1
|
Wang Y, Fu H, Shi XJ, Zhao GP, Lyu LD. Genome-wide screen reveals cellular functions that counteract rifampicin lethality in Escherichia coli. Microbiol Spectr 2024; 12:e0289523. [PMID: 38054714 PMCID: PMC10782999 DOI: 10.1128/spectrum.02895-23] [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: 07/19/2023] [Accepted: 10/31/2023] [Indexed: 12/07/2023] Open
Abstract
IMPORTANCE Rifamycins are a group of antibiotics with a wide antibacterial spectrum. Although the binding target of rifamycin has been well characterized, the mechanisms underlying the discrepant killing efficacy between gram-negative and gram-positive bacteria remain poorly understood. Using a high-throughput screen combined with targeted gene knockouts in the gram-negative model organism Escherichia coli, we established that rifampicin efficacy is strongly dependent on several cellular pathways, including iron acquisition, DNA repair, aerobic respiration, and carbon metabolism. In addition, we provide evidence that these pathways modulate rifampicin efficacy in a manner distinct from redox-related killing. Our findings provide insights into the mechanism of rifamycin efficacy and may aid in the development of new antimicrobial adjuvants.
Collapse
Affiliation(s)
- Yu Wang
- Key Laboratory of Medical Molecular Virology of the Ministry of Education/National Health Commission, School of Basic Medical Sciences and Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Han Fu
- Key Laboratory of Medical Molecular Virology of the Ministry of Education/National Health Commission, School of Basic Medical Sciences and Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai, China
- CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiao-Jie Shi
- Key Laboratory of Medical Molecular Virology of the Ministry of Education/National Health Commission, School of Basic Medical Sciences and Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Guo-Ping Zhao
- Key Laboratory of Medical Molecular Virology of the Ministry of Education/National Health Commission, School of Basic Medical Sciences and Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai, China
- CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Liang-Dong Lyu
- Key Laboratory of Medical Molecular Virology of the Ministry of Education/National Health Commission, School of Basic Medical Sciences and Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Tuberculosis, Shanghai Clinical Research Center for Infectious Disease (Tuberculosis), Shanghai Pulmonary Hospital, Shanghai, China
| |
Collapse
|
2
|
Wan Y, Wai Chi Chan E, Chen S. Maintenance and generation of proton motive force are both essential for expression of phenotypic antibiotic tolerance in bacteria. Microbiol Spectr 2023; 11:e0083223. [PMID: 37623371 PMCID: PMC10580908 DOI: 10.1128/spectrum.00832-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 07/11/2023] [Indexed: 08/26/2023] Open
Abstract
Bacterial antibiotic tolerance, a phenomenon first observed in 1944, is known to be responsible for both onset and exacerbation of recurrent and chronic bacterial infections. The development of antibiotic tolerance was previously thought to be due to a switch to physiological dormancy when bacteria encounter adverse growth conditions. Our recent laboratory findings, however, showed that a set of genes related to the maintenance of proton motive force (PMF) are up-regulated under starvation, indicating that the tolerant sub-population, which are commonly known as persisters, can actively maintain their tolerance phenotypes. In this study, we investigated the relative functional roles of proteins involved in the maintenance and active generation of PMF in mediating tolerance formation in bacteria and found that the PspA and RcsB proteins play a key role in PMF maintenance in persisters, as deletion of genes encoding these two proteins resulted in significantly lower tolerance levels. Consistently, expression of the OsmC and Bdm proteins, which is under regulation by RcsB, is required to maintain PMF and the antibiotic tolerance phenotypes. On the other hand, the NuoL, Ndh, AppC, CyoB, and NuoF proteins, which are electron transport chain (ETC) components, were also found to be actively expressed in persisters in order to generate PMF to support functioning of various tolerance mechanisms such as efflux activities. Our data show that active generation of PMF is even more important than the PMF maintenance functions of PspA and RcsB in the expression of antibiotic tolerance phenotypes in persisters. Assessment of double- and triple-gene knockout strains, in which the PMF maintenance genes and those encoding ETC components were simultaneously deleted, confirms that these two groups of genes are both required for the expression of antibiotic tolerance phenotypes and that a lack of these functions would result in complete PMF dissipation and accumulation of antibiotics in the intracellular compartment of persisters and eventually cell death. Products of these genes are, therefore, ideal targets for future development of anti-tolerance agents. IMPORTANCE In this work, bacteria were found to undergo active generation and maintenance of proton motive force (PMF) under adverse conditions, such as starvation so as to support a range of physiological functions in order to survive under such conditions for a prolonged period. The ability to maintain a substantial level of PMF was found to be directly linked to that exhibiting phenotypic antibiotic tolerance under nutrient starvation or other adverse conditions. These findings infer that bacteria do not simply become physiologically dormant when they become antibiotic tolerant, instead they need to produce a wide range of proteins including those which help prevent PMF dissipation, such as PspA and RcsB, and the electron transport chain components, such as NuoL and Ndh, that actively generate PMF even during long-term starvation. As antibiotic tolerant sub-population is known to play a role in eliciting recurrent and chronic infections, especially among patients with a weakened immune system, the PMF maintenance mechanisms identified in this work are potential targets for the development of new strategies to control recurrent and chronic infections.
Collapse
Affiliation(s)
- Yingkun Wan
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Edward Wai Chi Chan
- Department of Applied Biology and Chemical Technology, State Key Lab of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - Sheng Chen
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong
- Department of Applied Biology and Chemical Technology, State Key Lab of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
- City University of Hong Kong Chendu Research Institute, Chengdu, China
- Shenzhen Key Lab for Food Biological Safety Control, Hong Kong PolyU Shenzhen Research Institute, Shenzhen, China
| |
Collapse
|
3
|
Gagnon JC, Beauregard-Tousignant S, Marcil JS, Lazar CS. Deep Isolated Aquifer Brines Harbor Atypical Halophilic Microbial Communities in Quebec, Canada. Genes (Basel) 2023; 14:1529. [PMID: 37628582 PMCID: PMC10454208 DOI: 10.3390/genes14081529] [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: 06/15/2023] [Revised: 07/21/2023] [Accepted: 07/24/2023] [Indexed: 08/27/2023] Open
Abstract
The deep terrestrial subsurface, hundreds of meters to kilometers below the surface, is characterized by oligotrophic conditions, dark and often anoxic settings, with fluctuating pH, salinity, and water availability. Despite this, microbial populations are detected and active, contributing to biogeochemical cycles over geological time. Because it is extremely difficult to access the deep biosphere, little is known about the identity and metabolisms of these communities, although they likely possess unknown pathways and might interfere with deep waste deposits. Therefore, we analyzed rock and groundwater microbial communities from deep, isolated brine aquifers in two regions dating back to the Ordovician and Devonian, using amplicon and whole genome sequencing. We observed significant differences in diversity and community structure between both regions, suggesting an impact of site age and composition. The deep hypersaline groundwater did not contain typical halophilic bacteria, and genomes suggested pathways involved in protein and hydrocarbon degradation, and carbon fixation. We identified mainly one strategy to cope with osmotic stress: compatible solute uptake and biosynthesis. Finally, we detected many bacteriophage families, potentially indicating that bacteria are infected. However, we also found auxiliary metabolic genes in the viral genomes, probably conferring an advantage to the infected hosts.
Collapse
Affiliation(s)
- Jean-Christophe Gagnon
- Department of Biological Sciences, University of Québec at Montréal (UQAM), C.P. 8888, Succ. Centre-Ville, Montréal, QC H3C 3P8, Canada; (J.-C.G.); (S.B.-T.)
- Interuniversity Research Group in Limnology/Groupe de Recherche Interuniversitaire en Limnologie (GRIL), Montréal, QC H3C 3P8, Canada
| | - Samuel Beauregard-Tousignant
- Department of Biological Sciences, University of Québec at Montréal (UQAM), C.P. 8888, Succ. Centre-Ville, Montréal, QC H3C 3P8, Canada; (J.-C.G.); (S.B.-T.)
| | - Jean-Sébastien Marcil
- Derena Geosciences, Quebec, QC G7A 3Y5, Canada;
- Ressources Utica Inc., Quebec, QC G1V 4M7, Canada
| | - Cassandre Sara Lazar
- Department of Biological Sciences, University of Québec at Montréal (UQAM), C.P. 8888, Succ. Centre-Ville, Montréal, QC H3C 3P8, Canada; (J.-C.G.); (S.B.-T.)
| |
Collapse
|
4
|
Cho SG, Song M, Chuon K, Shim JG, Meas S, Jung KH. Heliorhodopsin binds and regulates glutamine synthetase activity. PLoS Biol 2022; 20:e3001817. [PMID: 36190943 PMCID: PMC9529153 DOI: 10.1371/journal.pbio.3001817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 09/06/2022] [Indexed: 11/05/2022] Open
Abstract
Photoreceptors are light-sensitive proteins found in various organisms that respond to light and relay signals into the cells. Heliorhodopsin, a retinal-binding membrane protein, has been recently discovered, however its function remains unknown. Herein, we investigated the relationship between Actinobacteria bacterium IMCC26103 heliorhodopsin (AbHeR) and an adjacent glutamine synthetase (AbGS) in the same operon. We demonstrate that AbHeR binds to AbGS and regulates AbGS activity. More specifically, the dissociation constant (Kd) value of the binding between AbHeR and AbGS is 6.06 μM. Moreover, the absence of positively charged residues within the intracellular loop of AbHeR impacted Kd value as they serve as critical binding sites for AbGS. We also confirm that AbHeR up-regulates the biosynthetic enzyme activity of AbGS both in vitro and in vivo in the presence of light. GS is a key enzyme involved in nitrogen assimilation that catalyzes the conversion of glutamate and ammonia to glutamine. Hence, the interaction between AbHeR and AbGS may be critical for nitrogen assimilation in Actinobacteria bacterium IMCC26103 as it survives in low-nutrient environments. Overall, the findings of our study describe, for the first time, to the best of our knowledge, a novel function of heliorhodopsin as a regulatory rhodopsin with the capacity to bind and regulate enzyme activity required for nitrogen assimilation. A study of heliorhodopsin, an actinobacterial photoreceptor of unknown function, reveals that it interacts with glutamine synthetase, an enzyme involved in nitrogen assimilation, and regulates its activity in the presence of light, highlighting the diverse functions of rhodopsins in different organisms.
Collapse
Affiliation(s)
- Shin-Gyu Cho
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul, Korea,Research Institute for Basic Science, Sogang University, Seoul, Korea
| | - Myungchul Song
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul, Korea
| | - Kimleng Chuon
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul, Korea
| | - Jin-gon Shim
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul, Korea
| | - Seanghun Meas
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul, Korea,Department of Biology, Faculty of Science, Royal University of Phnom Penh, Phnom Penh, Cambodia
| | - Kwang-Hwan Jung
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul, Korea,* E-mail:
| |
Collapse
|
5
|
Tang Z, Chen H, Chen W, Zhong Q, Zhang M, Chen W, Yun YH. Unraveling the antibacterial mechanism of 3-carene against Pseudomonas fragi by integrated proteomics and metabolomics analyses and its application in pork. Int J Food Microbiol 2022; 379:109846. [PMID: 35908494 DOI: 10.1016/j.ijfoodmicro.2022.109846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 06/11/2022] [Accepted: 07/18/2022] [Indexed: 11/25/2022]
Abstract
Pseudomonas fragi is primarily responsible for the spoilage of various foods, especially meat. The aim of this study was to investigate the antibacterial mechanism of 3-carene against P. fragi. 3-Carene treatment decreased the phospholipid content and the fluidity of the cell membrane, induced reactive oxygen species (ROS) generation and affected respiratory chain dehydrogenase, oxoglutarate dehydrogenase and citrate synthase in P. fragi. Metabolomics and proteomics analyses further showed that in the presence of 3-carene, 519 proteins, 136 metabolites in positive ion mode and 100 metabolites in negative ion mode were differentially expressed. These proteins and metabolites were primarily involved in amino acid metabolism, fatty acid degradation, the tricarboxylic acid cycle (TCA cycle) and other processes. Consequently, the stimulation of 3-carene altered cell membrane properties, disturbed important amino acid and energy metabolism, and even caused oxidative stress. Additionally, the results of total viable counts and the total volatile base nitrogen indicated that 3-carene could significantly improve the preservation of refrigerated pork. This study suggested that 3-carene has promising potential to be developed as a food preservative.
Collapse
Affiliation(s)
- Zhiling Tang
- School of Food Sciences & Engineering, Hainan University, 58 People Road, Haikou 570228, PR China
| | - Haiming Chen
- School of Food Sciences & Engineering, Hainan University, 58 People Road, Haikou 570228, PR China
| | - Weijun Chen
- School of Food Sciences & Engineering, Hainan University, 58 People Road, Haikou 570228, PR China
| | - Qiuping Zhong
- School of Food Sciences & Engineering, Hainan University, 58 People Road, Haikou 570228, PR China
| | - Ming Zhang
- School of Food Sciences & Engineering, Hainan University, 58 People Road, Haikou 570228, PR China
| | - Wenxue Chen
- School of Food Sciences & Engineering, Hainan University, 58 People Road, Haikou 570228, PR China.
| | - Yong-Huan Yun
- School of Food Sciences & Engineering, Hainan University, 58 People Road, Haikou 570228, PR China.
| |
Collapse
|
6
|
Ranjani J, Sivakumar R, Gunasekaran P, Velmurugan G, Ramasamy S, Rajendhran J. Genome-wide identification of genetic requirements of Pseudomonas aeruginosa PAO1 for rat cardiomyocyte (H9C2) infection by insertion sequencing. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 98:105231. [PMID: 35104681 DOI: 10.1016/j.meegid.2022.105231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 12/18/2021] [Accepted: 01/25/2022] [Indexed: 10/19/2022]
Abstract
Pseudomonas aeruginosa is a major infectious agent among Gram-negative bacteria, which causes both acute and chronic infections. Infections due to P. aeruginosa are hard to treat, as it entails various strategies like virulence factors synthesis, drug efflux systems & resistance and protein secretion systems during pathogenesis. Despite extensive research in Pseudomonas pathogenesis, novel drug targets and potential therapeutic strategies are urgently needed. In this study, we investigated the genetic requirements of P. aeruginosa PAO1 for rat cardiomyocyte (H9C2) infection by insertion sequencing (INSeq). A mutant library comprising ~70,000 mutants of PAO1 was generated and the differentiated form of H9C2 cells (d-H9C2) was infected with the library. The infected d-H9C2 cells were maintained with antibiotic-protection and without any antibiotics in the growth media for 24 h. Subsequently, DNA library for INSeq was prepared, sequenced and fitness analysis was performed. One hundred and thirteen mutants were negatively selected in the infection condition with antibiotic-protection, whereas 143 mutants were negatively selected in antibiotic-free condition. Surprisingly, a higher number of mutants showed enriched fitness than the mutants of reduced fitness during the infection. We demonstrated that the genes associated with flagella and T3SS are important for adhesion and invasion of cardiomyocytes, while pili and proteases are conditionally essential during host cell lysis. Hence, our findings highlight the essential genes for cardiomyocyte infection, particularly during the intracellular phase. The aerotaxis receptor Aer, plays a critical role during intracellular life. Genes such as flgE, flgF, flhA, flhB, fliA, fliC, fliF, motA, aotJ, aer, wbpJ, ponA, fleQ, PA5205, hmgA, trkH and pslH are essential for infection.
Collapse
Affiliation(s)
- Jothi Ranjani
- Department of Genetics, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai 625021, Tamil Nadu, India
| | - Ramamoorthy Sivakumar
- Department of Genetics, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai 625021, Tamil Nadu, India
| | - Paramasamy Gunasekaran
- Department of Genetics, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai 625021, Tamil Nadu, India
| | - Ganesan Velmurugan
- Chemomicrobiomics Laboratory, Department of Biochemistry & Microbiology, KMCH Research Foundation, Coimbatore 641014, Tamil Nadu, India
| | - Subbiah Ramasamy
- Cardiac Hypertrophy Laboratory, Department of Molecular Biology, School of Biological Sciences, Madurai Kamaraj University, Madurai 625 021, Tamil Nadu, India
| | - Jeyaprakash Rajendhran
- Department of Genetics, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai 625021, Tamil Nadu, India.
| |
Collapse
|
7
|
Curtabbi A, Enríquez JA. The ins and outs of the flavin mononucleotide cofactor of respiratory complex I. IUBMB Life 2022; 74:629-644. [PMID: 35166025 DOI: 10.1002/iub.2600] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 01/23/2022] [Accepted: 01/24/2022] [Indexed: 12/12/2022]
Abstract
The flavin mononucleotide (FMN) cofactor of respiratory complex I occupies a key position in the electron transport chain. Here, the electrons coming from NADH start the sequence of oxidoreduction reactions, which drives the generation of the proton-motive force necessary for ATP synthesis. The overall architecture and the general catalytic proprieties of the FMN site are mostly well established. However, several aspects regarding the complex I flavin cofactor are still unknown. For example, the flavin binding to the N-module, the NADH-oxidizing portion of complex I, lacks a molecular description. The dissociation of FMN from the enzyme is beginning to emerge as an important regulatory mechanism of complex I activity and ROS production. Finally, how mitochondria import and metabolize FMN is still uncertain. This review summarizes the current knowledge on complex I flavin cofactor and discusses the open questions for future research.
Collapse
Affiliation(s)
- Andrea Curtabbi
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain
| | - José Antonio Enríquez
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain.,Centro de Investigación Biomédica en Red en Fragilidad y Envejecimiento Saludable (CIBERFES), Instituto de Salud Carlos III, Madrid, Spain
| |
Collapse
|
8
|
Ansari F, Yoval-Sánchez B, Niatsetskaya Z, Sosunov S, Stepanova A, Garcia C, Owusu-Ansah E, Ten V, Wittig I, Galkin A. Quantification of NADH:ubiquinone oxidoreductase (complex I) content in biological samples. J Biol Chem 2021; 297:101204. [PMID: 34543622 PMCID: PMC8503622 DOI: 10.1016/j.jbc.2021.101204] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/26/2021] [Accepted: 08/31/2021] [Indexed: 12/14/2022] Open
Abstract
Impairments in mitochondrial energy metabolism have been implicated in human genetic diseases associated with mitochondrial and nuclear DNA mutations, neurodegenerative and cardiovascular disorders, diabetes, and aging. Alteration in mitochondrial complex I structure and activity has been shown to play a key role in Parkinson's disease and ischemia/reperfusion tissue injury, but significant difficulty remains in assessing the content of this enzyme complex in a given sample. The present study introduces a new method utilizing native polyacrylamide gel electrophoresis in combination with flavin fluorescence scanning to measure the absolute content of complex I, as well as α-ketoglutarate dehydrogenase complex, in any preparation. We show that complex I content is 19 ± 1 pmol/mg of protein in the brain mitochondria, whereas varies up to 10-fold in different mouse tissues. Together with the measurements of NADH-dependent specific activity, our method also allows accurate determination of complex I catalytic turnover, which was calculated as 104 min-1 for NADH:ubiquinone reductase in mouse brain mitochondrial preparations. α-ketoglutarate dehydrogenase complex content was determined to be 65 ± 5 and 123 ± 9 pmol/mg protein for mouse brain and bovine heart mitochondria, respectively. Our approach can also be extended to cultured cells, and we demonstrated that about 90 × 103 complex I molecules are present in a single human embryonic kidney 293 cell. The ability to determine complex I content should provide a valuable tool to investigate the enzyme status in samples after in vivo treatment in mutant organisms, cells in culture, or human biopsies.
Collapse
Affiliation(s)
- Fariha Ansari
- Division of Neonatology, Department of Pediatrics, Columbia University Medical Center, New York, New York, USA
| | - Belem Yoval-Sánchez
- Division of Neonatology, Department of Pediatrics, Columbia University Medical Center, New York, New York, USA
| | - Zoya Niatsetskaya
- Division of Neonatology, Department of Pediatrics, Columbia University Medical Center, New York, New York, USA
| | - Sergey Sosunov
- Division of Neonatology, Department of Pediatrics, Columbia University Medical Center, New York, New York, USA
| | - Anna Stepanova
- Division of Neonatology, Department of Pediatrics, Columbia University Medical Center, New York, New York, USA
| | - Christian Garcia
- Department of Physiology & Cellular Biophysics, Columbia University, New York, New York, USA
| | - Edward Owusu-Ansah
- Department of Physiology & Cellular Biophysics, Columbia University, New York, New York, USA
| | - Vadim Ten
- Division of Neonatology, Department of Pediatrics, Columbia University Medical Center, New York, New York, USA
| | - Ilka Wittig
- Functional Proteomics, Institute of Cardiovascular Physiology, Goethe University, Frankfurt am Main, Germany; German Center for Cardiovascular Research (DZHK), Partner site RheinMain, Frankfurt am Main, Germany
| | - Alexander Galkin
- Division of Neonatology, Department of Pediatrics, Columbia University Medical Center, New York, New York, USA; Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, New York, USA.
| |
Collapse
|
9
|
Schimpf J, Oppermann S, Gerasimova T, Santos Seica AF, Hellwig P, Grishkovskaya I, Wohlwend D, Haselbach D, Friedrich T. Structure of the peripheral arm of a minimalistic respiratory complex I. Structure 2021; 30:80-94.e4. [PMID: 34562374 DOI: 10.1016/j.str.2021.09.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 07/09/2021] [Accepted: 09/08/2021] [Indexed: 10/20/2022]
Abstract
Respiratory complex I drives proton translocation across energy-transducing membranes by NADH oxidation coupled with (ubi)quinone reduction. In humans, its dysfunction is associated with neurodegenerative diseases. The Escherichia coli complex represents the structural minimal form of an energy-converting NADH:ubiquinone oxidoreductase. Here, we report the structure of the peripheral arm of the E. coli complex I consisting of six subunits, the FMN cofactor, and nine iron-sulfur clusters at 2.7 Å resolution obtained by cryo electron microscopy. While the cofactors are in equivalent positions as in the complex from other species, individual subunits are adapted to the absence of supernumerary proteins to guarantee structural stability. The catalytically important subunits NuoC and D are fused resulting in a specific architecture of functional importance. Striking features of the E. coli complex are scrutinized by mutagenesis and biochemical characterization of the variants. Moreover, the arrangement of the subunits sheds light on the unknown assembly of the complex.
Collapse
Affiliation(s)
- Johannes Schimpf
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104 Freiburg, Germany
| | - Sabrina Oppermann
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104 Freiburg, Germany
| | - Tatjana Gerasimova
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104 Freiburg, Germany; Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, CMC, Université de Strasbourg CNRS, 4 Rue Blaise Pascal, 67081 Strasbourg, France
| | - Ana Filipa Santos Seica
- Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, CMC, Université de Strasbourg CNRS, 4 Rue Blaise Pascal, 67081 Strasbourg, France
| | - Petra Hellwig
- Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, CMC, Université de Strasbourg CNRS, 4 Rue Blaise Pascal, 67081 Strasbourg, France; University of Strasbourg, Institute for Advanced Studies (USIAS), 5 Allée du Général Rouvillois, 67083 Strasbourg, France
| | - Irina Grishkovskaya
- Research Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Daniel Wohlwend
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104 Freiburg, Germany
| | - David Haselbach
- Research Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Thorsten Friedrich
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104 Freiburg, Germany.
| |
Collapse
|
10
|
Active maintenance of proton motive force mediates starvation-induced bacterial antibiotic tolerance in Escherichia coli. Commun Biol 2021; 4:1068. [PMID: 34521984 PMCID: PMC8440630 DOI: 10.1038/s42003-021-02612-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 08/26/2021] [Indexed: 12/15/2022] Open
Abstract
Recent evidence suggests that metabolic shutdown alone does not fully explain how bacteria exhibit phenotypic antibiotic tolerance. In an attempt to investigate the range of starvation-induced physiological responses underlying tolerance development, we found that active maintenance of the transmembrane proton motive force (PMF) is essential for prolonged expression of antibiotic tolerance in bacteria. Eradication of tolerant sub-population could be achieved by disruption of PMF using the ionophore CCCP, or through suppression of PMF maintenance mechanisms by simultaneous inhibition of the phage shock protein (Psp) response and electron transport chain (ETC) complex activities. We consider disruption of bacterial PMF a feasible strategy for treatment of chronic and recurrent bacterial infections. The proton motive force (PMF) is a critical electrochemical gradient involved in bacterial energy metabolism. Here, Miaomiao Wang, Edward Wai Chi Chan et al. demonstrate that the PMF plays a key role in starvation-induced antibiotic tolerance in E. coli, suggesting that PMF disruption could be a future strategy to treat bacterial infection.
Collapse
|
11
|
Ahn D, Bhushan G, McConville TH, Annavajhala MK, Soni RK, Wong Fok Lung T, Hofstaedter CE, Shah SS, Chong AM, Castano VG, Ernst RK, Uhlemann AC, Prince A. An acquired acyltransferase promotes Klebsiella pneumoniae ST258 respiratory infection. Cell Rep 2021; 35:109196. [PMID: 34077733 PMCID: PMC8283688 DOI: 10.1016/j.celrep.2021.109196] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 02/12/2021] [Accepted: 05/10/2021] [Indexed: 12/18/2022] Open
Abstract
Klebsiella pneumoniae ST258 is a human pathogen associated with poor outcomes worldwide. We identify a member of the acyltransferase superfamily 3 (atf3), enriched within the ST258 clade, that provides a major competitive advantage for the proliferation of these organisms in vivo. Comparison of a wild-type ST258 strain (KP35) and a Δatf3 isogenic mutant generated by CRISPR-Cas9 targeting reveals greater NADH:ubiquinone oxidoreductase transcription and ATP generation, fueled by increased glycolysis. The acquisition of atf3 induces changes in the bacterial acetylome, promoting lysine acetylation of multiple proteins involved in central metabolism, specifically Zwf (glucose-6 phosphate dehydrogenase). The atf3-mediated metabolic boost leads to greater consumption of glucose in the host airway and increased bacterial burden in the lung, independent of cytokine levels and immune cell recruitment. Acquisition of this acyltransferase enhances fitness of a K. pneumoniae ST258 isolate and may contribute to the success of this clonal complex as a healthcare-associated pathogen.
Collapse
Affiliation(s)
- Danielle Ahn
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA.
| | - Gitanjali Bhushan
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Thomas H McConville
- Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Medini K Annavajhala
- Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Rajesh Kumar Soni
- Proteomics and Macromolecular Crystallography Shared Resource, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Tania Wong Fok Lung
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Casey E Hofstaedter
- Department of Microbial Pathogenesis, University of Maryland, Baltimore, Baltimore, MD 21201, USA
| | - Shivang S Shah
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Alexander M Chong
- Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Victor G Castano
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Robert K Ernst
- Department of Microbial Pathogenesis, University of Maryland, Baltimore, Baltimore, MD 21201, USA
| | - Anne-Catrin Uhlemann
- Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Alice Prince
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| |
Collapse
|
12
|
Abstract
Bacteria possess a sophisticated arsenal of defense mechanisms that allow them to survive in adverse conditions. Adaptation to acid stress and hypoxia is crucial for the enterobacterial transmission in the gastrointestinal tract of their human host. When subjected to low pH, Escherichia coli and many other enterobacteria activate a proton-consuming resistance system based on the acid stress-inducible lysine decarboxylase LdcI. Here we develop generally applicable tools to uncover the spatial localization of LdcI inside the cell by superresolution fluorescence microscopy and investigate the in vitro supramolecular organization of this enzyme by cryo-EM. We build on these results to propose a mechanistic model for LdcI function and offer tools for further in vivo investigations. Pathogenic and commensal bacteria often have to resist the harsh acidity of the host stomach. The inducible lysine decarboxylase LdcI buffers the cytosol and the local extracellular environment to ensure enterobacterial survival at low pH. Here, we investigate the acid stress-response regulation of Escherichia coli LdcI by combining biochemical and biophysical characterization with negative stain and cryoelectron microscopy (cryo-EM) and wide-field and superresolution fluorescence imaging. Due to deleterious effects of fluorescent protein fusions on native LdcI decamers, we opt for three-dimensional localization of nanobody-labeled endogenous wild-type LdcI in acid-stressed E. coli cells and show that it organizes into distinct patches at the cell periphery. Consistent with recent hypotheses that in vivo clustering of metabolic enzymes often reflects their polymerization as a means of stimulus-induced regulation, we show that LdcI assembles into filaments in vitro at physiologically relevant low pH. We solve the structures of these filaments and of the LdcI decamer formed at neutral pH by cryo-EM and reveal the molecular determinants of LdcI polymerization, confirmed by mutational analysis. Finally, we propose a model for LdcI function inside the enterobacterial cell, providing a structural and mechanistic basis for further investigation of the role of its supramolecular organization in the acid stress response.
Collapse
|
13
|
Zhang F, Vik SB. Analysis of the assembly pathway for membrane subunits of Complex I reveals that subunit L (ND5) can assemble last in E. coli. BBA ADVANCES 2021; 1. [DOI: 10.1016/j.bbadva.2021.100027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
|
14
|
Skorupa P, Lindenstrauß U, Burschel S, Blumenscheit C, Friedrich T, Pinske C. The N-terminal domains of the paralogous HycE and NuoCD govern assembly of the respective formate hydrogenlyase and NADH dehydrogenase complexes. FEBS Open Bio 2020; 10:371-385. [PMID: 31925988 PMCID: PMC7050243 DOI: 10.1002/2211-5463.12787] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 12/17/2019] [Accepted: 01/08/2020] [Indexed: 11/23/2022] Open
Abstract
Formate hydrogenlyase (FHL) is the main hydrogen-producing enzyme complex in enterobacteria. It converts formate to CO2 and H2 via a formate dehydrogenase and a [NiFe]-hydrogenase. FHL and complex I are evolutionarily related and share a common core architecture. However, complex I catalyses the fundamentally different electron transfer from NADH to quinone and pumps protons. The catalytic FHL subunit, HycE, resembles NuoCD of Escherichia coli complex I; a fusion of NuoC and NuoD present in other organisms. The C-terminal domain of HycE harbours the [NiFe]-active site and is similar to other hydrogenases, while this domain in NuoCD is involved in quinone binding. The N-terminal domains of these proteins do not bind cofactors and are not involved in electron transfer. As these N-terminal domains are separate proteins in some organisms, we removed them in E. coli and observed that both FHL and complex I activities were essentially absent. This was due to either a disturbed assembly or to complex instability. Replacing the N-terminal domain of HycE with a 180 amino acid E. coli NuoC protein fusion did not restore activity, indicating that the domains have complex-specific functions. A FHL complex in which the N- and C-terminal domains of HycE were physically separated still retained most of its FHL activity, while the separation of NuoCD abolished complex I activity completely. Only the FHL complex tolerates physical separation of the HycE domains. Together, the findings strongly suggest that the N-terminal domains of these proteins are key determinants in complex assembly.
Collapse
Affiliation(s)
- Philipp Skorupa
- Institute of Biology/MicrobiologyMartin‐Luther University Halle‐WittenbergGermany
| | - Ute Lindenstrauß
- Institute of Biology/MicrobiologyMartin‐Luther University Halle‐WittenbergGermany
| | - Sabrina Burschel
- Institute of Biochemistry/Molecular BioenergeticsAlbert‐Ludwigs‐University FreiburgGermany
| | | | - Thorsten Friedrich
- Institute of Biochemistry/Molecular BioenergeticsAlbert‐Ludwigs‐University FreiburgGermany
| | - Constanze Pinske
- Institute of Biology/MicrobiologyMartin‐Luther University Halle‐WittenbergGermany
| |
Collapse
|
15
|
Zhou S, Lama S, Sankaranarayanan M, Park S. Metabolic engineering of Pseudomonas denitrificans for the 1,3-propanediol production from glycerol. BIORESOURCE TECHNOLOGY 2019; 292:121933. [PMID: 31404755 DOI: 10.1016/j.biortech.2019.121933] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 07/27/2019] [Accepted: 07/29/2019] [Indexed: 06/10/2023]
Abstract
Bio-production of 1,3-propanediol (1,3-PDO) from glycerol was studied using Pseudomonas denitrificans as host, which aerobically synthesizes coenzyme B12, an essential cofactor of glycerol dehydratase (GDHt). P. denitrificans was transformed with the 1,3-PDO synthesis pathway composed of GDHt and 1,3-PDO oxidoreductase (PDOR), and its putative 3-hydroxypropionaldehyde (3-HPA) dehydrogenase(s), leading to the production of 3-hydroxypropioninc acid form the intermediary 3-HPA, was identified and deleted. In addition, to improve the availability of NADH for PDOR, oxidation of NADH in the electron transport chain was disturbed by deletion of the nuo operon and/or ndh gene. Finally, acetate formation pathway was eliminated. One resulting strain could produce 68.95 mM 1,3-PDO with the yield of 0.92 mol 1,3-PDO/mol glycerol on flask scale and 440 mM with the yield of 0.89 mol 1,3-PDO/mol glycerol in a fed-batch bioreactor experiment. This study demonstrates that P. denitrificans is a promising recombinant host for the production of 1,3-PDO from glycerol.
Collapse
Affiliation(s)
- Shengfang Zhou
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, China; School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Suman Lama
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Mugesh Sankaranarayanan
- Department of Biotechnology, Vel Tech Rangarajan Dr. Sagunthala R&D Institute of Science and Technology, Avadi, Chennai 600062, India
| | - Sunghoon Park
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea.
| |
Collapse
|
16
|
Wilmaerts D, Dewachter L, De Loose PJ, Bollen C, Verstraeten N, Michiels J. HokB Monomerization and Membrane Repolarization Control Persister Awakening. Mol Cell 2019; 75:1031-1042.e4. [DOI: 10.1016/j.molcel.2019.06.015] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 05/21/2019] [Accepted: 06/12/2019] [Indexed: 11/15/2022]
|
17
|
Gu M, Yin Q, Wang Z, He K, Wu G. Color and nitrogen removal from synthetic dye wastewater in an integrated mesophilic hydrolysis/acidification and multiple anoxic/aerobic process. CHEMOSPHERE 2018; 212:881-889. [PMID: 30195168 DOI: 10.1016/j.chemosphere.2018.08.162] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 06/30/2018] [Accepted: 08/31/2018] [Indexed: 06/08/2023]
Abstract
Dye wastewater is one kind of refractory pollutant and it is commonly treated by the integrated anaerobic and aerobic process. A new integrated hydrolysis/acidification and multiple anoxic/aerobic (AO) process was proposed for the removal of color and nitrogen from azo dye wastewater. System performance, the degradation pathway of azo dye and nitrogen metabolic pathway were investigated with quadrupole-time-of-flight and metagenomic analyses. The proposed process removed color and nitrogen efficiently, with the removal percentages of 89.4% and 54.0%, respectively. A colorful intermediate C16H11N3O7S2 during the degradation of azo dye was detected. Controlling a low dissolved oxygen concentration in the multiple AO process could enhance nitrogen removal. The detected bacteria possessing azoreductase for the azo dye degradation included Desulfovibrio aminophilus, Thermoanaerobacter, Lactococcus raffinolactis, Ruminiclostridium and Rhodopirellula. The nitrifying genes of amo and hao were mainly detected in Nitrosomonas, while the denitrifying genes were detected in Thauera, Candidatus Accumulibacter and Rhodothermus marinus.
Collapse
Affiliation(s)
- Mengqi Gu
- Guangdong Province Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, China
| | - Qidong Yin
- Guangdong Province Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, China
| | - Zhongzhong Wang
- Guangdong Province Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, China
| | - Kai He
- Research Centre for Environmental Quality Management, Kyoto University, 1-2 Yumihama, Otsu, Shiga, 520-0811, Japan
| | - Guangxue Wu
- Guangdong Province Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, China.
| |
Collapse
|
18
|
Shewanella oneidensis MR-1 Utilizes both Sodium- and Proton-Pumping NADH Dehydrogenases during Aerobic Growth. Appl Environ Microbiol 2018; 84:AEM.00415-18. [PMID: 29654176 PMCID: PMC5981069 DOI: 10.1128/aem.00415-18] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 04/05/2018] [Indexed: 02/02/2023] Open
Abstract
Shewanella oneidensis MR-1 is a metal-reducing bacterium with the ability to utilize many different terminal electron acceptors, including oxygen and solid-metal oxides. Both metal oxide reduction and aerobic respiration have been studied extensively in this organism. However, electron transport chain processes upstream of the terminal oxidoreductases have been relatively understudied in this organism, especially electron transfer from NADH to respiratory quinones. Genome annotation indicates that S. oneidensis MR-1 encodes four NADH dehydrogenases, a proton-translocating dehydrogenase (Nuo), two sodium ion-translocating dehydrogenases (Nqr1 and Nqr2), and an “uncoupling” dehydrogenase (Ndh), but none of these complexes have been studied. Therefore, we conducted a study specifically focused on the effects of individual NADH dehydrogenase knockouts in S. oneidensis MR-1. We observed that two of the single-mutant strains, the ΔnuoN and ΔnqrF1 mutants, exhibited significant growth defects compared with the wild type. However, the defects were minor and only apparent under certain growth conditions. Further testing of the ΔnuoN ΔnqrF1 double-mutant strain yielded no growth in minimal medium under oxic conditions, indicating that Nuo and Nqr1 have overlapping functions, but at least one is necessary for aerobic growth. Coutilization of proton- and sodium ion-dependent energetics has important implications for the growth of this organism in environments with varied pH and salinity, including microbial electrochemical systems. IMPORTANCE Bacteria utilize a wide variety of metabolic pathways that allow them to take advantage of different energy sources, and to do so with varied efficiency. The efficiency of a metabolic process determines the growth yield of an organism, or the amount of biomass it produces per amount of substrate consumed. This parameter has important implications in biotechnology and wastewater treatment, where low growth yields are often preferred to minimize the production of microbial biomass. In this study, we investigated respiratory pathways containing NADH dehydrogenases with varied efficiency (i.e., the number of ions translocated per NADH oxidized) in the metal-reducing bacterium Shewanella oneidensis MR-1. We observed that two different respiratory pathways are used concurrently, and at least one pathway must be functional for growth under oxic conditions.
Collapse
|
19
|
Dörner K, Vranas M, Schimpf J, Straub IR, Hoeser J, Friedrich T. Significance of [2Fe-2S] Cluster N1a for Electron Transfer and Assembly of Escherichia coli Respiratory Complex I. Biochemistry 2017; 56:2770-2778. [DOI: 10.1021/acs.biochem.6b01058] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Katerina Dörner
- Institut
für Biochemie, Albert-Ludwigs-Universität, Albertstraße 21, 79104 Freiburg, Germany
| | - Marta Vranas
- Spemann
Graduate School of Biology and Medicine (SGBM), Albert-Ludwigs-University, Freiburg, Germany
| | - Johannes Schimpf
- Institut
für Biochemie, Albert-Ludwigs-Universität, Albertstraße 21, 79104 Freiburg, Germany
| | - Isabella R. Straub
- Institut
für Biochemie, Albert-Ludwigs-Universität, Albertstraße 21, 79104 Freiburg, Germany
| | - Jo Hoeser
- Institut
für Biochemie, Albert-Ludwigs-Universität, Albertstraße 21, 79104 Freiburg, Germany
| | - Thorsten Friedrich
- Spemann
Graduate School of Biology and Medicine (SGBM), Albert-Ludwigs-University, Freiburg, Germany
| |
Collapse
|
20
|
Wheatley NM, Eden KD, Ngo J, Rosinski JS, Sawaya MR, Cascio D, Collazo M, Hoveida H, Hubbell WL, Yeates TO. A PII-Like Protein Regulated by Bicarbonate: Structural and Biochemical Studies of the Carboxysome-Associated CPII Protein. J Mol Biol 2016; 428:4013-4030. [PMID: 27464895 PMCID: PMC5048545 DOI: 10.1016/j.jmb.2016.07.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 07/11/2016] [Accepted: 07/18/2016] [Indexed: 11/18/2022]
Abstract
Autotrophic bacteria rely on various mechanisms to increase intracellular concentrations of inorganic forms of carbon (i.e., bicarbonate and CO2) in order to improve the efficiency with which they can be converted to organic forms. Transmembrane bicarbonate transporters and carboxysomes play key roles in accumulating bicarbonate and CO2, but other regulatory elements of carbon concentration mechanisms in bacteria are less understood. In this study, after analyzing the genomic regions around α-type carboxysome operons, we characterize a protein that is conserved across these operons but has not been previously studied. On the basis of a series of apo- and ligand-bound crystal structures and supporting biochemical data, we show that this protein, which we refer to as the carboxysome-associated PII protein (CPII), represents a new and distinct subfamily within the broad superfamily of previously studied PII regulatory proteins, which are generally involved in regulating nitrogen metabolism in bacteria. CPII undergoes dramatic conformational changes in response to ADP binding, and the affinity for nucleotide binding is strongly enhanced by the presence of bicarbonate. CPII therefore appears to be a unique type of PII protein that senses bicarbonate availability, consistent with its apparent genomic association with the carboxysome and its constituents.
Collapse
Affiliation(s)
- Nicole M Wheatley
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA 90095, USA
| | - Kevin D Eden
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Joanna Ngo
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Justin S Rosinski
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Michael R Sawaya
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA 90095, USA
| | - Duilio Cascio
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA 90095, USA
| | - Michael Collazo
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA 90095, USA
| | - Hamidreza Hoveida
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Wayne L Hubbell
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA; Jules Stein Eye Institute, University of California, Los Angeles, CA 90095, USA
| | - Todd O Yeates
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA 90095, USA; Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA.
| |
Collapse
|
21
|
Chan SWS, Yau J, Ing C, Liu K, Farber P, Won A, Bhandari V, Kara-Yacoubian N, Seraphim TV, Chakrabarti N, Kay LE, Yip CM, Pomès R, Sharpe S, Houry WA. Mechanism of Amyloidogenesis of a Bacterial AAA+ Chaperone. Structure 2016; 24:1095-109. [PMID: 27265850 DOI: 10.1016/j.str.2016.05.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 04/27/2016] [Accepted: 05/01/2016] [Indexed: 10/21/2022]
Abstract
Amyloids are fibrillar protein superstructures that are commonly associated with diseases in humans and with physiological functions in various organisms. The precise mechanisms of amyloid formation remain to be elucidated. Surprisingly, we discovered that a bacterial Escherichia coli chaperone-like ATPase, regulatory ATPase variant A (RavA), and specifically the LARA domain in RavA, forms amyloids under acidic conditions at elevated temperatures. RavA is involved in modulating the proper assembly of membrane respiratory complexes. LARA contains an N-terminal loop region followed by a β-sandwich-like folded core. Several approaches, including nuclear magnetic resonance spectroscopy and molecular dynamics simulations, were used to determine the mechanism by which LARA switches to an amyloid state. These studies revealed that the folded core of LARA is amyloidogenic and is protected by its N-terminal loop. At low pH and high temperatures, the interaction of the N-terminal loop with the folded core is disrupted, leading to amyloid formation.
Collapse
Affiliation(s)
- Sze Wah Samuel Chan
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Medical Sciences Building, Toronto, ON M5S 1A8, Canada
| | - Jason Yau
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Medical Sciences Building, Toronto, ON M5S 1A8, Canada; Molecular Structure and Function Program, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Christopher Ing
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Medical Sciences Building, Toronto, ON M5S 1A8, Canada; Molecular Structure and Function Program, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Kaiyin Liu
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Medical Sciences Building, Toronto, ON M5S 1A8, Canada
| | - Patrick Farber
- Molecular Structure and Function Program, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Amy Won
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Vaibhav Bhandari
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Medical Sciences Building, Toronto, ON M5S 1A8, Canada
| | - Nareg Kara-Yacoubian
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Medical Sciences Building, Toronto, ON M5S 1A8, Canada
| | - Thiago V Seraphim
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Medical Sciences Building, Toronto, ON M5S 1A8, Canada
| | - Nilmadhab Chakrabarti
- Molecular Structure and Function Program, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Lewis E Kay
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Medical Sciences Building, Toronto, ON M5S 1A8, Canada; Molecular Structure and Function Program, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Christopher M Yip
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Medical Sciences Building, Toronto, ON M5S 1A8, Canada; Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Régis Pomès
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Medical Sciences Building, Toronto, ON M5S 1A8, Canada; Molecular Structure and Function Program, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Simon Sharpe
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Medical Sciences Building, Toronto, ON M5S 1A8, Canada; Molecular Structure and Function Program, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada.
| | - Walid A Houry
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Medical Sciences Building, Toronto, ON M5S 1A8, Canada.
| |
Collapse
|
22
|
Structural insights into the Escherichia coli lysine decarboxylases and molecular determinants of interaction with the AAA+ ATPase RavA. Sci Rep 2016; 6:24601. [PMID: 27080013 PMCID: PMC4832331 DOI: 10.1038/srep24601] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 04/01/2016] [Indexed: 11/09/2022] Open
Abstract
The inducible lysine decarboxylase LdcI is an important enterobacterial acid stress
response enzyme whereas LdcC is its close paralogue thought to play mainly a
metabolic role. A unique macromolecular cage formed by two decamers of the
Escherichia coli LdcI and five hexamers of the AAA+ ATPase RavA was shown
to counteract acid stress under starvation. Previously, we proposed a pseudoatomic
model of the LdcI-RavA cage based on its cryo-electron microscopy map and crystal
structures of an inactive LdcI decamer and a RavA monomer. We now present
cryo-electron microscopy 3D reconstructions of the E. coli LdcI and LdcC, and
an improved map of the LdcI bound to the LARA domain of RavA, at pH optimal for
their enzymatic activity. Comparison with each other and with available structures
uncovers differences between LdcI and LdcC explaining why only the acid stress
response enzyme is capable of binding RavA. We identify interdomain movements
associated with the pH-dependent enzyme activation and with the RavA binding.
Multiple sequence alignment coupled to a phylogenetic analysis reveals that certain
enterobacteria exert evolutionary pressure on the lysine decarboxylase towards the
cage-like assembly with RavA, implying that this complex may have an important
function under particular stress conditions.
Collapse
|
23
|
Wessels HJCT, de Almeida NM, Kartal B, Keltjens JT. Bacterial Electron Transfer Chains Primed by Proteomics. Adv Microb Physiol 2016; 68:219-352. [PMID: 27134025 DOI: 10.1016/bs.ampbs.2016.02.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Electron transport phosphorylation is the central mechanism for most prokaryotic species to harvest energy released in the respiration of their substrates as ATP. Microorganisms have evolved incredible variations on this principle, most of these we perhaps do not know, considering that only a fraction of the microbial richness is known. Besides these variations, microbial species may show substantial versatility in using respiratory systems. In connection herewith, regulatory mechanisms control the expression of these respiratory enzyme systems and their assembly at the translational and posttranslational levels, to optimally accommodate changes in the supply of their energy substrates. Here, we present an overview of methods and techniques from the field of proteomics to explore bacterial electron transfer chains and their regulation at levels ranging from the whole organism down to the Ångstrom scales of protein structures. From the survey of the literature on this subject, it is concluded that proteomics, indeed, has substantially contributed to our comprehending of bacterial respiratory mechanisms, often in elegant combinations with genetic and biochemical approaches. However, we also note that advanced proteomics offers a wealth of opportunities, which have not been exploited at all, or at best underexploited in hypothesis-driving and hypothesis-driven research on bacterial bioenergetics. Examples obtained from the related area of mitochondrial oxidative phosphorylation research, where the application of advanced proteomics is more common, may illustrate these opportunities.
Collapse
Affiliation(s)
- H J C T Wessels
- Nijmegen Center for Mitochondrial Disorders, Radboud Proteomics Centre, Translational Metabolic Laboratory, Radboud University Medical Center, Nijmegen, The Netherlands
| | - N M de Almeida
- Institute of Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - B Kartal
- Institute of Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands; Laboratory of Microbiology, Ghent University, Ghent, Belgium
| | - J T Keltjens
- Institute of Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands.
| |
Collapse
|
24
|
Different Functions of Phylogenetically Distinct Bacterial Complex I Isozymes. J Bacteriol 2016; 198:1268-80. [PMID: 26833419 PMCID: PMC4859585 DOI: 10.1128/jb.01025-15] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 01/28/2016] [Indexed: 12/12/2022] Open
Abstract
UNLABELLED NADH:quinone oxidoreductase (complex I) is a bioenergetic enzyme that transfers electrons from NADH to quinone, conserving the energy of this reaction by contributing to the proton motive force. While the importance of NADH oxidation to mitochondrial aerobic respiration is well documented, the contribution of complex I to bacterial electron transport chains has been tested in only a few species. Here, we analyze the function of two phylogenetically distinct complex I isozymes in Rhodobacter sphaeroides, an alphaproteobacterium that contains well-characterized electron transport chains. We found that R. sphaeroides complex I activity is important for aerobic respiration and required for anaerobic dimethyl sulfoxide (DMSO) respiration (in the absence of light), photoautotrophic growth, and photoheterotrophic growth (in the absence of an external electron acceptor). Our data also provide insight into the functions of the phylogenetically distinct R. sphaeroidescomplex I enzymes (complex IA and complex IE) in maintaining a cellular redox state during photoheterotrophic growth. We propose that the function of each isozyme during photoheterotrophic growth is either NADH synthesis (complex IA) or NADH oxidation (complex IE). The canonical alphaproteobacterial complex I isozyme (complex IA) was also shown to be important for routing electrons to nitrogenase-mediated H2 production, while the horizontally acquired enzyme (complex IE) was dispensable in this process. Unlike the singular role of complex I in mitochondria, we predict that the phylogenetically distinct complex I enzymes found across bacterial species have evolved to enhance the functions of their respective electron transport chains. IMPORTANCE Cells use a proton motive force (PMF), NADH, and ATP to support numerous processes. In mitochondria, complex I uses NADH oxidation to generate a PMF, which can drive ATP synthesis. This study analyzed the function of complex I in bacteria, which contain more-diverse and more-flexible electron transport chains than mitochondria. We tested complex I function in Rhodobacter sphaeroides, a bacterium predicted to encode two phylogenetically distinct complex I isozymes. R. sphaeroides cells lacking both isozymes had growth defects during all tested modes of growth, illustrating the important function of this enzyme under diverse conditions. We conclude that the two isozymes are not functionally redundant and predict that phylogenetically distinct complex I enzymes have evolved to support the diverse lifestyles of bacteria.
Collapse
|
25
|
Zhu S, Canales A, Bedair M, Vik SB. Loss of Complex I activity in the Escherichia coli enzyme results from truncating the C-terminus of subunit K, but not from cross-linking it to subunits N or L. J Bioenerg Biomembr 2016; 48:325-33. [PMID: 26931547 DOI: 10.1007/s10863-016-9655-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 02/25/2016] [Indexed: 12/16/2022]
Abstract
Complex I is a multi-subunit enzyme of the respiratory chain with seven core subunits in its membrane arm (A, H, J, K, L, M, and N). In the enzyme from Escherichia coli the C-terminal ten amino acids of subunit K lie along the lateral helix of subunit L, and contribute to a junction of subunits K, L and N on the cytoplasmic surface. Using double cysteine mutagenesis, the cross-linking of subunit K (R99C) to either subunit L (K581C) or subunit N (T292C) was attempted. A partial yield of cross-linked product had no effect on the activity of the enzyme, or on proton translocation, suggesting that the C-terminus of subunit K has no dynamic role in function. To further elucidate the role of subunit K genetic deletions were constructed at the C-terminus. Upon the serial deletion of the last 4 residues of the C-terminus of subunit K, various results were obtained. Deletion of one amino acid had little effect on the activity of Complex I, but deletions of 2 or more amino acids led to total loss of enzyme activity and diminished levels of subunits L, M, and N in preparations of membrane vesicles. Together these results suggest that while the C-terminus of subunit K has no dynamic role in energy transduction by Complex I, it is vital for the correct assembly of the enzyme.
Collapse
Affiliation(s)
- Shaotong Zhu
- Department of Biological Sciences, Southern Methodist University, Dallas, TX, 75275-0376, USA.,Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Alejandra Canales
- Department of Biological Sciences, Southern Methodist University, Dallas, TX, 75275-0376, USA.,Department of Biochemistry, University of Wisconsin, Madison, WI, 53706, USA
| | - Mai Bedair
- Department of Biological Sciences, Southern Methodist University, Dallas, TX, 75275-0376, USA.,University of Texas Southwestern Medical School, Dallas, TX, 75390, USA
| | - Steven B Vik
- Department of Biological Sciences, Southern Methodist University, Dallas, TX, 75275-0376, USA.
| |
Collapse
|
26
|
Subrahmanian N, Remacle C, Hamel PP. Plant mitochondrial Complex I composition and assembly: A review. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:1001-14. [PMID: 26801215 DOI: 10.1016/j.bbabio.2016.01.009] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 01/18/2016] [Accepted: 01/18/2016] [Indexed: 12/31/2022]
Abstract
In the mitochondrial inner membrane, oxidative phosphorylation generates ATP via the operation of several multimeric enzymes. The proton-pumping Complex I (NADH:ubiquinone oxidoreductase) is the first and most complicated enzyme required in this process. Complex I is an L-shaped enzyme consisting of more than 40 subunits, one FMN molecule and eight Fe-S clusters. In recent years, genetic and proteomic analyses of Complex I mutants in various model systems, including plants, have provided valuable insights into the assembly of this multimeric enzyme. Assisted by a number of key players, referred to as "assembly factors", the assembly of Complex I takes place in a sequential and modular manner. Although a number of factors have been identified, their precise function in mediating Complex I assembly still remains to be elucidated. This review summarizes our current knowledge of plant Complex I composition and assembly derived from studies in plant model systems such as Arabidopsis thaliana and Chlamydomonas reinhardtii. Plant Complex I is highly conserved and comprises a significant number of subunits also present in mammalian and fungal Complexes I. Plant Complex I also contains additional subunits absent from the mammalian and fungal counterpart, whose function in enzyme activity and assembly is not clearly understood. While 14 assembly factors have been identified for human Complex I, only two proteins, namely GLDH and INDH, have been established as bona fide assembly factors for plant Complex I. This article is part of a Special Issue entitled Respiratory complex I, edited by Volker Zickermann and Ulrich Brandt.
Collapse
Affiliation(s)
- Nitya Subrahmanian
- The Ohio State University, Department of Molecular Genetics, 500 Aronoff Laboratory, 318 W. 12th Avenue, Columbus, OH 43210, USA
| | - Claire Remacle
- Institute of Botany, Department of Life Sciences, University of Liège, 4000 Liège, Belgium
| | - Patrice Paul Hamel
- The Ohio State University, Department of Molecular Genetics, 500 Aronoff Laboratory, 318 W. 12th Avenue, Columbus, OH 43210, USA; The Ohio State University, Department of Biological Chemistry and Pharmacology, 500 Aronoff Laboratory, 318 W. 12th Avenue, Columbus, OH 43210, USA.
| |
Collapse
|
27
|
Friedrich T, Dekovic DK, Burschel S. Assembly of the Escherichia coli NADH:ubiquinone oxidoreductase (respiratory complex I). BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1857:214-23. [PMID: 26682761 DOI: 10.1016/j.bbabio.2015.12.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Revised: 12/03/2015] [Accepted: 12/07/2015] [Indexed: 12/13/2022]
Abstract
Energy-converting NADH:ubiquinone oxidoreductase, respiratory complex I, couples the electron transfer from NADH to ubiquinone with the translocation of four protons across the membrane. The Escherichia coli complex I is made up of 13 different subunits encoded by the so-called nuo-genes. The electron transfer is catalyzed by nine cofactors, a flavin mononucleotide and eight iron-sulfur (Fe/S)-clusters. The individual subunits and the cofactors have to be assembled together in a coordinated way to guarantee the biogenesis of the active holoenzyme. Only little is known about the assembly of the bacterial complex compared to the mitochondrial one. Due to the presence of so many Fe/S-clusters the assembly of complex I is intimately connected with the systems responsible for the biogenesis of these clusters. In addition, a few other proteins have been reported to be required for an effective assembly of the complex in other bacteria. The proposed role of known bacterial assembly factors is discussed and the information from other bacterial species is used in this review to draw an as complete as possible model of bacterial complex I assembly. In addition, the supramolecular organization of the complex in E. coli is briefly described. This article is part of a Special Issue entitled Organization and dynamics of bioenergetic systems in bacteria, edited by Prof. Conrad Mullineaux.
Collapse
Affiliation(s)
- Thorsten Friedrich
- Albert-Ludwigs-Universität Freiburg, Institut für Biochemie, 79104 Freiburg i. Br., Germany; Spemann Graduate School of Biology and Medicine, Albertstr. 19A, 79104 Freiburg i. Br., Germany.
| | - Doris Kreuzer Dekovic
- Albert-Ludwigs-Universität Freiburg, Institut für Biochemie, 79104 Freiburg i. Br., Germany; Spemann Graduate School of Biology and Medicine, Albertstr. 19A, 79104 Freiburg i. Br., Germany
| | - Sabrina Burschel
- Albert-Ludwigs-Universität Freiburg, Institut für Biochemie, 79104 Freiburg i. Br., Germany
| |
Collapse
|
28
|
Sensitizing Pseudomonas aeruginosa to antibiotics by electrochemical disruption of membrane functions. Biomaterials 2015; 74:267-79. [PMID: 26461119 DOI: 10.1016/j.biomaterials.2015.10.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 09/29/2015] [Accepted: 10/01/2015] [Indexed: 11/20/2022]
Abstract
Recently, we reported synergistic effects between 70 μA/cm(2) direct current and tobramycin in killing Pseudomonas aeruginosa PAO1 persister cells, a phenomenon we named electrochemical control of persister cells (ECCP; Niepa et al. Biomaterials 33: 7356-7365, 2012). To understand the mechanism of ECCP, the effects of electrochemical treatments mediated via stainless steel 304 and carbon electrodes on P. aeruginosa PAO1 were systematically compared using complementary approaches in this study. Electron microscopic analysis revealed that μA/cm(2) level direct current (DC) caused substantial changes in the structure and membrane integrity of P. aeruginosa PAO1 cells. DC treatments using SS304 electrodes induced cell lysis, while the same level of DC generated using carbon electrodes led to aggregation of intracellular proteins and increased permeabilization of P. aeruginosa PAO1 cells to antibiotics. The profound effects of DC on the physiology of persister cells were corroborated with DNA microarray analysis, which revealed the induction of genes associated with pyocin production and SOS response in DC-treated persister cells. Interestingly, sequential treatment using DC mediated with carbon electrodes followed by tobramycin was found more effective than concurrent treatment; and total eradication of persister cells was achieved.
Collapse
|
29
|
Phylogenomic analysis and predicted physiological role of the proton-translocating NADH:quinone oxidoreductase (complex I) across bacteria. mBio 2015; 6:mBio.00389-15. [PMID: 25873378 PMCID: PMC4453560 DOI: 10.1128/mbio.00389-15] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The proton-translocating NADH:quinone oxidoreductase (complex I) is a multisubunit integral membrane enzyme found in the respiratory chains of both bacteria and eukaryotic organelles. Although much research has focused on the enzyme's central role in the mitochondrial respiratory chain, comparatively little is known about its role in the diverse energetic lifestyles of different bacteria. Here, we used a phylogenomic approach to better understand the distribution of complex I across bacteria, the evolution of this enzyme, and its potential roles in shaping the physiology of different bacterial groups. By surveying 970 representative bacterial genomes, we predict complex I to be present in ~50% of bacteria. While this includes bacteria with a wide range of energetic schemes, the presence of complex I is associated with specific lifestyles, including aerobic respiration and specific types of phototrophy (bacteria with only a type II reaction center). A phylogeny of bacterial complex I revealed five main clades of enzymes whose evolution is largely congruent with the evolution of the bacterial groups that encode complex I. A notable exception includes the gammaproteobacteria, whose members encode one of two distantly related complex I enzymes predicted to participate in different types of respiratory chains (aerobic versus anaerobic). Comparative genomic analyses suggest a broad role for complex I in reoxidizing NADH produced from various catabolic reactions, including the tricarboxylic acid (TCA) cycle and fatty acid beta-oxidation. Together, these findings suggest diverse roles for complex I across bacteria and highlight the importance of this enzyme in shaping diverse physiologies across the bacterial domain. IMPORTANCE Living systems use conserved energy currencies, including a proton motive force (PMF), NADH, and ATP. The respiratory chain enzyme, complex I, connects these energy currencies by using NADH produced during nutrient breakdown to generate a PMF, which is subsequently used for ATP synthesis. Our goal is to better understand the role of complex I in bacteria, whose energetic diversity allows us to view its function in a range of biological contexts. We analyzed sequenced bacterial genomes to predict the presence, evolution, and function of complex I in bacteria. We identified five main classes of bacterial complex I and predict that different classes participate in different types of respiratory chains (aerobic and anaerobic). We also predict that complex I helps maintain a cellular redox state by reoxidizing NADH produced from central metabolism. Our findings suggest diverse roles for complex I in bacterial physiology, highlighting the need for future laboratory-based studies.
Collapse
|
30
|
Respiratory complex I fromEscherichia colidoes not transport Na+in the absence of its NuoL subunit. FEBS Lett 2014; 588:4520-5. [DOI: 10.1016/j.febslet.2014.10.030] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Revised: 10/24/2014] [Accepted: 10/27/2014] [Indexed: 12/23/2022]
|
31
|
Massoz S, Larosa V, Plancke C, Lapaille M, Bailleul B, Pirotte D, Radoux M, Leprince P, Coosemans N, Matagne RF, Remacle C, Cardol P. Inactivation of genes coding for mitochondrial Nd7 and Nd9 complex I subunits in Chlamydomonas reinhardtii. Impact of complex I loss on respiration and energetic metabolism. Mitochondrion 2014; 19 Pt B:365-74. [DOI: 10.1016/j.mito.2013.11.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Revised: 11/22/2013] [Accepted: 11/26/2013] [Indexed: 02/04/2023]
|
32
|
Malet H, Liu K, El Bakkouri M, Chan SWS, Effantin G, Bacia M, Houry WA, Gutsche I. Assembly principles of a unique cage formed by hexameric and decameric E. coli proteins. eLife 2014; 3:e03653. [PMID: 25097238 PMCID: PMC4145799 DOI: 10.7554/elife.03653] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A 3.3 MDa macromolecular cage between two Escherichia coli proteins with seemingly incompatible symmetries-the hexameric AAA+ ATPase RavA and the decameric inducible lysine decarboxylase LdcI-is reconstructed by cryo-electron microscopy to 11 Å resolution. Combined with a 7.5 Å resolution reconstruction of the minimal complex between LdcI and the LdcI-binding domain of RavA, and the previously solved crystal structures of the individual components, this work enables to build a reliable pseudoatomic model of this unusual architecture and to identify conformational rearrangements and specific elements essential for complex formation. The design of the cage created via lateral interactions between five RavA rings is unique for the diverse AAA+ ATPase superfamily.
Collapse
Affiliation(s)
- Hélène Malet
- European Molecular Biology Laboratory, Grenoble, France Unit for Virus Host-Cell Interactions, Université Grenoble Alpes, Grenoble, France Unit for Virus Host-Cell Interactions, CNRS, Grenoble, France
| | - Kaiyin Liu
- Department of Biochemistry, University of Toronto, Toronto, Canada
| | | | | | - Gregory Effantin
- Unit for Virus Host-Cell Interactions, Université Grenoble Alpes, Grenoble, France Unit for Virus Host-Cell Interactions, CNRS, Grenoble, France
| | - Maria Bacia
- Université Grenoble Alpes, Institut de Biologie Structurale, Grenoble, France Institut de Biologie Structurale, CNRS, Grenoble, France Institut de Biologie Structurale, CEA, Grenoble, France
| | - Walid A Houry
- Department of Biochemistry, University of Toronto, Toronto, Canada
| | - Irina Gutsche
- Unit for Virus Host-Cell Interactions, Université Grenoble Alpes, Grenoble, France Unit for Virus Host-Cell Interactions, CNRS, Grenoble, France
| |
Collapse
|
33
|
Colony-live--a high-throughput method for measuring microbial colony growth kinetics--reveals diverse growth effects of gene knockouts in Escherichia coli. BMC Microbiol 2014; 14:171. [PMID: 24964927 PMCID: PMC4096534 DOI: 10.1186/1471-2180-14-171] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Accepted: 06/06/2014] [Indexed: 11/11/2022] Open
Abstract
Background Precise quantitative growth measurements and detection of small growth changes in high-throughput manner is essential for fundamental studies of bacterial cell. However, an inherent tradeoff for measurement quality in high-throughput methods sacrifices some measurement quality. A key challenge has been how to enhance measurement quality without sacrificing throughput. Results We developed a new high-throughput measurement system, termed Colony-live. Here we show that Colony-live provides accurate measurement of three growth values (lag time of growth (LTG), maximum growth rate (MGR), and saturation point growth (SPG)) by visualizing colony growth over time. By using a new normalization method for colony growth, Colony-live gives more precise and accurate growth values than the conventional method. We demonstrated the utility of Colony-live by measuring growth values for the entire Keio collection of Escherichia coli single-gene knockout mutants. By using Colony-live, we were able to identify subtle growth defects of single-gene knockout mutants that were undetectable by the conventional method quantified by fixed time-point camera imaging. Further, Colony-live can reveal genes that influence the length of the lag-phase and the saturation point of growth. Conclusions Measurement quality is critical to achieving the resolution required to identify unique phenotypes among a diverse range of phenotypes. Sharing high-quality genome-wide datasets should benefit many researchers who are interested in specific gene functions or the architecture of cellular systems. Our Colony-live system provides a new powerful tool to accelerate accumulation of knowledge of microbial growth phenotypes.
Collapse
|
34
|
Genes of the N-methylglutamate pathway are essential for growth of Methylobacterium extorquens DM4 with monomethylamine. Appl Environ Microbiol 2014; 80:3541-50. [PMID: 24682302 DOI: 10.1128/aem.04160-13] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Monomethylamine (MMA, CH3NH2) can be used as a carbon and nitrogen source by many methylotrophic bacteria. Methylobacterium extorquens DM4 lacks the MMA dehydrogenase encoded by mau genes, which in M. extorquens AM1 is essential for growth on MMA. Identification and characterization of minitransposon mutants with an MMA-dependent phenotype showed that strain DM4 grows with MMA as the sole source of carbon, energy, and nitrogen by the N-methylglutamate (NMG) pathway. Independent mutations were found in a chromosomal region containing the genes gmaS, mgsABC, and mgdABCD for the three enzymes of the pathway, γ-glutamylmethylamide (GMA) synthetase, NMG synthase, and NMG dehydrogenase, respectively. Reverse transcription-PCR confirmed the operonic structure of the two divergent gene clusters mgsABC-gmaS and mgdABCD and their induction during growth with MMA. The genes mgdABCD and mgsABC were found to be essential for utilization of MMA as a carbon and nitrogen source. The gene gmaS was essential for MMA utilization as a carbon source, but residual growth of mutant DM4gmaS growing with succinate and MMA as a nitrogen source was observed. Plasmid copies of gmaS and the gmaS homolog METDI4690, which encodes a protein 39% identical to GMA synthetase, fully restored the ability of mutants DM4gmaS and DM4gmaSΔmetdi4690 to use MMA as a carbon and nitrogen source. Similarly, chemically synthesized GMA, the product of GMA synthetase, could be used as a nitrogen source for growth in the wild-type strain, as well as in DM4gmaS and DM4gmaSΔmetdi4690 mutants. The NADH:ubiquinone oxidoreductase respiratory complex component NuoG was also found to be essential for growth with MMA as a carbon source.
Collapse
|
35
|
Wong KS, Snider JD, Graham C, Greenblatt JF, Emili A, Babu M, Houry WA. The MoxR ATPase RavA and its cofactor ViaA interact with the NADH:ubiquinone oxidoreductase I in Escherichia coli. PLoS One 2014; 9:e85529. [PMID: 24454883 PMCID: PMC3893208 DOI: 10.1371/journal.pone.0085529] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Accepted: 11/27/2013] [Indexed: 12/26/2022] Open
Abstract
MoxR ATPases are widespread throughout bacteria and archaea. The experimental evidence to date suggests that these proteins have chaperone-like roles in facilitating the maturation of dedicated protein complexes that are functionally diverse. In Escherichia coli, the MoxR ATPase RavA and its putative cofactor ViaA are found to exist in early stationary-phase cells at 37 °C at low levels of about 350 and 90 molecules per cell, respectively. Both proteins are predominantly localized to the cytoplasm, but ViaA was also unexpectedly found to localize to the cell membrane. Whole genome microarrays and synthetic lethality studies both indicated that RavA-ViaA are genetically linked to Fe-S cluster assembly and specific respiratory pathways. Systematic analysis of mutant strains of ravA and viaA indicated that RavA-ViaA sensitizes cells to sublethal concentrations of aminoglycosides. Furthermore, this effect was dependent on RavA's ATPase activity, and on the presence of specific subunits of NADH:ubiquinone oxidoreductase I (Nuo Complex, or Complex I). Importantly, both RavA and ViaA were found to physically interact with specific Nuo subunits. We propose that RavA-ViaA facilitate the maturation of the Nuo complex.
Collapse
Affiliation(s)
- Keith S. Wong
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Jamie D. Snider
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Chris Graham
- Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, Saskatchewan, Canada
| | - Jack F. Greenblatt
- Banting and Best Department of Medical Research, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Andrew Emili
- Banting and Best Department of Medical Research, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Mohan Babu
- Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, Saskatchewan, Canada
| | - Walid A. Houry
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
- * E-mail:
| |
Collapse
|
36
|
Paul CE, Lavandera I, Gotor-Fernández V, Kroutil W, Gotor V. Escherichia coli/ADH-A: An All-Inclusive Catalyst for the Selective Biooxidation and Deracemisation of Secondary Alcohols. ChemCatChem 2013. [DOI: 10.1002/cctc.201300409] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|