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Yu Z, Zhang W, Yang H, Chou SH, Galperin MY, He J. Gas and light: triggers of c-di-GMP-mediated regulation. FEMS Microbiol Rev 2023; 47:fuad034. [PMID: 37339911 PMCID: PMC10505747 DOI: 10.1093/femsre/fuad034] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 06/01/2023] [Accepted: 06/17/2023] [Indexed: 06/22/2023] Open
Abstract
The widespread bacterial second messenger c-di-GMP is responsible for regulating many important physiological functions such as biofilm formation, motility, cell differentiation, and virulence. The synthesis and degradation of c-di-GMP in bacterial cells depend, respectively, on diguanylate cyclases and c-di-GMP-specific phosphodiesterases. Since c-di-GMP metabolic enzymes (CMEs) are often fused to sensory domains, their activities are likely controlled by environmental signals, thereby altering cellular c-di-GMP levels and regulating bacterial adaptive behaviors. Previous studies on c-di-GMP-mediated regulation mainly focused on downstream signaling pathways, including the identification of CMEs, cellular c-di-GMP receptors, and c-di-GMP-regulated processes. The mechanisms of CME regulation by upstream signaling modules received less attention, resulting in a limited understanding of the c-di-GMP regulatory networks. We review here the diversity of sensory domains related to bacterial CME regulation. We specifically discuss those domains that are capable of sensing gaseous or light signals and the mechanisms they use for regulating cellular c-di-GMP levels. It is hoped that this review would help refine the complete c-di-GMP regulatory networks and improve our understanding of bacterial behaviors in changing environments. In practical terms, this may eventually provide a way to control c-di-GMP-mediated bacterial biofilm formation and pathogenesis in general.
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Affiliation(s)
- Zhaoqing Yu
- National Key Laboratory of Agricultural Microbiology and Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, 1 Shizishan Street, Wuhan, Hubei 430070, PR China
- Institute of Agro-Product Processing, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing, Jiangsu 210014, PR China
| | - Wei Zhang
- National Key Laboratory of Agricultural Microbiology and Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, 1 Shizishan Street, Wuhan, Hubei 430070, PR China
| | - He Yang
- National Key Laboratory of Agricultural Microbiology and Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, 1 Shizishan Street, Wuhan, Hubei 430070, PR China
| | - Shan-Ho Chou
- National Key Laboratory of Agricultural Microbiology and Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, 1 Shizishan Street, Wuhan, Hubei 430070, PR China
| | - Michael Y Galperin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Jin He
- National Key Laboratory of Agricultural Microbiology and Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, 1 Shizishan Street, Wuhan, Hubei 430070, PR China
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2
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Zhang J, Li Q, Wang Q, Zhao J, Zhu Y, Su T, Qi Q, Wang Q. Heme biosensor-guided in vivo pathway optimization and directed evolution for efficient biosynthesis of heme. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:33. [PMID: 36859288 PMCID: PMC9979517 DOI: 10.1186/s13068-023-02285-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 02/18/2023] [Indexed: 03/03/2023]
Abstract
BACKGROUND Heme has attracted much attention because of its wide applications in medicine and food. The products of genes hemBCDEFY convert 5-aminolevulinic acid to protoporphyrin IX (PPIX; the immediate precursor of heme); protoporphyrin ferrochelatase (FECH) inserts Fe2+ into PPIX to generate heme. Biosynthesis of heme is limited by the need for optimized expression levels of multiple genes, complex regulatory mechanisms, and low enzymatic activity; these problems need to be overcome in metabolic engineering to improve heme synthesis. RESULTS We report a heme biosensor-guided screening strategy using the heme-responsive protein HrtR to regulate tcR expression in Escherichia coli, providing a quantifiable link between the intracellular heme concentration and cell survival in selective conditions (i.e., the presence of tetracycline). This system was used for rapid enrichment screening of heme-producing strains from a library with random ribosome binding site (RBS) variants and from a FECH mutant library. Through up to four rounds of iterative evolution, strains with optimal RBS intensities for the combination of hemBCDEFY were screened; we obtained a PPIX titer of 160.8 mg/L, the highest yield yet reported in shaken-flask fermentation. A high-activity FECH variant was obtained from the saturation mutagenesis library. Fed-batch fermentation of strain SH20C, harboring the optimized hemBCDEFY and the FECH mutant, produced 127.6 mg/L of heme. CONCLUSION We sequentially improved the multigene biosynthesis pathway of PPIX and performed in vivo directed evolution of FECH, based on a heme biosensor, which demonstrated the effectiveness of the heme biosensor-based pathway optimization strategy and broadens our understanding of the mechanism of heme synthesis.
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Affiliation(s)
- Jian Zhang
- grid.27255.370000 0004 1761 1174National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237 People’s Republic of China
| | - Qingbin Li
- grid.27255.370000 0004 1761 1174National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237 People’s Republic of China
| | - Qi Wang
- grid.27255.370000 0004 1761 1174National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237 People’s Republic of China
| | - Jingyu Zhao
- grid.27255.370000 0004 1761 1174National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237 People’s Republic of China
| | - Yuan Zhu
- grid.27255.370000 0004 1761 1174National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237 People’s Republic of China
| | - Tianyuan Su
- grid.27255.370000 0004 1761 1174National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237 People’s Republic of China
| | - Qingsheng Qi
- grid.27255.370000 0004 1761 1174National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237 People’s Republic of China ,grid.9227.e0000000119573309CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
| | - Qian Wang
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, People's Republic of China. .,CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, People's Republic of China.
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3
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Nitric Oxide Signaling for Aerial Mycelium Formation in Streptomyces coelicolor A3(2) M145. Appl Environ Microbiol 2022; 88:e0122222. [PMID: 36354316 PMCID: PMC9746327 DOI: 10.1128/aem.01222-22] [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] [Indexed: 11/12/2022] Open
Abstract
Nitric oxide (NO) is a well-known signaling molecule in various organisms. Streptomyces undergoes complex morphological differentiation, similar to that of fungi. A recent study revealed a nitrogen oxide metabolic cycle that forms NO in Streptomyces coelicolor A3(2) M145. Further, endogenously produced NO serves as a signaling molecule. Here, we report that endogenously produced NO regulates cyclic 3',5'-diguanylate (c-di-GMP) levels and controls aerial mycelium formation through the c-di-GMP-binding transcriptional regulator BldD in S. coelicolor A3(2) M145. These observations provide important insights into the mechanisms regulating morphological differentiation. This is the first study to demonstrate a link between NO and c-di-GMP in S. coelicolor A3(2) M145. Morphological differentiation is closely linked to the initiation of secondary metabolism in actinomycetes. Thus, the NO signaling-based regulation of aerial mycelium formation has potential applications in the fermentation industry employing useful actinomycetes. IMPORTANCE Eukaryotic and prokaryotic cells utilize nitric oxide (NO) to regulate physiological functions. Besides its role as a producer of different bioactive substances, Streptomyces is suggested to be involved in mycelial development regulated by endogenously produced NO. However, the regulatory mechanisms are unclear. In this study, we proposed that NO signaling is involved in aerial mycelium formation in S. coelicolor A3(2) M145. NO serves as a signaling molecule for the regulation of intracellular cyclic 3',5'-diguanylate (c-di-GMP) levels, resulting in aerial mycelium formation controlled by a c-di-GMP receptor, BldD. As the abundant production of valuable secondary metabolites is closely related to the initiation of morphological differentiation in Streptomyces, NO may provide value for application in industrial fermentation by serving as a tool for regulating secondary metabolism.
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4
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Wang J, Rao L, Huang Z, Ma L, Yang T, Yu Z, Sun A, Ge Y. The nitric oxide synthase gene negatively regulates biofilm formation in Staphylococcus epidermidis. Front Cell Infect Microbiol 2022; 12:1015859. [PMID: 36405963 PMCID: PMC9669438 DOI: 10.3389/fcimb.2022.1015859] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 10/12/2022] [Indexed: 11/07/2023] Open
Abstract
Staphylococcus epidermidis (S. epidermidis) is a clinically important conditioned pathogen that can cause a troublesome chronic implant-related infection once a biofilm is formed. The nitric oxide synthase (NOS) gene, which is responsible for endogenous nitric oxide synthesis, has already been found in the genome of S. epidermidis; however, the specific mechanisms associated with the effects of NOS on S. epidermidis pathogenicity are still unknown. The purpose of the current study was to investigate whether the NOS gene has an impact on biofilm formation in S. epidermidis. Bioinformatics analysis of the NOS gene was performed, and homologous recombination was subsequently employed to delete this gene. The effects of the NOS gene on biofilm formation of S. epidermidis and its underlying mechanisms were analyzed by bacterial growth assays, biofilm semiquantitative determination, Triton X-100-induced autolysis assays, and bacterial biofilm dispersal assays. Additionally, the transcription levels of fbe, aap, icaA, icaR and sigB, which are related to biofilm formation, were further investigated by qRT-PCR following NOS deletion. Phylogenetic analysis revealed that the NOS gene was conserved between bacterial species originating from different genera. The NOS deletion strain of S. epidermidis 1457 and its counterpart were successfully constructed. Disruption of the NOS gene resulted in significantly enhanced biofilm formation, slightly retarded bacterial growth, a markedly decreased autolysis rate, and drastically weakened bacterial biofilm dispersal. Our data showed that the fbe, aap and icaA genes were significantly upregulated, while the icaR and sigB genes were significantly downregulated, compared with the wild strain. Therefore, these data strongly suggested that the NOS gene can negatively regulate biofilm formation in S. epidermidis by affecting biofilm aggregation and dispersal.
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Affiliation(s)
- Jiaxue Wang
- School of Laboratory Medicine and Bioengineering, Hangzhou Medical College, Hangzhou, Zhejiang, China
- Department of Clinical Laboratory, Laboratory Medicine Center, Zhejiang Provincial People’s Hospital (Affiliated People’s Hospital, Hangzhou Medical College), Hangzhou, Zhejiang, China
- Key Laboratory of Biomarkers and In Vitro Diagnosis Translation of Zhejiang province, Hangzhou, Zhejiang, China
- Institute of Clinical Microbiology, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Lulin Rao
- School of Laboratory Medicine and Bioengineering, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Zhuoan Huang
- School of Laboratory Medicine and Bioengineering, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Lili Ma
- School of Laboratory Medicine and Bioengineering, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Tian Yang
- School of Laboratory Medicine and Bioengineering, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Zhongqi Yu
- School of Laboratory Medicine and Bioengineering, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Aihua Sun
- Department of basic medicine, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Yumei Ge
- Department of Clinical Laboratory, Laboratory Medicine Center, Zhejiang Provincial People’s Hospital (Affiliated People’s Hospital, Hangzhou Medical College), Hangzhou, Zhejiang, China
- Key Laboratory of Biomarkers and In Vitro Diagnosis Translation of Zhejiang province, Hangzhou, Zhejiang, China
- Institute of Clinical Microbiology, Hangzhou Medical College, Hangzhou, Zhejiang, China
- Department of basic medicine, Hangzhou Medical College, Hangzhou, Zhejiang, China
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5
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Omer R, Mohsin MZ, Mohsin A, Mushtaq BS, Huang X, Guo M, Zhuang Y, Huang J. Engineered Bacteria-Based Living Materials for Biotherapeutic Applications. Front Bioeng Biotechnol 2022; 10:870675. [PMID: 35573236 PMCID: PMC9096031 DOI: 10.3389/fbioe.2022.870675] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 03/11/2022] [Indexed: 11/10/2022] Open
Abstract
Future advances in therapeutics demand the development of dynamic and intelligent living materials. The past static monofunctional materials shall be unable to meet the requirements of future medical development. Also, the demand for precision medicine has increased with the progressively developing human society. Therefore, engineered living materials (ELMs) are vitally important for biotherapeutic applications. These ELMs can be cells, microbes, biofilms, and spores, representing a new platform for treating intractable diseases. Synthetic biology plays a crucial role in the engineering of these living entities. Hence, in this review, the role of synthetic biology in designing and creating genetically engineered novel living materials, particularly bacteria, has been briefly summarized for diagnostic and targeted delivery. The main focus is to provide knowledge about the recent advances in engineered bacterial-based therapies, especially in the treatment of cancer, inflammatory bowel diseases, and infection. Microorganisms, particularly probiotics, have been engineered for synthetic living therapies. Furthermore, these programmable bacteria are designed to sense input signals and respond to disease-changing environments with multipronged therapeutic outputs. These ELMs will open a new path for the synthesis of regenerative medicines as they release therapeutics that provide in situ drug delivery with lower systemic effects. In last, the challenges being faced in this field and the future directions requiring breakthroughs have been discussed. Conclusively, the intent is to present the recent advances in research and biomedical applications of engineered bacteria-based therapies during the last 5 years, as a novel treatment for uncontrollable diseases.
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Affiliation(s)
- Rabia Omer
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Muhammad Zubair Mohsin
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Ali Mohsin
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Bilal Sajid Mushtaq
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, China
| | - Xumeng Huang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Meijin Guo
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Yingping Zhuang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Jiaofang Huang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China,*Correspondence: Jiaofang Huang,
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6
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Chen J, Xie P, Huang Y, Gao H. Complex Interplay of Heme-Copper Oxidases with Nitrite and Nitric Oxide. Int J Mol Sci 2022; 23:979. [PMID: 35055165 PMCID: PMC8780969 DOI: 10.3390/ijms23020979] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/13/2022] [Accepted: 01/15/2022] [Indexed: 12/19/2022] Open
Abstract
Nitrite and nitric oxide (NO), two active and critical nitrogen oxides linking nitrate to dinitrogen gas in the broad nitrogen biogeochemical cycle, are capable of interacting with redox-sensitive proteins. The interactions of both with heme-copper oxidases (HCOs) serve as the foundation not only for the enzymatic interconversion of nitrogen oxides but also for the inhibitory activity. From extensive studies, we now know that NO interacts with HCOs in a rapid and reversible manner, either competing with oxygen or not. During interconversion, a partially reduced heme/copper center reduces the nitrite ion, producing NO with the heme serving as the reductant and the cupric ion providing a Lewis acid interaction with nitrite. The interaction may lead to the formation of either a relatively stable nitrosyl-derivative of the enzyme reduced or a more labile nitrite-derivative of the enzyme oxidized through two different pathways, resulting in enzyme inhibition. Although nitrite and NO show similar biochemical properties, a growing body of evidence suggests that they are largely treated as distinct molecules by bacterial cells. NO seemingly interacts with all hemoproteins indiscriminately, whereas nitrite shows high specificity to HCOs. Moreover, as biologically active molecules and signal molecules, nitrite and NO directly affect the activity of different enzymes and are perceived by completely different sensing systems, respectively, through which they are linked to different biological processes. Further attempts to reconcile this apparent contradiction could open up possible avenues for the application of these nitrogen oxides in a variety of fields, the pharmaceutical industry in particular.
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Affiliation(s)
| | | | | | - Haichun Gao
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou 310058, China; (J.C.); (P.X.); (Y.H.)
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7
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H-NOX proteins in the virulence of pathogenic bacteria. Biosci Rep 2021; 42:230559. [PMID: 34939646 PMCID: PMC8738867 DOI: 10.1042/bsr20212014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 12/17/2021] [Accepted: 12/21/2021] [Indexed: 12/05/2022] Open
Abstract
Nitric oxide (NO) is a toxic gas encountered by bacteria as a product of their own metabolism or as a result of a host immune response. Non-toxic concentrations of NO have been shown to initiate changes in bacterial behaviors such as the transition between planktonic and biofilm-associated lifestyles. The heme nitric oxide/oxygen binding proteins (H-NOX) are a widespread family of bacterial heme-based NO sensors that regulate biofilm formation in response to NO. The presence of H-NOX in several human pathogens combined with the importance of planktonic–biofilm transitions to virulence suggests that H-NOX sensing may be an important virulence factor in these organisms. Here we review the recent data on H-NOX NO signaling pathways with an emphasis on H-NOX homologs from pathogens and commensal organisms. The current state of the field is somewhat ambiguous regarding the role of H-NOX in pathogenesis. However, it is clear that H-NOX regulates biofilm in response to environmental factors and may promote persistence in the environments that serve as reservoirs for these pathogens. Finally, the evidence that large subgroups of H-NOX proteins may sense environmental signals besides NO is discussed within the context of a phylogenetic analysis of this large and diverse family.
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8
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Kitanishi K, Shimonaka M, Unno M. Characterization of a Cobalt-Substituted Globin-Coupled Oxygen Sensor Histidine Kinase from Anaeromyxobacter sp. Fw109-5: Insights into Catalytic Regulation by Its Heme Coordination Structure. ACS OMEGA 2021; 6:34912-34919. [PMID: 34963974 PMCID: PMC8697598 DOI: 10.1021/acsomega.1c05564] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 11/24/2021] [Indexed: 05/09/2023]
Abstract
Heme-based gas sensors are an emerging class of heme proteins. AfGcHK, a globin-coupled histidine kinase from Anaeromyxobacter sp. Fw109-5, is an oxygen sensor enzyme in which oxygen binding to Fe(II) heme in the globin sensor domain substantially enhances its autophosphorylation activity. Here, we reconstituted AfGcHK with cobalt protoporphyrin IX (Co-AfGcHK) in place of heme (Fe-AfGcHK) and characterized the spectral and catalytic properties of the full-length proteins. Spectroscopic analyses indicated that Co(III) and Co(II)-O2 complexes were in a 6-coordinated low-spin state in Co-AfGcHK, like Fe(III) and Fe(II)-O2 complexes of Fe-AfGcHK. Although both Fe(II) and Co(II) complexes were in a 5-coordinated state, Fe(II) and Co(II) complexes were in high-spin and low-spin states, respectively. The autophosphorylation activity of Co(III) and Co(II)-O2 complexes of Co-AfGcHK was fully active, whereas that of the Co(II) complex was moderately active. This contrasts with Fe-AfGcHK, where Fe(III) and Fe(II)-O2 complexes were fully active and the Fe(II) complex was inactive. Collectively, activity data and coordination structures of Fe-AfGcHK and Co-AfGcHK indicate that all fully active forms were in a 6-coordinated low-spin state, whereas the inactive form was in a 5-coordinated high-spin state. The 5-coordinated low-spin complex was moderately active-a novel finding of this study. These results suggest that the catalytic activity of AfGcHK is regulated by its heme coordination structure, especially the spin state of its heme iron. Our study presents the first successful preparation and characterization of a cobalt-substituted globin-coupled oxygen sensor enzyme and may lead to a better understanding of the molecular mechanisms of catalytic regulation in this family.
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Affiliation(s)
- Kenichi Kitanishi
- Department
of Chemistry, Faculty of Science, Tokyo
University of Science, 1-3 Kagurazaka, Shinjuku-ku, Tokyo 162-8601, Japan
- . Tel: +81-3-3260-4272 (ex. 5738)
| | - Motoyuki Shimonaka
- Department
of Chemistry, Faculty of Science, Tokyo
University of Science, 1-3 Kagurazaka, Shinjuku-ku, Tokyo 162-8601, Japan
| | - Masaki Unno
- Graduate
School of Science and Engineering, Ibaraki
University, 4-12-1 Nakanarusawa, Hitachi, Ibaraki 316-8511, Japan
- Frontier
Research Center for Applied Atomic Sciences, Ibaraki University, 162-1 Shirakata, Tokai, Naka, Ibaraki 319-1106, Japan
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9
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Chen XJ, Wang B, Thompson IP, Huang WE. Rational Design and Characterization of Nitric Oxide Biosensors in E. coli Nissle 1917 and Mini SimCells. ACS Synth Biol 2021; 10:2566-2578. [PMID: 34551261 DOI: 10.1021/acssynbio.1c00223] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nitric oxide (NO) is an important disease biomarker found in many chronic inflammatory diseases and cancers. A well-characterized nitric sensing system is useful to aid the rapid development of bacteria therapy and synthetic biology. In this work, we engineered a set of NO-responsive biosensors based on the PnorV promoter and its NorR regulator in the norRVW operon; the circuits were characterized and optimized in probiotic Escherichia coli Nissle 1917 and mini SimCells (minicells containing designed gene circuits for specific tasks). Interestingly, the expression level of NorR displayed an inverse correlation to the PnorV promoter activation, as a strong expression of the NorR regulator resulted in a low amplitude of NO-inducible gene expression. This could be explained by a competitive binding mechanism where the activated and inactivated NorR competitively bind to the same site on the PnorV promoter. To overcome such issues, the NO induction performance was further improved by making a positive feedback loop that fine-tuned the level of NorR. In addition, by examining two integration host factor (IHF) binding sites of the PnorV promoter, we demonstrated that the deletion of the second IHF site increased the maximum signal output by 25% (500 μM DETA/NO) with no notable increase in the basal expression level. The optimized NO-sensing gene circuit in anucleate mini SimCells exhibited increased robustness against external fluctuation in medium composition. The NO detection limit of the optimized gene circuit pPnorVβ was also improved from 25.6 to 1.3 nM in mini SimCells. Moreover, lyophilized mini SimCells can maintain function for over 2 months. Hence, SimCell-based NO biosensors could be used as safe sensor chassis for synthetic biology.
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Affiliation(s)
- Xiaoyu J. Chen
- Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, United Kingdom
| | - Baojun Wang
- Hangzhou Innovation Center and College of Chemical & Biological Engineering, Zhejiang University, Hangzhou 311200, China
- School of Biological Sciences, University of Edinburgh, G20 Roger Land Building, The Kingʼs Buildings, Edinburgh EH9 3FF, United Kingdom
- ZJU-UoE Joint Research Centre for Engineering Biology, Zhejiang University, Haining 314400, China
| | - Ian P. Thompson
- Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, United Kingdom
| | - Wei E. Huang
- Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, United Kingdom
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10
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Gonzaga de França Lopes L, Gouveia Júnior FS, Karine Medeiros Holanda A, Maria Moreira de Carvalho I, Longhinotti E, Paulo TF, Abreu DS, Bernhardt PV, Gilles-Gonzalez MA, Cirino Nogueira Diógenes I, Henrique Silva Sousa E. Bioinorganic systems responsive to the diatomic gases O2, NO, and CO: From biological sensors to therapy. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2021.214096] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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11
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Guo K, Gao H. Physiological Roles of Nitrite and Nitric Oxide in Bacteria: Similar Consequences from Distinct Cell Targets, Protection, and Sensing Systems. Adv Biol (Weinh) 2021; 5:e2100773. [PMID: 34310085 DOI: 10.1002/adbi.202100773] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 06/19/2021] [Indexed: 12/22/2022]
Abstract
Nitrite and nitric oxide (NO) are two active nitrogen oxides that display similar biochemical properties, especially when interacting with redox-sensitive proteins (i.e., hemoproteins), an observation serving as the foundation of the notion that the antibacterial effect of nitrite is largely attributed to NO formation. However, a growing body of evidence suggests that they are largely treated as distinct molecules by bacterial cells. Although both nitrite and NO are formed and decomposed by enzymes participating in the transformation of these nitrogen species, NO can also be generated via amino acid metabolism by bacterial NO synthetase and scavenged by flavohemoglobin. NO seemingly interacts with all hemoproteins indiscriminately, whereas nitrite shows high specificity to heme-copper oxidases. Consequently, the homeostasis of redox-sensitive proteins may be responsible for the substantial difference in NO-targets identified to date among different bacteria. In addition, most protective systems against NO damage have no significant role in alleviating inhibitory effects of nitrite. Furthermore, when functioning as signal molecules, nitrite and NO are perceived by completely different sensing systems, through which they are linked to different biological processes.
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Affiliation(s)
- Kailun Guo
- Institute of Microbiology and College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Haichun Gao
- Institute of Microbiology and College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
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12
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Hassett DJ, Kovall RA, Schurr MJ, Kotagiri N, Kumari H, Satish L. The Bactericidal Tandem Drug, AB569: How to Eradicate Antibiotic-Resistant Biofilm Pseudomonas aeruginosa in Multiple Disease Settings Including Cystic Fibrosis, Burns/Wounds and Urinary Tract Infections. Front Microbiol 2021; 12:639362. [PMID: 34220733 PMCID: PMC8245851 DOI: 10.3389/fmicb.2021.639362] [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: 12/08/2020] [Accepted: 04/07/2021] [Indexed: 11/13/2022] Open
Abstract
The life-threatening pandemic concerning multi-drug resistant (MDR) bacteria is an evolving problem involving increased hospitalizations, billions of dollars in medical costs and a remarkably high number of deaths. Bacterial pathogens have demonstrated the capacity for spontaneous or acquired antibiotic resistance and there is virtually no pool of organisms that have not evolved such potentially clinically catastrophic properties. Although many diseases are linked to such organisms, three include cystic fibrosis (CF), burn/blast wounds and urinary tract infections (UTIs), respectively. Thus, there is a critical need to develop novel, effective antimicrobials for the prevention and treatment of such problematic infections. One of the most formidable, naturally MDR bacterial pathogens is Pseudomonas aeruginosa (PA) that is particularly susceptible to nitric oxide (NO), a component of our innate immune response. This susceptibility sets the translational stage for the use of NO-based therapeutics during the aforementioned human infections. First, we discuss how such NO therapeutics may be able to target problematic infections in each of the aforementioned infectious scenarios. Second, we describe a recent discovery based on years of foundational information, a novel drug known as AB569. AB569 is capable of forming a "time release" of NO from S-nitrosothiols (RSNO). AB569, a bactericidal tandem consisting of acidified NaNO2 (A-NO2 -) and Na2-EDTA, is capable of killing all pathogens that are associated with the aforementioned disorders. Third, we described each disease state in brief, the known or predicted effects of AB569 on the viability of PA, its potential toxicity and highly remote possibility for resistance to develop. Finally, we conclude that AB569 can be a viable alternative or addition to conventional antibiotic regimens to treat such highly problematic MDR bacterial infections for civilian and military populations, as well as the economical burden that such organisms pose.
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Affiliation(s)
- Daniel J Hassett
- Department of Molecular Genetics, Biochemistry and Microbiology, Cincinnati, OH, United States
| | - Rhett A Kovall
- Department of Molecular Genetics, Biochemistry and Microbiology, Cincinnati, OH, United States
| | - Michael J Schurr
- Department of Immunology and Microbiology, University of Colorado Health Sciences, Denver, CO, United States
| | - Nalinikanth Kotagiri
- Division of Pharmacy, University of Colorado Health Sciences, Denver, CO, United States
| | - Harshita Kumari
- Division of Pharmacy, University of Colorado Health Sciences, Denver, CO, United States
| | - Latha Satish
- Department of Pathology and Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, United States.,Shriners Hospitals for Children-Cincinnati, Cincinnati, OH, United States
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13
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Fu J, Hall S, Boon EM. Recent evidence for multifactorial biofilm regulation by heme sensor proteins NosP and H-NOX. CHEM LETT 2021; 50:1095-1103. [PMID: 36051866 PMCID: PMC9432776 DOI: 10.1246/cl.200945] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
Abstract
Heme is involved in signal transduction by either acting as a cofactor of heme-based gas/redox sensors or binding reversely to heme-responsive proteins. Bacteria respond to low concentrations of nitric oxide (NO) to modulate group behaviors such as biofilms through the well-characterized H-NOX family and the newly discovered heme sensor protein NosP. NosP shares functional similarities with H-NOX as a heme-based NO sensor; both regulate two-component systems and/or cyclic-di-GMP metabolizing enzymes, playing roles in processes such as quorum sensing and biofilm regulation. Interestingly, aside from its role in NO signaling, recent studies suggest that NosP may also sense labile heme. In this Highlight Review, we briefly summarize H-NOX-dependent NO signaling in bacteria, then focus on recent advances in NosP-mediated NO signaling and labile heme sensing.
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Affiliation(s)
| | | | - Elizabeth M. Boon
- To whom correspondence should be addressed: Elizabeth M. Boon: Tel.: (631) 632-7945. Fax: (631) 632-7960.
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14
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The solution chemistry of nitric oxide and other reactive nitrogen species. Nitric Oxide 2020; 103:31-46. [DOI: 10.1016/j.niox.2020.07.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 07/14/2020] [Accepted: 07/16/2020] [Indexed: 12/17/2022]
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15
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Layer G. Heme biosynthesis in prokaryotes. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1868:118861. [PMID: 32976912 DOI: 10.1016/j.bbamcr.2020.118861] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 09/17/2020] [Accepted: 09/18/2020] [Indexed: 12/21/2022]
Abstract
The cyclic tetrapyrrole heme is used as a prosthetic group in a broad variety of different proteins in almost all organisms. Often, it is essential for vital biochemical processes such as aerobic and anaerobic respiration as well as photosynthesis. In Nature, heme is made from the common tetrapyrrole precursor 5-aminolevulinic acid, and for a long time it was assumed that heme is biosynthesized by a single, common pathway in all organisms. However, although this is indeed the case in eukaryotes, heme biosynthesis is more diverse in the prokaryotic world, where two additional pathways exist. The final elucidation of the two 'alternative' heme biosynthesis routes operating in some bacteria and archaea was achieved within the last decade. This review summarizes the three different heme biosynthesis pathways with a special emphasis on the two 'new' prokaryotic routes.
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Affiliation(s)
- Gunhild Layer
- Albert-Ludwigs-Universität Freiburg, Institut für Pharmazeutische Wissenschaften, Stefan-Meier-Strasse 19, 79104 Freiburg, Germany.
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16
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Fang K, Park OJ, Hong SH. Controlling biofilms using synthetic biology approaches. Biotechnol Adv 2020; 40:107518. [PMID: 31953206 PMCID: PMC7125041 DOI: 10.1016/j.biotechadv.2020.107518] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 01/09/2020] [Accepted: 01/11/2020] [Indexed: 12/22/2022]
Abstract
Bacterial biofilms are formed by the complex but ordered regulation of intra- or inter-cellular communication, environmentally responsive gene expression, and secretion of extracellular polymeric substances. Given the robust nature of biofilms due to the non-growing nature of biofilm bacteria and the physical barrier provided by the extracellular matrix, eradicating biofilms is a very difficult task to accomplish with conventional antibiotic or disinfectant treatments. Synthetic biology holds substantial promise for controlling biofilms by improving and expanding existing biological tools, introducing novel functions to the system, and re-conceptualizing gene regulation. This review summarizes synthetic biology approaches used to eradicate biofilms via protein engineering of biofilm-related enzymes, utilization of synthetic genetic circuits, and the development of functional living agents. Synthetic biology also enables beneficial applications of biofilms through the production of biomaterials and patterning biofilms with specific temporal and spatial structures. Advances in synthetic biology will add novel biofilm functionalities for future therapeutic, biomanufacturing, and environmental applications.
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Affiliation(s)
- Kuili Fang
- Department of Chemical and Biological Engineering, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Oh-Jin Park
- Department of Chemical and Biological Engineering, Illinois Institute of Technology, Chicago, IL 60616, USA; Department of Biological and Chemical Engineering, Yanbian University of Science and Technology, Yanji, Jilin, People's Republic of China
| | - Seok Hoon Hong
- Department of Chemical and Biological Engineering, Illinois Institute of Technology, Chicago, IL 60616, USA.
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17
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Shimizu T, Lengalova A, Martínek V, Martínková M. Heme: emergent roles of heme in signal transduction, functional regulation and as catalytic centres. Chem Soc Rev 2019; 48:5624-5657. [DOI: 10.1039/c9cs00268e] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Molecular mechanisms of unprecedented functions of exchangeable/labile heme and heme proteins including transcription, DNA binding, protein kinase activity, K+ channel functions, cis–trans isomerization, N–N bond formation, and other functions are described.
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Affiliation(s)
- Toru Shimizu
- Department of Biochemistry
- Faculty of Science
- Charles University
- Prague 2
- Czech Republic
| | - Alzbeta Lengalova
- Department of Biochemistry
- Faculty of Science
- Charles University
- Prague 2
- Czech Republic
| | - Václav Martínek
- Department of Biochemistry
- Faculty of Science
- Charles University
- Prague 2
- Czech Republic
| | - Markéta Martínková
- Department of Biochemistry
- Faculty of Science
- Charles University
- Prague 2
- Czech Republic
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18
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Williams DE, Boon EM. Towards Understanding the Molecular Basis of Nitric Oxide-Regulated Group Behaviors in Pathogenic Bacteria. J Innate Immun 2018; 11:205-215. [PMID: 30557874 DOI: 10.1159/000494740] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 10/04/2018] [Indexed: 12/18/2022] Open
Abstract
Pathogenic bacteria have many strategies for causing disease in humans. One such strategy is the ability to live both as single-celled motile organisms or as part of a community of bacteria called a biofilm. Biofilms are frequently adhered to biotic or abiotic surfaces and are extremely antibiotic resistant. Upon biofilm dispersal, bacteria become more antibiotic susceptible but are also able to readily infect another host. Various studies have shown that low, nontoxic levels of nitric oxide (NO) may induce biofilm dispersal in many bacterial species. While the molecular details of this phenotype remain largely unknown, in several species, NO has been implicated in biofilm-to-planktonic cell transitions via ligation to 1 of 2 characterized NO sensors, NosP or H-NOX. Based on the data available to date, it appears that NO binding to H-NOX or NosP triggers a downstream response based on changes in cellular cyclic di-GMP concentrations and/or the modulation of quorum sensing. In order to develop applications for control of biofilm infections, the identification and characterization of biofilm dispersal mechanisms is vital. This review focuses on the efforts made to understand NO-mediated control of H-NOX and NosP pathways in the 3 pathogenic bacteria Legionella pneumophila, Vibrio cholerae, and Pseudomonas aeruginosa.
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Affiliation(s)
- Dominique E Williams
- Department of Chemistry and Institute of Chemical Biology and Drug Design, Stony Brook University, Stony Brook, New York, USA
| | - Elizabeth M Boon
- Department of Chemistry and Institute of Chemical Biology and Drug Design, Stony Brook University, Stony Brook, New York, USA,
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19
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Bacon BA, Liu Y, Kincaid JR, Boon EM. Spectral Characterization of a Novel NO Sensing Protein in Bacteria: NosP. Biochemistry 2018; 57:6187-6200. [PMID: 30272959 DOI: 10.1021/acs.biochem.8b00451] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
A novel family of bacterial hemoproteins named NosP has been discovered recently; its members are proposed to function as nitric oxide (NO) responsive proteins involved in bacterial group behaviors such as quorum sensing and biofilm growth and dispersal. Currently, little is known about molecular activation mechanisms in NosP. Here, functional studies were performed utilizing the distinct spectroscopic characteristics associated with the NosP heme cofactor. NosPs from Pseudomonas aeruginosa ( Pa), Vibrio cholerae ( Vc), and Legionella pneumophila ( Lpg) were studied in their ferrous unligated forms as well as their ferrous CO, ferrous NO, and ferric CN adducts. The resonance Raman (rR) data collected on the ferric forms strongly support the existence of a distorted heme cofactor, which is a common feature in NO sensors. The ferrous spectra exhibit a 213 cm-1 feature, which is assigned to the Fe-Nhis stretching mode. The Fe-C and C-O frequencies in the spectra of ferrous CO NosP complexes are inversely correlated with relatively similar frequencies, consistent with a proximal histidine ligand and a relatively hydrophobic environment. The rR spectra obtained for isotopically labeled ferrous NO adducts provide evidence of formation of a 5-coordinate NO complex, resulting from proximal Fe-Nhis cleavage, which is believed to play a role in biological heme-NO signal transduction. Additionally, we found that of the three NosPs studied, Lpg NosP contains the most electropositive ligand binding pocket, while Pa NosP has the most electronegative ligand binding pocket. This pattern is also observed in the measured heme reduction potentials for these three proteins, which may indicate distinct functions for each.
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Affiliation(s)
- Bezalel A Bacon
- Graduate program in Biochemistry and Structural Biology , Stony Brook University , Stony Brook , New York 11790-3400 , United States
| | - Yilin Liu
- Department of Chemistry , Marquette University , Milwaukee , Wisconsin 53233 , United States
| | - James R Kincaid
- Department of Chemistry , Marquette University , Milwaukee , Wisconsin 53233 , United States
| | - Elizabeth M Boon
- Graduate program in Biochemistry and Structural Biology , Stony Brook University , Stony Brook , New York 11790-3400 , United States.,Department of Chemistry and Institute of Chemical Biology and Drug Discovery , Stony Brook University , Stony Brook , New York 11794-3400 , United States
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