupesh Taneja
- CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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3
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Dawson CC, Cummings JE, Starkey JM, Slayden RA. Discovery of a novel type IIb RelBE toxin-antitoxin system in Mycobacterium tuberculosis defined by co-regulation with an antisense RNA. Mol Microbiol 2022; 117:1419-1433. [PMID: 35526138 PMCID: PMC9325379 DOI: 10.1111/mmi.14917] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 04/30/2022] [Accepted: 05/05/2022] [Indexed: 11/29/2022]
Abstract
Toxin‐antitoxin loci regulate adaptive responses to stresses associated with the host environment and drug exposure. Phylogenomic studies have shown that Mycobacterium tuberculosis encodes a naturally expanded type II toxin‐antitoxin system, including ParDE/RelBE superfamily members. Type II toxins are presumably regulated exclusively through protein–protein interactions with type II antitoxins. However, experimental observations in M. tuberculosis indicated that additional control mechanisms regulate RelBE2 type II loci under host‐associated stress conditions. Herein, we describe for the first time a novel antisense RNA, termed asRelE2, that co‐regulates RelE2 production via targeted processing by the Mtb RNase III, Rnc. We find that convergent expression of this coding‐antisense hybrid TA locus, relBE2‐asrelE2, is controlled in a cAMP‐dependent manner by the essential cAMP receptor protein transcription factor, Crp, in response to the host‐associated stresses of low pH and nutrient limitation. Ex vivo survival studies with relE2 and asrelE2 knockout strains showed that RelE2 contributes to Mtb survival in activated macrophages and low pH to nutrient limitation. To our knowledge, this is the first report of a novel tripartite type IIb TA loci and antisense post‐transcriptional regulation of a type II TA loci.
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Affiliation(s)
- Clinton C Dawson
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins.,Endolytix Technology, Inc. Beverly, 01915
| | - Jason E Cummings
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins
| | - Julie M Starkey
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins
| | - Richard A Slayden
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins
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4
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Experimental confirmation that an uncommon
rrs
gene mutation (g878a) of
Mycobacterium tuberculosis
confers resistance to streptomycin. Antimicrob Agents Chemother 2022; 66:e0191521. [DOI: 10.1128/aac.01915-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The effective treatment of patients diagnosed with drug resistant tuberculosis is highly dependent upon the ability to rapidly and accurately determine the antibiotic susceptibility profile of the
Mycobacterium tuberculosis
isolate(s) involved. Thus, as more clinical microbiology laboratories advance towards the use of DNA sequence-based diagnostics, it is imperative that their predictive functions extend beyond the well-known resistance mutations, in order to also encompass as many of the lower-frequency mutations as possible. However, in most cases, the fundamental experimental proof that links these uncommon mutations with phenotypic resistance is lacking. One such example is the g878a polymorphism within the
rrs
16s rRNA gene. We, and others, have identified this mutation within a small number of drug-resistant isolates, although a consensus regarding exactly which aminoglycoside antibiotic(s) it confers resistance toward has not previously been reached. Here we have employed oligo-mediated recombineering to introduce the g878a polymorphism into the
rrs
gene of
M. bovis
BCG - a close relative of
M. tuberculosis
- and demonstrate that it confers low-level resistance to streptomycin alone. It does not confer cross-resistance towards amikacin, capreomycin, nor kanamycin. We also demonstrate that the
rrs
g878a
mutation exerts a substantial fitness defect
in vitro
, that may at least in part explain why clinical isolates bearing this mutation appear to be quite rare. Overall, this study provides clarity to the phenotype attributable to the
rrs
g878a
mutation and is relevant to the future implementation of genomics-based diagnostics, as well as the clinical management of patients where this particular polymorphism is encountered.
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5
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Elimination of PknL and MSMEG_4242 in Mycobacterium smegmatis alters the character of the outer cell envelope and selects for mutations in Lsr2. ACTA ACUST UNITED AC 2021; 7:100060. [PMID: 34485766 PMCID: PMC8408660 DOI: 10.1016/j.tcsw.2021.100060] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 08/12/2021] [Accepted: 08/13/2021] [Indexed: 11/23/2022]
Abstract
Elimination of pknL and adjacent gene MSMEG_4242 in M. smegmatis produces rough & smooth colonies. All smooth colony mutants have inactivated lsr2 genes. Inactivated lsr2 leads to high expression of MSMEG_4727 and increased synthesis of LOS. Smooth mutants don’t form biofilms, have longer bacilli and increased sliding motility. Rough strains deleted for pknL and MSMEG_4242 form biofilms but have aberrant sliding motility. We propose a phosphorylation cascade of PknB phosphorylating PknL that then phosphorylates Lsr2.
Four serine/threonine kinases are present in all mycobacteria: PknA, PknB, PknG and PknL. PknA and PknB are essential for growth and replication, PknG regulates metabolism, but little is known about PknL. Inactivation of pknL and adjacent regulator MSMEG_4242 in rough colony M. smegmatis mc2155 produced both smooth and rough colonies. Upon restreaking rough colonies, smooth colonies appeared at a frequency of ~ 1/250. Smooth mutants did not form biofilms, showed increased sliding motility and anomalous lipids on thin-layer chromatography, identified by mass spectrometry as lipooligosaccharides and perhaps also glycopeptidolipids. RNA-seq and Sanger sequencing revealed that all smooth mutants had inactivated lsr2 genes due to mutations and different IS1096 insertions. When complemented with lsr2, the colonies became rough, anomalous lipids disappeared and sliding motility decreased. Smooth mutants showed increased expression of IS1096 transposase TnpA and MSMEG_4727, which encodes a protein similar to PKS5. When MSMEG_4727 was deleted, smooth pknL/MSMEG_4242/lsr2 mutants reverted to rough, formed good biofilms, their motility decreased slightly and their anomalous lipids disappeared. Rough delpknL/del4242 mutants formed poor biofilms and showed decreased, aberrant sliding motility and both phenotypes were complemented with the two deleted genes. Inactivation of lsr2 changes colony morphology from rough to smooth, augments sliding motility and increases expression of MSMEG_4727 and other enzymes synthesizing lipooligosaccharides, apparently preventing biofilm formation. Similar morphological phase changes occur in other mycobacteria, likely reflecting environmental adaptations. PknL and MSMEG_4242 regulate lipid components of the outer cell envelope and their absence selects for lsr2 inactivation. A regulatory, phosphorylation cascade model is proposed.
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6
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Martín C, Marinova D, Aguiló N, Gonzalo-Asensio J. MTBVAC, a live TB vaccine poised to initiate efficacy trials 100 years after BCG. Vaccine 2021; 39:7277-7285. [PMID: 34238608 DOI: 10.1016/j.vaccine.2021.06.049] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 06/03/2021] [Accepted: 06/21/2021] [Indexed: 01/06/2023]
Abstract
At its 100th birthday of its first administration to a newborn, BCG has been (and continues being) an inspiration for the construction and development of hundreds of new TB vaccine candidates in the last two and a half decades. Today, 14 candidates are in clinical development inside the global TB vaccine pipeline. MTBVAC is one of these candidates. Based on a live-attenuated Mycobacterium tuberculosis clinical isolate, MTBVAC's 25 years of vaccine discovery, construction and characterisation have followed Pasteur principles, and in the process, BCG has served as a reference gold standard for establishing the safety and protective efficacy of new TB vaccine candidates. MTBVAC, which contains the antigen repertoire of M. tuberculosis, is now poised to initiate Phase 3 efficacy trials in newborns in TB-endemic countries. BCG's efficacy extends beyond that against TB, shown to confer heterologous non-specific immunity to other diseases and reduce all-cause mortality in the first months of life. Today, WHO recognises the importance that any new TB vaccine designed for administration at birth, should show similar non-specific benefits as BCG vía mechanisms of trained immunity and/or cross-reactivity of adaptive immune responses to other pathogens. Key recent studies provide strong support for MTBVAC's ability of inducing trained immunity and conferring non-specific heterologous protection similar to BCG. Research on alternative delivery routes of MTBVAC, such as a clinically feasible aerosol route, could facilitate vaccine administration for long-term TB eradication programmes in the future.
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Affiliation(s)
- Carlos Martín
- Grupo de Genética de Micobacterias, Microbiología, Facultad de Medicina Universidad de Zaragoza, Spain; CIBERES Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain; Servicio de Microbiología, Hospital Universitario Miguel Servet, ISS Aragón, Zaragoza, Spain.
| | - Dessislava Marinova
- Grupo de Genética de Micobacterias, Microbiología, Facultad de Medicina Universidad de Zaragoza, Spain; CIBERES Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Nacho Aguiló
- Grupo de Genética de Micobacterias, Microbiología, Facultad de Medicina Universidad de Zaragoza, Spain; CIBERES Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Jesús Gonzalo-Asensio
- Grupo de Genética de Micobacterias, Microbiología, Facultad de Medicina Universidad de Zaragoza, Spain; CIBERES Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
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7
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Abstract
Current models of horizontal gene transfer (HGT) in mycobacteria are based on “distributive conjugal transfer” (DCT), an HGT type described in the fast-growing, saprophytic model organism Mycobacterium smegmatis, which creates genome mosaicism in resulting strains and depends on an ESX-1 type VII secretion system. In contrast, only few data on interstrain DNA transfer are available for tuberculosis-causing mycobacteria, for which chromosomal DNA transfer between two Mycobacterium canettii strains was reported, a process which, however, was not observed for Mycobacterium tuberculosis strains. Here, we have studied a wide range of human- and animal-adapted members of the Mycobacterium tuberculosis complex (MTBC) using an optimized filter-based mating assay together with three selected strains of M. canettii that acted as DNA recipients. Unlike in previous approaches, we obtained a high yield of thousands of recombinants containing transferred chromosomal DNA fragments from various MTBC donor strains, as confirmed by whole-genome sequence analysis of 38 randomly selected clones. While the genome organizations of the obtained recombinants showed mosaicisms of donor DNA fragments randomly integrated into a recipient genome backbone, reminiscent of those described as being the result of ESX-1-mediated DCT in M. smegmatis, we observed similar transfer efficiencies when ESX-1-deficient donor and/or recipient mutants were used, arguing that in tubercle bacilli, HGT is an ESX-1-independent process. These findings provide new insights into the genetic events driving the pathoevolution of M. tuberculosis and radically change our perception of HGT in mycobacteria, particularly for those species that show recombinogenic population structures despite the natural absence of ESX-1 secretion systems.
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8
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Feng S, Hong Z, Zhang G, Li J, Tian GB, Zhou H, Huang X. Mycobacterium PPE31 Contributes to Host Cell Death. Front Cell Infect Microbiol 2021; 11:629836. [PMID: 33928042 PMCID: PMC8078103 DOI: 10.3389/fcimb.2021.629836] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 03/23/2021] [Indexed: 12/03/2022] Open
Abstract
Genome scale mutagenesis identifies many genes required for mycobacterial infectivity and survival, but their contributions and mechanisms of action within the host are poorly understood. Using CRISPR interference, we created a knockdown of ppe31Mm gene in Mycobacterium marinum (M. marinum), which reduced the resistance to acid medium. To further explore the function of PPE31, the ppe31 mutant strain was generated in M. marinum and Mycobacterium tuberculosis (M. tuberculosis), respectively. Macrophages infected with the ppe31Mm mutant strain caused a reduced inflammatory mediator expressions. In addition, macrophages infected with M. marinum Δppe31Mm had decreased host cell death dependent on JNK signaling. Consistent with these results, deletion of ppe31Mtb from M. tuberculosis increased the sensitivity to acid medium and reduced cell death in macrophages. Furthermore, we demonstrate that both ppe31 mutants from M. marinum and M. tuberculosis resulted in reduced survival in macrophages, and the survivability of M. marinum was deceased in zebrafish due to loss of ppe31Mm. Our findings confirm that PPE31 as a virulence associated factor that modulates innate immune responses to mycobacterial infection.
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Affiliation(s)
- Siyuan Feng
- Center for Infection and Immunity, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhongshan School of Medicine, Sun Yat-sen University, Zhuhai, China.,Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, China
| | - Zhongsi Hong
- Center for Infection and Immunity, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhongshan School of Medicine, Sun Yat-sen University, Zhuhai, China
| | - Guoliang Zhang
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China
| | - Jiachen Li
- Center for Infection and Immunity, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhongshan School of Medicine, Sun Yat-sen University, Zhuhai, China.,Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, China
| | - Guo-Bao Tian
- Center for Infection and Immunity, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhongshan School of Medicine, Sun Yat-sen University, Zhuhai, China.,Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, China
| | - Haibo Zhou
- The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, China
| | - Xi Huang
- Center for Infection and Immunity, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhongshan School of Medicine, Sun Yat-sen University, Zhuhai, China.,Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, China.,Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China.,The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, China.,Sino-French Hoffmann Institute of Immunology, College of Basic Medical Science, Guangzhou Medical University, Guangzhou, China
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9
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Liang Y, Yu H. Genetic toolkits for engineering Rhodococcus species with versatile applications. Biotechnol Adv 2021; 49:107748. [PMID: 33823269 DOI: 10.1016/j.biotechadv.2021.107748] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 03/31/2021] [Accepted: 03/31/2021] [Indexed: 02/09/2023]
Abstract
Rhodococcus spp. are a group of non-model gram-positive bacteria with diverse catabolic activities and strong adaptive capabilities, which enable their wide application in whole-cell biocatalysis, environmental bioremediation, and lignocellulosic biomass conversion. Compared with model microorganisms, the engineering of Rhodococcus is challenging because of the lack of universal molecular tools, high genome GC content (61% ~ 71%), and low transformation and recombination efficiencies. Nevertheless, because of the high interest in Rhodococcus species for bioproduction, various genetic elements and engineering tools have been recently developed for Rhodococcus spp., including R. opacus, R. jostii, R. ruber, and R. erythropolis, leading to the expansion of the genetic toolkits for Rhodococcus engineering. In this article, we provide a comprehensive review of the important developed genetic elements for Rhodococcus, including shuttle vectors, promoters, antibiotic markers, ribosome binding sites, and reporter genes. In addition, we also summarize gene transfer techniques and strategies to improve transformation efficiency, as well as random and precise genome editing tools available for Rhodococcus, including transposition, homologous recombination, recombineering, and CRISPR/Cas9. We conclude by discussing future trends in Rhodococcus engineering. We expect that more synthetic and systems biology tools (such as multiplex genome editing, dynamic regulation, and genome-scale metabolic models) will be adapted and optimized for Rhodococcus.
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Affiliation(s)
- Youxiang Liang
- Department of Chemical Engineering, Tsinghua University, Beijing 100084, China; Key Laboratory of Industrial Biocatalysis (Tsinghua University), the Ministry of Education, Beijing 100084, China
| | - Huimin Yu
- Department of Chemical Engineering, Tsinghua University, Beijing 100084, China; Key Laboratory of Industrial Biocatalysis (Tsinghua University), the Ministry of Education, Beijing 100084, China; Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China.
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10
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Qi N, She GL, Du W, Ye BC. Mycobacterium smegmatis GlnR Regulates the Glyoxylate Cycle and the Methylcitrate Cycle on Fatty Acid Metabolism by Repressing icl Transcription. Front Microbiol 2021; 12:603835. [PMID: 33613477 PMCID: PMC7886694 DOI: 10.3389/fmicb.2021.603835] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 01/12/2021] [Indexed: 12/23/2022] Open
Abstract
Mycobacterium smegmatis (Msm), along with its pathogenic counterpart Mycobacterium tuberculosis (Mtb), utilizes fatty acids and cholesterol as important carbon and energy sources during the persistence within host cells. As a dual-functional enzyme in the glyoxylate cycle and the methylcitrate cycle, isocitrate lyase (ICL, encoded by icl or MSMEG_0911) is indispensable for the growth of Msm and Mtb on short-chain fatty acids. However, regulation of icl in mycobacteria in response to nutrient availability remains largely unknown. Here, we report that the global nitrogen metabolism regulator GlnR represses icl expression by binding to an atypical binding motif in the icl promoter region under nitrogen-limiting conditions. We further show that GlnR competes with PrpR, a transcriptional activator of icl, and dominantly occupies the co-binding motif in the icl promoter region. In the absence of GlnR or in response to the excess nitrogen condition, Msm cells elongate and exhibit robust growth on short-chain fatty acids due to the PrpR-mediated activation of icl, thereby inducing enhanced apoptosis in infected macrophages. Taken together, our findings reveal the GlnR-mediated repression of icl on fatty acid metabolism, which might be a general strategy of nutrient sensing and environmental adaptation employed by mycobacteria.
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Affiliation(s)
- Nan Qi
- Institute of Engineering Biology and Health, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, China
| | - Guo-Lan She
- Institute of Engineering Biology and Health, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, China
| | - Wei Du
- Institute of Engineering Biology and Health, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, China
| | - Bang-Ce Ye
- Institute of Engineering Biology and Health, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, China.,Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, Institute of Engineering Biology and Health, East China University of Science and Technology, Shanghai, China
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11
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Dalberto PF, de Souza EV, Abbadi BL, Neves CE, Rambo RS, Ramos AS, Macchi FS, Machado P, Bizarro CV, Basso LA. Handling the Hurdles on the Way to Anti-tuberculosis Drug Development. Front Chem 2020; 8:586294. [PMID: 33330374 PMCID: PMC7710551 DOI: 10.3389/fchem.2020.586294] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 09/25/2020] [Indexed: 12/17/2022] Open
Abstract
The global epidemic of tuberculosis (TB) imposes a sustained epidemiologic vigilance and investments in research by governments. Mycobacterium tuberculosis, the main causative agent of TB in human beings, is a very successful pathogen, being the main cause of death in the population among infectious agents. In 2018, ~10 million individuals were contaminated with this bacillus and became ill with TB, and about 1.2 million succumbed to the disease. Most of the success of the M. tuberculosis to linger in the population comes from its ability to persist in an asymptomatic latent state into the host and, in fact, the majority of the individuals are unaware of being contaminated. Even though TB is a treatable disease and is curable in most cases, the treatment is lengthy and laborious. In addition, the rise of resistance to first-line anti-TB drugs elicits a response from TB research groups to discover new chemical entities, preferably with novel mechanisms of action. The pathway to find a new TB drug, however, is arduous and has many barriers that are difficult to overcome. Fortunately, several approaches are available today to be pursued by scientists interested in anti-TB drug development, which goes from massively testing chemical compounds against mycobacteria, to discovering new molecular targets by genetic manipulation. This review presents some difficulties found along the TB drug development process and illustrates different approaches that might be used to try to identify new molecules or targets that are able to impair M. tuberculosis survival.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Luiz A. Basso
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF) and Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
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12
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Loss of U1498 methylation in 16S rRNA by RsmE methyltransferase associates its role with aminoglycoside resistance in mycobacteria. J Glob Antimicrob Resist 2020; 23:359-369. [PMID: 33186785 DOI: 10.1016/j.jgar.2020.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 05/28/2020] [Accepted: 10/06/2020] [Indexed: 11/23/2022] Open
Abstract
OBJECTIVES Modulation of methylation pattern through mutations in ribosomal methyltransferases is a key mechanism of bacterial drug resistance. However, RsmG (GidB), which specifically methylates G527 in 16S rRNA, remains the only conserved methyltransferase known to be associated with low-level drug resistance in mycobacterial isolates. The mycobacterial RsmE homologue methylates U1498 in 16S rRNA in a highly specific manner. U1498 lies in the vicinity of the binding site for various aminoglycosides in the ribosome. However, the association of methylation at U1498 with altered drug response remains poorly understood. METHODS A deletion mutant of the RsmE homologue in Mycobacterium smegmatis was generated by a suicidal vector strategy and drug susceptibility assays were performed on wild-type, knockout and complemented strains with varying concentrations of ribosomal- and non-ribosomal-targeting drugs. RESULTS Deletion of the RsmE homologue of M. smegmatis led to an at least two-fold increase in the minimum inhibitory concentrations (MICs) of aminoglycosides that bind in the decoding centre proximal to U1498 in the 30S subunit. The change in MICs was highly specific and reproducible and did not show any cross-resistance to other drug classes. Surprisingly, Rv2372c, the RsmE homologue of Mycobacterium tuberculosis, has the largest number of mutations among conserved ribosomal methyltransferases, after gidB, highlighting the role of mutations in RsmE methyltransferase as a key emerging mechanism of resistance in clinical strains. CONCLUSION We present the first evidence of an association of methylation of U1498 in 16S rRNA with development of low-level resistance in mycobacteria that must be tackled in a timely manner.
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13
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Harnagel A, Lopez Quezada L, Park SW, Baranowski C, Kieser K, Jiang X, Roberts J, Vaubourgeix J, Yang A, Nelson B, Fay A, Rubin E, Ehrt S, Nathan C, Lupoli TJ. Nonredundant functions of Mycobacterium tuberculosis chaperones promote survival under stress. Mol Microbiol 2020; 115:272-289. [PMID: 32996193 DOI: 10.1111/mmi.14615] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 09/21/2020] [Accepted: 09/22/2020] [Indexed: 12/12/2022]
Abstract
Bacterial chaperones ClpB and DnaK, homologs of the respective eukaryotic heat shock proteins Hsp104 and Hsp70, are essential in the reactivation of toxic protein aggregates that occur during translation or periods of stress. In the pathogen Mycobacterium tuberculosis (Mtb), the protective effect of chaperones extends to survival in the presence of host stresses, such as protein-damaging oxidants. However, we lack a full understanding of the interplay of Hsps and other stress response genes in mycobacteria. Here, we employ genome-wide transposon mutagenesis to identify the genes that support clpB function in Mtb. In addition to validating the role of ClpB in Mtb's response to oxidants, we show that HtpG, a homolog of Hsp90, plays a distinct role from ClpB in the proteotoxic stress response. While loss of neither clpB nor htpG is lethal to the cell, loss of both through genetic depletion or small molecule inhibition impairs recovery after exposure to host-like stresses, especially reactive nitrogen species. Moreover, defects in cells lacking clpB can be complemented by overexpression of other chaperones, demonstrating that Mtb's stress response network depends upon finely tuned chaperone expression levels. These results suggest that inhibition of multiple chaperones could work in concert with host immunity to disable Mtb.
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Affiliation(s)
- Alexa Harnagel
- Department of Chemistry, New York University, New York, NY, USA
| | - Landys Lopez Quezada
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
| | - Sae Woong Park
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
| | - Catherine Baranowski
- Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Karen Kieser
- Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Xiuju Jiang
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
| | - Julia Roberts
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
| | - Julien Vaubourgeix
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
| | - Amy Yang
- Department of Chemistry, New York University, New York, NY, USA
| | - Brock Nelson
- Department of Chemistry, New York University, New York, NY, USA
| | - Allison Fay
- Immunology Program, Sloan Kettering Institute, New York, NY, USA
| | - Eric Rubin
- Immunology Program, Sloan Kettering Institute, New York, NY, USA
| | - Sabine Ehrt
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
| | - Carl Nathan
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
| | - Tania J Lupoli
- Department of Chemistry, New York University, New York, NY, USA.,Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
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14
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Colangeli R, Gupta A, Vinhas SA, Chippada Venkata UD, Kim S, Grady C, Jones-López EC, Soteropoulos P, Palaci M, Marques-Rodrigues P, Salgame P, Ellner JJ, Dietze R, Alland D. Mycobacterium tuberculosis progresses through two phases of latent infection in humans. Nat Commun 2020; 11:4870. [PMID: 32978384 PMCID: PMC7519141 DOI: 10.1038/s41467-020-18699-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 09/03/2020] [Indexed: 12/21/2022] Open
Abstract
Little is known about the physiology of latent Mycobacterium tuberculosis infection. We studied the mutational rates of 24 index tuberculosis (TB) cases and their latently infected household contacts who developed active TB up to 5.25 years later, as an indication of bacterial physiological state and possible generation times during latent TB infection in humans. Here we report that the rate of new mutations in the M. tuberculosis genome decline dramatically after two years of latent infection (two-sided p < 0.001, assuming an 18 h generation time equal to log phase M. tuberculosis, with latency period modeled as a continuous variable). Alternatively, assuming a fixed mutation rate, the generation time increases over the latency duration. Mutations indicative of oxidative stress do not increase with increasing latency duration suggesting a lack of host or bacterial derived mutational stress. These results suggest that M. tuberculosis enters a quiescent state during latency, decreasing the risk for mutational drug resistance and increasing generation time, but potentially increasing bacterial tolerance to drugs that target actively growing bacteria.
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Affiliation(s)
- Roberto Colangeli
- Department of Medicine, Rutgers-New Jersey Medical School, Newark, NJ, USA
| | - Aditi Gupta
- Department of Medicine, Rutgers-New Jersey Medical School, Newark, NJ, USA
| | - Solange Alves Vinhas
- Núcleo de Doenças Infecciosas, Universidade Federal do Espírito Santo (UFES), Vitória, Brazil
| | | | - Soyeon Kim
- Frontier Science Foundation, 1371 Beacon Street, Suite #203, Brookline, MA, 02446, USA
| | - Courtney Grady
- Department of Medicine, Rutgers-New Jersey Medical School, Newark, NJ, USA
| | - Edward C Jones-López
- Division of Infectious Diseases, Department of Medicine. Keck School of Medicine of USC, University of Southern California Los Angeles, Los Angeles, CA, USA
| | - Patricia Soteropoulos
- The Genomics Center, Rutgers-New Jersey Medical School, Newark, NJ, USA
- Department of Microbiology, Biochemistry, and Molecular Genetics, Rutgers-New Jersey Medical School, Newark, NJ, USA
| | - Moisés Palaci
- Núcleo de Doenças Infecciosas, Universidade Federal do Espírito Santo (UFES), Vitória, Brazil
| | | | - Padmini Salgame
- Department of Medicine, Rutgers-New Jersey Medical School, Newark, NJ, USA
| | - Jerrold J Ellner
- Department of Medicine, Rutgers-New Jersey Medical School, Newark, NJ, USA
| | - Reynaldo Dietze
- Núcleo de Doenças Infecciosas, Universidade Federal do Espírito Santo (UFES), Vitória, Brazil
- Global Health & Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
| | - David Alland
- Department of Medicine, Rutgers-New Jersey Medical School, Newark, NJ, USA.
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15
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Andrews ESV, Rzoska-Smith E, Arcus VL. Post-transcriptional modulation of the SigF regulon in Mycobacterium smegmatis by the PhoH2 toxin-antitoxin. PLoS One 2020; 15:e0236551. [PMID: 32726339 PMCID: PMC7390352 DOI: 10.1371/journal.pone.0236551] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 07/06/2020] [Indexed: 01/03/2023] Open
Abstract
PhoH2 proteins are highly conserved across bacteria and archaea yet their biological function is poorly characterised. We examined the growth profiles of Mycobacterium smegmatis strains mc2155 and mc2155 ΔphoH2 and observed the same growth profile and growth rate in a variety of conditions. In light of the comparable growth, we used RNAseq to provide a snapshot of the differences between the transcriptomes of M. smegmatis mc2155 and M. smegmatis mc2155 ΔphoH2 during normal growth. At 48 hours, elevated expression of the sigF regulon was observed in ΔphoH2 relative to wild type. In biochemical assays, PhoH2 showed activity toward sigF mRNA insinuating a role of PhoH2 in modulating the pool of sigF mRNA in the cell during normal growth, adding further complexity to the repertoire of reported mechanisms of post-translational regulation. Multiple copies of the preferred target site of PhoH2 were identified in loops of the sigF mRNA structure, leading us to propose a mechanism for the activity of PhoH2 that is initiated after assembly on specific single-stranded loops of RNA. We hypothesise that PhoH2 is a toxin-antitoxin that contributes to the regulation of SigF at a post-transcriptional level through targeted activity on sigF mRNA. This work presents the first evidence for post-transcriptional regulation of SigF along with the biological function of PhoH2 from M. smegmatis. This has implications for the highly conserved PhoH2 toxin-antitoxin module across the mycobacteria including the important human pathogen M. tuberculosis.
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Affiliation(s)
- Emma S. V. Andrews
- School of Science, Division of Health, Engineering, Computing and Science, University of Waikato, Hamilton, New Zealand
- * E-mail:
| | - Elizabeth Rzoska-Smith
- School of Science, Division of Health, Engineering, Computing and Science, University of Waikato, Hamilton, New Zealand
| | - Vickery L. Arcus
- School of Science, Division of Health, Engineering, Computing and Science, University of Waikato, Hamilton, New Zealand
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16
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Lopez Quezada L, Smith R, Lupoli TJ, Edoo Z, Li X, Gold B, Roberts J, Ling Y, Park SW, Nguyen Q, Schoenen FJ, Li K, Hugonnet JE, Arthur M, Sacchettini JC, Nathan C, Aubé J. Activity-Based Protein Profiling Reveals That Cephalosporins Selectively Active on Non-replicating Mycobacterium tuberculosis Bind Multiple Protein Families and Spare Peptidoglycan Transpeptidases. Front Microbiol 2020; 11:1248. [PMID: 32655524 PMCID: PMC7324553 DOI: 10.3389/fmicb.2020.01248] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 05/15/2020] [Indexed: 11/13/2022] Open
Abstract
As β-lactams are reconsidered for the treatment of tuberculosis (TB), their targets are assumed to be peptidoglycan transpeptidases, as verified by adduct formation and kinetic inhibition of Mycobacterium tuberculosis (Mtb) transpeptidases by carbapenems active against replicating Mtb. Here, we investigated the targets of recently described cephalosporins that are selectively active against non-replicating (NR) Mtb. NR-active cephalosporins failed to inhibit recombinant Mtb transpeptidases. Accordingly, we used alkyne analogs of NR-active cephalosporins to pull down potential targets through unbiased activity-based protein profiling and identified over 30 protein binders. None was a transpeptidase. Several of the target candidates are plausibly related to Mtb's survival in an NR state. However, biochemical tests and studies of loss of function mutants did not identify a unique target that accounts for the bactericidal activity of these beta-lactams against NR Mtb. Instead, NR-active cephalosporins appear to kill Mtb by collective action on multiple targets. These results highlight the ability of these β-lactams to target diverse classes of proteins.
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Affiliation(s)
- Landys Lopez Quezada
- Department of Microbiology & Immunology, Weill Cornell Medical College, New York, NY, United States
| | - Robert Smith
- Chemical Methodologies & Library Development Center, The University of Kansas, Lawrence, KS, United States
| | - Tania J Lupoli
- Department of Microbiology & Immunology, Weill Cornell Medical College, New York, NY, United States
| | - Zainab Edoo
- Sorbonne Université, Sorbonne Paris Cité, Université de Paris, INSERM, Centre de Recherche des Cordeliers, CRC, Paris, France
| | - Xiaojun Li
- Departments of Biochemistry and Biophysics, Texas A&M University, College Station, TX, United States
| | - Ben Gold
- Department of Microbiology & Immunology, Weill Cornell Medical College, New York, NY, United States
| | - Julia Roberts
- Department of Microbiology & Immunology, Weill Cornell Medical College, New York, NY, United States
| | - Yan Ling
- Department of Microbiology & Immunology, Weill Cornell Medical College, New York, NY, United States
| | - Sae Woong Park
- Department of Microbiology & Immunology, Weill Cornell Medical College, New York, NY, United States
| | - Quyen Nguyen
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Frank J Schoenen
- Chemical Methodologies & Library Development Center, The University of Kansas, Lawrence, KS, United States
| | - Kelin Li
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Jean-Emmanuel Hugonnet
- Sorbonne Université, Sorbonne Paris Cité, Université de Paris, INSERM, Centre de Recherche des Cordeliers, CRC, Paris, France
| | - Michel Arthur
- Sorbonne Université, Sorbonne Paris Cité, Université de Paris, INSERM, Centre de Recherche des Cordeliers, CRC, Paris, France
| | - James C Sacchettini
- Departments of Biochemistry and Biophysics, Texas A&M University, College Station, TX, United States
| | - Carl Nathan
- Department of Microbiology & Immunology, Weill Cornell Medical College, New York, NY, United States
| | - Jeffrey Aubé
- Chemical Methodologies & Library Development Center, The University of Kansas, Lawrence, KS, United States.,Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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17
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Monomeric NADH-Oxidizing Methylenetetrahydrofolate Reductases from Mycobacterium smegmatis Lack Flavin Coenzyme. J Bacteriol 2020; 202:JB.00709-19. [PMID: 32253341 DOI: 10.1128/jb.00709-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 03/27/2020] [Indexed: 01/16/2023] Open
Abstract
5,10-Methylenetetrahydrofolate reductase (MetF/MTHFR) is an essential enzyme in one-carbon metabolism for de novo biosynthesis of methionine. Our in vivo and in vitro analyses of MSMEG_6664/MSMEI_6484, annotated as putative MTHFR in Mycobacterium smegmatis, failed to reveal their function as MTHFRs. However, we identified two hypothetical proteins, MSMEG_6596 and MSMEG_6649, as noncanonical MTHFRs in the bacterium. MTHFRs are known to be oligomeric flavoproteins. Both MSMEG_6596 and MSMEG_6649 are monomeric proteins and lack flavin coenzymes. In vitro, the catalytic efficiency (k cat/Km ) of MSMEG_6596 (MTHFR1) for 5,10-CH2-THF and NADH was ∼13.5- and 15.3-fold higher than that of MSMEG_6649 (MTHFR2). Thus, MSMEG_6596 is the major MTHFR. This interpretation was further supported by better rescue of the E. coli Δmthfr strain by MTHFR1 than by MTHFR2. As identified by liquid chromatography-tandem mass spectrometry, the product of MTHFR1- or MTHFR2-catalyzed reactions was 5-CH3-THF. The M. smegmatis Δmsmeg_6596 strain was partially auxotrophic for methionine and grew only poorly without methionine or without being complemented with a functional copy of MTHFR1 or MTHFR2. Furthermore, the Δmsmeg_6596 strain was more sensitive to folate pathway inhibitors (sulfachloropyridazine, p-aminosalicylic acid, sulfamethoxazole, and trimethoprim). The studies reveal that MTHFR1 and MTHFR2 are two noncanonical MTHFR proteins that are monomeric and lack flavin coenzyme. Both MTHFR1 and MTHFR2 are involved in de novo methionine biosynthesis and required for antifolate resistance in mycobacteria.IMPORTANCE MTHFR/MetF is an essential enzyme in a one-carbon metabolic pathway for de novo biosynthesis of methionine. MTHFRs are known to be oligomeric flavoproteins. Our in vivo and in vitro analyses of Mycobacterium smegmatis MSMEG_6664/MSMEI_6484, annotated as putative MTHFR, failed to reveal their function as MTHFRs. However, we identified two of the hypothetical proteins, MSMEG_6596 and MSMEG_6649, as MTHFR1 and MTHFR2, respectively. Interestingly, both MTHFRs are monomeric and lack flavin coenzymes. M. smegmatis deleted for the major mthfr (mthfr1) was partially auxotroph for methionine and more sensitive to folate pathway inhibitors (sulfachloropyridazine, para-aminosalicylic acid, sulfamethoxazole, and trimethoprim). The studies reveal that MTHFR1 and MTHFR2 are novel MTHFRs involved in de novo methionine biosynthesis and required for antifolate resistance in mycobacteria.
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18
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Alonso MN, Malaga W, Mc Neil M, Jackson M, Romano MI, Guilhot C, Santangelo MP. Efficient method for targeted gene disruption by homologous recombination in Mycobacterium avium subspecie paratuberculosis. Res Microbiol 2020; 171:203-210. [PMID: 32283218 DOI: 10.1016/j.resmic.2020.04.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 04/02/2020] [Accepted: 04/03/2020] [Indexed: 10/24/2022]
Abstract
Targeted gene disruption by homologous recombination, has been widely used in mycobacterium species to understand the genetic basis of virulence and persistence in the host and to develop efficacious potential live vaccines. However, in slow growing pathogenic mycobacteria as Mycobacterium avium subsp paratuberculosis (MAP), these methods have been inefficient, in part due to the low frequency of legitimate homologous recombination. Another feature of mycobacteria is the low efficiency of transformation; therefore, some years ago, a phage-mediated transduction process was developed to introduce DNA into mycobacteria. This strategy is very efficient, due to the high rate of infection of the phage. This report describes a genetic method for the generation of targeted deletion mutations in MAP by allelic exchange using in vitro-generated specialized transducing mycobacteriophages, which does not require the critical packaging step and that could also be applied to other mycobacteria. We provide a detailed gene deletion methodology and demonstrate the use of this genetic system by deleting the mce4 operon of MAP. Finally, our results showed that the deletion of mce4 in MAP induces triacylglycerol accumulation; alter morphology and aggregation in liquid culture.
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Affiliation(s)
- Maria Natalia Alonso
- IABIMO Instituto de Agrobiotecnología y Biología Molecular, INTA-CONICET, Los Reseros y Nicolas Repetto 1686, Hurlingham, Buenos Aires, Argentina.
| | - Wladimir Malaga
- Institut de Pharmacologie et de Biologie Structurale, IPBS, University of Toulouse, CNRS, UPS, BP64182 205 Route de Narbonne, 31077 Toulouse Cedex 04, France.
| | - Michael Mc Neil
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523-1682, USA.
| | - Mary Jackson
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523-1682, USA.
| | - Maria Isabel Romano
- IABIMO Instituto de Agrobiotecnología y Biología Molecular, INTA-CONICET, Los Reseros y Nicolas Repetto 1686, Hurlingham, Buenos Aires, Argentina.
| | - Christophe Guilhot
- Institut de Pharmacologie et de Biologie Structurale, IPBS, University of Toulouse, CNRS, UPS, BP64182 205 Route de Narbonne, 31077 Toulouse Cedex 04, France.
| | - María Paz Santangelo
- IABIMO Instituto de Agrobiotecnología y Biología Molecular, INTA-CONICET, Los Reseros y Nicolas Repetto 1686, Hurlingham, Buenos Aires, Argentina.
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19
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Wang Q, Boshoff HIM, Harrison JR, Ray PC, Green SR, Wyatt PG, Barry CE. PE/PPE proteins mediate nutrient transport across the outer membrane of Mycobacterium tuberculosis. Science 2020; 367:1147-1151. [PMID: 32139546 PMCID: PMC11036889 DOI: 10.1126/science.aav5912] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 10/31/2019] [Accepted: 02/05/2020] [Indexed: 12/19/2022]
Abstract
Mycobacterium tuberculosis has an unusual outer membrane that lacks canonical porin proteins for the transport of small solutes to the periplasm. We discovered that 3,3-bis-di(methylsulfonyl)propionamide (3bMP1) inhibits the growth of M. tuberculosis, and resistance to this compound is conferred by mutation within a member of the proline-proline-glutamate (PPE) family, PPE51. Deletion of PPE51 rendered M. tuberculosis cells unable to replicate on propionamide, glucose, or glycerol. Growth was restored upon loss of the mycobacterial cell wall component phthiocerol dimycocerosate. Mutants in other proline-glutamate (PE)/PPE clusters, responsive to magnesium and phosphate, also showed a phthiocerol dimycocerosate-dependent growth compromise upon limitation of the corresponding substrate. Phthiocerol dimycocerosate determined the low permeability of the mycobacterial outer membrane, and the PE/PPE proteins apparently act as solute-specific channels.
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Affiliation(s)
- Qinglan Wang
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Helena I M Boshoff
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Justin R Harrison
- Drug Discovery Unit, College of Life Sciences, James Black Centre, University of Dundee, Dundee DD1 5EH, UK
| | - Peter C Ray
- Drug Discovery Unit, College of Life Sciences, James Black Centre, University of Dundee, Dundee DD1 5EH, UK
- Exscientia Ltd., Oxford OX1 3LD, UK
| | - Simon R Green
- Drug Discovery Unit, College of Life Sciences, James Black Centre, University of Dundee, Dundee DD1 5EH, UK
| | - Paul G Wyatt
- Drug Discovery Unit, College of Life Sciences, James Black Centre, University of Dundee, Dundee DD1 5EH, UK
| | - Clifton E Barry
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town 7925, South Africa
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20
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Riggs-Shute SD, Falkinham JO, Yang Z. Construction and Use of Transposon MycoTetOP 2 for Isolation of Conditional Mycobacteria Mutants. Front Microbiol 2020; 10:3091. [PMID: 32038540 PMCID: PMC6985430 DOI: 10.3389/fmicb.2019.03091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 12/20/2019] [Indexed: 11/13/2022] Open
Abstract
Mycobacteria are unique in many aspects of their biology. The development of genetic tools to identify genes critical for their growth by forward genetic analysis holds great promises to advance our understanding of their cellular, physiological and biochemical processes. Here we report the development of a novel transposon, MycoTetOP2, to aid the identification of such genes by direct transposon mutagenesis. This mariner-based transposon contains nested anhydrotetracycline (ATc)-inducible promoters to drive transcription outward from both of its ends. In addition, it includes the Escherichia coli R6Kγ origin to facilitate the identification of insertion sites. MycoTetOP2 was placed in a shuttle plasmid with a temperature-sensitive DNA replication origin in mycobacteria. This allows propagation of mycobacteria harboring the plasmid at a permissive temperature. The resulting population of cells can then be subjected to a temperature shift to select for transposon mutants. This transposon and its delivery system, once constructed, were tested in the fast-growing model Mycobacterium smegmatis and 13 mutants with ATc-dependent growth were isolated. The identification of the insertion sites in these mutants led to nine unique genetic loci with genes critical for essential processes in both M. smegmatis and Mycobacterium tuberculosis. These results demonstrate that MycoTetOP2 and its delivery vector provide valuable tools for the studies of mycobacteria by forward genetics.
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Affiliation(s)
- Sarah D Riggs-Shute
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, United States.,Department of Biology, Tidewater Community College, Portsmouth, VA, United States
| | - Joseph O Falkinham
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, United States
| | - Zhaomin Yang
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, United States
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21
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Biosynthesis of Galactan in Mycobacterium tuberculosis as a Viable TB Drug Target? Antibiotics (Basel) 2020; 9:antibiotics9010020. [PMID: 31935842 PMCID: PMC7168186 DOI: 10.3390/antibiotics9010020] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 12/27/2019] [Accepted: 01/02/2020] [Indexed: 12/21/2022] Open
Abstract
While target-based drug design has proved successful in several therapeutic areas, this approach has not yet provided compelling outcomes in the field of antibacterial agents. This statement remains especially true for the development of novel therapeutic interventions against tuberculosis, an infectious disease that is among the top ten leading causes of death globally. Mycobacterial galactan is an important component of the protective cell wall core of the tuberculosis pathogen and it could provide a promising target for the design of new drugs. In this review, we summarize the current knowledge on galactan biosynthesis in Mycobacterium tuberculosis, including landmark findings that led to the discovery and understanding of three key enzymes in this pathway: UDP-galactose mutase, and galactofuranosyl transferases GlfT1 and GlfT2. Moreover, we recapitulate the efforts aimed at their inhibition. The predicted common transition states of the three enzymes provide the lucrative possibility of multitargeting in pharmaceutical development, a favourable property in the mitigation of drug resistance. We believe that a tight interplay between target-based computational approaches and experimental methods will result in the development of original inhibitors that could serve as the basis of a new generation of drugs against tuberculosis.
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22
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Kapoor I, Varada R, Aroli S, Varshney U. Nudix hydrolases with Coenzyme A (CoA) and acyl-CoA pyrophosphatase activities confer growth advantage to Mycobacterium smegmatis. MICROBIOLOGY (READING, ENGLAND) 2019; 165:1219-1232. [PMID: 31526453 DOI: 10.1099/mic.0.000850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Nudix hydrolase family proteins hydrolyse toxic by-products of cellular metabolism such as mutagenic nucleoside triphosphates, sugar nucleotides and signalling molecules. We studied the substrate specificities of Nudix hydrolases encoded by rv3672c and rv3040c from Mycobacterium tuberculosis and their respective homologues, msmeg_6185 and msmeg_2327 from M. smegmatis. The rv3672c- and msmeg_6185-encoded proteins (Rv3672 and MSMEG_6185, respectively) showed CoA pyrophosphatase (CoAse) activity that converted acyl-CoA to adenosine-3',5'-diphosphate (3', 5'-ADP) and 4-acyl phosphopantetheine. The efficiencies of Rv3672 and MSMEG_6185 in hydrolysing CoA derivatives were found to be higher than those of the Rv3040 and MSMEG_2327 (encoded by rv3040c and msmeg_2327, respectively). Further, amongst the substrates tested, Rv3672 and MSMEG_6185 used CoA and oxidized CoA as the most preferred substrates. Use of the M. smegmatis model showed that the expression of msmeg_6185 occurs in the log and stationary phases but declines during the late stationary phase and becomes undetectable during hypoxia. The co-culture competition experiments performed between the wild-type and Δmsmeg_6185 strains of M. smegmatis in different carbon sources revealed that the presence of msmeg_6185 provided growth fitness advantage to M. smegmatis, irrespective of the carbon source, implicating its function in regulation for the optimal physiological levels of acyl-CoAs in the cell.
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Affiliation(s)
- Indu Kapoor
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
| | - Rajagopal Varada
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
| | - Shashanka Aroli
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
| | - Umesh Varshney
- Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, 560064, India
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
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23
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Gifford I, Vance S, Nguyen G, Berry AM. A Stable Genetic Transformation System and Implications of the Type IV Restriction System in the Nitrogen-Fixing Plant Endosymbiont Frankia alni ACN14a. Front Microbiol 2019; 10:2230. [PMID: 31608043 PMCID: PMC6769113 DOI: 10.3389/fmicb.2019.02230] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 09/11/2019] [Indexed: 12/26/2022] Open
Abstract
Genus Frankia is comprised primarily of nitrogen-fixing actinobacteria that form root nodule symbioses with a group of hosts known as the actinorhizal plants. These plants are evolutionarily closely related to the legumes that are nodulated by the rhizobia. Both host groups utilize homologs of nodulation genes for root-nodule symbiosis, derived from common plant ancestors. The corresponding endosymbionts, Frankia and the rhizobia, however, are distantly related groups of bacteria, leading to questions about their symbiotic mechanisms and evolutionary history. To date, a stable system of electrotransformation has been lacking in Frankia despite numerous attempts by research groups worldwide. We have identified type IV methyl-directed restriction systems, highly-expressed in a range of actinobacteria, as a likely barrier to Frankia transformation. Here we report the successful electrotransformation of the model strain F. alni ACN14a with an unmethylated, broad host-range replicating plasmid, expressing chloramphenicol-resistance for selection and GFP as a marker of gene expression. This system circumvented the type IV restriction barrier and allowed the stable maintenance of the plasmid. During nitrogen limitation, Frankia differentiates into two cell types: the vegetative hyphae and nitrogen-fixing vesicles. When the expression of egfp under the control of the nif gene cluster promoter was localized using fluorescence imaging, the expression of nitrogen fixation in nitrogen-limited culture was localized in Frankia vesicles but not in hyphae. The ability to separate gene expression patterns between Frankia hyphae and vesicles will enable deeper comparisons of molecular signaling and metabolic exchange between Frankia-actinorhizal and rhizobia-legume symbioses to be made, and may broaden potential applications in agriculture. Further downstream applications are possible, including gene knock-outs and complementation, to open up a range of experiments in Frankia and its symbioses. Additionally, in the transcriptome of F. alni ACN14a, type IV restriction enzymes were highly expressed in nitrogen-replete culture but their expression strongly decreased during symbiosis. The down-regulation of type IV restriction enzymes in symbiosis suggests that horizontal gene transfer may occur more frequently inside the nodule, with possible new implications for the evolution of Frankia.
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Affiliation(s)
- Isaac Gifford
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
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24
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Borgers K, Vandewalle K, Festjens N, Callewaert N. A guide to Mycobacterium mutagenesis. FEBS J 2019; 286:3757-3774. [PMID: 31419030 DOI: 10.1111/febs.15041] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 07/05/2019] [Accepted: 08/12/2019] [Indexed: 12/18/2022]
Abstract
The genus Mycobacterium includes several pathogens that cause severe disease in humans, like Mycobacterium tuberculosis (M. tb), the infectious agent causing tuberculosis. Genetic tools to engineer mycobacterial genomes, in a targeted or random fashion, have provided opportunities to investigate M. tb infection and pathogenesis. Furthermore, they have allowed the identification and validation of potential targets for the diagnosis, prevention, and treatment of tuberculosis. This review describes the various methods that are available for the generation of mutants in Mycobacterium species, focusing specifically on tools for altering slow-growing mycobacteria from the M. tb complex. Among others, it incorporates the recent new molecular biological technologies (e.g. ORBIT) to rapidly and/or genome-wide comprehensively obtain targeted mutants in mycobacteria. As such, this review can be used as a guide to select the appropriate genetic tools to generate mycobacterial mutants of interest, which can be used as tools to aid understanding of M. tb infection or to help developing TB intervention strategies.
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Affiliation(s)
- Katlyn Borgers
- VIB-UGhent Center for Medical Biotechnology, Belgium.,Department of Biochemistry and Microbiology, Ghent University, Belgium
| | - Kristof Vandewalle
- VIB-UGhent Center for Medical Biotechnology, Belgium.,Department of Biochemistry and Microbiology, Ghent University, Belgium
| | - Nele Festjens
- VIB-UGhent Center for Medical Biotechnology, Belgium.,Department of Biochemistry and Microbiology, Ghent University, Belgium
| | - Nico Callewaert
- VIB-UGhent Center for Medical Biotechnology, Belgium.,Department of Biochemistry and Microbiology, Ghent University, Belgium
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25
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Minato Y, Gohl DM, Thiede JM, Chacón JM, Harcombe WR, Maruyama F, Baughn AD. Genomewide Assessment of Mycobacterium tuberculosis Conditionally Essential Metabolic Pathways. mSystems 2019; 4:e00070-19. [PMID: 31239393 PMCID: PMC6593218 DOI: 10.1128/msystems.00070-19] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 06/07/2019] [Indexed: 11/30/2022] Open
Abstract
A better understanding of essential cellular functions in pathogenic bacteria is important for the development of more effective antimicrobial agents. We performed a comprehensive identification of essential genes in Mycobacterium tuberculosis, the major causative agent of tuberculosis, using a combination of transposon insertion sequencing (Tn-seq) and comparative genomic analysis. To identify conditionally essential genes by Tn-seq, we used media with different nutrient compositions. Although many conditional gene essentialities were affected by the presence of relevant nutrient sources, we also found that the essentiality of genes in a subset of metabolic pathways was unaffected by metabolite availability. Comparative genomic analysis revealed that not all essential genes identified by Tn-seq were fully conserved within the M. tuberculosis complex, including some existing antitubercular drug target genes. In addition, we utilized an available M. tuberculosis genome-scale metabolic model, iSM810, to predict M. tuberculosis gene essentiality in silico Comparing the sets of essential genes experimentally identified by Tn-seq to those predicted in silico reveals the capabilities and limitations of gene essentiality predictions, highlighting the complexity of M. tuberculosis essential metabolic functions. This study provides a promising platform to study essential cellular functions in M. tuberculosis IMPORTANCE Mycobacterium tuberculosis causes 10 million cases of tuberculosis (TB), resulting in over 1 million deaths each year. TB therapy is challenging because it requires a minimum of 6 months of treatment with multiple drugs. Protracted treatment times and the emergent spread of drug-resistant M. tuberculosis necessitate the identification of novel targets for drug discovery to curb this global health threat. Essential functions, defined as those indispensable for growth and/or survival, are potential targets for new antimicrobial drugs. In this study, we aimed to define gene essentialities of M. tuberculosis on a genomewide scale to comprehensively identify potential targets for drug discovery. We utilized a combination of experimental (functional genomics) and in silico approaches (comparative genomics and flux balance analysis). Our functional genomics approach identified sets of genes whose essentiality was affected by nutrient availability. Comparative genomics revealed that not all essential genes were fully conserved within the M. tuberculosis complex. Comparing sets of essential genes identified by functional genomics to those predicted by flux balance analysis highlighted gaps in current knowledge regarding M. tuberculosis metabolic capabilities. Thus, our study identifies numerous potential antitubercular drug targets and provides a comprehensive picture of the complexity of M. tuberculosis essential cellular functions.
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Affiliation(s)
- Yusuke Minato
- Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Daryl M Gohl
- University of Minnesota Genomics Center, Minneapolis, Minnesota, USA
| | - Joshua M Thiede
- Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Jeremy M Chacón
- Biotechnology Institute and Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, USA
| | - William R Harcombe
- Biotechnology Institute and Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, USA
| | - Fumito Maruyama
- Department of Microbiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- The Japan Science and Technology Agency/Japan International Cooperation Agency, Science and Technology Research Partnership for Sustainable Development (JST/JICA, SATREPS), Tokyo, Japan
- Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco, Chile
| | - Anthony D Baughn
- Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
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26
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Gheibi A, Khanahmad H, Kardar GA, Boshtam M, Rezaie S, Kazemi B, Khorramizadeh MR. Optimization and Comparison of Different Methods and Factors for Efficient Transformation of Brucella abortus RB51strain. Adv Biomed Res 2019; 8:37. [PMID: 31198771 PMCID: PMC6555225 DOI: 10.4103/abr.abr_14_19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Background: The development of protective vaccines for Brucella spp. has been hampered by the difficulty in transformation of Brucella cells with foreign DNA for genetic manipulation. It seems that the formation of Brucella spheroplasts would increase the efficiency of transformation. The aim of this study was to devise an efficient method for the transformation of Brucella spp. Materials and Methods: At first, spheroplast of Brucella was prepared by glycine and ampicillin induction and transformed using optimized protocols of CaCl2, electroporation, and lipofection methods. Then, the efficacy of transformation was compared between the three-mentioned methods. Results: Ampicillin-induced spheroplasts from early-log phase culture of brucella when incubated in a medium-containing 0.2 M sucrose during cell recovery had higher transformation efficiency in three different methods. Comparison of the transformation efficiency of Brucella abortus RB51 using the CaCl2, lipofection, and electroporation methods revealed that the transformation efficiency with the lipofection method was significantly higher than with other two methods (P < 0.05). Conclusions: Lipofection method by lipofectamine 2000 on ampicillin-induced spheroplasts can be a suitable approach for Brucella transformation.
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Affiliation(s)
- Azam Gheibi
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Hossein Khanahmad
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Gholam Ali Kardar
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran.,Department of Immunology, Asthma and Allergy Research Institute, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Maryam Boshtam
- Isfahan Cardiovascular Research Center, Cardiovascular Research Institute, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Sassan Rezaie
- Department of Mycology and Parasitology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Bahram Kazemi
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Khorramizadeh
- Biosensor Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
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27
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Palčeková Z, Angala SK, Belardinelli JM, Eskandarian HA, Joe M, Brunton R, Rithner C, Jones V, Nigou J, Lowary TL, Gilleron M, McNeil M, Jackson M. Disruption of the SucT acyltransferase in Mycobacterium smegmatis abrogates succinylation of cell envelope polysaccharides. J Biol Chem 2019; 294:10325-10335. [PMID: 31110045 DOI: 10.1074/jbc.ra119.008585] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 05/14/2019] [Indexed: 12/22/2022] Open
Abstract
Similar to other prokaryotes, mycobacteria decorate their major cell envelope glycans with minor covalent substituents whose biological significance remains largely unknown. We report on the discovery of a mycobacterial enzyme, named here SucT, that adds succinyl groups to the arabinan domains of both arabinogalactan (AG) and lipoarabinomannan (LAM). Disruption of the SucT-encoding gene in Mycobacterium smegmatis abolished AG and LAM succinylation and altered the hydrophobicity and rigidity of the cell envelope of the bacilli without significantly altering AG and LAM biosynthesis. The changes in the cell surface properties of the mutant were consistent with earlier reports of transposon mutants of the closely related species Mycobacterium marinum and Mycobacterium avium harboring insertions in the orthologous gene whose ability to microaggregate and form biofilms were altered. Our findings point to an important role of SucT-mediated AG and LAM succinylation in modulating the cell surface properties of mycobacteria.
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Affiliation(s)
- Zuzana Palčeková
- From the Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado 80523-1682
| | - Shiva K Angala
- From the Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado 80523-1682
| | - Juan Manuel Belardinelli
- From the Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado 80523-1682
| | - Haig A Eskandarian
- the Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne VD, Switzerland
| | - Maju Joe
- the Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Richard Brunton
- the Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Christopher Rithner
- the Central Instrumentation Facility, Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523-1872, and
| | - Victoria Jones
- From the Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado 80523-1682
| | - Jérôme Nigou
- the Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, 205 Route de Narbonne, 31077 Toulouse, France
| | - Todd L Lowary
- the Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Martine Gilleron
- the Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, 205 Route de Narbonne, 31077 Toulouse, France
| | - Michael McNeil
- From the Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado 80523-1682
| | - Mary Jackson
- From the Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado 80523-1682,
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28
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Chen Y, Xu Y, Yang S, Li S, Ding W, Zhang W. Deficiency of D-alanyl-D-alanine ligase A attenuated cell division and greatly altered the proteome of Mycobacterium smegmatis. Microbiologyopen 2019; 8:e00819. [PMID: 30828981 PMCID: PMC6741128 DOI: 10.1002/mbo3.819] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 01/24/2019] [Accepted: 01/25/2019] [Indexed: 12/14/2022] Open
Abstract
D‐Alanyl‐D‐alanine ligase A (DdlA) catalyses the dimerization of two D‐alanines yielding D‐alanyl‐D‐alanine required for mycobacterial peptidoglycan biosynthesis, and is a promising antimycobacterial drug target. To better understand the roles of DdlA in mycobacteria in vivo, we established a cell model in which DdlA expression was specifically downregulated by ddlA antisense RNA by introducing a 380 bp ddlA fragment into pMind followed by transforming the construct into nonpathogenic Mycobacterium smegmatis. The M. smegmatis cell model was verified by plotting the growth inhibition curves and quantifying endogenous DdlA expression using a polyclonal anti‐DdlA antibody produced from the expressed DdlA. Scanning electron microscopy and transmission electron microscopy were used to investigate mycobacterial morphology. Bidimensional gel electrophoresis and mass spectrometry were used to analyze differentially expressed proteins. Consequently, the successful construction of the M. smegmatis cell model was verified. The morphological investigation of the model indicated that DdlA deficiency led to an increased number of Z rings and a rearrangement of intracellular content, including a clear nucleoid and visible filamentous DNA. Proteomic techniques identified six upregulated and 14 downregulated proteins that interacted with each other to permit cell survival by forming a regulatory network under DdlA deficiency. Finally, our data revealed that DdlA deficiency inhibited cell division in mycobacteria and attenuated the process of carbohydrate catabolism and the pathway of fatty acid anabolism, while maintaining active protein degradation and synthesis. N‐Nitrosodimethylamine (NDMA)‐dependent methanol dehydrogenase (MSMEG_6242) and fumonisin (MSMEG_1419) were identified as potential antimycobacterial drug targets.
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Affiliation(s)
- Yingfei Chen
- Dalian Yuming Senior High School, Liaoning, China
| | - Yuefei Xu
- Biochemistry and Molecular Biology Department of College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Shufeng Yang
- Department of Microbiology, Dalian Medical University, Dalian, China
| | - Sheng Li
- Biochemistry and Molecular Biology Department of College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Wenyong Ding
- Biochemistry and Molecular Biology Department of College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Wenli Zhang
- Biochemistry and Molecular Biology Department of College of Basic Medical Sciences, Dalian Medical University, Dalian, China
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29
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You D, Xu Y, Yin BC, Ye BC. Nitrogen Regulator GlnR Controls Redox Sensing and Lipids Anabolism by Directly Activating the whiB3 in Mycobacterium smegmatis. Front Microbiol 2019; 10:74. [PMID: 30761112 PMCID: PMC6361795 DOI: 10.3389/fmicb.2019.00074] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 01/15/2019] [Indexed: 11/30/2022] Open
Abstract
WhiB3 is a conserved cytoplasmic redox sensor which is required in the infection and lipid anabolism of Mycobacterium tuberculosis. The response of WhiB3 to environmental nutrient and its regulatory cascades are crucial during the persistent infection, while little is known about the relationship between WhiB3 and emergence of nutrient stress in this process. Here, we found that nitrogen regulator GlnR directly interacted with the WhiB3 promoter region and activated its transcription in response to nitrogen availability. In whiB3 promoter region, the typical GlnR-box was also identified. Moreover, GlnR controlled cell resistance to redox stress and SL-1 lipid anabolism by directly activating whiB3 expression. These results demonstrated that GlnR regulated redox sensor WhiB3 at the transcriptional level and mediated the interplay among nitrogen metabolism, redox sensing, and lipid anabolism.
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Affiliation(s)
- Di You
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Ying Xu
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Bin-Cheng Yin
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Bang-Ce Ye
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China.,Institute of Engineering Biology and Health, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, China
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30
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Sala C, Odermatt NT, Soler-Arnedo P, Gülen MF, von Schultz S, Benjak A, Cole ST. EspL is essential for virulence and stabilizes EspE, EspF and EspH levels in Mycobacterium tuberculosis. PLoS Pathog 2018; 14:e1007491. [PMID: 30571761 PMCID: PMC6319747 DOI: 10.1371/journal.ppat.1007491] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 01/04/2019] [Accepted: 11/28/2018] [Indexed: 12/03/2022] Open
Abstract
The ESX-1, type VII, secretion system represents the major virulence determinant of Mycobacterium tuberculosis, one of the most successful intracellular pathogens. Here, by combining genetic and high-throughput approaches, we show that EspL, a protein of 115 amino acids, is essential for mediating ESX-1-dependent virulence and for stabilization of EspE, EspF and EspH protein levels. Indeed, an espL knock-out mutant was unable to replicate intracellularly, secrete ESX-1 substrates or stimulate innate cytokine production. Moreover, proteomic studies detected greatly reduced amounts of EspE, EspF and EspH in the espL mutant as compared to the wild type strain, suggesting a role for EspL as a chaperone. The latter conclusion was further supported by discovering that EspL interacts with EspD, which was previously demonstrated to stabilize the ESX-1 substrates and effector proteins, EspA and EspC. Loss of EspL also leads to downregulation in M. tuberculosis of WhiB6, a redox-sensitive transcriptional activator of ESX-1 genes. Overall, our data highlight the importance of a so-far overlooked, though conserved, component of the ESX-1 secretion system and begin to delineate the role played by EspE, EspF and EspH in virulence and host-pathogen interaction. Mycobacterium tuberculosis is the etiological agent of human tuberculosis, a life-threatening disease which has seen a recrudescence in the last decades due to the spread of drug-resistant bacterial strains and to co-morbidities such as HIV and diabetes. To develop effective treatment and limit bacterial dissemination within and outside the host, it is pivotal to improve our understanding of the strategies used by the pathogen to colonize the host and subvert the immune defenses. The ESX-1 secretion system represents a key player in these processes. Here we show that the EspL protein, encoded by the ESX-1 gene cluster, is essential for bacterial virulence and for stabilizing the abundance of the EspE, EspF and EspH components of the ESX-1 system. Tubercle bacilli lacking EspL cannot multiply inside macrophages, do not secrete the major virulence factor EsxA and fail to trigger the ESX-1 dependent innate immune response. EspL is thus an important but so-far neglected contributor to ESX-1 function.
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Affiliation(s)
- Claudia Sala
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- * E-mail: (CS); (STC)
| | - Nina T. Odermatt
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Paloma Soler-Arnedo
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Muhammet F. Gülen
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Sofia von Schultz
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Andrej Benjak
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Stewart T. Cole
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- * E-mail: (CS); (STC)
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31
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Decout A, Silva-Gomes S, Drocourt D, Blattes E, Rivière M, Prandi J, Larrouy-Maumus G, Caminade AM, Hamasur B, Källenius G, Kaur D, Dobos KM, Lucas M, Sutcliffe IC, Besra GS, Appelmelk BJ, Gilleron M, Jackson M, Vercellone A, Tiraby G, Nigou J. Deciphering the molecular basis of mycobacteria and lipoglycan recognition by the C-type lectin Dectin-2. Sci Rep 2018; 8:16840. [PMID: 30443026 PMCID: PMC6237770 DOI: 10.1038/s41598-018-35393-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 11/05/2018] [Indexed: 01/04/2023] Open
Abstract
Dectin-2 is a C-type lectin involved in the recognition of several pathogens such as Aspergillus fumigatus, Candida albicans, Schistosoma mansonii, and Mycobacterium tuberculosis that triggers Th17 immune responses. Identifying pathogen ligands and understanding the molecular basis of their recognition is one of the current challenges. Purified M. tuberculosis mannose-capped lipoarabinomannan (ManLAM) was shown to induce signaling via Dectin-2, an activity that requires the (α1 → 2)-linked mannosides forming the caps. Here, using isogenic M. tuberculosis mutant strains, we demonstrate that ManLAM is a bona fide and actually the sole ligand mediating bacilli recognition by Dectin-2, although M. tuberculosis produces a variety of cell envelope mannoconjugates, such as phosphatidyl-myo-inositol hexamannosides, lipomannan or manno(lipo)proteins, that bear (α1 → 2)-linked mannosides. In addition, we found that Dectin-2 can recognize lipoglycans from other bacterial species, such as Saccharotrix aerocolonigenes or the human opportunistic pathogen Tsukamurella paurometabola, suggesting that lipoglycans are prototypical Dectin-2 ligands. Finally, from a structure/function relationship perspective, we show, using lipoglycan variants and synthetic mannodendrimers, that dimannoside caps and multivalent interaction are required for ligand binding to and signaling via Dectin-2. Better understanding of the molecular basis of ligand recognition by Dectin-2 will pave the way for the rational design of potent adjuvants targeting this receptor.
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Affiliation(s)
- Alexiane Decout
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, Université Paul Sabatier, 31077, Toulouse, France.,InvivoGen, Research Department, 31400, Toulouse, France.,Global Health Institute, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Sandro Silva-Gomes
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, Université Paul Sabatier, 31077, Toulouse, France.,GlaxoSmithKline (GSK), Stevenage Herts, SG1 2NY, UK
| | | | - Emilyne Blattes
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, Université Paul Sabatier, 31077, Toulouse, France.,Innovative Medecine for Tuberculosis (iM4TB), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Michel Rivière
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, Université Paul Sabatier, 31077, Toulouse, France
| | - Jacques Prandi
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, Université Paul Sabatier, 31077, Toulouse, France
| | - Gérald Larrouy-Maumus
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, Université Paul Sabatier, 31077, Toulouse, France.,Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London, SW7 2AZ, UK
| | - Anne-Marie Caminade
- Laboratoire de Chimie de Coordination, Université de Toulouse, CNRS, Université Paul Sabatier, 31077, Toulouse, France
| | - Beston Hamasur
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 77, Stockholm, Sweden.,Biopromic AB, 171 65, Solna, Sweden
| | - Gunilla Källenius
- Department of Medicine, Karolinska Institutet Solna 171 76, Stockholm, Sweden
| | - Devinder Kaur
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, 80523-1682, USA.,Massachusetts Supranational TB Reference Laboratory, University of Massachusetts Medical School, Jamaica Plain, MA, 0213, USA
| | - Karen M Dobos
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, 80523-1682, USA
| | - Megan Lucas
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, 80523-1682, USA
| | - Iain C Sutcliffe
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, NE1 8ST, UK
| | - Gurdyal S Besra
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Ben J Appelmelk
- Department of Medical Microbiology and Infection Control, VU University Medical Center, 1081 BT, Amsterdam, The Netherlands
| | - Martine Gilleron
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, Université Paul Sabatier, 31077, Toulouse, France
| | - Mary Jackson
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, 80523-1682, USA
| | - Alain Vercellone
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, Université Paul Sabatier, 31077, Toulouse, France
| | - Gérard Tiraby
- InvivoGen, Research Department, 31400, Toulouse, France
| | - Jérôme Nigou
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, Université Paul Sabatier, 31077, Toulouse, France.
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Naorem SS, Han J, Zhang SY, Zhang J, Graham LB, Song A, Smith CV, Rashid F, Guo H. Efficient transposon mutagenesis mediated by an IPTG-controlled conditional suicide plasmid. BMC Microbiol 2018; 18:158. [PMID: 30355324 PMCID: PMC6201506 DOI: 10.1186/s12866-018-1319-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 10/16/2018] [Indexed: 11/17/2022] Open
Abstract
Background Transposon mutagenesis is highly valuable for bacterial genetic and genomic studies. The transposons are usually delivered into host cells through conjugation or electroporation of a suicide plasmid. However, many bacterial species cannot be efficiently conjugated or transformed for transposon saturation mutagenesis. For this reason, temperature-sensitive (ts) plasmids have also been developed for transposon mutagenesis, but prolonged incubation at high temperatures to induce ts plasmid loss can be harmful to the hosts and lead to enrichment of mutants with adaptive genetic changes. In addition, the ts phenotype of a plasmid is often strain- or species-specific, as it may become non-ts or suicidal in different bacterial species. Results We have engineered several conditional suicide plasmids that have a broad host range and whose loss is IPTG-controlled. One construct, which has the highest stability in the absence of IPTG induction, was then used as a curable vector to deliver hyperactive miniTn5 transposons for insertional mutagenesis. Our analyses show that these new tools can be used for efficient and regulatable transposon mutagenesis in Escherichia coli, Acinetobacter baylyi and Pseudomonas aeruginosa. In P. aeruginosa PAO1, we have used this method to generate a Tn5 insertion library with an estimated diversity of ~ 108, which is ~ 2 logs larger than the best transposon insertional library of PAO1 and related Pseudomonas strains previously reported. Conclusion We have developed a number of IPTG-controlled conditional suicide plasmids. By exploiting one of them for transposon delivery, a highly efficient and broadly useful mutagenesis system has been developed. As the assay condition is mild, we believe that our methodology will have broad applications in microbiology research. Electronic supplementary material The online version of this article (10.1186/s12866-018-1319-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Santa S Naorem
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, MO, 65212, USA
| | - Jin Han
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, MO, 65212, USA
| | - Stephanie Y Zhang
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, MO, 65212, USA
| | - Junyi Zhang
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, MO, 65212, USA
| | - Lindsey B Graham
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, MO, 65212, USA
| | - Angelou Song
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, MO, 65212, USA
| | - Cameron V Smith
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, MO, 65212, USA
| | - Fariha Rashid
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, MO, 65212, USA
| | - Huatao Guo
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, MO, 65212, USA.
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A uniform cloning platform for mycobacterial genetics and protein production. Sci Rep 2018; 8:9539. [PMID: 29934571 PMCID: PMC6015033 DOI: 10.1038/s41598-018-27687-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 06/08/2018] [Indexed: 12/31/2022] Open
Abstract
Molecular research on mycobacteria relies on a multitude of tools for the genetic manipulation of these clinically important bacteria. However, a uniform set of vectors allowing for standardized cloning procedures is not available. Here, we developed a versatile series of mycobacterial vectors for gene deletion, complementation and protein production and purification. The vectors are compatible with fragment exchange (FX) cloning, a recently developed high-throughput cloning principle taking advantage of the type IIS restriction enzyme SapI and its capacity to generate sticky trinucleotide ends outside of its recognition sequence. FX cloning allows for the efficient cloning into an entry vector and the facile transfer of the sequenced insert into a variety of destination vectors. We generated a set of mycobacterial expression vectors spanning a wide range of expression strengths, tagging variants and selection markers to rapidly screen for the optimal expression construct in order to purify membrane proteins from the model organism Mycobacterium smegmatis. Further, we generated a series of suicide vectors containing two counterselection markers and used them to delete twenty genes encoding for potential drug efflux pumps in M. smegmatis. The vectors will further facilitate genetic and biochemical research on various mycobacterial species.
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Chhotaray C, Tan Y, Mugweru J, Islam MM, Adnan Hameed HM, Wang S, Lu Z, Wang C, Li X, Tan S, Liu J, Zhang T. Advances in the development of molecular genetic tools for Mycobacterium tuberculosis. J Genet Genomics 2018; 45:S1673-8527(18)30114-0. [PMID: 29941353 DOI: 10.1016/j.jgg.2018.06.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Mycobacterium tuberculosis, a clinically relevant Gram-positive bacterium of great clinical relevance, is a lethal pathogen owing to its complex physiological characteristics and development of drug resistance. Several molecular genetic tools have been developed in the past few decades to study this microorganism. These tools have been instrumental in understanding how M. tuberculosis became a successful pathogen. Advanced molecular genetic tools have played a significant role in exploring the complex pathways involved in M. tuberculosis pathogenesis. Here, we review various molecular genetic tools used in the study of M. tuberculosis. Further, we discuss the applications of clustered regularly interspaced short palindromic repeat interference (CRISPRi), a novel technology recently applied in M. tuberculosis research to study target gene functions. Finally, prospective outcomes of the applications of molecular techniques in the field of M. tuberculosis genetic research are also discussed.
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Affiliation(s)
- Chiranjibi Chhotaray
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yaoju Tan
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, Guangzhou Chest Hospital, Guangzhou 510095, China
| | - Julius Mugweru
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China; Department of Biological Sciences, University of Embu, P.O Box 6 -60100, Embu, Kenya
| | - Md Mahmudul Islam
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - H M Adnan Hameed
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuai Wang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhili Lu
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Changwei Wang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Xinjie Li
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, Guangzhou Chest Hospital, Guangzhou 510095, China
| | - Shouyong Tan
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, Guangzhou Chest Hospital, Guangzhou 510095, China
| | - Jianxiong Liu
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, Guangzhou Chest Hospital, Guangzhou 510095, China.
| | - Tianyu Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Abbadi BL, Rodrigues-Junior VDS, Dadda ADS, Pissinate K, Villela AD, Campos MM, Lopes LGDF, Bizarro CV, Machado P, Sousa EHS, Basso LA. Is IQG-607 a Potential Metallodrug or Metallopro-Drug With a Defined Molecular Target in Mycobacterium tuberculosis? Front Microbiol 2018; 9:880. [PMID: 29765372 PMCID: PMC5938375 DOI: 10.3389/fmicb.2018.00880] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 04/16/2018] [Indexed: 12/14/2022] Open
Abstract
The emergence of strains of Mycobacterium tuberculosis resistant to isoniazid (INH) has underscored the need for the development of new anti-tuberculosis agents. INH is activated by the mycobacterial katG-encoded catalase-peroxidase, forming an acylpyridine fragment that is covalently attached to the C4 of NADH. This isonicotinyl-NAD adduct inhibits the activity of 2-trans-enoyl-ACP(CoA) reductase (InhA), which plays a role in mycolic acid biosynthesis. A metal-based INH analog, Na3[FeII(CN)5(INH)]·4H2O, IQG-607, was designed to have an electronic redistribution on INH moiety that would lead to an intramolecular electron transfer to bypass KatG activation. HPLC and EPR studies showed that the INH moiety can be oxidized by superoxide or peroxide yielding similar metabolites and isonicotinoyl radical only when associated to IQG-607, thereby supporting redox-mediated drug activation as a possible mechanism of action. However, IQG-607 was shown to inhibit the in vitro activity of both wild-type and INH-resistant mutant InhA enzymes in the absence of KatG activation. IQG-607 given by the oral route to M. tuberculosis-infected mice reduced lung lesions. Experiments using early and late controls of infection revealed a bactericidal activity for IQG-607. HPLC and voltammetric methods were developed to quantify IQG-607. Pharmacokinetic studies showed short half-life, high clearance, moderate volume of distribution, and low oral bioavailability, which was not altered by feeding. Safety and toxic effects of IQG-607 after acute and 90-day repeated oral administrations in both rats and minipigs showed occurrence of mild to moderate toxic events. Eight multidrug-resistant strains (MDR-TB) were resistant to IQG-607, suggesting an association between katG mutation and increasing MIC values. Whole genome sequencing of three spontaneous IQG-607-resistant strains harbored katG gene mutations. MIC measurements and macrophage infection experiments with a laboratorial strain showed that katG mutation is sufficient to confer resistance to IQG-607 and that the macrophage intracellular environment cannot trigger the self-activation mechanism. Reduced activity of IQG-607 against an M. tuberculosis strain overexpressing S94A InhA mutant protein suggested both the need for KatG activation and InhA as its target. Further efforts are suggested to be pursued toward attempting to translate IQG-607 into a chemotherapeutic agent to treat tuberculosis.
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Affiliation(s)
- Bruno L Abbadi
- Centro de Pesquisas em Biologia Molecular e Funcional, Instituto Nacional de Ciência e Tecnologia em Tuberculose, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil.,Programa de Pós-Graduação em Biologia Celular e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - Valnês da Silva Rodrigues-Junior
- Centro de Pesquisas em Biologia Molecular e Funcional, Instituto Nacional de Ciência e Tecnologia em Tuberculose, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - Adilio da Silva Dadda
- Centro de Pesquisas em Biologia Molecular e Funcional, Instituto Nacional de Ciência e Tecnologia em Tuberculose, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil.,Programa de Pós-Graduação em Biologia Celular e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - Kenia Pissinate
- Centro de Pesquisas em Biologia Molecular e Funcional, Instituto Nacional de Ciência e Tecnologia em Tuberculose, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - Anne D Villela
- Centro de Pesquisas em Biologia Molecular e Funcional, Instituto Nacional de Ciência e Tecnologia em Tuberculose, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - Maria M Campos
- Centro de Pesquisas em Biologia Molecular e Funcional, Instituto Nacional de Ciência e Tecnologia em Tuberculose, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil.,Programa de Pós-Graduação em Medicina e Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - Luiz G de França Lopes
- Grupo de Bioinorgânica, Departamento de Química Orgânica e Inorgânica, Universidade Federal do Ceará, Fortaleza, Brazil
| | - Cristiano V Bizarro
- Centro de Pesquisas em Biologia Molecular e Funcional, Instituto Nacional de Ciência e Tecnologia em Tuberculose, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil.,Programa de Pós-Graduação em Biologia Celular e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - Pablo Machado
- Centro de Pesquisas em Biologia Molecular e Funcional, Instituto Nacional de Ciência e Tecnologia em Tuberculose, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil.,Programa de Pós-Graduação em Biologia Celular e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - Eduardo H S Sousa
- Grupo de Bioinorgânica, Departamento de Química Orgânica e Inorgânica, Universidade Federal do Ceará, Fortaleza, Brazil
| | - Luiz A Basso
- Centro de Pesquisas em Biologia Molecular e Funcional, Instituto Nacional de Ciência e Tecnologia em Tuberculose, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil.,Programa de Pós-Graduação em Biologia Celular e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil.,Programa de Pós-Graduação em Medicina e Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
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Sakatos A, Babunovic GH, Chase MR, Dills A, Leszyk J, Rosebrock T, Bryson B, Fortune SM. Posttranslational modification of a histone-like protein regulates phenotypic resistance to isoniazid in mycobacteria. SCIENCE ADVANCES 2018; 4:eaao1478. [PMID: 29732401 PMCID: PMC5931751 DOI: 10.1126/sciadv.aao1478] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 03/20/2018] [Indexed: 05/08/2023]
Abstract
There is increasing evidence that phenotypically drug-resistant bacteria may be important determinants of antibiotic treatment failure. Using high-throughput imaging, we defined distinct subpopulations of mycobacterial cells that exhibit heritable but semi-stable drug resistance. These subpopulations have distinct transcriptional signatures and growth characteristics at both bulk and single-cell levels, which are also heritable and semi-stable. We find that the mycobacterial histone-like protein HupB is required for the formation of these subpopulations. Using proteomic approaches, we further demonstrate that HupB is posttranslationally modified by lysine acetylation and lysine methylation. Mutation of a single posttranslational modification site specifically abolishes the formation of one of the drug-resistant subpopulations of cells, providing the first evidence in prokaryotes that posttranslational modification of a bacterial nucleoid-associated protein may epigenetically regulate cell state.
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Affiliation(s)
- Alexandra Sakatos
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Gregory H. Babunovic
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Michael R. Chase
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Alexander Dills
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - John Leszyk
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 02129, USA
| | - Tracy Rosebrock
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
- Stonehill College, North Easton, MA 02357, USA
| | - Bryan Bryson
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Sarah M. Fortune
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
- The Ragon Institute of Massachusetts General Hospital, Harvard, and Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Corresponding author.
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37
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Dalberto PF, Rodrigues-Junior V, Almeida Falcão VC, Pinto AFM, Abbadi BL, Bizarro CV, Basso LA, Villela AD, Santos DS. Assessing the role of deoD gene in Mycobacterium tuberculosis in vitro growth and macrophage infection. Microb Pathog 2018; 119:60-64. [PMID: 29608932 DOI: 10.1016/j.micpath.2018.03.056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 02/12/2018] [Accepted: 03/29/2018] [Indexed: 11/25/2022]
Abstract
Purine nucleoside phosphorylase from Mycobacterium tuberculosis (MtPNP), encoded by deoD gene (Rv3307), is an enzyme from the purine salvage pathway, which has been widely studied as a molecular target for the development of inhibitors with potential antimycobacterial activity. However, the role of MtPNP in tuberculosis pathogenesis and dormancy is still unknown. The present work aims to construct a deoD knockout strain from M. tuberculosis, to evaluate the role of MtPNP in the growth of M. tuberculosis under oxygenated condition and in a dormancy model, and to assess whether deoD gene is important for M. tuberculosis invasion and growth in macrophages. The construction of a knockout strain for deoD gene was confirmed at DNA level by PCR and protein level by Western blot and LC-MS/MS. The deoD gene is not required for M. tuberculosis growth and survival under oxygenated and hypoxic conditions. The disruption of deoD gene did not affect mycobacterial ability to invade and grow in RAW 264.7 cells under the experimental conditions employed here.
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Affiliation(s)
- Pedro Ferrari Dalberto
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Instituto de Pesquisas Biomédicas, Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil; Programa de Pós-Graduação em Biologia Celular e Molecular, PUCRS, Porto Alegre, Brazil
| | - Valnês Rodrigues-Junior
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Instituto de Pesquisas Biomédicas, Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
| | - Virginia Carla Almeida Falcão
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Instituto de Pesquisas Biomédicas, Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil; Programa de Pós-Graduação em Biologia Celular e Molecular, PUCRS, Porto Alegre, Brazil
| | - Antônio Frederico Michel Pinto
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Instituto de Pesquisas Biomédicas, Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
| | - Bruno Lopes Abbadi
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Instituto de Pesquisas Biomédicas, Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil; Programa de Pós-Graduação em Biologia Celular e Molecular, PUCRS, Porto Alegre, Brazil
| | - Cristiano Valim Bizarro
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Instituto de Pesquisas Biomédicas, Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
| | - Luiz Augusto Basso
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Instituto de Pesquisas Biomédicas, Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil; Programa de Pós-Graduação em Biologia Celular e Molecular, PUCRS, Porto Alegre, Brazil; Programa de Pós-Graduação em Medicina e Ciências da Saúde, PUCRS, Porto Alegre, Brazil
| | - Anne Drumond Villela
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Instituto de Pesquisas Biomédicas, Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil.
| | - Diógenes Santiago Santos
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Instituto de Pesquisas Biomédicas, Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil; Programa de Pós-Graduação em Biologia Celular e Molecular, PUCRS, Porto Alegre, Brazil
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Madacki J, Laval F, Grzegorzewicz A, Lemassu A, Záhorszká M, Arand M, McNeil M, Daffé M, Jackson M, Lanéelle MA, Korduláková J. Impact of the epoxide hydrolase EphD on the metabolism of mycolic acids in mycobacteria. J Biol Chem 2018; 293:5172-5184. [PMID: 29472294 DOI: 10.1074/jbc.ra117.000246] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 02/16/2018] [Indexed: 01/09/2023] Open
Abstract
Mycolic acids are the hallmark of the cell envelope in mycobacteria, which include the important human pathogens Mycobacterium tuberculosis and Mycobacterium leprae Mycolic acids are very long C60-C90 α-alkyl β-hydroxy fatty acids having a variety of functional groups on their hydrocarbon chain that define several mycolate types. Mycobacteria also produce an unusually large number of putative epoxide hydrolases, but the physiological functions of these enzymes are still unclear. Here, we report that the mycobacterial epoxide hydrolase EphD is involved in mycolic acid metabolism. We found that orthologs of EphD from M. tuberculosis and M. smegmatis are functional epoxide hydrolases, cleaving a lipophilic substrate, 9,10-cis-epoxystearic acid, in vitro and forming a vicinal diol. The results of EphD overproduction in M. smegmatis and M. bovis BCG Δhma strains producing epoxymycolic acids indicated that EphD is involved in the metabolism of these forms of mycolates in both fast- and slow-growing mycobacteria. Moreover, using MALDI-TOF-MS and 1H NMR spectroscopy of mycolic acids and lipids isolated from EphD-overproducing M. smegmatis, we identified new oxygenated mycolic acid species that accumulated during epoxymycolate depletion. Disruption of the ephD gene in M. tuberculosis specifically impaired the synthesis of ketomycolates and caused accumulation of their precursor, hydroxymycolate, indicating either direct or indirect involvement of EphD in ketomycolate biosynthesis. Our results clearly indicate that EphD plays a role in metabolism of oxygenated mycolic acids in mycobacteria.
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Affiliation(s)
- Jan Madacki
- From the Department of Biochemistry, Faculty of Natural Sciences, Comenius University, 842 15 Bratislava, Slovakia
| | - Françoise Laval
- the Tuberculosis & Infection Biology Department, Institut de Pharmacologie et de Biologie Structurale, CNRS, 31077 Toulouse, France
| | - Anna Grzegorzewicz
- the Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado 80523-1682, and
| | - Anne Lemassu
- the Tuberculosis & Infection Biology Department, Institut de Pharmacologie et de Biologie Structurale, CNRS, 31077 Toulouse, France
| | - Monika Záhorszká
- From the Department of Biochemistry, Faculty of Natural Sciences, Comenius University, 842 15 Bratislava, Slovakia
| | - Michael Arand
- the Institute of Pharmacology and Toxicology, University of Zürich, CH-8057 Zürich, Switzerland
| | - Michael McNeil
- the Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado 80523-1682, and
| | - Mamadou Daffé
- the Tuberculosis & Infection Biology Department, Institut de Pharmacologie et de Biologie Structurale, CNRS, 31077 Toulouse, France
| | - Mary Jackson
- the Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado 80523-1682, and
| | - Marie-Antoinette Lanéelle
- the Tuberculosis & Infection Biology Department, Institut de Pharmacologie et de Biologie Structurale, CNRS, 31077 Toulouse, France
| | - Jana Korduláková
- From the Department of Biochemistry, Faculty of Natural Sciences, Comenius University, 842 15 Bratislava, Slovakia,
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Abstract
Tuberculosis is responsible for more deaths worldwide than any other infectious disease. For anyone looking to learn more about this persistent public health threat, this conversational "frequently asked questions" style review addresses a breadth of questions. It offers a brief, somewhat opinionated, review of what is and is not known, particularly in light of how findings in the lab do or do not help inform the understanding of human tuberculosis.
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Affiliation(s)
- Kristine M Guinn
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Eric J Rubin
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
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40
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Cabruja M, Mondino S, Tsai YT, Lara J, Gramajo H, Gago G. A conditional mutant of the fatty acid synthase unveils unexpected cross talks in mycobacterial lipid metabolism. Open Biol 2017; 7:rsob.160277. [PMID: 28228470 PMCID: PMC5356441 DOI: 10.1098/rsob.160277] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 01/25/2017] [Indexed: 01/02/2023] Open
Abstract
Unlike most bacteria, mycobacteria rely on the multi-domain enzyme eukaryote-like fatty acid synthase I (FAS I) to make fatty acids de novo. These metabolites are precursors of the biosynthesis of most of the lipids present both in the complex mycobacteria cell wall and in the storage lipids inside the cell. In order to study the role of the type I FAS system in Mycobacterium lipid metabolism in vivo, we constructed a conditional mutant in the fas-acpS operon of Mycobacterium smegmatis and analysed in detail the impact of reduced de novo fatty acid biosynthesis on the global architecture of the cell envelope. As expected, the mutant exhibited growth defect in the non-permissive condition that correlated well with the lower expression of fas-acpS and the concomitant reduction of FAS I, confirming that FAS I is essential for survival. The reduction observed in FAS I provoked an accumulation of its substrates, acetyl-CoA and malonyl-CoA, and a strong reduction of C12 to C18 acyl-CoAs, but not of long-chain acyl-CoAs (C19 to C24). The most intriguing result was the ability of the mutant to keep synthesizing mycolic acids when fatty acid biosynthesis was impaired. A detailed comparative lipidomic analysis showed that although reduced FAS I levels had a strong impact on fatty acid and phospholipid biosynthesis, mycolic acids were still being synthesized in the mutant, although with a different relative species distribution. However, when triacylglycerol degradation was inhibited, mycolic acid biosynthesis was significantly reduced, suggesting that storage lipids could be an intracellular reservoir of fatty acids for the biosynthesis of complex lipids in mycobacteria. Understanding the interaction between FAS I and the metabolic pathways that rely on FAS I products is a key step to better understand how lipid homeostasis is regulated in this microorganism and how this regulation could play a role during infection in pathogenic mycobacteria.
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Affiliation(s)
- Matías Cabruja
- Laboratory of Physiology and Genetics of Actinomycetes, Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Sonia Mondino
- Laboratory of Physiology and Genetics of Actinomycetes, Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Yi Ting Tsai
- Laboratory of Physiology and Genetics of Actinomycetes, Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Julia Lara
- Laboratory of Physiology and Genetics of Actinomycetes, Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Hugo Gramajo
- Laboratory of Physiology and Genetics of Actinomycetes, Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Gabriela Gago
- Laboratory of Physiology and Genetics of Actinomycetes, Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
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Villela AD, Rodrigues-Junior VS, Pinto AFM, Falcão VCDA, Sánchez-Quitian ZA, Eichler P, Bizarro CV, Basso LA, Santos DS. Construction of Mycobacterium tuberculosis cdd knockout and evaluation of invasion and growth in macrophages. Mem Inst Oswaldo Cruz 2017; 112:785-789. [PMID: 29091140 PMCID: PMC5661903 DOI: 10.1590/0074-02760170105] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 05/30/2017] [Indexed: 12/26/2022] Open
Abstract
Cytidine deaminase (MtCDA), encoded by cdd gene (Rv3315c), is the only enzyme identified in nucleotide biosynthesis pathway of Mycobacterium tuberculosis that is able to recycle cytidine and deoxycytidine. An M. tuberculosis knockout strain for cdd gene was obtained by allelic replacement. Evaluation of mRNA expression validated cdd deletion and showed the absence of polar effect. MudPIT LC-MS/MS data indicated thymidine phosphorylase expression was decreased in knockout and complemented strains. The cdd disruption does not affect M. tuberculosis growth both in Mid- dlebrook 7H9 and in RAW 264.7 cells, which indicates that cdd is not important for macrophage invasion and virulence.
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Affiliation(s)
- Anne Drumond Villela
- Pontifícia Universidade Católica do Rio Grande do Sul, Centro de Pesquisas em Biologia Molecular e Funcional, Instituto Nacional de Ciência e Tecnologia em Tuberculose, Porto Alegre, RS, Brasil
| | - Valnês S Rodrigues-Junior
- Pontifícia Universidade Católica do Rio Grande do Sul, Centro de Pesquisas em Biologia Molecular e Funcional, Instituto Nacional de Ciência e Tecnologia em Tuberculose, Porto Alegre, RS, Brasil
| | - Antônio Frederico Michel Pinto
- Pontifícia Universidade Católica do Rio Grande do Sul, Centro de Pesquisas em Biologia Molecular e Funcional, Instituto Nacional de Ciência e Tecnologia em Tuberculose, Porto Alegre, RS, Brasil
| | - Virgínia Carla de Almeida Falcão
- Pontifícia Universidade Católica do Rio Grande do Sul, Centro de Pesquisas em Biologia Molecular e Funcional, Instituto Nacional de Ciência e Tecnologia em Tuberculose, Porto Alegre, RS, Brasil.,Pontifícia Universidade Católica do Rio Grande do Sul, Programa de Pós-Graduação em Biologia Celular e Molecular, Porto Alegre, RS, Brasil
| | - Zilpa Adriana Sánchez-Quitian
- Pontifícia Universidade Católica do Rio Grande do Sul, Centro de Pesquisas em Biologia Molecular e Funcional, Instituto Nacional de Ciência e Tecnologia em Tuberculose, Porto Alegre, RS, Brasil.,Pontifícia Universidade Católica do Rio Grande do Sul, Programa de Pós-Graduação em Biologia Celular e Molecular, Porto Alegre, RS, Brasil
| | - Paula Eichler
- Pontifícia Universidade Católica do Rio Grande do Sul, Centro de Pesquisas em Biologia Molecular e Funcional, Instituto Nacional de Ciência e Tecnologia em Tuberculose, Porto Alegre, RS, Brasil
| | - Cristiano Valim Bizarro
- Pontifícia Universidade Católica do Rio Grande do Sul, Centro de Pesquisas em Biologia Molecular e Funcional, Instituto Nacional de Ciência e Tecnologia em Tuberculose, Porto Alegre, RS, Brasil.,Pontifícia Universidade Católica do Rio Grande do Sul, Programa de Pós-Graduação em Biologia Celular e Molecular, Porto Alegre, RS, Brasil
| | - Luiz Augusto Basso
- Pontifícia Universidade Católica do Rio Grande do Sul, Centro de Pesquisas em Biologia Molecular e Funcional, Instituto Nacional de Ciência e Tecnologia em Tuberculose, Porto Alegre, RS, Brasil.,Pontifícia Universidade Católica do Rio Grande do Sul, Programa de Pós-Graduação em Biologia Celular e Molecular, Porto Alegre, RS, Brasil.,Pontifícia Universidade Católica do Rio Grande do Sul, Programa de Pós-Graduação em Medicina e Ciências da Saúde, Porto Alegre, RS, Brasil
| | - Diógenes Santiago Santos
- Pontifícia Universidade Católica do Rio Grande do Sul, Centro de Pesquisas em Biologia Molecular e Funcional, Instituto Nacional de Ciência e Tecnologia em Tuberculose, Porto Alegre, RS, Brasil.,Pontifícia Universidade Católica do Rio Grande do Sul, Programa de Pós-Graduação em Biologia Celular e Molecular, Porto Alegre, RS, Brasil
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42
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Gregoire SA, Byam J, Pavelka MS. galK-based suicide vector mediated allelic exchange in Mycobacterium abscessus. MICROBIOLOGY-SGM 2017; 163:1399-1408. [PMID: 28933689 DOI: 10.1099/mic.0.000528] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Mycobacterium abscessus is a fast-growing environmental organism and an important emerging pathogen. It is highly resistant to many antibiotics and undergoes a smooth to rough colony morphology change that appears to be important for pathogenesis. Smooth environmental strains have a glycopeptidolipid (GPL) on the surface, while certain types of clinical strains are often rough and lack this GPL, due to mutations in biosynthetic genes or the mmpL4b transporter gene. We report here the development and evaluation of an allelic exchange system for unmarked alleles in M. abscessus ATCC19977, using a suicide vector bearing the E. coli galK gene and 2-deoxygalactose counterselection. We describe here two variant galK suicide vectors, and demonstrate their utility in constructing a variety of mutants with deletion alleles of the mmpL4b GPL transporter gene, the mbtH GPL biosynthesis gene, the known β-lactamase gene MAB_2875 and a putative β-lactamase gene, MAB_2833. We also show that a novel allele of the E. coli aacC4 gene, conferring apramycin resistance (aacC41), can be used as a selectable marker in M. abscessus ATCC19977 at single copy.
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Affiliation(s)
- Stacy A Gregoire
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Joel Byam
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Martin S Pavelka
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA
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A Novel Calcium Uptake Transporter of Uncharacterized P-Type ATPase Family Supplies Calcium for Cell Surface Integrity in Mycobacterium smegmatis. mBio 2017; 8:mBio.01388-17. [PMID: 28951477 PMCID: PMC5615198 DOI: 10.1128/mbio.01388-17] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ca2+ plays an important role in the physiology of bacteria. Intracellular Ca2+ concentrations are tightly maintained in the nanomolar range. Molecular mechanisms of Ca2+ uptake in bacteria remain elusive. Here we show that CtpE is responsible for Ca2+ uptake in Mycobacterium smegmatis. It represents a previously uncharacterized P-type ATPase family in bacteria. Disruption of ctpE in M. smegmatis resulted in a mutant with impaired growth under Ca2+-deficient conditions. The growth defect of the mutant could be rescued by Ca2+ or by ectopic expression of ctpE from M. smegmatis or the orthologous gene (Rv0908) from Mycobacterium tuberculosis H37Rv. Radioactive transport assays revealed that CtpE is a Ca2+-specific transporter. Ca2+ deficiency increased expression of ctpE, resulting in increased 45Ca2+ accumulation in cells. ctpE is a gene that is part of an operon, which is negatively regulated by Ca2+. The ctpE mutant also showed hypersensitivity to polymyxin B, increased biofilm formation, and higher cell aggregation, indicating cell envelope defects. Our work establishes, for the first time, the presence of Ca2+ uptake pumps of the energy-dependent P-type ATPase superfamily in bacteria and also implicates that intracellular Ca2+ is essential for growth and cell envelope integrity in M. smegmatis. Ca2+ is essential for gene regulation, enzymatic activity, and maintenance of structural integrity of cell walls in bacteria. Bacteria maintain intracellular calcium concentrations in a narrow range, creating a gradient with low cytoplasmic calcium concentration and high extracellular calcium concentration. Due to this steep gradient, active pumps belonging to family 2 of P-type ATPases and antiporters are used for Ca2+ efflux, whereas Ca2+ uptake is usually carried out by channels. Molecular mechanisms of Ca2+ uptake in bacteria are still elusive and are mainly limited to a nonproteinaceous channel in Escherichia coli and a pH-dependent channel protein from Bacillus subtilis. Energy-dependent active transporters are not reported for Ca2+ uptake from any organism. Here we show that CtpE belonging to a family of previously uncharacterized bacterial P-type ATPases is involved in specific uptake of Ca2+ into Mycobacterium smegmatis. We also demonstrate that intracellular Ca2+ obtained through CtpE is essential for growth and maintenance of cell surface properties under Ca2+-deficient conditions.
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Villela AD, Rodrigues VDS, Pinto AFM, Wink PL, Sánchez-Quitian ZA, Petersen GO, Campos MM, Basso LA, Santos DS. Characterisation of iunH gene knockout strain from Mycobacterium tuberculosis. Mem Inst Oswaldo Cruz 2017; 112:203-208. [PMID: 28225907 PMCID: PMC5319374 DOI: 10.1590/0074-02760160462] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 12/02/2016] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Tuberculosis (TB) is an infectious disease caused mainly by the bacillus Mycobacterium tuberculosis. The better understanding of important metabolic pathways from M. tuberculosis can contribute to the development of novel therapeutic and prophylactic strategies to combat TB. Nucleoside hydrolase (MtIAGU-NH), encoded by iunH gene (Rv3393), is an enzyme from purine salvage pathway in M. tuberculosis. MtIAGU-NH accepts inosine, adenosine, guanosine, and uridine as substrates, which may point to a pivotal metabolic role. OBJECTIVES Our aim was to construct a M. tuberculosis knockout strain for iunH gene, to evaluate in vitro growth and the effect of iunH deletion in M. tuberculosis in non-activated and activated macrophages models of infection. METHODS A M. tuberculosis knockout strain for iunH gene was obtained by allelic replacement, using pPR27xylE plasmid. The complemented strain was constructed by the transformation of the knockout strain with pNIP40::iunH. MtIAGU-NH expression was analysed by Western blot and LC-MS/MS. In vitro growth was evaluated in Sauton’s medium. Bacterial load of non-activated and interferon-γ activated RAW 264.7 cells infected with knockout strain was compared with wild-type and complemented strains. FINDINGS Western blot and LC-MS/MS validated iunH deletion at protein level. The iunH knockout led to a delay in M. tuberculosis growth kinetics in Sauton’s medium during log phase, but did not affect bases and nucleosides pool in vitro. No significant difference in bacterial load of knockout strain was observed when compared with both wild-type and complemented strains after infection of non-activated and interferon-γ activated RAW 264.7 cells. MAIN CONCLUSION The disruption of iunH gene does not influence M. tuberculosis growth in both non-activated and activated RAW 264.7 cells, which show that iunH gene is not important for macrophage invasion and virulence. Our results indicated that MtIAGU-NH is not a target for drug development.
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Affiliation(s)
- Anne Drumond Villela
- Pontifícia Universidade Católica do Rio Grande do Sul, Centro de Pesquisas em Biologia Molecular e Funcional, Instituto Nacional de Ciência e Tecnologia em Tuberculose, Porto Alegre, RS, Brasil
| | - Valnês da Silva Rodrigues
- Pontifícia Universidade Católica do Rio Grande do Sul, Centro de Pesquisas em Biologia Molecular e Funcional, Instituto Nacional de Ciência e Tecnologia em Tuberculose, Porto Alegre, RS, Brasil.,Pontifícia Universidade Católica do Rio Grande do Sul, Programa de Pós-Graduação em Medicina e Ciências da Saúde, Porto Alegre, RS, Brasil.,Pontifícia Universidade Católica do Rio Grande do Sul, Instituto de Toxicologia e Farmacologia, Porto Alegre, RS, Brasil
| | - Antônio Frederico Michel Pinto
- Pontifícia Universidade Católica do Rio Grande do Sul, Centro de Pesquisas em Biologia Molecular e Funcional, Instituto Nacional de Ciência e Tecnologia em Tuberculose, Porto Alegre, RS, Brasil
| | - Priscila Lamb Wink
- Pontifícia Universidade Católica do Rio Grande do Sul, Centro de Pesquisas em Biologia Molecular e Funcional, Instituto Nacional de Ciência e Tecnologia em Tuberculose, Porto Alegre, RS, Brasil.,Pontifícia Universidade Católica do Rio Grande do Sul, Programa de Pós-Graduação em Biologia Celular e Molecular, Porto Alegre, RS, Brasil
| | - Zilpa Adriana Sánchez-Quitian
- Pontifícia Universidade Católica do Rio Grande do Sul, Centro de Pesquisas em Biologia Molecular e Funcional, Instituto Nacional de Ciência e Tecnologia em Tuberculose, Porto Alegre, RS, Brasil.,Pontifícia Universidade Católica do Rio Grande do Sul, Programa de Pós-Graduação em Biologia Celular e Molecular, Porto Alegre, RS, Brasil
| | - Guilherme Oliveira Petersen
- Pontifícia Universidade Católica do Rio Grande do Sul, Centro de Pesquisas em Biologia Molecular e Funcional, Instituto Nacional de Ciência e Tecnologia em Tuberculose, Porto Alegre, RS, Brasil
| | - Maria Martha Campos
- Pontifícia Universidade Católica do Rio Grande do Sul, Programa de Pós-Graduação em Medicina e Ciências da Saúde, Porto Alegre, RS, Brasil.,Pontifícia Universidade Católica do Rio Grande do Sul, Instituto de Toxicologia e Farmacologia, Porto Alegre, RS, Brasil.,Pontifícia Universidade Católica do Rio Grande do Sul, Programa de Pós-Graduação em Biologia Celular e Molecular, Porto Alegre, RS, Brasil
| | - Luiz Augusto Basso
- Pontifícia Universidade Católica do Rio Grande do Sul, Centro de Pesquisas em Biologia Molecular e Funcional, Instituto Nacional de Ciência e Tecnologia em Tuberculose, Porto Alegre, RS, Brasil.,Pontifícia Universidade Católica do Rio Grande do Sul, Programa de Pós-Graduação em Medicina e Ciências da Saúde, Porto Alegre, RS, Brasil.,Pontifícia Universidade Católica do Rio Grande do Sul, Programa de Pós-Graduação em Biologia Celular e Molecular, Porto Alegre, RS, Brasil
| | - Diógenes Santiago Santos
- Pontifícia Universidade Católica do Rio Grande do Sul, Centro de Pesquisas em Biologia Molecular e Funcional, Instituto Nacional de Ciência e Tecnologia em Tuberculose, Porto Alegre, RS, Brasil.,Pontifícia Universidade Católica do Rio Grande do Sul, Programa de Pós-Graduação em Biologia Celular e Molecular, Porto Alegre, RS, Brasil
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Rv3852 (H-NS) of Mycobacterium tuberculosis Is Not Involved in Nucleoid Compaction and Virulence Regulation. J Bacteriol 2017; 199:JB.00129-17. [PMID: 28559300 DOI: 10.1128/jb.00129-17] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 05/25/2017] [Indexed: 02/05/2023] Open
Abstract
A handful of nucleoid-associated proteins (NAPs) regulate the vast majority of genes in a bacterial cell. H-NS, the histone-like nucleoid-structuring protein, is one of these NAPs and protects Escherichia coli from foreign gene expression. Though lacking any sequence similarity with E. coli H-NS, Rv3852 was annotated as the H-NS ortholog in Mycobacterium tuberculosis, as it resembles human histone H1. The role of Rv3852 was thoroughly investigated by immunoblotting, subcellular localization, construction of an unmarked rv3852 deletion in the M. tuberculosis genome, and subsequent analysis of the resulting Δrv3852 strain. We found that Rv3852 was predominantly present in the logarithmic growth phase with a decrease in protein abundance in stationary phase. Furthermore, it was strongly associated with the cell membrane and not detected in the cytosolic fraction, nor was it secreted. The Δrv3852 strain displayed no growth defect or morphological abnormalities. Quantitative measurement of nucleoid localization in the Δrv3852 mutant strain compared to that in the parental H37Rv strain showed no difference in nucleoid position or spread. Infection of macrophages as well as severe combined immunodeficient (SCID) mice demonstrated that loss of Rv3852 had no detected influence on the virulence of M. tuberculosis We thus conclude that M. tuberculosis Rv3852 is not involved in pathogenesis and is not a typical NAP. The existence of an as yet undiscovered Rv3852 ortholog cannot be excluded, although this role is likely played by the well-characterized Lsr2 protein.IMPORTANCEMycobacterium tuberculosis is the causative agent of the lung infection tuberculosis, claiming more than 1.5 million lives each year. To understand the mechanisms of latent infection, where M. tuberculosis can stay dormant inside the human host, we require deeper knowledge of the basic biology and of the regulatory networks. In our work, we show that Rv3852, previously annotated as H-NS, is not a typical nucleoid-associated protein (NAP) as expected from its initial annotation. Rv3852 from M. tuberculosis has neither influence on nucleoid shape or compaction nor a role in virulence. Our findings reduce the repertoire of identified nucleoid-associated proteins in M. tuberculosis to four transcription regulators and underline the importance of genetic studies to assign a function to bacterial genes.
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Mugweru J, Makafe G, Cao Y, Zhang Y, Wang B, Huang S, Njire M, Chhotaray C, Tan Y, Li X, Liu J, Tan S, Deng J, Zhang T. A Cassette Containing Thiostrepton, Gentamicin Resistance Genes, and dif sequences Is Effective in Construction of Recombinant Mycobacteria. Front Microbiol 2017; 8:468. [PMID: 28392781 PMCID: PMC5364183 DOI: 10.3389/fmicb.2017.00468] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 03/07/2017] [Indexed: 11/24/2022] Open
Abstract
The genetic manipulation of Mycobacterium tuberculosis genome is limited by the availability of selection markers. Spontaneous resistance mutation rate of M. tuberculosis to the widely used kanamycin is relatively high which often leads to some false positive transformants. Due to the few available markers, we have created a cassette containing thiostrepton resistance gene (tsr) for selection in M. tuberculosis and M. bovis BCG, and gentamicin resistance gene (aacC1) for Escherichia coli and M. smegmatis mc2155, flanked with dif sequences recognized by the Xer system of mycobacteria. This cassette adds to the limited available selection markers for mycobacteria.
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Affiliation(s)
- Julius Mugweru
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of SciencesGuangzhou, China
- University of Chinese Academy of SciencesBeijing, China
| | - Gaelle Makafe
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of SciencesGuangzhou, China
- University of Chinese Academy of SciencesBeijing, China
| | - Yuanyuan Cao
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of SciencesGuangzhou, China
| | - Yang Zhang
- Key Laboratory of Biotechnology of Antibiotics, Ministry of Health, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing, China
| | - Bangxing Wang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of SciencesGuangzhou, China
| | - Shaobo Huang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of SciencesGuangzhou, China
| | - Moses Njire
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of SciencesGuangzhou, China
- University of Chinese Academy of SciencesBeijing, China
| | - Chiranjibi Chhotaray
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of SciencesGuangzhou, China
- University of Chinese Academy of SciencesBeijing, China
| | - Yaoju Tan
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, Guangzhou Chest HospitalGuangzhou, China
| | - Xinjie Li
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, Guangzhou Chest HospitalGuangzhou, China
| | - Jianxiong Liu
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, Guangzhou Chest HospitalGuangzhou, China
| | - Shouyong Tan
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, Guangzhou Chest HospitalGuangzhou, China
| | - Jiaoyu Deng
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of SciencesWuhan, China
| | - Tianyu Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of SciencesGuangzhou, China
- University of Chinese Academy of SciencesBeijing, China
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Otal I, Pérez-Herrán E, Garcia-Morales L, Menéndez MC, Gonzalez-Y-Merchand JA, Martín C, García MJ. Detection of a Putative TetR-Like Gene Related to Mycobacterium bovis BCG Growth in Cholesterol Using a gfp-Transposon Mutagenesis System. Front Microbiol 2017; 8:315. [PMID: 28321208 PMCID: PMC5337628 DOI: 10.3389/fmicb.2017.00315] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 02/15/2017] [Indexed: 11/13/2022] Open
Abstract
In vitro transposition is a powerful genetic tool for identifying mycobacterial virulence genes and studying virulence factors in relation to the host. Transposon shuttle mutagenesis is a method for constructing stable insertions in the genome of different microorganisms including mycobacteria. Using an IS1096 derivative, we have constructed the Tngfp, a transposon containing a promoterless green fluorescent protein (gfp) gene. This transposon was able to transpose randomly in Mycobacterium bovis BCG. Bacteria with a single copy of the gfp gene per chromosome from an M. bovis BCG::Tngfp library were analyzed and cells exhibiting high levels of fluorescence were detected by flow cytometry. Application of this approach allowed for the selection of a mutant, BCG_2177c::Tngfp (BCG-Tn), on the basis of high level of long-standing fluorescence at stationary phase. This BCG-Tn mutant showed some particular phenotypic features compared to the wild type strain, mainly during stationary phase, when cholesterol was used as a sole carbon source, thus supporting the relationships of the targeted gene with the regulation of cholesterol metabolism in this bacteria. This approach showed that Tngfp is a potentially useful tool for studying the involvement of the targeted loci in metabolic pathways of mycobacteria.
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Affiliation(s)
- Isabel Otal
- Grupo de Genética de Micobacterias, Departamento de Microbiologia, Medicina Preventiva y Salud Pública, Universidad de ZaragozaZaragoza, Spain; Centros de Investigación Biomédica en Red Enfermedades Respiratorias, Instituto de Salud Carlos IIIMadrid, Spain; Instituto de Investigación Sanitaria AragónZaragoza, Spain
| | - Esther Pérez-Herrán
- Grupo de Genética de Micobacterias, Departamento de Microbiologia, Medicina Preventiva y Salud Pública, Universidad de ZaragozaZaragoza, Spain; Diseases of the Developing World, GlaxoSmithKlineTres Cantos, Spain
| | - Lazaro Garcia-Morales
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional Ciudad de Mexico, Mexico
| | - María C Menéndez
- Departamento de Medicina Preventiva, Universidad Autónoma Madrid, Spain
| | - Jorge A Gonzalez-Y-Merchand
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional Ciudad de Mexico, Mexico
| | - Carlos Martín
- Grupo de Genética de Micobacterias, Departamento de Microbiologia, Medicina Preventiva y Salud Pública, Universidad de ZaragozaZaragoza, Spain; Centros de Investigación Biomédica en Red Enfermedades Respiratorias, Instituto de Salud Carlos IIIMadrid, Spain; Instituto de Investigación Sanitaria AragónZaragoza, Spain
| | - María J García
- Departamento de Medicina Preventiva, Universidad Autónoma Madrid, Spain
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Falcão VCA, Villela AD, Rodrigues-Junior VS, Pissinate K, Eichler P, Pinto AFM, Basso LA, Santos DS, Bizarro CV. Validation of Mycobacterium tuberculosis dihydroneopterin aldolase as a molecular target for anti-tuberculosis drug development. Biochem Biophys Res Commun 2017; 485:814-819. [PMID: 28257847 DOI: 10.1016/j.bbrc.2017.02.137] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 02/27/2017] [Indexed: 12/17/2022]
Abstract
An early step of target validation in antimicrobial drug discovery is to prove that a gene coding for a putative target is essential for pathogen's viability. However, little attention has been paid to demonstrate the causal links between gene essentiality and a particular protein function that will be the focus of a drug discovery effort. This should be considered an important step in target validation since a growing number of proteins are found to exhibit multiple and unrelated tasks. Here, we show that the Mycobacterium tuberculosis (Mtb) folB gene is essential and that this essentiality depends on the dihydroneopterin aldolase/epimerase activities of its protein product, the FolB protein from the folate biosynthesis pathway. The wild-type (WT) MtFolB and point mutants K99A and Y54F were cloned, expressed, purified and monitored for the aldolase, epimerase and oxygenase activities using HPLC. In contrast to the WT MtFolB, both mutants have neither aldolase nor epimerase activities in the conditions assayed. We then performed gene knockout experiments and showed that folB gene is essential for Mtb survival under the conditions tested. Moreover, only the WT folB sequence could be used as a rescue copy in gene complementation studies. When the sequences of mutants K99A or Y54F were used for complementation, no viable colonies were obtained, indicating that aldolase and/or epimerase activities are crucial for Mtb survival. These results provide a solid basis for further work aiming to develop new anti-TB agents acting as inhibitors of the aldolase/epimerase activities of MtFolB.
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Affiliation(s)
- V C A Falcão
- Instituto Nacional de Ciência e Tecnologia em Tuberculose, Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Brazil; Programa de Pós-Graduação em Biologia Celular e Molecular (PUCRS), Brazil
| | - A D Villela
- Instituto Nacional de Ciência e Tecnologia em Tuberculose, Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Brazil; Programa de Pós-Graduação em Medicina e Ciências da Saúde (PUCRS), Porto Alegre, RS, Brazil
| | - V S Rodrigues-Junior
- Instituto Nacional de Ciência e Tecnologia em Tuberculose, Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Brazil; Programa de Pós-Graduação em Medicina e Ciências da Saúde (PUCRS), Porto Alegre, RS, Brazil
| | - K Pissinate
- Instituto Nacional de Ciência e Tecnologia em Tuberculose, Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Brazil
| | - P Eichler
- Instituto Nacional de Ciência e Tecnologia em Tuberculose, Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Brazil
| | - A F M Pinto
- Instituto Nacional de Ciência e Tecnologia em Tuberculose, Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Brazil
| | - L A Basso
- Instituto Nacional de Ciência e Tecnologia em Tuberculose, Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Brazil; Programa de Pós-Graduação em Biologia Celular e Molecular (PUCRS), Brazil; Programa de Pós-Graduação em Medicina e Ciências da Saúde (PUCRS), Porto Alegre, RS, Brazil
| | - D S Santos
- Instituto Nacional de Ciência e Tecnologia em Tuberculose, Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Brazil; Programa de Pós-Graduação em Biologia Celular e Molecular (PUCRS), Brazil
| | - C V Bizarro
- Instituto Nacional de Ciência e Tecnologia em Tuberculose, Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Brazil; Programa de Pós-Graduação em Biologia Celular e Molecular (PUCRS), Brazil.
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Unique Regulation of the DosR Regulon in the Beijing Lineage of Mycobacterium tuberculosis. J Bacteriol 2016; 199:JB.00696-16. [PMID: 27799329 DOI: 10.1128/jb.00696-16] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 10/25/2016] [Indexed: 12/11/2022] Open
Abstract
The DosR regulon, a set of 48 genes normally expressed in Mycobacterium tuberculosis under conditions that inhibit aerobic respiration, is controlled via the DosR-DosS/DosT two-component system. While the regulon requires induction in most M. tuberculosis isolates, for members of the Beijing lineage, its expression is uncoupled from the need for signaling. In our attempts to understand the mechanistic basis for this uncoupling in the Beijing background, we previously reported the identification of two synonymous single-nucleotide polymorphisms (SNPs) within the adjacent Rv3134c gene. In the present study, we have interrogated the impact of these SNPs on dosR expression in wild-type strains, as well as a range of dosR-dosS-dosT mutants, for both Beijing and non-Beijing M. tuberculosis backgrounds. In this manner, we have unequivocally determined that the C601T dosR promoter SNP is the sole requirement for the dramatic shift in the pattern of DosR regulon expression seen in this globally important lineage. Interestingly, we also show that DosT is completely nonfunctional within these strains. Thus, a complex series of evolutionary steps has led to the present-day Beijing DosR phenotype that, in turn, potentially confers a fitness advantage in the face of some form of host-associated selective pressure. IMPORTANCE Mycobacterium tuberculosis strains of the Beijing lineage have been described as being of enhanced virulence compared to other lineages, and in certain regions, they are associated with the dramatic spread of multidrug-resistant tuberculosis (TB). In terms of trying to understand the functional basis for these broad epidemiological phenomena, it is interesting that, in contrast to the other major lineages, the Beijing strains all constitutively overexpress members of the DosR regulon. Here, we identify the mutational events that led to the evolution of this unique phenotype. In addition, our work highlights the fact that important phenotypic differences exist between distinct M. tuberculosis lineages, with the potential to impact the efficacy of diagnosis, vaccination, and treatment programs.
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Petridis M, Vickers C, Robson J, McKenzie JL, Bereza M, Sharrock A, Aung HL, Arcus VL, Cook GM. Structure and Function of AmtR in Mycobacterium smegmatis: Implications for Post-Transcriptional Regulation of Urea Metabolism through a Small Antisense RNA. J Mol Biol 2016; 428:4315-4329. [PMID: 27640309 DOI: 10.1016/j.jmb.2016.09.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2016] [Revised: 09/02/2016] [Accepted: 09/07/2016] [Indexed: 01/19/2023]
Abstract
Soil-dwelling bacteria of the phylum actinomycetes generally harbor either GlnR or AmtR as a global regulator of nitrogen metabolism. Mycobacterium smegmatis harbors both of these canonical regulators; GlnR regulates the expression of key genes involved in nitrogen metabolism, while the function and signal transduction pathway of AmtR in M. smegmatis remains largely unknown. Here, we report the structure and function of the M. smegmatis AmtR and describe the role of AmtR in the regulation of nitrogen metabolism in response to nitrogen availability. To determine the function of AmtR in M. smegmatis, we performed genome-wide expression profiling comparing the wild-type versus an ∆amtR mutant and identified significant changes in the expression of 11 genes, including an operon involved in urea degradation. An AmtR consensus-binding motif (CTGTC-N4-GACAG) was identified in the promoter region of this operon, and ligand-independent, high-affinity AmtR binding was validated by both electrophoretic mobility shift assays and surface plasmon resonance measurements. We confirmed the transcription of a cis-encoded small RNA complementary to the gene encoding AmtR under nitrogen excess, and we propose a post-transcriptional regulatory mechanism for AmtR. The three-dimensional X-ray structure of AmtR at 2.0Å revealed an overall TetR-like dimeric structure, and the alignment of the M. smegmatis AmtR and Corynebacterium glutamicum AmtR regulatory domains showed poor structural conservation, providing a potential explanation for the lack of M. smegmatis AmtR interaction with the adenylylated PII protein. Taken together, our data suggest an AmtR (repressor)/GlnR (activator) competitive binding mechanism for transcriptional regulation of urea metabolism that is controlled by a cis-encoded small antisense RNA.
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Affiliation(s)
- Michael Petridis
- Department of Microbiology and Immunology, Otago School of Medical Sciences, University of Otago, Dunedin 9054, New Zealand.
| | - Chelsea Vickers
- Department of Biological Sciences, University of Waikato, Hamilton 3240, New Zealand.
| | - Jennifer Robson
- Department of Microbiology and Immunology, Otago School of Medical Sciences, University of Otago, Dunedin 9054, New Zealand.
| | - Joanna L McKenzie
- Department of Biological Sciences, University of Waikato, Hamilton 3240, New Zealand.
| | - Magdalena Bereza
- Department of Biological Sciences, University of Waikato, Hamilton 3240, New Zealand.
| | - Abigail Sharrock
- Department of Biological Sciences, University of Waikato, Hamilton 3240, New Zealand.
| | - Htin Lin Aung
- Department of Microbiology and Immunology, Otago School of Medical Sciences, University of Otago, Dunedin 9054, New Zealand.
| | - Vickery L Arcus
- Department of Biological Sciences, University of Waikato, Hamilton 3240, New Zealand.
| | - Gregory M Cook
- Department of Microbiology and Immunology, Otago School of Medical Sciences, University of Otago, Dunedin 9054, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Auckland 1042, New Zealand.
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