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Simcox BS, Rohde KH. Orphan response regulator NnaR is critical for nitrate and nitrite assimilation in Mycobacterium abscessus. Front Cell Infect Microbiol 2024; 14:1411333. [PMID: 38854658 PMCID: PMC11162112 DOI: 10.3389/fcimb.2024.1411333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 05/10/2024] [Indexed: 06/11/2024] Open
Abstract
Mycobacterium abscessus (Mab) is an opportunistic pathogen afflicting individuals with underlying lung disease such as Cystic Fibrosis (CF) or immunodeficiencies. Current treatment strategies for Mab infections are limited by its inherent antibiotic resistance and limited drug access to Mab in its in vivo niches resulting in poor cure rates of 30-50%. Mab's ability to survive within macrophages, granulomas and the mucus laden airways of the CF lung requires adaptation via transcriptional remodeling to counteract stresses like hypoxia, increased levels of nitrate, nitrite, and reactive nitrogen intermediates. Mycobacterium tuberculosis (Mtb) is known to coordinate hypoxic adaptation via induction of respiratory nitrate assimilation through the nitrate reductase narGHJI. Mab, on the other hand, does not encode a respiratory nitrate reductase. In addition, our recent study of the transcriptional responses of Mab to hypoxia revealed marked down-regulation of a locus containing putative nitrate assimilation genes, including the orphan response regulator nnaR (nitrate/nitrite assimilation regulator). These putative nitrate assimilation genes, narK3 (nitrate/nitrite transporter), nirBD (nitrite reductase), nnaR, and sirB (ferrochelatase) are arranged contiguously while nasN (assimilatory nitrate reductase identified in this work) is encoded in a different locus. Absence of a respiratory nitrate reductase in Mab and down-regulation of nitrogen metabolism genes in hypoxia suggest interplay between hypoxia adaptation and nitrate assimilation are distinct from what was previously documented in Mtb. The mechanisms used by Mab to fine-tune the transcriptional regulation of nitrogen metabolism in the context of stresses e.g. hypoxia, particularly the role of NnaR, remain poorly understood. To evaluate the role of NnaR in nitrate metabolism we constructed a Mab nnaR knockout strain (MabΔnnaR ) and complement (MabΔnnaR+C ) to investigate transcriptional regulation and phenotypes. qRT-PCR revealed NnaR is necessary for regulating nitrate and nitrite reductases along with a putative nitrate transporter. Loss of NnaR compromised the ability of Mab to assimilate nitrate or nitrite as sole nitrogen sources highlighting its necessity. This work provides the first insights into the role of Mab NnaR setting a foundation for future work investigating NnaR's contribution to pathogenesis.
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Affiliation(s)
| | - Kyle H. Rohde
- Division of Immunity and Pathogenesis, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, United States
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Ensinck D, Gerhardt ECM, Rollan L, Huergo LF, Gramajo H, Diacovich L. The PII protein interacts with the Amt ammonium transport and modulates nitrate/nitrite assimilation in mycobacteria. Front Microbiol 2024; 15:1366111. [PMID: 38591044 PMCID: PMC11001197 DOI: 10.3389/fmicb.2024.1366111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 03/04/2024] [Indexed: 04/10/2024] Open
Abstract
PII proteins are signal transduction proteins that belong to a widely distributed family of proteins involved in the modulation of different metabolisms in bacteria. These proteins are homotrimers carrying a flexible loop, named T-loop, which changes its conformation due to the recognition of diverse key metabolites, ADP, ATP, and 2-oxoglutarate. PII proteins interact with different partners to primarily regulate a set of nitrogen pathways. In some organisms, PII proteins can also control carbon metabolism by interacting with the biotin carboxyl carrier protein (BCCP), a key component of the acetyl-CoA carboxylase (ACC) enzyme complex, inhibiting its activity with the consequent reduction of fatty acid biosynthesis. Most bacteria contain at least two PII proteins, named GlnB and GlnK, with different regulatory roles. In mycobacteria, only one PII protein was identified, and the three-dimensional structure was solved, however, its physiological role is unknown. In this study we purified the Mycobacterium tuberculosis (M. tb) PII protein, named GlnB, and showed that it weakly interacts with the AccA3 protein, the α subunit shared by the three different, and essential, Acyl-CoA carboxylase complexes (ACCase 4, 5, and 6) present in M. tb. A M. smegmatis deletion mutant, ∆MsPII, exhibited a growth deficiency on nitrate and nitrite as unique nitrogen sources, and accumulated nitrite in the culture supernatant. In addition, M. tb PII protein was able to interact with the C-terminal domain of the ammonium transporter Amt establishing the ancestral role for this PII protein as a GlnK functioning protein.
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Affiliation(s)
- Delfina Ensinck
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Edileusa C. M. Gerhardt
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Lara Rollan
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Luciano F. Huergo
- Setor Litoral, Federal University of Paraná, Universidade Federal do Paraná (UFPR), Matinhos, Paraná, Brazil
- Graduated Program in Sciences-Biochemistry, Universidade Federal do Paraná (UFPR), Curitiba, Paraná, Brazil
| | - Hugo Gramajo
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Lautaro Diacovich
- 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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3
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Fan J, Jia Y, He S, Tan Z, Li A, Li J, Zhang Z, Li B, Chu H. GlnR activated transcription of nitrogen metabolic pathway genes facilitates biofilm formation by mycobacterium abscessus. Int J Antimicrob Agents 2024; 63:107025. [PMID: 37926271 DOI: 10.1016/j.ijantimicag.2023.107025] [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: 06/12/2023] [Revised: 10/10/2023] [Accepted: 10/31/2023] [Indexed: 11/07/2023]
Abstract
OBJECTIVES Nitrogen is indispensable for the synthesis of biomacromolecules. The correlation between nitrogen metabolism and Mycobacterium abscessus (M. abscessus) biofilm formation is unclear. This study constructed global nitrogen regulator gene GlnR (Mab_0744) knockout (ΔglnR) and complementation (ΔglnR::glnR) M. abscessus strains. METHODS Global nitrogen regulator gene glnR (Mab_0744) knockout (ΔglnR) and complementation (ΔglnR::glnR) M. abscessus strains were constructed. Sauton's medium was used to culture M. abscessus pellicle biofilm. To test the antibiotic susceptibility of pellicle biofilm, clarithromycin, amikacin, cefoxitin or imipenem was added to the medium under biofilms after 14 days of incubation. RT-qPCR and ChIP-qPCR were performed to analyse the transcriptional regulatory function of GlnR. RESULTS GlnR knockout decreased the growth rate of planktonic cells, reduced biofilm mass and wrinkle formation, and diminished the resistance of biofilms to antibiotics. However, the susceptibility of planktonic cells to antibiotics was not changed by glnR knockout. The growth rate of planktonic ΔglnR cells was accelerated by adding nitrogen sources to the medium; the addition of glutamine or sodium glutamate rescued ΔglnR biofilm morphology and resistance to amikacin, cefoxitin, clarithromycin and imipenem. GlnR bound the promoter region and activated the transcription of eight nitrogen metabolic pathway genes (i.e. glnA, amt, ansP, nirB, nirD, glnD, glnK and narK3), which are closely related to glutamine/glutamate biosynthesis and, thus, regulate biofilm formation. CONCLUSION This study provides insights into the mechanisms of M. abscessus biofilm formation and its resistance to antibiotics.
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Affiliation(s)
- Junsheng Fan
- Department of Respiratory and Critical Care Medicine, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China; School of Medicine, Tongji University, Shanghai, China
| | - Yaping Jia
- Department of Respiratory and Critical Care Medicine, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China; School of Medicine, Tongji University, Shanghai, China
| | - Siyuan He
- Department of Respiratory and Critical Care Medicine, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China; School of Medicine, Tongji University, Shanghai, China
| | - Zhili Tan
- Department of Respiratory and Critical Care Medicine, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China; School of Medicine, Tongji University, Shanghai, China
| | - Anqi Li
- Department of Respiratory and Critical Care Medicine, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China; School of Medicine, Tongji University, Shanghai, China
| | - Juan Li
- Department of Respiratory and Critical Care Medicine, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China; School of Medicine, Tongji University, Shanghai, China
| | - Zhemin Zhang
- Department of Respiratory and Critical Care Medicine, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China; School of Medicine, Tongji University, Shanghai, China
| | - Bing Li
- Department of Respiratory and Critical Care Medicine, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China; School of Medicine, Tongji University, Shanghai, China.
| | - Haiqing Chu
- Department of Respiratory and Critical Care Medicine, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China; School of Medicine, Tongji University, Shanghai, China; Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China.
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Zhao X, Song Y, Wang T, Hua C, Hu R, Shang Y, Shi H, Chen S. Glutamine synthetase and GlnR regulate nitrogen metabolism in Paenibacillus polymyxa WLY78. Appl Environ Microbiol 2023; 89:e0013923. [PMID: 37668407 PMCID: PMC10537745 DOI: 10.1128/aem.00139-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 07/12/2023] [Indexed: 09/06/2023] Open
Abstract
Paenibacillus polymyxa WLY78, a N2-fixing bacterium, has great potential use as a biofertilizer in agriculture. Recently, we have revealed that GlnR positively and negatively regulates the transcription of the nif (nitrogen fixation) operon (nifBHDKENXhesAnifV) in P. polymyxa WLY78 by binding to two loci of the nif promoter according to nitrogen availability. However, the regulatory mechanisms of nitrogen metabolism mediated by GlnR in the Paenibacillus genus remain unclear. In this study, we have revealed that glutamine synthetase (GS) and GlnR in P. polymyxa WLY78 play a key role in the regulation of nitrogen metabolism. P. polymyxa GS (encoded by glnA within glnRA) and GS1 (encoded by glnA1) belong to distinct groups: GSI-α and GSI-β. Both GS and GS1 have the enzyme activity to convert NH4+ and glutamate into glutamine, but only GS is involved in the repression by GlnR. GlnR represses transcription of glnRA under excess nitrogen, while it activates the expression of glnA1 under nitrogen limitation. GlnR simultaneously activates and represses the expression of amtBglnK and gcvH in response to nitrogen availability. Also, GlnR regulates the expression of nasA, nasD1D2, nasT, glnQHMP, and glnS. IMPORTANCE In this study, we have revealed that Paenibacillus polymyxa GlnR uses multiple mechanisms to regulate nitrogen metabolism. GlnR activates or represses or simultaneously activates and inhibits the transcription of nitrogen metabolism genes in response to nitrogen availability. The multiple regulation mechanisms employed by P. polymyxa GlnR are very different from Bacillus subtilis GlnR which represses nitrogen metabolism under excess nitrogen. Both GS encoded by glnA within the glnRA operon and GS1 encoded by glnA1 in P. polymyxa WLY78 are involved in ammonium assimilation, but only GS is required for regulating GlnR activity. The work not only provides significant insight into understanding the interplay of GlnR and GS in nitrogen metabolism but also provides guidance for improving nitrogen fixation efficiency by modulating nitrogen metabolism.
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Affiliation(s)
- Xiyun Zhao
- Key Laboratory of Soil Microbiology of Agriculture Ministry and College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yi Song
- Key Laboratory of Soil Microbiology of Agriculture Ministry and College of Biological Sciences, China Agricultural University, Beijing, China
| | - Tianshu Wang
- Key Laboratory of Soil Microbiology of Agriculture Ministry and College of Biological Sciences, China Agricultural University, Beijing, China
| | - Chongchong Hua
- Key Laboratory of Soil Microbiology of Agriculture Ministry and College of Biological Sciences, China Agricultural University, Beijing, China
| | - Rui Hu
- Key Laboratory of Soil Microbiology of Agriculture Ministry and College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yimin Shang
- Key Laboratory of Soil Microbiology of Agriculture Ministry and College of Biological Sciences, China Agricultural University, Beijing, China
| | - Haowen Shi
- Key Laboratory of Soil Microbiology of Agriculture Ministry and College of Biological Sciences, China Agricultural University, Beijing, China
| | - Sanfeng Chen
- Key Laboratory of Soil Microbiology of Agriculture Ministry and College of Biological Sciences, China Agricultural University, Beijing, China
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Shi J, Feng Z, Xu J, Li F, Zhang Y, Wen A, Wang F, Song Q, Wang L, Cui H, Tong S, Chen P, Zhu Y, Zhao G, Wang S, Feng Y, Lin W. Structural insights into the transcription activation mechanism of the global regulator GlnR from actinobacteria. Proc Natl Acad Sci U S A 2023; 120:e2300282120. [PMID: 37216560 PMCID: PMC10235972 DOI: 10.1073/pnas.2300282120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 04/27/2023] [Indexed: 05/24/2023] Open
Abstract
In actinobacteria, an OmpR/PhoB subfamily protein called GlnR acts as an orphan response regulator and globally coordinates the expression of genes responsible for nitrogen, carbon, and phosphate metabolism in actinobacteria. Although many researchers have attempted to elucidate the mechanisms of GlnR-dependent transcription activation, progress is impeded by lacking of an overall structure of GlnR-dependent transcription activation complex (GlnR-TAC). Here, we report a co-crystal structure of the C-terminal DNA-binding domain of GlnR (GlnR_DBD) in complex with its regulatory cis-element DNA and a cryo-EM structure of GlnR-TAC which comprises Mycobacterium tuberculosis RNA polymerase, GlnR, and a promoter containing four well-characterized conserved GlnR binding sites. These structures illustrate how four GlnR protomers coordinate to engage promoter DNA in a head-to-tail manner, with four N-terminal receiver domains of GlnR (GlnR-RECs) bridging GlnR_DBDs and the RNAP core enzyme. Structural analysis also unravels that GlnR-TAC is stabilized by complex protein-protein interactions between GlnR and the conserved β flap, σAR4, αCTD, and αNTD domains of RNAP, which are further confirmed by our biochemical assays. Taken together, these results reveal a global transcription activation mechanism for the master regulator GlnR and other OmpR/PhoB subfamily proteins and present a unique mode of bacterial transcription regulation.
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Affiliation(s)
- Jing Shi
- Department of Pathogen Biology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, 210023Nanjing, China
- Department of Biophysics, Zhejiang University School of Medicine, 310058Hangzhou, China
- Department of Infectious Disease of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, 310058Hangzhou, China
| | - Zhenzhen Feng
- Department of Pathogen Biology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, 210023Nanjing, China
| | - Juncao Xu
- Key Laboratory of Synthetic Biology, Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 200032Shanghai, China
| | - Fangfang Li
- Department of Pathogen Biology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, 210023Nanjing, China
| | - Yuqiong Zhang
- MOE Key Laboratory of Laser Life Science and Institute of Laser Life Science, College of Biophotonics, South China Normal University, 510631Guangzhou, Guangdong, China
- Guangdong Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, 510631Guangzhou, Guangdong, China
- Songshan Lake Materials Laboratory, 523808Dongguan, Guangdong, China
| | - Aijia Wen
- Department of Biophysics, Zhejiang University School of Medicine, 310058Hangzhou, China
- Department of Infectious Disease of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, 310058Hangzhou, China
| | - Fulin Wang
- Department of Pathogen Biology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, 210023Nanjing, China
| | - Qian Song
- Department of Pathogen Biology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, 210023Nanjing, China
| | - Lu Wang
- Department of Pathogen Biology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, 210023Nanjing, China
| | - Hong Cui
- Pasteurien College, Suzhou Medical College of Soochow University, Soochow University, 251000Soochow, China
| | - Shujuan Tong
- Department of Pathogen Biology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, 210023Nanjing, China
| | - Peiying Chen
- Department of Pathogen Biology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, 210023Nanjing, China
| | - Yejin Zhu
- Department of Pathogen Biology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, 210023Nanjing, China
| | - Guoping Zhao
- Key Laboratory of Synthetic Biology, Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 200032Shanghai, China
| | - Shuang Wang
- Songshan Lake Materials Laboratory, 523808Dongguan, Guangdong, China
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, 100190Beijing, China
| | - Yu Feng
- Department of Biophysics, Zhejiang University School of Medicine, 310058Hangzhou, China
- Department of Infectious Disease of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, 310058Hangzhou, China
| | - Wei Lin
- Department of Pathogen Biology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, 210023Nanjing, China
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai200237, China
- Nanjing Drum Tower Hospital Clinical College, Nanjing University of Chinese Medicine, 210023Nanjing, China
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He J, Kang X, Wu J, Shao Z, Zhang Z, Wu Y, Yuan H, Zhao G, Wang J. Transcriptional Self-Regulation of the Master Nitrogen Regulator GlnR in Mycobacteria. J Bacteriol 2023; 205:e0047922. [PMID: 36943048 PMCID: PMC10127674 DOI: 10.1128/jb.00479-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 02/27/2023] [Indexed: 03/23/2023] Open
Abstract
As a master nitrogen regulator in most actinomycetes, GlnR both governs central nitrogen metabolism and regulates many carbon, phosphate, and secondary metabolic pathways. To date, most studies have been focused on the GlnR regulon, while little is known about the transcriptional regulator for glnR itself. It has been observed that glnR transcription can be upregulated in Mycobacterium smegmatis under nitrogen-limited growth conditions; however, the detailed regulatory mechanism is still unclear. Here, we demonstrate that the glnR gene in M. smegmatis is transcriptionally activated by its product GlnR in response to nitrogen limitation. The precise GlnR binding site was successfully characterized in its promoter region using the electrophoretic mobility shift assay and the DNase I footprinting assay. Site mutagenesis and genetic analyses confirmed that the binding site was essential for in vivo self-activation of glnR transcription. Moreover, based on bioinformatic analyses, we discovered that most of the mycobacterial glnR promoter regions (144 out of 147) contain potential GlnR binding sites, and we subsequently proved that the purified M. smegmatis GlnR protein could specifically bind 16 promoter regions that represent 119 mycobacterial species, including Mycobacterium tuberculosis. Together, our findings not only elucidate the transcriptional self-regulation mechanism of glnR transcription in M. smegmatis but also indicate the ubiquity of the mechanism in other mycobacterial species. IMPORTANCE In actinomycetes, the nitrogen metabolism not only is essential for the construction of life macromolecules but also affects the biosynthesis of secondary metabolites and even virulence (e.g., Mycobacterium tuberculosis). The transcriptional regulation of genes involved in nitrogen metabolism has been thoroughly studied and involves the master nitrogen regulator GlnR. However, the transcriptional regulation of glnR itself remains elusive. Here, we demonstrated that GlnR functions as a transcriptional self-activator in response to nitrogen starvation in the fast-growing model Mycobacterium species Mycobacterium smegmatis. We further showed that this self-regulation mechanism could be widespread in other mycobacteria, which might be beneficial for those slow-growing mycobacteria to adapt to the nitrogen-starvation environments such as within human macrophages for M. tuberculosis.
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Affiliation(s)
- Juanmei He
- CAS Key Laboratory of Synthetic Biology, Centre of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xiaoman Kang
- CAS Key Laboratory of Synthetic Biology, Centre of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jiacheng Wu
- CAS Key Laboratory of Synthetic Biology, Centre of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Zhihui Shao
- CAS Key Laboratory of Synthetic Biology, Centre of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | | | - Yuqian Wu
- Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Hua Yuan
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Guoping Zhao
- CAS Key Laboratory of Synthetic Biology, Centre of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jin Wang
- Department of Clinical Laboratory, Shenzhen Second People’s Hospital & Institute of Translational Medicine/the First Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, China
- Guangdong Provincial Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People’s Hospital (Shenzhen Institute of Translational Medicine), Shenzhen, China
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von Rosen T, Keller LM, Weber-Ban E. Survival in Hostile Conditions: Pupylation and the Proteasome in Actinobacterial Stress Response Pathways. Front Mol Biosci 2021; 8:685757. [PMID: 34179091 PMCID: PMC8223512 DOI: 10.3389/fmolb.2021.685757] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 05/04/2021] [Indexed: 12/31/2022] Open
Abstract
Bacteria employ a multitude of strategies to cope with the challenges they face in their natural surroundings, be it as pathogens, commensals or free-living species in rapidly changing environments like soil. Mycobacteria and other Actinobacteria acquired proteasomal genes and evolved a post-translational, ubiquitin-like modification pathway called pupylation to support their survival under rapidly changing conditions and under stress. The proteasomal 20S core particle (20S CP) interacts with ring-shaped activators like the hexameric ATPase Mpa that recruits pupylated substrates. The proteasomal subunits, Mpa and pupylation enzymes are encoded in the so-called Pup-proteasome system (PPS) gene locus. Genes in this locus become vital for bacteria to survive during periods of stress. In the successful human pathogen Mycobacterium tuberculosis, the 20S CP is essential for survival in host macrophages. Other members of the PPS and proteasomal interactors are crucial for cellular homeostasis, for example during the DNA damage response, iron and copper regulation, and heat shock. The multiple pathways that the proteasome is involved in during different stress responses suggest that the PPS plays a vital role in bacterial protein quality control and adaptation to diverse challenging environments.
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Affiliation(s)
- Tatjana von Rosen
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Lena Ml Keller
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Eilika Weber-Ban
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
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Mallick I, Santucci P, Poncin I, Point V, Kremer L, Cavalier JF, Canaan S. Intrabacterial lipid inclusions in mycobacteria: unexpected key players in survival and pathogenesis? FEMS Microbiol Rev 2021; 45:6283747. [PMID: 34036305 DOI: 10.1093/femsre/fuab029] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 05/21/2021] [Indexed: 12/12/2022] Open
Abstract
Mycobacterial species, including Mycobacterium tuberculosis, rely on lipids to survive and chronically persist within their hosts. Upon infection, opportunistic and strict pathogenic mycobacteria exploit metabolic pathways to import and process host-derived free fatty acids, subsequently stored as triacylglycerols under the form of intrabacterial lipid inclusions (ILI). Under nutrient-limiting conditions, ILI constitute a critical source of energy that fuels the carbon requirements and maintain redox homeostasis, promoting bacterial survival for extensive periods of time. In addition to their basic metabolic functions, these organelles display multiple other biological properties, emphasizing their central role in the mycobacterial lifecycle. However, despite of their importance, the dynamics of ILI metabolism and their contribution to mycobacterial adaptation/survival in the context of infection has not been thoroughly documented. Herein, we provide an overview of the historical ILI discoveries, their characterization, and current knowledge regarding the micro-environmental stimuli conveying ILI formation, storage and degradation. We also review new biological systems to monitor the dynamics of ILI metabolism in extra- and intracellular mycobacteria and describe major molecular actors in triacylglycerol biosynthesis, maintenance and breakdown. Finally, emerging concepts regarding to the role of ILI in mycobacterial survival, persistence, reactivation, antibiotic susceptibility and inter-individual transmission are also discuss.
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Affiliation(s)
- Ivy Mallick
- Aix-Marseille Univ, CNRS, LISM, IMM FR3479, Marseille, France.,IHU Méditerranée Infection, Aix-Marseille Univ., Marseille, France
| | - Pierre Santucci
- Aix-Marseille Univ, CNRS, LISM, IMM FR3479, Marseille, France
| | - Isabelle Poncin
- Aix-Marseille Univ, CNRS, LISM, IMM FR3479, Marseille, France
| | - Vanessa Point
- Aix-Marseille Univ, CNRS, LISM, IMM FR3479, Marseille, France
| | - Laurent Kremer
- Institut de Recherche en Infectiologie de Montpellier (IRIM), CNRS, UMR 9004, Université de Montpellier, Montpellier, France.,IRIM, INSERM, Montpellier, France
| | | | - Stéphane Canaan
- Aix-Marseille Univ, CNRS, LISM, IMM FR3479, Marseille, France
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Ma H, Liu WB, Zhang XP, Hu HQ, Gu SD, Yuan H, Ye BC. GlnR-mediated regulation of KstR controls cholesterol catabolism in Mycobacterium smegmatis. Biotechnol Appl Biochem 2021; 69:1209-1216. [PMID: 34008246 DOI: 10.1002/bab.2197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 05/12/2021] [Indexed: 11/10/2022]
Abstract
Tuberculosis, caused by mycobacteria, continues to pose a substantial public health threat. Mycobacteria typically use cholesterol from the membranes of host macrophages as a carbon and energy source. Most genes that control cholesterol degradation are regulated by KstR, which is highly conserved in Mycobacterium tuberculosis and Mycobacterium smegmatis. Through bioinformatic analysis, we found a typical global nitrogen regulator (GlnR)-binding motif (CCGAC-AACAGT-GACAC) in the promoter region of kstR of M. smegmatis, and we determined its binding activity in vitro using electrophoretic mobility shift assays. Using RT-qPCR, we found that nine genes involved in side-chain or sterol-ring oxidation were upregulated in a ΔglnR M. smegmatis strain compared to the WT strain and glnR-complemented strains under nitrogen limitation. ATP assays in macrophages revealed that coordinated GlnR-KstR regulation significantly reduced the viability of M. smegmatis in macrophages. Thus, we found that various genes involved in cholesterol catabolism are regulated by GlnR via KstR in response to environmental nitrogen, and that they further affect the invasive ability of M. smegmatis. These findings revealed a novel regulatory mechanism of cholesterol catabolism, which may be useful in the development of new strategies for controlling tuberculosis.
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Affiliation(s)
- Heng Ma
- School of Chemistry and Chemical Engineering, Shihezi University, Xinjiang, China
| | - Wei-Bing Liu
- Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Xiao-Peng Zhang
- Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Hao-Qi Hu
- Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Sheng-Di Gu
- Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Hao Yuan
- Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Bang-Ce Ye
- School of Chemistry and Chemical Engineering, Shihezi University, Xinjiang, China.,Lab 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, Zhejiang, 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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Sousa EH, Carepo MS, Moura JJ. Nitrate-nitrite fate and oxygen sensing in dormant Mycobacterium tuberculosis: A bioinorganic approach highlighting the importance of transition metals. Coord Chem Rev 2020. [DOI: 10.1016/j.ccr.2020.213476] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
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12
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Cereijo AE, Kuhn ML, Hernández MA, Ballicora MA, Iglesias AA, Alvarez HM, Asencion Diez MD. Study of duplicated galU genes in Rhodococcus jostii and a putative new metabolic node for glucosamine-1P in rhodococci. Biochim Biophys Acta Gen Subj 2020; 1865:129727. [PMID: 32890704 DOI: 10.1016/j.bbagen.2020.129727] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 08/11/2020] [Accepted: 08/30/2020] [Indexed: 01/10/2023]
Abstract
BACKGOUND Studying enzymes that determine glucose-1P fate in carbohydrate metabolism is important to better understand microorganisms as biotechnological tools. One example ripe for discovery is the UDP-glucose pyrophosphorylase enzyme from Rhodococcus spp. In the R. jostii genome, this gene is duplicated, whereas R. fascians contains only one copy. METHODS We report the molecular cloning of galU genes from R. jostii and R. fascians to produce recombinant proteins RjoGalU1, RjoGalU2, and RfaGalU. Substrate saturation curves were conducted, kinetic parameters were obtained and the catalytic efficiency (kcat/Km) was used to analyze enzyme promiscuity. We also investigated the response of R. jostii GlmU pyrophosphorylase activity with different sugar-1Ps, which may compete for substrates with RjoGalU2. RESULTS All enzymes were active as pyrophosphorylases and exhibited substrate promiscuity toward sugar-1Ps. Remarkably, RjoGalU2 exhibited one order of magnitude higher activity with glucosamine-1P than glucose-1P, the canonical substrate. Glucosamine-1P activity was also significant in RfaGalU. The efficient use of the phospho-amino-sugar suggests the feasibility of the reaction to occur in vivo. Also, RjoGalU2 and RfaGalU represent enzymatic tools for the production of (amino)glucosyl precursors for the putative synthesis of novel molecules. CONCLUSIONS Results support the hypothesis that partitioning of glucosamine-1P includes an uncharacterized metabolic node in Rhodococcus spp., which could be important for producing diverse alternatives for carbohydrate metabolism in biotechnological applications. GENERAL SIGNIFICANCE Results presented here provide a model to study evolutionary enzyme promiscuity, which could be used as a tool to expand an organism's metabolic repertoire by incorporating non-canonical substrates into novel metabolic pathways.
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Affiliation(s)
- A E Cereijo
- Instituto de Agrobiotecnología del Litoral (UNL-CONICET), Facultad de Bioquímica y Ciencias Biológicas, CCT-Santa Fe, Colectora Ruta Nac 168 km 0, 3000 Santa Fe, Argentina
| | - M L Kuhn
- Department of Chemistry and Biochemistry, San Francisco State University, 1600 Holloway Ave., San Francisco, CA, United States
| | - M A Hernández
- Instituto de Biociencias de la Patagonia (INBIOP), Universidad Nacional de la Patagonia San Juan Bosco y CONICET, Km 4-Ciudad Universitaria 9000, Comodoro Rivadavia, Chubut, Argentina
| | - M A Ballicora
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1068 W. Sheridan Rd., Chicago, IL 60660, United States
| | - A A Iglesias
- Instituto de Agrobiotecnología del Litoral (UNL-CONICET), Facultad de Bioquímica y Ciencias Biológicas, CCT-Santa Fe, Colectora Ruta Nac 168 km 0, 3000 Santa Fe, Argentina
| | - H M Alvarez
- Instituto de Biociencias de la Patagonia (INBIOP), Universidad Nacional de la Patagonia San Juan Bosco y CONICET, Km 4-Ciudad Universitaria 9000, Comodoro Rivadavia, Chubut, Argentina.
| | - M D Asencion Diez
- Instituto de Agrobiotecnología del Litoral (UNL-CONICET), Facultad de Bioquímica y Ciencias Biológicas, CCT-Santa Fe, Colectora Ruta Nac 168 km 0, 3000 Santa Fe, Argentina.
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13
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GlnR Negatively Regulates Glutamate-Dependent Acid Resistance in Lactobacillus brevis. Appl Environ Microbiol 2020; 86:AEM.02615-19. [PMID: 31953336 DOI: 10.1128/aem.02615-19] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 01/08/2020] [Indexed: 11/20/2022] Open
Abstract
Lactic acid bacteria often encounter a variety of multiple stresses in their natural and industrial fermentation environments. The glutamate decarboxylase (GAD) system is one of the most important acid resistance systems in lactic acid bacteria. In this study, we demonstrated that GlnR, a nitrogen regulator in Gram-positive bacteria, directly modulated γ-aminobutyric acid (GABA) conversion from glutamate and was involved in glutamate-dependent acid resistance in Lactobacillus brevis The glnR deletion strain (ΔglnR mutant) achieved a titer of 284.7 g/liter GABA, which is 9.8-fold higher than that of the wild-type strain. The cell survival of the glnR deletion strain was significantly higher than that of the wild-type strain under the condition of acid challenge and was positively correlated with initial glutamate concentration and GABA production. Quantitative reverse transcription-PCR assays demonstrated that GlnR inhibited the transcription of the glutamate decarboxylase-encoding gene (gadB), glutamate/GABA antiporter-encoding gene (gadC), glutamine synthetase-encoding gene (glnA), and specific transcriptional regulator-encoding gene (gadR) involved in gadCB operon regulation. Moreover, GABA production and glutamate-dependent acid resistance were absolutely abolished in the gadR glnR deletion strain. Electrophoretic mobility shift and DNase I footprinting assays revealed that GlnR directly bound to the 5'-untranslated regions of the gadR gene and gadCB operon, thus inhibiting their transcription. These results revealed a novel regulatory mechanism of GlnR on glutamate-dependent acid resistance in Lactobacillus IMPORTANCE Free-living lactic acid bacteria often encounter acid stresses because of their organic acid-producing features. Several acid resistance mechanisms, such as the glutamate decarboxylase system, F1Fo-ATPase proton pump, and alkali production, are usually employed to relieve growth inhibition caused by acids. The glutamate decarboxylase system is vital for GAD-containing lactic acid bacteria to protect cells from DNA damage, enzyme inactivation, and product yield loss in acidic habitats. In this study, we found that a MerR-type regulator, GlnR, was involved in glutamate-dependent acid resistance by directly regulating the transcription of the gadR gene and gadCB operon, resulting in an inhibition of GABA conversion from glutamate in L. brevis This study represents a novel mechanism for GlnR's regulation of glutamate-dependent acid resistance and also provides a simple and novel strategy to engineer Lactobacillus strains to elevate their acid resistance as well as GABA conversion from glutamate.
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14
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Metabolic Switching of Mycobacterium tuberculosis during Hypoxia Is Controlled by the Virulence Regulator PhoP. J Bacteriol 2020; 202:JB.00705-19. [PMID: 31932312 DOI: 10.1128/jb.00705-19] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 01/06/2020] [Indexed: 11/20/2022] Open
Abstract
Mycobacterium tuberculosis retains the ability to establish an asymptomatic latent infection. A fundamental question in mycobacterial physiology is to understand the mechanisms involved in hypoxic stress, a critical player in persistence. Here, we show that the virulence regulator PhoP responds to hypoxia, the dormancy signal, and effectively integrates hypoxia with nitrogen metabolism. We also provide evidence to demonstrate that both under nitrogen limiting conditions and during hypoxia, phoP locus controls key genes involved in nitrogen metabolism. Consistently, under hypoxia a ΔphoP strain shows growth attenuation even with surplus nitrogen, the alternate electron acceptor, and complementation of the mutant restores bacterial growth. Together, our observations provide new biological insights into the role of PhoP in integrating nitrogen metabolism with hypoxia by the assistance of the hypoxia regulator DosR. The results have significant implications on the mechanism of intracellular survival and growth of the tubercle bacilli under a hypoxic environment within the phagosome.IMPORTANCE M. tuberculosis retains the unique ability to establish an asymptomatic latent infection. To understand the mechanisms involved in hypoxic stress which play a critical role in persistence, we show that the virulence regulator PhoP is linked to hypoxia, the dormancy signal. In keeping with this, phoP was shown to play a major role in M. tuberculosis growth under hypoxia even in the presence of surplus nitrogen, the alternate electron acceptor. Our results showing regulation of hypoxia-responsive genes provide new biological insights into role of the virulence regulator in metabolic switching by sensing hypoxia and integrating nitrogen metabolism with hypoxia by the assistance of the hypoxia regulator DosR.
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15
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Tan W, Liao TH, Wang J, Ye Y, Wei YC, Zhou HK, Xiao Y, Zhi XY, Shao ZH, Lyu LD, Zhao GP. A recently evolved diflavin-containing monomeric nitrate reductase is responsible for highly efficient bacterial nitrate assimilation. J Biol Chem 2020; 295:5051-5066. [PMID: 32111737 DOI: 10.1074/jbc.ra120.012859] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 02/25/2020] [Indexed: 12/11/2022] Open
Abstract
Nitrate is one of the major inorganic nitrogen sources for microbes. Many bacterial and archaeal lineages have the capacity to express assimilatory nitrate reductase (NAS), which catalyzes the rate-limiting reduction of nitrate to nitrite. Although a nitrate assimilatory pathway in mycobacteria has been proposed and validated physiologically and genetically, the putative NAS enzyme has yet to be identified. Here, we report the characterization of a novel NAS encoded by Mycolicibacterium smegmatis Msmeg_4206, designated NasN, which differs from the canonical NASs in its structure, electron transfer mechanism, enzymatic properties, and phylogenetic distribution. Using sequence analysis and biochemical characterization, we found that NasN is an NADPH-dependent, diflavin-containing monomeric enzyme composed of a canonical molybdopterin cofactor-binding catalytic domain and an FMN-FAD/NAD-binding, electron-receiving/transferring domain, making it unique among all previously reported hetero-oligomeric NASs. Genetic studies revealed that NasN is essential for aerobic M. smegmatis growth on nitrate as the sole nitrogen source and that the global transcriptional regulator GlnR regulates nasN expression. Moreover, unlike the NADH-dependent heterodimeric NAS enzyme, NasN efficiently supports bacterial growth under nitrate-limiting conditions, likely due to its significantly greater catalytic activity and oxygen tolerance. Results from a phylogenetic analysis suggested that the nasN gene is more recently evolved than those encoding other NASs and that its distribution is limited mainly to Actinobacteria and Proteobacteria. We observed that among mycobacterial species, most fast-growing environmental mycobacteria carry nasN, but that it is largely lacking in slow-growing pathogenic mycobacteria because of multiple independent genomic deletion events along their evolution.
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Affiliation(s)
- Wei Tan
- Department of Microbiology and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong 999077, China.,Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences and Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai 200032, China
| | - Tian-Hua Liao
- Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Jin Wang
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Yu Ye
- Department of Microbiology and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong 999077, China
| | - Yu-Chen Wei
- Department of Microbiology and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong 999077, China
| | - Hao-Kui Zhou
- Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Youli Xiao
- CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Xiao-Yang Zhi
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming 650091, China
| | - Zhi-Hui Shao
- CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Liang-Dong Lyu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences and Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai 200032, China
| | - Guo-Ping Zhao
- Department of Microbiology and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong 999077, China .,Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences and Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai 200032, China.,Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.,Bio-Med Big Data Center, Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China.,Shanghai-MOST Key Laboratory for Health and Disease Genomics, Chinese National Human Genome Center, Shanghai 201203, China
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16
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Zhang Y, Zhou X, Wang X, Wang L, Xia M, Luo J, Shen Y, Wang M. Improving phytosterol biotransformation at low nitrogen levels by enhancing the methylcitrate cycle with transcriptional regulators PrpR and GlnR of Mycobacterium neoaurum. Microb Cell Fact 2020; 19:13. [PMID: 31992309 PMCID: PMC6986058 DOI: 10.1186/s12934-020-1285-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 01/16/2020] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Androstenedione (AD) is an important steroid medicine intermediate that is obtained via the degradation of phytosterols by mycobacteria. The production process of AD is mainly the degradation of the phytosterol aliphatic side chain, which is accompanied by the production of propionyl CoA. Excessive accumulation of intracellular propionyl-CoA produces a toxic effect in mycobacteria, which restricts the improvement of production efficiency. The 2-methylcitrate cycle pathway (MCC) plays a significant role in the detoxification of propionyl-CoA in bacterial. The effect of the MCC on phytosterol biotransformation in mycobacteria has not been elucidated in detail. Meanwhile, reducing fermentation cost has always been an important issue to be solved in the optimizing of the bioprocess. RESULTS There is a complete MCC in Mycobacterium neoaurum (MNR), prpC, prpD and prpB in the prp operon encode methylcitrate synthase, methylcitrate dehydratase and methylisocitrate lyase involved in MCC, and PrpR is a specific transcriptional activator of prp operon. After the overexpression of prpDCB and prpR in MNR, the significantly improved transcription levels of prpC, prpD and prpB were observed. The highest conversion ratios of AD obtained by MNR-prpDBC and MNR-prpR increased from 72.3 ± 2.5% to 82.2 ± 2.2% and 90.6 ± 2.6%, respectively. Through enhanced the PrpR of MNR, the in intracellular propionyl-CoA levels decreased by 43 ± 3%, and the cell viability improved by 22 ± 1% compared to MNR at 96 h. The nitrogen transcription regulator GlnR repressed prp operon transcription in a nitrogen-limited medium. The glnR deletion enhanced the transcription level of prpDBC and the biotransformation ability of MNR. MNR-prpR/ΔglnR was constructed by the overexpression of prpR in the glnR-deleted strain showed adaptability to low nitrogen. The highest AD conversion ratio by MNR-prpR/ΔglnR was 92.8 ± 2.7% at low nitrogen level, which was 1.4 times higher than that of MNR. CONCLUSION Improvement in phytosterol biotransformation after the enhancement of propionyl-CoA metabolism through the combined modifications of the prp operon and glnR of mycobacteria was investigated for the first time. The overexpress of prpR in MNR can increase the transcription of essential genes (prpC, prpD and prpB) of MCC, reduce the intracellular propionyl-CoA level and improve bacterial viability. The knockout of glnR can enhance the adaptability of MNR to the nitrogen source. In the MNRΔglnR strain, overexpress of prpR can achieve efficient production of AD at low nitrogen levels, thus reducing the production cost. This strategy provides a reference for the economic and effective production of other valuable steroid metabolites from phytosterol in the pharmaceutical industry.
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Affiliation(s)
- Yang Zhang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China. .,College of Life Science, Liaocheng University, Liaocheng, 252059, Shandong, China.
| | - Xiuling Zhou
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Xuemei Wang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Lu Wang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Menglei Xia
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Jianmei Luo
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Yanbing Shen
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China.
| | - Min Wang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China.
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Initial Metabolic Step of a Novel Ethanolamine Utilization Pathway and Its Regulation in Streptomyces coelicolor M145. mBio 2019; 10:mBio.00326-19. [PMID: 31113893 PMCID: PMC6529630 DOI: 10.1128/mbio.00326-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Until now, knowledge of the utilization of ethanolamine in Streptomyces was limited. Our work represents the first attempt to reveal a novel ethanolamine utilization pathway in the actinobacterial model organism S. coelicolor through the characterization of the key enzyme gamma-glutamylethanolamide synthetase GlnA4, which is absolutely required for growth in the presence of ethanolamine. The novel ethanolamine utilization pathway is dissimilar to the currently known ethanolamine utilization pathway, which occurs in metabolome. The novel ethanolamine utilization pathway does not result in the production of toxic by-products (such as acetaldehyde); thus, it is not encapsulated. We believe that this contribution is a milestone in understanding the ecology of Streptomyces and the utilization of alternative nitrogen sources. Our report provides new insight into bacterial primary metabolism, which remains complex and partially unexplored. Streptomyces coelicolor is a Gram-positive soil bacterium with a high metabolic and adaptive potential that is able to utilize a variety of nitrogen sources. However, little is known about the utilization of the alternative nitrogen source ethanolamine. Our study revealed that S. coelicolor can utilize ethanolamine as a sole nitrogen or carbon (N/C) source, although it grows poorly on this nitrogen source due to the absence of a specific ethanolamine permease. Heterologous expression of a putative ethanolamine permease (SPRI_5940) from Streptomycespristinaespiralis positively influenced the biomass accumulation of the overexpression strain grown in defined medium with ethanolamine. In this study, we demonstrated that a glutamine synthetase-like protein, GlnA4 (SCO1613), is involved in the initial metabolic step of a novel ethanolamine utilization pathway in S. coelicolor M145. GlnA4 acts as a gamma-glutamylethanolamide synthetase. Transcriptional analysis revealed that expression of glnA4 was induced by ethanolamine and repressed in the presence of ammonium. Regulation of glnA4 is governed by the transcriptional repressor EpuRI (SCO1614). The ΔglnA4 mutant strain was unable to grow on defined liquid Evans medium supplemented with ethanolamine. High-performance liquid chromatography (HPLC) analysis demonstrated that strain ΔglnA4 is unable to utilize ethanolamine. GlnA4-catalyzed glutamylation of ethanolamine was confirmed in an enzymatic in vitro assay, and the GlnA4 reaction product, gamma-glutamylethanolamide, was detected by HPLC/electrospray ionization-mass spectrometry (HPLC/ESI-MS). In this work, the first step of ethanolamine utilization in S. coelicolor M145 was elucidated, and a putative ethanolamine utilization pathway was deduced based on the sequence similarity and genomic localization of homologous genes.
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18
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The Nitrogen Regulator GlnR Directly Controls Transcription of the prpDBC Operon Involved in Methylcitrate Cycle in Mycobacterium smegmatis. J Bacteriol 2019; 201:JB.00099-19. [PMID: 30745367 DOI: 10.1128/jb.00099-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 02/03/2019] [Indexed: 12/13/2022] Open
Abstract
Mycobacterium tuberculosis utilizes fatty acids of the host as the carbon source. Metabolism of odd-chain fatty acids by Mycobacterium tuberculosis produces propionyl coenzyme A (propionyl-CoA). The methylcitrate cycle is essential for mycobacteria to utilize the propionyl-CoA to persist and grow on these fatty acids. In M. smegmatis, methylcitrate synthase, methylcitrate dehydratase, and methylisocitrate lyase involved in the methylcitrate cycle are encoded by prpC, prpD, and prpB, respectively, in operon prpDBC In this study, we found that the nitrogen regulator GlnR directly binds to the promoter region of the prpDBC operon and inhibits its transcription. The binding motif of GlnR was identified by bioinformatic analysis and validated using DNase I footprinting and electrophoretic mobility shift assays. The GlnR-binding motif is separated by a 164-bp sequence from the binding site of PrpR, a pathway-specific transcriptional activator of methylcitrate cycle, but the binding affinity of GlnR to prpDBC is much stronger than that of PrpR. Deletion of glnR resulted in faster growth in propionate or cholesterol medium compared with the wild-type strain. The ΔglnR mutant strain also showed a higher survival rate in macrophages. These results illustrated that the nitrogen regulator GlnR regulates the methylcitrate cycle through direct repression of the transcription of the prpDBC operon. This finding not only suggests an unprecedented link between nitrogen metabolism and the methylcitrate pathway but also reveals a potential target for controlling the growth of pathogenic mycobacteria.IMPORTANCE The success of mycobacteria survival in macrophage depends on its ability to assimilate fatty acids and cholesterol from the host. The cholesterol and fatty acids are catabolized via β-oxidation to generate propionyl coenzyme A (propionyl-CoA), which is then primarily metabolized via the methylcitrate cycle. Here, we found a typical GlnR binding box in the prp operon, and the affinity is much stronger than that of PrpR, a transcriptional activator of methylcitrate cycle. Furthermore, GlnR repressed the transcription of the prp operon. Deletion of glnR significantly enhanced the growth of Mycobacterium tuberculosis in propionate or cholesterol medium, as well as viability in macrophages. These findings provide new insights into the regulatory mechanisms underlying the cross talk of nitrogen and carbon metabolisms in mycobacteria.
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19
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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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20
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Antczak M, Płocińska R, Płociński P, Rumijowska-Galewicz A, Żaczek A, Strapagiel D, Dziadek J. The NnaR orphan response regulator is essential for the utilization of nitrate and nitrite as sole nitrogen sources in mycobacteria. Sci Rep 2018; 8:17552. [PMID: 30510199 PMCID: PMC6277429 DOI: 10.1038/s41598-018-35844-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 11/05/2018] [Indexed: 12/12/2022] Open
Abstract
Nitrogen is an essential component of biological molecules and an indispensable microelement required for the growth of cells. Nitrogen metabolism of Mycobacterium smegmatis is regulated by a number of transcription factors, with the glnR gene product playing a major role. Under nitrogen-depletion conditions, GlnR controls the expression of many genes involved in nitrogen assimilation, including the msmeg_0432 gene encoding NnaR, the homologue of a nitrite/nitrate transport regulator from Streptomyces coelicolor. In the present study, the role of NnaR in the nitrogen metabolism of M. smegmatis was evaluated. The ∆glnR and ∆nnaR mutant strains were generated and cultured under nitrogen-depletion conditions. Total RNA profiling was used to investigate the potential role of NnaR in the GlnR regulon under nitrogen-depletion and in nitrogen-rich media. We found that disruption of MSMEG_0432 affected the expression of genes involved in nitrite/nitrate uptake, and its removal rendered mycobacteria unable to assimilate nitrogen from those sources, leading to cell death. RNA-Seq results were validated using quantitative real-time polymerase chain reaction (qRT-PCR) and electrophoretic mobility shift assays (EMSAs). The ability of mutants to grow on various nitrogen sources was evaluated using the BIOLOG Phenotype screening platform and confirmed on minimal Sauton's medium containing various sources of nitrogen. The ∆glnR mutant was not able to convert nitrates to nitrites. Interestingly, NnaR required active GlnR to prevent nitrogen starvation, and both proteins cooperated in the regulation of gene expression associated with nitrate/nitrite assimilation. The ∆nnaR mutant was able to convert nitrates to nitrites, but it could not assimilate the products of this conversion. Importantly, NnaR was the key regulator of the expression of the truncated haemoglobin trHbN, which is required to improve the survival of bacteria under nitrosative stress.
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Affiliation(s)
- Magdalena Antczak
- Institute for Medical Biology, Polish Academy of Sciences, Łódź, Poland
| | - Renata Płocińska
- Institute for Medical Biology, Polish Academy of Sciences, Łódź, Poland
| | | | | | - Anna Żaczek
- Department of Biochemistry and Cell Biology, University of Rzeszów, Rzeszów, Poland
| | - Dominik Strapagiel
- Biobank Lab, Department of Molecular Biophysics, University of Łódź, Łódź, Poland
| | - Jarosław Dziadek
- Institute for Medical Biology, Polish Academy of Sciences, Łódź, Poland.
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21
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Rakovitsky N, Bar Oz M, Goldberg K, Gibbons S, Zimhony O, Barkan D. The Unexpected Essentiality of glnA2 in Mycobacterium smegmatis Is Salvaged by Overexpression of the Global Nitrogen Regulator glnR, but Not by L-, D- or Iso-Glutamine. Front Microbiol 2018; 9:2143. [PMID: 30271391 PMCID: PMC6142876 DOI: 10.3389/fmicb.2018.02143] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 08/21/2018] [Indexed: 01/14/2023] Open
Abstract
Nitrogen metabolism plays a central role in the physiology of microorganisms, and Glutamine Synthetase (GS) genes are present in virtually all bacteria. In M. tuberculosis, four GS genes are present, but only glnA1 is essential, whereas glnA2 was shown to be non-essential for in-vitro as well as in-vivo growth and pathogenesis, and is postulated to be involved in D-glutamine and iso-glutamine synthesis. Whilst investigating the activity of an antimicrobial compound in M. smegmatis, we found a spontaneous temperature-sensitive mutant in glnA2 (I133F), and used it to investigate the role of glnA2 in M. smegmatis. We deleted the native glnA2 and replaced it with a mutated allele. This re-created the temperature sensitivity—as after 3–4 seemingly normal division cycles, glnA2 became essential for growth. This essentiality could not be salvaged by neither L, D- nor iso-glutamine, suggesting an additional role of glnA2 in M. smegmatis over its role in M. tuberculosis. We also found that overexpression of the global nitrogen regulator glnR enabled bypassing the essentiality of glnA2, allowing the creation of a complete deletion mutant. The discrepancy between the importance of glnA2 in Mtb and M. smegmatis stresses the caution in which results in one are extrapolated to the other.
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Affiliation(s)
- Nadya Rakovitsky
- Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Michal Bar Oz
- Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Karin Goldberg
- Department of Pharmaceutical Engineering, Azrieli College of Engineering, Jerusalem, Israel
| | - Simon Gibbons
- Research Department of Pharmaceutical and Biological Chemistry, UCL School of Pharmacy, London, United Kingdom
| | - Oren Zimhony
- Kaplan Medical Center, Rehovot, Israel.,The Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Daniel Barkan
- Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Jerusalem, Israel
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22
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Zhang Y, Zhang Y, Li P, Wang Y, Wang J, Shao Z, Zhao G. GlnR positive transcriptional regulation of the phosphate-specific transport system pstSCAB in Amycolatopsis mediterranei U32. Acta Biochim Biophys Sin (Shanghai) 2018; 50:757-765. [PMID: 30007316 DOI: 10.1093/abbs/gmy073] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Indexed: 11/14/2022] Open
Abstract
Amycolatopsis mediterranei U32 is an important industrial strain for the production of rifamycin SV. Rifampicin, a derivative of rifamycin SV, is commonly used to treat mycobacterial infections. Although phosphate has long been known to affect rifamycin biosynthesis, phosphate transport, metabolism, and regulation are poorly understood in A. mediterranei. In this study, the functional phosphate transport system pstSCAB was isolated by RNA sequencing and inactivated by insertion mutation in A. mediterranei U32. The mycelium morphology changed from a filamentous shape in the wild-type and pstS1+ strains to irregular swollen shape at the end of filamentous in the ΔpstS1 strain. RT-PCR assay revealed that pstSCAB genes are co-transcribed as a polycistronic messenger. The pstSCAB transcription was significantly activated by nitrate supplementation and positively regulated by GlnR which is a global regulator of nitrogen metabolism in actinomycetes. At the same time, the yield of rifamycin SV decreased after mutation (ΔpstS1) compared with wild-type U32, which indicated a strong connection among phosphate metabolism, nitrogen metabolism, and rifamycin production in actinomycetes.
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Affiliation(s)
- Yuhui Zhang
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang, China
- Department of Life Sciences, Henan Institute of Science and Technology, Xinxiang, China
| | - Yixuan Zhang
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang, China
| | - Peng Li
- Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Ying Wang
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Jin Wang
- Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Zhihui Shao
- Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Guoping Zhao
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang, China
- Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
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23
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Yang Y, Richards JP, Gundrum J, Ojha AK. GlnR Activation Induces Peroxide Resistance in Mycobacterial Biofilms. Front Microbiol 2018; 9:1428. [PMID: 30022971 PMCID: PMC6039565 DOI: 10.3389/fmicb.2018.01428] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 06/11/2018] [Indexed: 12/31/2022] Open
Abstract
Mycobacteria spontaneously form surface-associated multicellular communities, called biofilms, which display resistance to a wide range of exogenous stresses. A causal relationship between biofilm formation and emergence of stress resistance is not known. Here, we report that activation of a nitrogen starvation response regulator, GlnR, during the development of Mycobacterium smegmatis biofilms leads to peroxide resistance. The resistance arises from induction of a GlnR-dependent peroxide resistance (gpr) gene cluster comprising of 8 ORFs (MSMEG_0565-0572). Expression of gpr increases the NADPH to NADP ratio, suggesting that a reduced cytosolic environment of nitrogen-starved cells in biofilms contributes to peroxide resistance. Increased NADPH levels from gpr activity likely support the activity of enzymes involved in nitrogen assimilation, as suggested by a higher threshold of nitrogen supplement required by a gpr mutant to form biofilms. Together, our study uniquely interlinks a nutrient sensing mechanism with emergence of stress resistance during mycobacterial biofilm development. The gpr gene cluster is conserved in several mycobacteria that can cause nosocomial infections, offering a possible explanation for their resistance to peroxide-based sterilization of medical equipment.
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Affiliation(s)
- Yong Yang
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, NY, United States
| | - Jacob P. Richards
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, NY, United States
- Department of Infectious Diseases and Microbiology, University of Pittsburgh, Pittsburgh, PA, United States
| | - Jennifer Gundrum
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, NY, United States
| | - Anil K. Ojha
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, NY, United States
- Department of Biomedical Sciences, University at Albany, Albany, NY, United States
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24
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Liu XX, Shen MJ, Liu WB, Ye BC. GlnR-Mediated Regulation of Short-Chain Fatty Acid Assimilation in Mycobacterium smegmatis. Front Microbiol 2018; 9:1311. [PMID: 29988377 PMCID: PMC6023979 DOI: 10.3389/fmicb.2018.01311] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 05/29/2018] [Indexed: 11/20/2022] Open
Abstract
Assimilation of short-chain fatty acids (SCFAs) plays an important role in the survival and lipid biosynthesis of Mycobacteria. However, regulation of this process has not been thoroughly described. In the present work, we demonstrate that GlnR as a well-known nitrogen-sensing regulator transcriptionally modulates the AMP-forming propionyl-CoA synthetase (MsPrpE), and acetyl-CoA synthetases (MsAcs) is associated with SCFAs assimilation in Mycobacterium smegmatis, a model Mycobacterium. GlnR can directly activate the expression of MsprpE and Msacs by binding to their promoter regions based upon sensed nitrogen starvation in the host. Moreover, GlnR can activate the expression of lysine acetyltransferase encoding Mspat, which significantly decreases the activity of MsPrpE and MsAcs through increased acylation. Next, growth curves and resazurin assay show that GlnR can further regulate the growth of M. smegmatis on different SCFAs to control the viability. These results demonstrate that GlnR-mediated regulation of SCFA assimilation in response to the change of nitrogen signal serves to control the survival of M. smegmatis. These findings provide insights into the survival and nutrient utilization mechanisms of Mycobacteria in their host, which may enable new strategies in drug discovery for the control of tuberculosis.
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Affiliation(s)
- Xin-Xin Liu
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Meng-Jia Shen
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Wei-Bing Liu
- 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.,Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, China
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25
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Romero-Rodríguez A, Maldonado-Carmona N, Ruiz-Villafán B, Koirala N, Rocha D, Sánchez S. Interplay between carbon, nitrogen and phosphate utilization in the control of secondary metabolite production in Streptomyces. Antonie van Leeuwenhoek 2018; 111:761-781. [PMID: 29605896 DOI: 10.1007/s10482-018-1073-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Accepted: 03/21/2018] [Indexed: 12/21/2022]
Abstract
Streptomyces species are a wide and diverse source of many therapeutic agents (antimicrobials, antineoplastic and antioxidants, to name a few) and represent an important source of compounds with potential applications in medicine. The effect of nitrogen, phosphate and carbon on the production of secondary metabolites has long been observed, but it was not until recently that the molecular mechanisms on which these effects rely were ascertained. In addition to the specific macronutrient regulatory mechanisms, there is a complex network of interactions between these mechanisms influencing secondary metabolism. In this article, we review the recent advances in our understanding of the molecular mechanisms of regulation exerted by nitrogen, phosphate and carbon sources, as well as the effects of their interconnections, on the synthesis of secondary metabolites by members of the genus Streptomyces.
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Affiliation(s)
- Alba Romero-Rodríguez
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Tercer circuito Exterior de Ciudad Universitaria, 04510, Mexico City, Mexico.
| | - Nidia Maldonado-Carmona
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Tercer circuito Exterior de Ciudad Universitaria, 04510, Mexico City, Mexico
| | - Beatriz Ruiz-Villafán
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Tercer circuito Exterior de Ciudad Universitaria, 04510, Mexico City, Mexico
| | - Niranjan Koirala
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Tercer circuito Exterior de Ciudad Universitaria, 04510, Mexico City, Mexico
| | - Diana Rocha
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Tercer circuito Exterior de Ciudad Universitaria, 04510, Mexico City, Mexico
| | - Sergio Sánchez
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Tercer circuito Exterior de Ciudad Universitaria, 04510, Mexico City, Mexico
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26
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A semi-synthetic regulon enables rapid growth of yeast on xylose. Nat Commun 2018; 9:1233. [PMID: 29581426 PMCID: PMC5964326 DOI: 10.1038/s41467-018-03645-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 03/01/2018] [Indexed: 01/27/2023] Open
Abstract
Nutrient assimilation is the first step that allows biological systems to proliferate and produce value-added products. Yet, implementation of heterologous catabolic pathways has so far relied on constitutive gene expression without consideration for global regulatory systems that may enhance nutrient assimilation and cell growth. In contrast, natural systems prefer nutrient-responsive gene regulation (called regulons) that control multiple cellular functions necessary for cell survival and growth. Here, in Saccharomyces cerevisiae, by partially- and fully uncoupling galactose (GAL)-responsive regulation and metabolism, we demonstrate the significant growth benefits conferred by the GAL regulon. Next, by adapting the various aspects of the GAL regulon for a non-native nutrient, xylose, we build a semi-synthetic regulon that exhibits higher growth rate, better nutrient consumption, and improved growth fitness compared to the traditional and ubiquitous constitutive expression strategy. This work provides an elegant paradigm to integrate non-native nutrient catabolism with native, global cellular responses to support fast growth. Efficient assimilation of nutrients is essential for the production of value-added products in microbial fermentation. Here the authors design a semi-synthetic xylose regulon to improve growth characteristics of Saccharomyces cerevisiae on this non-native sugar.
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27
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Xu Y, You D, Ye BC. Nitrogen regulator GlnR directly controls transcription of genes encoding lysine deacetylases in Actinobacteria. MICROBIOLOGY-SGM 2017; 163:1702-1710. [PMID: 29058657 DOI: 10.1099/mic.0.000553] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
N-Lysine acetylation is a dynamic, reversible and regulatory post-translational modification (PTM) in prokaryotes, which integrates and coordinates metabolisms responding to environmental clues. However, the molecular mechanism underlying the signalling pathway from nutrient sensing to protein acetylation remains incompletely understood in micro-organisms. Here we found that global nitrogen regulator GlnR directly controls transcription of genes encoding lysine deacetylases in Actinobacteria. Electrophoretic mobility shift assays and real-time PCR (RT-PCR) in three Actinobacteria species (Saccharopolyspora erythraea, Streptomyces coelicolor and Mycobacterium smegmatis) revealed that GlnR regulator protein is able to interact with the promoter regions of these genes and activate their transcription. Furthermore, it was demonstrated that cellular acetylation status (acetylome) is modulated by extracellular nitrogen availability. Our results present an example of the novel complete signal transduction mechanism of regulating protein deacetylation through a nutrient-sensing pleiotropic regulator in response to nutrient availability.
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Affiliation(s)
- Ying Xu
- Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, PR China
| | - Di You
- Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, PR China
| | - Bang-Ce Ye
- Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, PR China.,Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, PR China
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28
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Hernández MA, Gleixner G, Sachse D, Alvarez HM. Carbon Allocation in Rhodococcus jostii RHA1 in Response to Disruption and Overexpression of nlpR Regulatory Gene, Based on 13C-labeling Analysis. Front Microbiol 2017; 8:1992. [PMID: 29075252 PMCID: PMC5641563 DOI: 10.3389/fmicb.2017.01992] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 09/27/2017] [Indexed: 12/23/2022] Open
Abstract
Nitrogen lipid regulator (NlpR) is a pleiotropic regulator that positively controls genes associated with both nitrogen and lipid metabolism in the oleaginous bacterium Rhodococcus jostii RHA1. In this study, we investigated the effect of nlpR disruption and overexpression on the assimilation of 13C-labeled glucose as carbon source, during cultivation of cells under nitrogen-limiting and nitrogen-rich conditions, respectively. Label incorporation into the total lipid extract (TLE) fraction was about 30% lower in the mutant strain in comparison with the wild type strain under low-nitrogen conditions. Moreover, a higher 13C abundance (∼60%) into the extracellular polymeric substance fraction was observed in the mutant strain. nlpR disruption also promoted a decrease in the label incorporation into several TLE-derivative fractions including neutral lipids (NL), glycolipids (GL), phospholipids (PL), triacylglycerols (TAG), diacylglycerols (DAG), and free fatty acids (FFA), with the DAG being the most affected. In contrast, the nlpR overexpression in RHA1 cells under nitrogen-rich conditions produced an increase of the label incorporation into the TLE and its derivative NL and PL fractions, the last one being the highest 13C enriched. In addition, a higher 13C enrichment occurred in the TAG, DAG, and FFA fractions after nlpR induction, with the FFA fraction being the most affected within the TLE. Isotopic-labeling experiments demonstrated that NlpR regulator is contributing in oleaginous phenotype of R. jostii RHA1 to the allocation of carbon into the different lipid fractions in response to nitrogen levels, increasing the rate of carbon flux into lipid metabolism.
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Affiliation(s)
- Martín A Hernández
- Instituto de Biociencias de la Patagonia, Consejo Nacional de Investigaciones Científicas y Técnicas, Facultad de Ciencias Naturales, Universidad Nacional de la Patagonia San Juan Bosco, Comodoro Rivadavia, Argentina
| | - Gerd Gleixner
- Department of Biogeochemical Processes, Max Planck Institute for Biogeochemistry, Jena, Germany
| | - Dirk Sachse
- Section 5.1: Geomorphology, GFZ German Research Centre for Geosciences, Potsdam, Germany.,Institute of Earth and Environmental Science, University of Potsdam, Potsdam, Germany
| | - Héctor M Alvarez
- Instituto de Biociencias de la Patagonia, Consejo Nacional de Investigaciones Científicas y Técnicas, Facultad de Ciencias Naturales, Universidad Nacional de la Patagonia San Juan Bosco, Comodoro Rivadavia, Argentina
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29
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Yang Y, Thomas J, Li Y, Vilchèze C, Derbyshire KM, Jacobs WR, Ojha AK. Defining a temporal order of genetic requirements for development of mycobacterial biofilms. Mol Microbiol 2017. [PMID: 28628249 DOI: 10.1111/mmi.13734] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Most mycobacterial species spontaneously form biofilms, inducing unique growth physiologies and reducing drug sensitivity. Biofilm growth progresses through three genetically programmed stages: substratum attachment, intercellular aggregation and architecture maturation. Growth of Mycobacterium smegmatis biofilms requires multiple factors including a chaperonin (GroEL1) and a nucleoid-associated protein (Lsr2), although how their activities are linked remains unclear. Here it is shown that Lsr2 participates in intercellular aggregation, but substratum attachment of Lsr2 mutants is unaffected, thereby genetically distinguishing these developmental stages. Further, a suppressor mutation in a glycopeptidolipid synthesis gene (mps) that results in hyperaggregation of cells and fully restores the form and functions of Δlsr2 mutant biofilms was identified. Suppression by the mps mutation is specific to Δlsr2; it does not rescue the maturation-deficient biofilms of a ΔgroEL1 mutant, thereby differentiating the process of aggregation from maturation. Gene expression analysis supports a stepwise process of maturation, highlighted by temporally separated, transient inductions of iron and nitrogen import genes. Furthermore, GroEL1 activity is required for induction of nitrogen, but not iron, import genes. Together, the findings begin to define molecular checkpoints during development of mycobacterial biofilms.
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Affiliation(s)
- Yong Yang
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Joseph Thomas
- Department of Infectious Diseases and Microbiology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yunlong Li
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Catherine Vilchèze
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Keith M Derbyshire
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - William R Jacobs
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA.,Howard Hughes Medical Institute, Bronx, NY, USA
| | - Anil K Ojha
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, NY, USA.,Department of Infectious Diseases and Microbiology, University of Pittsburgh, Pittsburgh, PA, USA
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30
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Enhancement of antibiotic productions by engineered nitrate utilization in actinomycetes. Appl Microbiol Biotechnol 2017; 101:5341-5352. [DOI: 10.1007/s00253-017-8292-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 03/28/2017] [Accepted: 04/06/2017] [Indexed: 10/19/2022]
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31
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Marshall DD, Halouska S, Zinniel DK, Fenton RJ, Kenealy K, Chahal HK, Rathnaiah G, Barletta RG, Powers R. Assessment of Metabolic Changes in Mycobacterium smegmatis Wild-Type and alr Mutant Strains: Evidence of a New Pathway of d-Alanine Biosynthesis. J Proteome Res 2017; 16:1270-1279. [PMID: 28121156 DOI: 10.1021/acs.jproteome.6b00871] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
In mycobacteria, d-alanine is an essential precursor for peptidoglycan biosynthesis. The only confirmed enzymatic pathway to form d-alanine is through the racemization of l-alanine by alanine racemase (Alr, EC 5.1.1.1). Nevertheless, the essentiality of Alr in Mycobacterium tuberculosis and Mycobacterium smegmatis for cell survivability in the absence of d-alanine has been a point of controversy with contradictory results reported in the literature. To address this issue, we examined the effects of alr inactivation on the cellular metabolism of M. smegmatis. The M. smegmatis alr insertion mutant TAM23 exhibited essentially identical growth to wild-type mc2155 in the absence of d-alanine. NMR metabolomics revealed drastically distinct phenotypes between mc2155 and TAM23. A metabolic switch was observed for TAM23 as a function of supplemented d-alanine. In the absence of d-alanine, the metabolic response directed carbon through an unidentified transaminase to provide the essential d-alanine required for survival. The process is reversed when d-alanine is available, in which the d-alanine is directed to peptidoglycan biosynthesis. Our results provide further support for the hypothesis that Alr is not an essential function of M. smegmatis and that specific Alr inhibitors will have no bactericidal action.
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Affiliation(s)
- Darrell D Marshall
- Department of Chemistry, University of Nebraska-Lincoln , Lincoln, Nebraska 68588-0304, United States
| | - Steven Halouska
- Department of Chemistry, University of Nebraska-Lincoln , Lincoln, Nebraska 68588-0304, United States
| | - Denise K Zinniel
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln , Lincoln, Nebraska 68583-0905, United States
| | - Robert J Fenton
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln , Lincoln, Nebraska 68583-0905, United States
| | - Katie Kenealy
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln , Lincoln, Nebraska 68583-0905, United States
| | - Harpreet K Chahal
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln , Lincoln, Nebraska 68583-0905, United States
| | - Govardhan Rathnaiah
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln , Lincoln, Nebraska 68583-0905, United States
| | - Raúl G Barletta
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln , Lincoln, Nebraska 68583-0905, United States.,Center for Redox Biology, University of Nebraska-Lincoln , Lincoln, Nebraska 68588-0662, United States
| | - Robert Powers
- Department of Chemistry, University of Nebraska-Lincoln , Lincoln, Nebraska 68588-0304, United States.,Center for Redox Biology, University of Nebraska-Lincoln , Lincoln, Nebraska 68588-0662, United States
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32
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Hernández MA, Lara J, Gago G, Gramajo H, Alvarez HM. The pleiotropic transcriptional regulator NlpR contributes to the modulation of nitrogen metabolism, lipogenesis and triacylglycerol accumulation in oleaginous rhodococci. Mol Microbiol 2016; 103:366-385. [DOI: 10.1111/mmi.13564] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/22/2016] [Indexed: 01/04/2023]
Affiliation(s)
- Martín A. Hernández
- INBIOP (Instituto de Biociencias de la Patagonia), Consejo Nacional de Investigaciones Científicas y Técnicas, Facultad de Ciencias Naturales; Universidad Nacional de la Patagonia San Juan Bosco; Ruta Provincial N° 1, Km 4-Ciudad Universitaria 9000 Comodoro Rivadavia Chubut Argentina
| | - Julia Lara
- IBR (Instituto de Biología Molecular y Celular de Rosario), Consejo Nacional de Investigaciones Científicas y Técnicas. Facultad de Ciencias Bioquímicas y Farmacéuticas; Universidad Nacional de Rosario; Ocampo y Esmeralda 2000 Rosario Santa Fe Argentina
| | - Gabriela Gago
- IBR (Instituto de Biología Molecular y Celular de Rosario), Consejo Nacional de Investigaciones Científicas y Técnicas. Facultad de Ciencias Bioquímicas y Farmacéuticas; Universidad Nacional de Rosario; Ocampo y Esmeralda 2000 Rosario Santa Fe Argentina
| | - Hugo Gramajo
- IBR (Instituto de Biología Molecular y Celular de Rosario), Consejo Nacional de Investigaciones Científicas y Técnicas. Facultad de Ciencias Bioquímicas y Farmacéuticas; Universidad Nacional de Rosario; Ocampo y Esmeralda 2000 Rosario Santa Fe Argentina
| | - Héctor M. Alvarez
- INBIOP (Instituto de Biociencias de la Patagonia), Consejo Nacional de Investigaciones Científicas y Técnicas, Facultad de Ciencias Naturales; Universidad Nacional de la Patagonia San Juan Bosco; Ruta Provincial N° 1, Km 4-Ciudad Universitaria 9000 Comodoro Rivadavia Chubut Argentina
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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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34
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Amin R, Franz-Wachtel M, Tiffert Y, Heberer M, Meky M, Ahmed Y, Matthews A, Krysenko S, Jakobi M, Hinder M, Moore J, Okoniewski N, Maček B, Wohlleben W, Bera A. Post-translational Serine/Threonine Phosphorylation and Lysine Acetylation: A Novel Regulatory Aspect of the Global Nitrogen Response Regulator GlnR in S. coelicolor M145. Front Mol Biosci 2016; 3:38. [PMID: 27556027 PMCID: PMC4977719 DOI: 10.3389/fmolb.2016.00038] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 07/25/2016] [Indexed: 01/03/2023] Open
Abstract
Soil-dwelling Streptomyces bacteria such as S.coelicolor have to constantly adapt to the nitrogen (N) availability in their habitat. Thus, strict transcriptional and post-translational control of the N-assimilation is fundamental for survival of this species. GlnR is a global response regulator that controls transcription of the genes related to the N-assimilation in S. coelicolor and other members of the Actinomycetales. GlnR represents an atypical orphan response regulator that is not activated by the phosphorylation of the conserved aspartate residue (Asp 50). We have applied transcriptional analysis, LC-MS/MS analysis and electrophoretic mobility shift assays (EMSAs) to understand the regulation of GlnR in S. coelicolor M145. The expression of glnR and GlnR-target genes was revisited under four different N-defined conditions and a complex N-rich condition. Although, the expression of selected GlnR-target genes was strongly responsive to changing N-concentrations, the glnR expression itself was independent of the N-availability. Using LC-MS/MSanalysis we demonstrated that GlnR was post-translationally modified. The post-translational modifications of GlnR comprise phosphorylation of the serine/threonine residues and acetylation of lysine residues. In the complex N-rich medium GlnR was phosphorylated on six serine/threonine residues and acetylated on one lysine residue. Under defined N-excess conditions only two phosphorylated residues were detected whereas under defined N-limiting conditions no phosphorylation was observed. GlnR phosphorylation is thus clearly correlated with N-rich conditions. Furthermore, GlnR was acetylated on four lysine residues independently of the N-concentration in the defined media and on only one lysine residue in the complex N-rich medium. Using EMSAs we demonstrated that phosphorylation inhibited the binding of GlnR to its targets genes, whereas acetylation had little influence on the formation of GlnR-DNA complex. This study clearly demonstrated that GlnR DNA-binding affinity is modulated by post-translational modifications in response to changing N-conditions in order to elicit a proper transcriptional response to the latter.
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Affiliation(s)
- Rafat Amin
- Department of Pathology, Dow International Medical College, Dow Research Institute of Biotechnology and Biomedical Sciences, Dow University of Health Sciences Karachi, Pakistan
| | - Mirita Franz-Wachtel
- Proteome Center Tübingen, Interdepartmental Institute for Cell Biology (IFIZ), University of Tübingen Tübingen, Germany
| | - Yvonne Tiffert
- B.R.A.I.N. Biotechnology Research and Information Network AG Zwingenberg, Germany
| | - Martin Heberer
- Microbiology and Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen Tübingen, Germany
| | - Mohamed Meky
- Microbiology and Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen Tübingen, Germany
| | - Yousra Ahmed
- Microbiology and Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, University of TübingenTübingen, Germany; Department of Pharmaceutical Biotechnology, Helmholtz Institute for Pharmaceutical Research Saarland, Saarland University CampusSaarbrücken, Germany
| | - Arne Matthews
- Microbiology and Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen Tübingen, Germany
| | - Sergii Krysenko
- Microbiology and Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen Tübingen, Germany
| | - Marco Jakobi
- Microbiology and Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen Tübingen, Germany
| | - Markus Hinder
- Microbiology and Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen Tübingen, Germany
| | - Jane Moore
- John Innes Center, Norwich Research Park Norwich, UK
| | - Nicole Okoniewski
- Microbiology and Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen Tübingen, Germany
| | - Boris Maček
- Proteome Center Tübingen, Interdepartmental Institute for Cell Biology (IFIZ), University of Tübingen Tübingen, Germany
| | - Wolfgang Wohlleben
- Microbiology and Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen Tübingen, Germany
| | - Agnieszka Bera
- Microbiology and Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen Tübingen, Germany
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Fascellaro G, Petrera A, Lai ZW, Nanni P, Grossmann J, Burger S, Biniossek ML, Gomez-Auli A, Schilling O, Imkamp F. Comprehensive Proteomic Analysis of Nitrogen-Starved Mycobacterium smegmatis Δpup Reveals the Impact of Pupylation on Nitrogen Stress Response. J Proteome Res 2016; 15:2812-25. [PMID: 27378031 DOI: 10.1021/acs.jproteome.6b00378] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Pupylation is a bacterial ubiquitin-like protein modification pathway, which results in the attachment of the small protein Pup to specific lysine residues of cellular targets. Pup was shown to serve as a degradation signal, directing proteins toward the bacterial proteasome for turnover. Recently, it was hypothesized that pupylation and proteasomal protein degradation support the survival of Mycobacterium smegmatis (Msm) during nitrogen starvation by supplying recycled amino acids. In the present study we generated a Pup deletion strain to investigate the influence of pupylation on Msm proteome in the absence of nitrogen sources. Quantitative proteomic analyses revealed a relatively low impact of Pup on MsmΔpup proteome immediately after exposure to growth medium lacking nitrogen. Less than 5.4% of the proteins displayed altered cellular levels when compared to Msm wild type. In contrast, post 24 h of nitrogen starvation 501 proteins (41% of the total quantified proteome) of Msm pup deletion strain showed significant changes in abundance. Noteworthy, important players involved in nitrogen assimilation were significantly affected in MsmΔpup. Furthermore, we quantified pupylated proteins of nitrogen-starved Msm to gain more detailed insights in the role of pupylation in surviving and overcoming the lack of nitrogen.
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Affiliation(s)
| | - Agnese Petrera
- Institute of Molecular Medicine and Cell Research, University of Freiburg , Freiburg, Germany
| | - Zon Weng Lai
- Institute of Molecular Medicine and Cell Research, University of Freiburg , Freiburg, Germany
| | - Paolo Nanni
- Functional Genomic Center, University of Zurich/ETH , Zurich, Switzerland
| | - Jonas Grossmann
- Functional Genomic Center, University of Zurich/ETH , Zurich, Switzerland
| | - Sibylle Burger
- Institute of Medical Microbiology, University of Zurich , Zurich, Switzerland
| | - Martin L Biniossek
- BIOSS Centre for Biological Signaling Studies, University of Freiburg , Freiburg, Germany
| | - Alejandro Gomez-Auli
- Institute of Molecular Medicine and Cell Research, University of Freiburg , Freiburg, Germany.,Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg , Freiburg, Germany.,Faculty of Biology, University of Freiburg , Freiburg, Germany
| | - Oliver Schilling
- Institute of Molecular Medicine and Cell Research, University of Freiburg , Freiburg, Germany.,BIOSS Centre for Biological Signaling Studies, University of Freiburg , Freiburg, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) , Heidelberg, Germany
| | - Frank Imkamp
- Institute of Medical Microbiology, University of Zurich , Zurich, Switzerland
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36
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Li Q, Ge F, Tan Y, Zhang G, Li W. Genome-Wide Transcriptome Profiling of Mycobacterium smegmatis MC² 155 Cultivated in Minimal Media Supplemented with Cholesterol, Androstenedione or Glycerol. Int J Mol Sci 2016; 17:E689. [PMID: 27164097 PMCID: PMC4881515 DOI: 10.3390/ijms17050689] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 04/12/2016] [Accepted: 04/28/2016] [Indexed: 11/16/2022] Open
Abstract
Mycobacterium smegmatis strain MC² 155 is an attractive model organism for the study of M. tuberculosis and other mycobacterial pathogens, as it can grow well using cholesterol as a carbon resource. However, its global transcriptomic response remains largely unrevealed. In this study, M. smegmatis MC² 155 cultivated in androstenedione, cholesterol and glycerol supplemented media were collected separately for a RNA-Sequencing study. The results showed that 6004, 6681 and 6348 genes were expressed in androstenedione, cholesterol and glycerol supplemented media, and 5891 genes were expressed in all three conditions, with 237 specially expressed in cholesterol added medium. A total of 1852 and 454 genes were significantly up-regulated by cholesterol compared with the other two supplements. Only occasional changes were observed in basic carbon and nitrogen metabolism, while almost all of the genes involved in cholesterol catabolism and mammalian cell entry (MCE) were up-regulated by cholesterol, but not by androstenedione. Eleven and 16 gene clusters were induced by cholesterol when compared with glycerol or androstenedione, respectively. This study provides a comprehensive analysis of the cholesterol responsive transcriptome of M. smegmatis. Our results indicated that cholesterol induced many more genes and increased the expression of the majority of genes involved in cholesterol degradation and MCE in M. smegmatis, while androstenedione did not have the same effect.
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Affiliation(s)
- Qun Li
- College of Life Sciences, Sichuan Normal University, Chengdu 610101, China.
| | - Fanglan Ge
- College of Life Sciences, Sichuan Normal University, Chengdu 610101, China.
| | - Yunya Tan
- College of Life Sciences, Sichuan Normal University, Chengdu 610101, China.
| | - Guangxiang Zhang
- College of Life Sciences, Sichuan Normal University, Chengdu 610101, China.
| | - Wei Li
- College of Life Sciences, Sichuan Normal University, Chengdu 610101, China.
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37
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Cen XF, Wang JZ, Zhao GP, Wang Y, Wang J. Molecular evidence for the coordination of nitrogen and carbon metabolisms, revealed by a study on the transcriptional regulation of the agl3EFG operon that encodes a putative carbohydrate transporter in Streptomyces coelicolor. Biochem Biophys Res Commun 2016; 471:510-4. [DOI: 10.1016/j.bbrc.2016.02.044] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 02/12/2016] [Indexed: 11/25/2022]
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38
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Petridis M, Benjak A, Cook GM. Defining the nitrogen regulated transcriptome of Mycobacterium smegmatis using continuous culture. BMC Genomics 2015; 16:821. [PMID: 26482235 PMCID: PMC4617892 DOI: 10.1186/s12864-015-2051-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 10/06/2015] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Nitrogen is essential for microbial growth and its importance is demonstrated by the complex regulatory systems used to control the transport, assimilation and metabolism of nitrogen. Recent studies are beginning to shed light on how mycobacteria respond to nitrogen limitation and several regulators (e.g., GlnR, PII) have been characterized at a molecular level. However, despite this progress, our knowledge of the transcriptional response of mycobacteria to nitrogen limitation and its regulation is confined to batch culture. METHODS To gain further insight into the response of mycobacteria to nitrogen limitation, we developed a nitrogen-limited chemostat. We compared the transcriptional response of nitrogen-limited cells to carbon-limited cells using RNA-seq analysis in a continuous culture model at a constant growth rate. CONCLUSIONS Our findings revealed significant changes in the expression of 357 genes (208 upregulated, 149 downregulated; >2-fold change, false discovery rate <5 %) in response to nitrogen limitation in continuous culture. The vast majority of the GlnR regulon (68 %) was differentially expressed under nitrogen limitation in continuous culture and approximately 52 % of the 357 genes overlapped with a previously published study investigating the response of M. smegmatis to nitrogen limitation in batch culture, while expression of only 17 % of the genes identified in batch culture were affected in our chemostat model. Moreover, we identified a unique set of 45 genes involved in the uptake and metabolism of nitrogen that were exclusive to our chemostat model. We observed strong downregulation of pathways for amino acid catabolism (i.e., alanine, aspartate, valine, proline and lysine), suggesting preservation of these amino acids for critical cellular function. We found 16 novel transcriptional regulators that were directly or indirectly involved in the global transcriptomic response of M. smegmatis to nitrogen limitation and identified several non-coding RNAs that might be involved in the transcriptional or post-transcriptional regulation of nitrogen-regulated gene expression. RESULTS Using nitrogen-limited continuous culture we identified the nitrogen-responsive transcriptome of M. smegmatis, including a number of small non-coding RNAs implicated in controlling nitrogen-regulated gene expression.
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Affiliation(s)
- Michael Petridis
- Department of Microbiology and Immunology, Otago School of Medical Sciences, University of Otago, P.O. Box 56, Dunedin, New Zealand. .,Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Auckland, 1042, New Zealand.
| | - Andrej Benjak
- Global Health Institute, École Polytechnique Fédérale de Lausanne, Lausanne, 1015, Switzerland.
| | - Gregory M Cook
- Department of Microbiology and Immunology, Otago School of Medical Sciences, University of Otago, P.O. Box 56, Dunedin, New Zealand. .,Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Auckland, 1042, New Zealand.
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39
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Hampel A, Huber C, Geffers R, Spona-Friedl M, Eisenreich W, Bange FC. Mycobacterium tuberculosis Is a Natural Ornithine Aminotransferase (rocD) Mutant and Depends on Rv2323c for Growth on Arginine. PLoS One 2015; 10:e0136914. [PMID: 26368558 PMCID: PMC4569260 DOI: 10.1371/journal.pone.0136914] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 08/10/2015] [Indexed: 11/18/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) possesses a genetic repertoire for metabolic pathways, which are specific and fit to its intracellular life style. Under in vitro conditions, Mtb is known to use arginine as a nitrogen source, but the metabolic pathways for arginine utilization have not been identified. Here we show that, in the presence of arginine, Mtb upregulates a gene cluster which includes an ornithine aminotransferase (rocD) and Rv2323c, a gene of unknown function. Isotopologue analysis by using 13C- or 15N-arginine revealed that in Mtb arginine is not only used as nitrogen source but also as carbon source for the formation of amino acids, in particular of proline. Surprisingly, rocD, which is widespread in other bacteria and is part of the classical arginase pathway turned out to be naturally deleted in Mtb, but not in non-tuberculous mycobacteria. Mtb lacking Rv2323c showed a growth defect on arginine, did not produce proline from arginine, and incorporated less nitrogen derived from arginine in its core nitrogen metabolism. We conclude that the highly induced pathway for arginine utilization in Mtb differs from that of other bacteria including non-tuberculous mycobacteria, probably reflecting a specific metabolic feature of intracellular Mtb.
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Affiliation(s)
- Annegret Hampel
- Department of Medical Microbiology and Hospital Epidemiology, Medical School Hannover, 30625 Hanover, Germany
| | - Claudia Huber
- Lehrstuhl für Biochemie, Technische Universität München, Garching, Germany
| | - Robert Geffers
- Research Group Genome Analytics, Helmholtz Center for Infection Research, 38124 Braunschweig, Germany
| | | | | | - Franz-Christoph Bange
- Department of Medical Microbiology and Hospital Epidemiology, Medical School Hannover, 30625 Hanover, Germany
- * E-mail:
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40
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Williams KJ, Jenkins VA, Barton GR, Bryant WA, Krishnan N, Robertson BD. Deciphering the metabolic response of Mycobacterium tuberculosis to nitrogen stress. Mol Microbiol 2015; 97:1142-57. [PMID: 26077160 PMCID: PMC4950008 DOI: 10.1111/mmi.13091] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/12/2014] [Indexed: 12/21/2022]
Abstract
A key component to the success of Mycobacterium tuberculosis as a pathogen is the ability to sense and adapt metabolically to the diverse range of conditions encountered in vivo, such as oxygen tension, environmental pH and nutrient availability. Although nitrogen is an essential nutrient for every organism, little is known about the genes and pathways responsible for nitrogen assimilation in M. tuberculosis. In this study we have used transcriptomics and chromatin immunoprecipitation and high‐throughput sequencing to address this. In response to nitrogen starvation, a total of 185 genes were significantly differentially expressed (96 up‐regulated and 89 down regulated; 5% genome) highlighting several significant areas of metabolic change during nitrogen limitation such as nitrate/nitrite metabolism, aspartate metabolism and changes in cell wall biosynthesis. We identify GlnR as a regulator involved in the nitrogen response, controlling the expression of at least 33 genes in response to nitrogen limitation. We identify a consensus GlnR binding site and relate its location to known transcriptional start sites. We also show that the GlnR response regulator plays a very different role in M. tuberculosis to that in non‐pathogenic mycobacteria, controlling genes involved in nitric oxide detoxification and intracellular survival instead of genes involved in nitrogen scavenging.
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Affiliation(s)
- Kerstin J Williams
- MRC Centre for Molecular Bacteriology and Infection, Department of Medicine, Imperial College London, London, SW7 2AZ, UK
| | - Victoria A Jenkins
- MRC Centre for Molecular Bacteriology and Infection, Department of Medicine, Imperial College London, London, SW7 2AZ, UK
| | - Geraint R Barton
- Centre for Integrative Systems Biology and Bioinformatics, Imperial College London, London, SW7 2AZ, UK
| | - William A Bryant
- Centre for Integrative Systems Biology and Bioinformatics, Imperial College London, London, SW7 2AZ, UK
| | - Nitya Krishnan
- MRC Centre for Molecular Bacteriology and Infection, Department of Medicine, Imperial College London, London, SW7 2AZ, UK
| | - Brian D Robertson
- MRC Centre for Molecular Bacteriology and Infection, Department of Medicine, Imperial College London, London, SW7 2AZ, UK.,Centre for Integrative Systems Biology and Bioinformatics, Imperial College London, London, SW7 2AZ, UK
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41
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GlnR-Mediated Regulation of ectABCD Transcription Expands the Role of the GlnR Regulon to Osmotic Stress Management. J Bacteriol 2015; 197:3041-7. [PMID: 26170409 DOI: 10.1128/jb.00185-15] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2015] [Accepted: 07/03/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Ectoine and hydroxyectoine are excellent compatible solutes for bacteria to deal with environmental osmotic stress and temperature damages. The biosynthesis cluster of ectoine and hydroxyectoine is widespread among microorganisms, and its expression is activated by high salinity and temperature changes. So far, little is known about the mechanism of the regulation of the transcription of ect genes and only two MarR family regulators (EctR1 in methylobacteria and the EctR1-related regulator CosR in Vibrio cholerae) have been found to negatively regulate the expression of ect genes. Here, we characterize GlnR, the global regulator for nitrogen metabolism in actinomycetes, as a negative regulator for the transcription of ectoine/hydroxyectoine biosynthetic genes (ect operon) in Streptomyces coelicolor. The physiological role of this transcriptional repression by GlnR is proposed to protect the intracellular glutamate pool, which acts as a key nitrogen donor for both the nitrogen metabolism and the ectoine/hydroxyectoine biosynthesis. IMPORTANCE High salinity is deleterious, and cells must evolve sophisticated mechanisms to cope with this osmotic stress. Although production of ectoine and hydroxyectoine is one of the most frequently adopted strategies, the in-depth mechanism of regulation of their biosynthesis is less understood. So far, only two MarR family negative regulators, EctR1 and CosR, have been identified in methylobacteria and Vibrio, respectively. Here, our work demonstrates that GlnR, the global regulator for nitrogen metabolism, is a negative transcriptional regulator for ect genes in Streptomyces coelicolor. Moreover, a close relationship is found between nitrogen metabolism and osmotic resistance, and GlnR-mediated regulation of ect transcription is proposed to protect the intracellular glutamate pool. Meanwhile, the work reveals the multiple roles of GlnR in bacterial physiology.
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42
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Shao ZH, Ren SX, Liu XQ, Xu J, Yan H, Zhao GP, Wang J. A preliminary study of the mechanism of nitrate-stimulated remarkable increase of rifamycin production in Amycolatopsis mediterranei U32 by RNA-seq. Microb Cell Fact 2015; 14:75. [PMID: 26041361 PMCID: PMC4453227 DOI: 10.1186/s12934-015-0264-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 05/11/2015] [Indexed: 01/15/2023] Open
Abstract
Background Rifamycin is an important antibiotic for the treatment of infectious disease caused by Mycobacteria tuberculosis. It was found that in Amycolatopsis mediterranei U32, an industrial producer for rifamycin SV, supplementation of nitrate into the medium remarkably stimulated the yield of rifamycin SV. However, the molecular mechanism of this nitrate-mediated stimulation remains unknown. Results In this study, RNA-sequencing (RNA-seq) technology was employed for investigation of the genome-wide differential gene expression in U32 cultured with or without nitrate supplementation. In the presence of nitrate, U32 maintained a high transcriptional level of genes both located in the rifamycin biosynthetic cluster and involved in the biosynthesis of rifamycin precursors, including 3-amino-5-dihydroxybenzoic acid, malonyl-CoA and (S)-methylmalonyl-CoA. However, when nitrate was omitted from the medium, the transcription of these genes declined sharply during the transition from the mid-logarithmic phase to the early stationary phase. With these understandings, one may easily propose that nitrate stimulates the rifamycin SV production through increasing both the precursors supply and the enzymes for rifamycin biosynthesis. Conclusion It is the first time to thoroughly illustrate the mechanism of the nitrate-mediated stimulation of rifamycin production at the transcriptional level, which may facilitate improvement of the industrial production of rifamycin SV, e.g. through optimizing the global rifamycin biosynthetic pathways on the basis of RNA-seq data. Electronic supplementary material The online version of this article (doi:10.1186/s12934-015-0264-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zhi Hui Shao
- CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 20032, China.
| | - Shuang Xi Ren
- CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 20032, China.
| | - Xin Qiang Liu
- CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 20032, China.
| | - Jian Xu
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China.
| | - Han Yan
- CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 20032, China.
| | - Guo Ping Zhao
- CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 20032, China. .,State Key Lab of Genetic Engineering and Center for Synthetic Biology, Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai, 200032, China. .,Shanghai-MOST Key Laboratory of Disease and Health Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, 201203, China. .,Department of Microbiology and Li KaShing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong Sar, China.
| | - Jin Wang
- CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 20032, China.
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Wang J, Wang Y, Zhao GP. Precise characterization of GlnR Box in actinomycetes. Biochem Biophys Res Commun 2015; 458:605-607. [PMID: 25684190 DOI: 10.1016/j.bbrc.2015.02.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 02/03/2015] [Indexed: 11/16/2022]
Abstract
GlnR has been characterized as a central regulator governing most nitrogen metabolisms in many important actinomycetes. So far, the GlnR binding consensus sequences have been extensively studied, but with different motifs proposed, which has therefore brought confusion and impeded the understanding of the in-depth molecular mechanisms of GlnR-mediated transcriptional regulation. Here, a 30-nt GlnR-protected DNA sequence in the promoter of glnA in Amycolatopsis mediterranei was employed for precise characterization of GlnR binding consensus sequences. Site-by-site mutagenesis strategy combining with the Electrophoretic Mobility Shift Assay were employed, and a 5-nt GlnR Box was precisely defined as the basic unit for GlnR binding.
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Affiliation(s)
- Jin Wang
- CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.
| | - Ying Wang
- CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Guo-Ping Zhao
- CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China; State Key Laboratory of Genetic Engineering, Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai, China; Shanghai-MOST Key Laboratory for Health and Disease Genomics, Chinese National Human Genome Center, Shanghai, China; Department of Microbiology and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong Special Administrative Region
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Drapal M, Perez-Fons L, Wheeler PR, Fraser PD. The application of metabolite profiling to Mycobacterium spp.: Determination of metabolite changes associated with growth. J Microbiol Methods 2014; 106:23-32. [DOI: 10.1016/j.mimet.2014.07.037] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Revised: 07/29/2014] [Accepted: 07/29/2014] [Indexed: 11/27/2022]
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Abstract
Several major pathogens, including Mycobacterium tuberculosis, parasitize host cells and exploit host-derived nutrients to sustain their own metabolism. Although the carbon sources that are used by M. tuberculosis have been extensively studied, the mechanisms by which mycobacteria capture and metabolize nitrogen, which is another essential constituent of biomolecules, have only recently been revisited. In this Progress article, we discuss central nitrogen metabolism in M. tuberculosis, the mechanisms that are used by this pathogen to obtain nitrogen from its host and the potential role of nitrogen capture and metabolism in virulence.
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GlnR negatively regulates the transcription of the alanine dehydrogenase encoding gene ald in Amycolatopsis mediterranei U32 under nitrogen limited conditions via specific binding to its major transcription initiation site. PLoS One 2014; 9:e104811. [PMID: 25144373 PMCID: PMC4140684 DOI: 10.1371/journal.pone.0104811] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 07/14/2014] [Indexed: 11/25/2022] Open
Abstract
Ammonium assimilation is catalyzed by two enzymatic pathways, i.e., glutamine synthetase/glutamate synthase (GS/GOGAT) and alanine dehydrogenase (AlaDH) in Amycolatopsis mediterranei U32. Under nitrogen-rich conditions, the AlaDH pathway is the major route for ammonium assimilation, while the GS/GOGAT pathway takes over when the extracellular nitrogen supply is limited. The global nitrogen regulator GlnR was previously characterized to activate the transcription of the GS encoding gene glnA in response to nitrogen limitation and is demonstrated in this study as a repressor for the transcription of the AlaDH encoding gene ald, whose regulation is consistent with the switch of the ammonium assimilation pathways from AlaDH to GS/GOGAT responding to nitrogen limitation. Three transcription initiation sites (TISs) of ald were determined with primer extension assay, among which transcription from aldP2 contributed the major transcripts under nitrogen-rich conditions but was repressed to an undetectable level in response to nitrogen limitation. Through DNase I footprinting assay, two separate regions were found to be protected by GlnR within ald promoter, within which three GlnR binding sites (a1, b1 sites in region I and a2 site in region II) were defined. Interestingly, the major TIS aldP2 is located in the middle of a2 site within region II. Therefore, one may easily conclude that GlnR represses the transcription of ald via specific binding to the GlnR binding sites, which obviously blocks the transcription initiation from aldP2 and therefore reduces ald transcripts.
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Elharar Y, Roth Z, Hermelin I, Moon A, Peretz G, Shenkerman Y, Vishkautzan M, Khalaila I, Gur E. Survival of mycobacteria depends on proteasome-mediated amino acid recycling under nutrient limitation. EMBO J 2014; 33:1802-14. [PMID: 24986881 DOI: 10.15252/embj.201387076] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Intracellular protein degradation is an essential process in all life domains. While in all eukaryotes regulated protein degradation involves ubiquitin tagging and the 26S-proteasome, bacterial prokaryotic ubiquitin-like protein (Pup) tagging and proteasomes are conserved only in species belonging to the phyla Actinobacteria and Nitrospira. In Mycobacterium tuberculosis, the Pup-proteasome system (PPS) is important for virulence, yet its physiological role in non-pathogenic species has remained an enigma. We now report, using Mycobacterium smegmatis as a model organism, that the PPS is essential for survival under starvation. Upon nitrogen limitation, PPS activity is induced, leading to accelerated tagging and degradation of many cytoplasmic proteins. We suggest a model in which the PPS functions to recycle amino acids under nitrogen starvation, thereby enabling the cell to maintain basal metabolic activities. We also find that the PPS auto-regulates its own activity via pupylation and degradation of its components in a manner that promotes the oscillatory expression of PPS components. As such, the destructive activity of the PPS is carefully balanced to maintain cellular functions during starvation.
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Affiliation(s)
- Yifat Elharar
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Ziv Roth
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Inna Hermelin
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Alexandra Moon
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Gabriella Peretz
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Yael Shenkerman
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Marina Vishkautzan
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Isam Khalaila
- The Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Eyal Gur
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
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Ventura M, Rieck B, Boldrin F, Degiacomi G, Bellinzoni M, Barilone N, Alzaidi F, Alzari PM, Manganelli R, O'Hare HM. GarA is an essential regulator of metabolism in Mycobacterium tuberculosis. Mol Microbiol 2013; 90:356-66. [PMID: 23962235 DOI: 10.1111/mmi.12368] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/15/2013] [Indexed: 01/16/2023]
Abstract
Alpha-ketoglutarate is a key metabolic intermediate at the crossroads of carbon and nitrogen metabolism, whose fate is tightly regulated. In mycobacteria the protein GarA regulates the tricarboxylic acid cycle and glutamate synthesis by direct binding and regulation of three enzymes that use α-ketoglutarate. GarA, in turn, is thought to be regulated via phosphorylation by protein kinase G and other kinases. We have investigated the requirement for GarA for metabolic regulation during growth in vitro and in macrophages. GarA was found to be essential to Mycobacterium tuberculosis, but dispensable in non-pathogenic Mycobacterium smegmatis. Disruption of garA caused a distinctive, nutrient-dependent phenotype, fitting with its proposed role in regulating glutamate metabolism. The data underline the importance of the TCA cycle and the balance with glutamate synthesis in M. tuberculosis and reveal vulnerability to disruption of these pathways.
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Affiliation(s)
- Marcello Ventura
- Department of Molecular Medicine, University of Padua, Via Gabelli 63, Padova, Italy
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Williams KJ, Bryant WA, Jenkins VA, Barton GR, Witney AA, Pinney JW, Robertson BD. Deciphering the response of Mycobacterium smegmatis to nitrogen stress using bipartite active modules. BMC Genomics 2013; 14:436. [PMID: 23819599 PMCID: PMC3706326 DOI: 10.1186/1471-2164-14-436] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Accepted: 06/20/2013] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND The ability to adapt to environments with fluctuating nutrient availability is vital for bacterial survival. Although essential for growth, few nitrogen metabolism genes have been identified or fully characterised in mycobacteria and nitrogen stress survival mechanisms are unknown. RESULTS A global transcriptional analysis of the mycobacterial response to nitrogen stress, showed a significant change in the differential expression of 16% of the Mycobacterium smegmatis genome. Gene expression changes were mapped onto the metabolic network using Active Modules for Bipartite Networks (AMBIENT) to identify metabolic pathways showing coordinated transcriptional responses to the stress. AMBIENT revealed several key features of the metabolic response not identified by KEGG enrichment alone. Down regulated reactions were associated with the general reduction in cellular metabolism as a consequence of reduced growth rate. Up-regulated modules highlighted metabolic changes in nitrogen assimilation and scavenging, as well as reactions involved in hydrogen peroxide metabolism, carbon scavenging and energy generation. CONCLUSIONS Application of an Active Modules algorithm to transcriptomic data identified key metabolic reactions and pathways altered in response to nitrogen stress, which are central to survival under nitrogen limiting environments.
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Affiliation(s)
- Kerstin J Williams
- Department of Medicine, MRC Centre for Molecular Bacteriology and Infection, South Kensington, London SW7 2AZ, UK
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