1
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Muduli S, Karmakar S, Mishra S. The coordinated action of the enzymes in the L-lysine biosynthetic pathway and how to inhibit it for antibiotic targets. Biochim Biophys Acta Gen Subj 2023; 1867:130320. [PMID: 36813209 DOI: 10.1016/j.bbagen.2023.130320] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 01/19/2023] [Accepted: 02/02/2023] [Indexed: 02/22/2023]
Abstract
BACKGROUND Antimicrobial resistance is a global health issue that requires immediate attention in terms of new antibiotics and new antibiotic targets. The l-lysine biosynthesis pathway (LBP) is a promising avenue for drug discovery as it is essential for bacterial growth and survival and is not required by human beings. SCOPE OF REVIEW The LBP involves a coordinated action of fourteen different enzymes distributed over four distinct sub-pathways. The enzymes involved in this pathway belong to different classes, such as aspartokinase, dehydrogenase, aminotransferase, epimerase, etc. This review provides a comprehensive account of the secondary and tertiary structure, conformational dynamics, active site architecture, mechanism of catalytic action, and inhibitors of all enzymes involved in LBP of different bacterial species. MAJOR CONCLUSIONS LBP offers a wide scope for novel antibiotic targets. The enzymology of a majority of the LBP enzymes is well understood, although these enzymes are less widely studied in the critical pathogens (according to the 2017 WHO report) that require immediate attention. In particular, the enzymes in the acetylase pathway, DapAT, DapDH, and Aspartokinase in critical pathogens have received little attention. High throughput screening for inhibitor design against the enzymes of lysine biosynthetic pathway is rather limited, both in number and in the extent of success. GENERAL SIGNIFICANCE This review can serve as a guide for the enzymology of LBP and help in identifying new drug targets and designing potential inhibitors.
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Affiliation(s)
- Sunita Muduli
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Soumyajit Karmakar
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Sabyashachi Mishra
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, India.
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2
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Yu HY, Rhim DB, Kim SK, Ban OH, Oh SK, Seo J, Hong SK. Growth promotion effect of red ginseng dietary fiber to probiotics and transcriptome analysis of Lactiplantibacillus plantarum. J Ginseng Res 2023; 47:159-165. [PMID: 36644380 PMCID: PMC9834016 DOI: 10.1016/j.jgr.2022.09.003] [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: 10/14/2021] [Revised: 09/15/2022] [Accepted: 09/27/2022] [Indexed: 11/19/2022] Open
Abstract
Background Red ginseng marc, the residue of red ginseng left after water extraction, is rich in dietary fiber. Dietary fiber derived from fruits or vegetables can promote the proliferation of probiotics, and it is a key technology in the food industry to increase the productivity of probiotics by adding growth-enhancing substances such as dietary fiber. In this study, the effect of red ginseng dietary fiber (RGDF) on the growth of probiotic bacterial strains was investigated at the phenotypic and genetic levels. Methods We performed transcriptome profiling of Lactiplantibacillus plantarum IDCC3501 in two phases of culture (logarithmic (L)-phase and stationary (S)-phase) in two culture conditions (with or without RGDF) using RNA-seq. Differentially expressed genes (DEGs) were identified and classified according to Gene Ontology terms. Results The growth of L.plantarum IDCC3501 was enhanced in medium supplemented with RGDF up to 2%. As a result of DEG analysis, 29 genes were upregulated and 30 were downregulated in the RGDF-treated group in the L-phase. In the S-phase, 57 genes were upregulated and 126 were downregulated in the RGDF-treated group. Among the upregulated genes, 5 were upregulated only in the L-phase, 10 were upregulated only in the S-phase, and 3 were upregulated in both the L- and S-phases. Conclusions Transcriptome analysis could be a valuable tool for elucidating the molecular mechanisms by which RGDF promotes the proliferation of L.plantarum IDCC3501. This growth-promoting effect of RGDF is important, since RGDF could be used as a prebiotic source without additional chemical or enzymatic processing.
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Affiliation(s)
- Hye-Young Yu
- Laboratory of Red Ginseng Products, Korea Ginseng Corporation, Daejeon, Republic of Korea
| | - Dong-Bin Rhim
- Laboratory of Red Ginseng Products, Korea Ginseng Corporation, Daejeon, Republic of Korea
| | - Sang-Kyu Kim
- Laboratory of Red Ginseng Products, Korea Ginseng Corporation, Daejeon, Republic of Korea
- Corresponding author. Sang-Kyu Kim, Laboratory of Red Ginseng Products, Korea Ginseng Corporation, 30, Gajeong-ro, Shinseong-dong, Yuseong-gu, Daejeon, 34128, Republic of Korea.
| | - O-Hyun Ban
- Ildong Bioscience, Pyeongteak, Republic of Korea
| | - Sang-Ki Oh
- Ildong Bioscience, Pyeongteak, Republic of Korea
| | - Jiho Seo
- Laboratory of Red Ginseng Products, Korea Ginseng Corporation, Daejeon, Republic of Korea
| | - Soon-Ki Hong
- Laboratory of Red Ginseng Products, Korea Ginseng Corporation, Daejeon, Republic of Korea
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3
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Arif SM, Floto RA, Blundell TL. Using Structure-guided Fragment-Based Drug Discovery to Target Pseudomonas aeruginosa Infections in Cystic Fibrosis. Front Mol Biosci 2022; 9:857000. [PMID: 35433835 PMCID: PMC9006449 DOI: 10.3389/fmolb.2022.857000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 02/23/2022] [Indexed: 11/13/2022] Open
Abstract
Cystic fibrosis (CF) is progressive genetic disease that predisposes lungs and other organs to multiple long-lasting microbial infections. Pseudomonas aeruginosa is the most prevalent and deadly pathogen among these microbes. Lung function of CF patients worsens following chronic infections with P. aeruginosa and is associated with increased mortality and morbidity. Emergence of multidrug-resistant, extensively drug-resistant and pandrug-resistant strains of P. aeruginosa due to intrinsic and adaptive antibiotic resistance mechanisms has failed the current anti-pseudomonal antibiotics. Hence new antibacterials are urgently needed to treat P. aeruginosa infections. Structure-guided fragment-based drug discovery (FBDD) is a powerful approach in the field of drug development that has succeeded in delivering six FDA approved drugs over the past 20 years targeting a variety of biological molecules. However, FBDD has not been widely used in the development of anti-pseudomonal molecules. In this review, we first give a brief overview of our structure-guided FBDD pipeline and then give a detailed account of FBDD campaigns to combat P. aeruginosa infections by developing small molecules having either bactericidal or anti-virulence properties. We conclude with a brief overview of the FBDD efforts in our lab at the University of Cambridge towards targeting P. aeruginosa infections.
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Affiliation(s)
| | - R. Andres Floto
- Molecular Immunity Unit, Department of Medicine University of Cambridge, MRC-Laboratory of Molecular Biology, Cambridge, United Kingdom
- Cambridge Centre for Lung Infection, Royal Papworth Hospital, Cambridge, United Kingdom
| | - Tom L. Blundell
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
- *Correspondence: Tom L. Blundell,
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4
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Ali S, Alam M, Hasan GM, Hassan MI. Potential therapeutic targets of Klebsiella pneumoniae: a multi-omics review perspective. Brief Funct Genomics 2021; 21:63-77. [PMID: 34448478 DOI: 10.1093/bfgp/elab038] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/03/2021] [Accepted: 08/04/2021] [Indexed: 11/15/2022] Open
Abstract
The multidrug resistance developed in many organisms due to the prolonged use of antibiotics has been an increasing global health crisis. Klebsiella pneumoniae is a causal organism for various infections, including respiratory, urinary tract and biliary diseases. Initially, immunocompromised individuals are primarily affected by K. pneumoniae. Due to the emergence of hypervirulent strains recently, both healthy and immunocompetent individuals are equally susceptible to K. pneumoniae infections. The infections caused by multidrug-resistant and hypervirulent K. pneumoniae strains are complicated to treat, illustrating an urgent need to develop novel and more practical approaches to combat the pathogen. We focused on the previously performed high-throughput analyses by other groups to discover several novel enzymes that may be considered attractive drug targets of K. pneumoniae. These targets qualify most of the selection criteria for drug targeting, including an absence of its homolog's gene in the host. The capsule, lipopolysaccharide, fimbriae, siderophores and essential virulence factors facilitate the pathogen entry, infection and survival inside the host. This review discusses K. pneumoniae pathophysiology, including its virulence determinants and further the potential drug targets that might facilitate the discovery of novel drugs and effective treatment regimens shortly.
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Affiliation(s)
- Sabeeha Ali
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar New Delhi 110025, India
| | - Manzar Alam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar New Delhi 110025, India
| | - Gulam Mustafa Hasan
- Department of Biochemistry, College of Medicine, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar New Delhi 110025, India
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5
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Trouillon J, Sentausa E, Ragno M, Robert-Genthon M, Lory S, Attrée I, Elsen S. Species-specific recruitment of transcription factors dictates toxin expression. Nucleic Acids Res 2020; 48:2388-2400. [PMID: 31925438 PMCID: PMC7049718 DOI: 10.1093/nar/gkz1232] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 12/17/2019] [Accepted: 12/21/2019] [Indexed: 12/13/2022] Open
Abstract
Tight and coordinate regulation of virulence determinants is essential for bacterial biology and involves dynamic shaping of transcriptional regulatory networks during evolution. The horizontally transferred two-partner secretion system ExlB-ExlA is instrumental in the virulence of different Pseudomonas species, ranging from soil- and plant-dwelling biocontrol agents to the major human pathogen Pseudomonas aeruginosa. Here, we identify a Cro/CI-like repressor, named ErfA, which together with Vfr, a CRP-like activator, controls exlBA expression in P. aeruginosa. The characterization of ErfA regulon across P. aeruginosa subfamilies revealed a second conserved target, the ergAB operon, with functions unrelated to virulence. To gain insights into this functional dichotomy, we defined the pan-regulon of ErfA in several Pseudomonas species and found ergAB as the sole conserved target of ErfA. The analysis of 446 exlBA promoter sequences from all exlBA+ genomes revealed a wide variety of regulatory sequences, as ErfA- and Vfr-binding sites were found to have evolved specifically in P. aeruginosa and nearly each species carries different regulatory sequences for this operon. We propose that the emergence of different regulatory cis-elements in the promoters of horizontally transferred genes is an example of plasticity of regulatory networks evolving to provide an adapted response in each individual niche.
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Affiliation(s)
- Julian Trouillon
- Université Grenoble Alpes, CNRS ERL5261, CEA-IRIG-BCI, INSERM UMR1036, Grenoble 38000, France
| | - Erwin Sentausa
- Université Grenoble Alpes, CNRS ERL5261, CEA-IRIG-BCI, INSERM UMR1036, Grenoble 38000, France
| | - Michel Ragno
- Université Grenoble Alpes, CNRS ERL5261, CEA-IRIG-BCI, INSERM UMR1036, Grenoble 38000, France
| | - Mylène Robert-Genthon
- Université Grenoble Alpes, CNRS ERL5261, CEA-IRIG-BCI, INSERM UMR1036, Grenoble 38000, France
| | - Stephen Lory
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Ina Attrée
- Université Grenoble Alpes, CNRS ERL5261, CEA-IRIG-BCI, INSERM UMR1036, Grenoble 38000, France
| | - Sylvie Elsen
- Université Grenoble Alpes, CNRS ERL5261, CEA-IRIG-BCI, INSERM UMR1036, Grenoble 38000, France
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6
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Tillery LM, Barrett KF, Dranow DM, Craig J, Shek R, Chun I, Barrett LK, Phan IQ, Subramanian S, Abendroth J, Lorimer DD, Edwards TE, Van Voorhis WC. Toward a structome of Acinetobacter baumannii drug targets. Protein Sci 2020; 29:789-802. [PMID: 31930600 DOI: 10.1002/pro.3826] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 01/06/2020] [Accepted: 01/08/2020] [Indexed: 12/13/2022]
Abstract
Acinetobacter baumannii is well known for causing hospital-associated infections due in part to its intrinsic antibiotic resistance as well as its ability to remain viable on surfaces and resist cleaning agents. In a previous publication, A. baumannii strain AB5075 was studied by transposon mutagenesis and 438 essential gene candidates for growth on rich-medium were identified. The Seattle Structural Genomics Center for Infectious Disease entered 342 of these candidate essential genes into our pipeline for structure determination, in which 306 were successfully cloned into expression vectors, 192 were detectably expressed, 165 screened as soluble, 121 were purified, 52 crystalized, 30 provided diffraction data, and 29 structures were deposited in the Protein Data Bank. Here, we report these structures, compare them with human orthologs where applicable, and discuss their potential as drug targets for antibiotic development against A. baumannii.
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Affiliation(s)
- Logan M Tillery
- Department of Medicine, Division of Allergy and Infectious Disease, Center for Emerging and Re-emerging Infectious Disease (CERID), University of Washington, Seattle, Washington.,Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington
| | - Kayleigh F Barrett
- Department of Medicine, Division of Allergy and Infectious Disease, Center for Emerging and Re-emerging Infectious Disease (CERID), University of Washington, Seattle, Washington.,Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington
| | - David M Dranow
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington.,UCB Pharma, Bainbridge Island, Washington
| | - Justin Craig
- Department of Medicine, Division of Allergy and Infectious Disease, Center for Emerging and Re-emerging Infectious Disease (CERID), University of Washington, Seattle, Washington.,Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington
| | - Roger Shek
- Department of Medicine, Division of Allergy and Infectious Disease, Center for Emerging and Re-emerging Infectious Disease (CERID), University of Washington, Seattle, Washington.,Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington
| | - Ian Chun
- Department of Medicine, Division of Allergy and Infectious Disease, Center for Emerging and Re-emerging Infectious Disease (CERID), University of Washington, Seattle, Washington.,Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington
| | - Lynn K Barrett
- Department of Medicine, Division of Allergy and Infectious Disease, Center for Emerging and Re-emerging Infectious Disease (CERID), University of Washington, Seattle, Washington.,Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington
| | - Isabelle Q Phan
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington.,Seattle Children's Research Institute, Seattle, Washington
| | - Sandhya Subramanian
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington.,Seattle Children's Research Institute, Seattle, Washington
| | - Jan Abendroth
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington.,UCB Pharma, Bainbridge Island, Washington
| | - Donald D Lorimer
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington.,UCB Pharma, Bainbridge Island, Washington
| | - Thomas E Edwards
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington.,UCB Pharma, Bainbridge Island, Washington
| | - Wesley C Van Voorhis
- Department of Medicine, Division of Allergy and Infectious Disease, Center for Emerging and Re-emerging Infectious Disease (CERID), University of Washington, Seattle, Washington.,Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington
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7
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Alaei L, Moosavi-Movahedi AA. Stability of multi-subunit proteins and conformational lock. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2020; 150:145-152. [DOI: 10.1016/j.pbiomolbio.2019.08.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Revised: 08/17/2019] [Accepted: 08/21/2019] [Indexed: 12/24/2022]
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8
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Impey RE, Panjikar S, Hall CJ, Bock LJ, Sutton JM, Perugini MA, Soares da Costa TP. Identification of two dihydrodipicolinate synthase isoforms from Pseudomonas aeruginosa that differ in allosteric regulation. FEBS J 2019; 287:386-400. [PMID: 31330085 DOI: 10.1111/febs.15014] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 06/12/2019] [Accepted: 07/19/2019] [Indexed: 12/13/2022]
Abstract
Pseudomonas aeruginosa is one of the leading causes of nosocomial infections, accounting for 10% of all hospital-acquired infections. Current antibiotics against P. aeruginosa are becoming increasingly ineffective due to the exponential rise in drug resistance. Thus, there is an urgent need to validate and characterize novel drug targets to guide the development of new classes of antibiotics against this pathogen. One such target is the diaminopimelate (DAP) pathway, which is responsible for the biosynthesis of bacterial cell wall and protein building blocks, namely meso-DAP and lysine. The rate-limiting step of this pathway is catalysed by the enzyme dihydrodipicolinate synthase (DHDPS), typically encoded for in bacteria by a single dapA gene. Here, we show that P. aeruginosa encodes two functional DHDPS enzymes, PaDHDPS1 and PaDHDPS2. Although these isoforms have similar catalytic activities (kcat = 29 s-1 and 44 s-1 for PaDHDPS1 and PaDHDPS2, respectively), they are differentially allosterically regulated by lysine, with only PaDHDPS2 showing inhibition by the end product of the DAP pathway (IC50 = 130 μm). The differences in allostery are attributed to a single amino acid difference in the allosteric binding pocket at position 56. This is the first example of a bacterium that contains multiple bona fide DHDPS enzymes, which differ in allosteric regulation. We speculate that the presence of the two isoforms allows an increase in the metabolic flux through the DAP pathway when required in this clinically important pathogen. DATABASES: PDB ID: 6P90.
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Affiliation(s)
- Rachael E Impey
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
| | - Santosh Panjikar
- Australian Synchrotron, ANSTO, Clayton, Australia.,Department of Molecular Biology and Biochemistry, Monash University, Melbourne, Australia
| | - Cody J Hall
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
| | - Lucy J Bock
- National Infection Service, Public Health England, Porton Down, Salisbury, UK
| | - J Mark Sutton
- National Infection Service, Public Health England, Porton Down, Salisbury, UK
| | - Matthew A Perugini
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
| | - Tatiana P Soares da Costa
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
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9
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Christoff RM, Gardhi CK, Soares da Costa TP, Perugini MA, Abbott BM. Pursuing DHDPS: an enzyme of unrealised potential as a novel antibacterial target. MEDCHEMCOMM 2019. [DOI: 10.1039/c9md00107g] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
DHDPS represents a novel enzyme target for the development of new antibiotics to combat multidrug resistance.
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Affiliation(s)
- Rebecca M. Christoff
- Department of Chemistry and Physics
- La Trobe Institute for Molecular Science
- La Trobe University
- Melbourne
- Australia
| | - Chamodi K. Gardhi
- Department of Chemistry and Physics
- La Trobe Institute for Molecular Science
- La Trobe University
- Melbourne
- Australia
| | - Tatiana P. Soares da Costa
- Department of Biochemistry and Genetics
- La Trobe Institute for Molecular Science
- La Trobe University
- Melbourne
- Australia
| | - Matthew A. Perugini
- Department of Biochemistry and Genetics
- La Trobe Institute for Molecular Science
- La Trobe University
- Melbourne
- Australia
| | - Belinda M. Abbott
- Department of Chemistry and Physics
- La Trobe Institute for Molecular Science
- La Trobe University
- Melbourne
- Australia
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10
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Bonomi M, Hanot S, Greenberg CH, Sali A, Nilges M, Vendruscolo M, Pellarin R. Bayesian Weighing of Electron Cryo-Microscopy Data for Integrative Structural Modeling. Structure 2018; 27:175-188.e6. [PMID: 30393052 DOI: 10.1016/j.str.2018.09.011] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 08/07/2018] [Accepted: 09/19/2018] [Indexed: 10/28/2022]
Abstract
Cryo-electron microscopy (cryo-EM) has become a mainstream technique for determining the structures of complex biological systems. However, accurate integrative structural modeling has been hampered by the challenges in objectively weighing cryo-EM data against other sources of information due to the presence of random and systematic errors, as well as correlations, in the data. To address these challenges, we introduce a Bayesian scoring function that efficiently and accurately ranks alternative structural models of a macromolecular system based on their consistency with a cryo-EM density map as well as other experimental and prior information. The accuracy of this approach is benchmarked using complexes of known structure and illustrated in three applications: the structural determination of the GroEL/GroES, RNA polymerase II, and exosome complexes. The approach is implemented in the open-source Integrative Modeling Platform (http://integrativemodeling.org), thus enabling integrative structure determination by combining cryo-EM data with other sources of information.
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Affiliation(s)
| | - Samuel Hanot
- Institut Pasteur, Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, CNRS UMR 3528, C3BI USR 3756 CNRS & IP, Paris, France
| | - Charles H Greenberg
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Sciences, and California Institute for Quantitative Biomedical Sciences, University of California, San Francisco, CA 94158, USA
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Sciences, and California Institute for Quantitative Biomedical Sciences, University of California, San Francisco, CA 94158, USA
| | - Michael Nilges
- Institut Pasteur, Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, CNRS UMR 3528, C3BI USR 3756 CNRS & IP, Paris, France
| | | | - Riccardo Pellarin
- Institut Pasteur, Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, CNRS UMR 3528, C3BI USR 3756 CNRS & IP, Paris, France.
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11
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Desbois S, John UP, Perugini MA. Dihydrodipicolinate synthase is absent in fungi. Biochimie 2018; 152:73-84. [PMID: 29959064 DOI: 10.1016/j.biochi.2018.06.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Accepted: 06/21/2018] [Indexed: 02/07/2023]
Abstract
The class I aldolase dihydrodipicolinate synthase (DHDPS) catalyzes the first committed step of the diaminopimelate (DAP) lysine biosynthesis pathway in bacteria, archaea and plants. Despite the existence, in databases, of numerous fungal sequences annotated as DHDPS, its presence in fungi has been the subject of contradictory claims. We report the characterization of DHDPS candidates from fungi. Firstly, the putative DHDPS from Coccidioides immitis (PDB ID: 3QFE) was shown to have negligible enzyme activity. Sequence analysis of 3QFE showed that three out of the seven amino acid residues critical for DHDPS activity are absent; however, exact matches to catalytic residues from two other class I aldolases, 2-keto-3-deoxygluconate aldolase (KDGA), and 4-hydroxy-2-oxoglutarate aldolase (HOGA), were identified. The presence of both KDGA and HOGA activity in 3QFE was confirmed in vitro using enzyme assays, the first report of such dual activity. Subsequent analyses of all publically available fungal sequences revealed that no entry contains all seven residues important for DHDPS function. The candidate with the highest number of identities (6 of 7), KIW77228 from Fonsecaea pedrosoi, was shown to have trace DHDPS activity in vitro, partially restored by substitution of the seventh critical residue, and to be incapable of complementing DHDPS-deficient E. coli cells. Combined with the presence of all seven sequences for the alternative α-aminoadipate (AAA) lysine biosynthesis pathway in C. immitis and F. pedrosoi, we believe that DHDPS and the DAP pathway are absent in fungi, and further, that robust informed methods for annotating genes need to be implemented.
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Affiliation(s)
- Sebastien Desbois
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, VIC, 3086, Australia
| | - Ulrik P John
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, VIC, 3086, Australia; Agriculture Victoria Research, Department of Economic Development, Jobs, Transport and Resources, AgriBio, La Trobe University, VIC, 3086, Australia
| | - Matthew A Perugini
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, VIC, 3086, Australia.
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12
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Manning ME, Danson EJ, Calderone CT. Functional chararacterization of the enzymes TabB and TabD involved in tabtoxin biosynthesis by Pseudomonas syringae. Biochem Biophys Res Commun 2018; 496:212-217. [PMID: 29307827 DOI: 10.1016/j.bbrc.2018.01.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 01/04/2018] [Indexed: 10/18/2022]
Abstract
Pseudomonas syringae pv. tabaci ATCC 11528 produces tabtoxin, a β-lactam-containing dipeptide phytotoxin. Tabtoxinine-β-lactam (TβL), one of tabtoxin's constituent amino acids, structurally mimics lysine, and many of the proteins encoded by the tabtoxin biosynthetic gene cluster are homologs of lysine biosynthetic enzymes, suggesting that the tabtoxin and lysine biosynthetic routes parallel one another. We cloned and expressed TabB and TabD, predicted homologs of tetrahydrodipicolinate (THDPA)-N-acyltransferase and N-acyl-THDPA aminotransferase, respectively, to determine their activities in vitro. We confirmed that TabB succinylates THDPA and that TabD is a PLP-dependent aminotransferase that utilizes glutamate as an amine donor. Surprisingly, we also found that though TabD could utilize the TabB product N-succinyl-THDPA as a substrate, THDPA itself was also recognized. These observations reveal that TabB functionally duplicates DapD, the THDPA-N-succinyltransferase involved in lysine biosynthesis, and reinforce the close relationship between the metabolic logics underpinning the respective biosynthetic pathways.
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Affiliation(s)
- Margot E Manning
- Department of Chemistry, Carleton College, 1 North College Street, Northfield, MN 55057, United States
| | - Eli J Danson
- Department of Chemistry, Carleton College, 1 North College Street, Northfield, MN 55057, United States
| | - Christopher T Calderone
- Department of Chemistry, Carleton College, 1 North College Street, Northfield, MN 55057, United States.
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13
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Chebotareva NA, Roman SG, Kurganov BI. Dissociative mechanism for irreversible thermal denaturation of oligomeric proteins. Biophys Rev 2016; 8:397-407. [PMID: 28510015 PMCID: PMC5418479 DOI: 10.1007/s12551-016-0220-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 09/13/2016] [Indexed: 01/09/2023] Open
Abstract
Protein stability is a fundamental characteristic essential for understanding conformational transformations of the proteins in the cell. When using protein preparations in biotechnology and biomedicine, the problem of protein stability is of great importance. The kinetics of denaturation of oligomeric proteins may have characteristic properties determined by the quaternary structure. The kinetic schemes of denaturation can include the multiple stages of conformational transitions in the protein oligomer and stages of reversible dissociation of the oligomer. In this case, the shape of the kinetic curve of denaturation or the shape of the melting curve registered by differential scanning calorimetry can vary with varying the protein concentration. The experimental data illustrating dissociative mechanism for irreversible thermal denaturation of oligomeric proteins have been summarized in the present review. The use of test systems based on thermal aggregation of oligomeric proteins for screening of agents possessing anti-aggregation activity is discussed.
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Affiliation(s)
- Natalia A Chebotareva
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky pr. 33, Moscow, 119071, Russia.
| | - Svetlana G Roman
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky pr. 33, Moscow, 119071, Russia
| | - Boris I Kurganov
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky pr. 33, Moscow, 119071, Russia
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14
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Skovpen YV, Conly CJT, Sanders DAR, Palmer DRJ. Biomimetic Design Results in a Potent Allosteric Inhibitor of Dihydrodipicolinate Synthase from Campylobacter jejuni. J Am Chem Soc 2016; 138:2014-20. [DOI: 10.1021/jacs.5b12695] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yulia V. Skovpen
- Department of Chemistry, University of Saskatchewan, 110 Science
Place, Saskatoon, Saskatchewan, Canada S7N 5C9
| | - Cuylar J. T. Conly
- Department of Chemistry, University of Saskatchewan, 110 Science
Place, Saskatoon, Saskatchewan, Canada S7N 5C9
| | - David A. R. Sanders
- Department of Chemistry, University of Saskatchewan, 110 Science
Place, Saskatoon, Saskatchewan, Canada S7N 5C9
| | - David R. J. Palmer
- Department of Chemistry, University of Saskatchewan, 110 Science
Place, Saskatoon, Saskatchewan, Canada S7N 5C9
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15
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Dogovski C, Gorman MA, Ketaren NE, Praszkier J, Zammit LM, Mertens HD, Bryant G, Yang J, Griffin MDW, Pearce FG, Gerrard JA, Jameson GB, Parker MW, Robins-Browne RM, Perugini MA. From knock-out phenotype to three-dimensional structure of a promising antibiotic target from Streptococcus pneumoniae. PLoS One 2013; 8:e83419. [PMID: 24349508 PMCID: PMC3862839 DOI: 10.1371/journal.pone.0083419] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Accepted: 11/13/2013] [Indexed: 11/18/2022] Open
Abstract
Given the rise in drug-resistant Streptococcus pneumoniae, there is an urgent need to discover new antimicrobials targeting this pathogen and an equally urgent need to characterize new drug targets. A promising antibiotic target is dihydrodipicolinate synthase (DHDPS), which catalyzes the rate-limiting step in lysine biosynthesis. In this study, we firstly show by gene knock out studies that S. pneumoniae (sp) lacking the DHDPS gene is unable to grow unless supplemented with lysine-rich media. We subsequently set out to characterize the structure, function and stability of the enzyme drug target. Our studies show that sp-DHDPS is folded and active with a k(cat) = 22 s(-1), K(M)(PYR) = 2.55 ± 0.05 mM and K(M)(ASA) = 0.044 ± 0.003 mM. Thermal denaturation experiments demonstrate sp-DHDPS exhibits an apparent melting temperature (T(M)(app)) of 72 °C, which is significantly greater than Escherichia coli DHDPS (Ec-DHDPS) (T(M)(app) = 59 °C). Sedimentation studies show that sp-DHDPS exists in a dimer-tetramer equilibrium with a K(D)(4→2) = 1.7 nM, which is considerably tighter than its E. coli ortholog (K(D)(4→2) = 76 nM). To further characterize the structure of the enzyme and probe its enhanced stability, we solved the high resolution (1.9 Å) crystal structure of sp-DHDPS (PDB ID 3VFL). The enzyme is tetrameric in the crystal state, consistent with biophysical measurements in solution. Although the sp-DHDPS and Ec-DHDPS active sites are almost identical, the tetramerization interface of the s. pneumoniae enzyme is significantly different in composition and has greater buried surface area (800 Å(2)) compared to its E. coli counterpart (500 Å(2)). This larger interface area is consistent with our solution studies demonstrating that sp-DHDPS is considerably more thermally and thermodynamically stable than Ec-DHDPS. Our study describe for the first time the knock-out phenotype, solution properties, stability and crystal structure of DHDPS from S. pneumoniae, a promising antimicrobial target.
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Affiliation(s)
- Con Dogovski
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria, Australia
| | - Michael A. Gorman
- St Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia
| | - Natalia E. Ketaren
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria, Australia
| | - Judy Praszkier
- Department of Microbiology & Immunology, University of Melbourne, Victoria, Australia
| | - Leanne M. Zammit
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | | | - Gary Bryant
- School of Applied Sciences, RMIT University, Melbourne, Victoria, Australia
| | - Ji Yang
- Department of Microbiology & Immunology, University of Melbourne, Victoria, Australia
| | - Michael D. W. Griffin
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria, Australia
| | - F. Grant Pearce
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Juliet A. Gerrard
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Callaghan Innovation, Lower Hutt, New Zealand
| | - Geoffrey B. Jameson
- Centre for Structural Biology, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Michael W. Parker
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria, Australia
- St Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia
| | - Roy M. Robins-Browne
- Department of Microbiology & Immunology, University of Melbourne, Victoria, Australia
| | - Matthew A. Perugini
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria, Australia
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16
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Moynie L, Schnell R, McMahon SA, Sandalova T, Boulkerou WA, Schmidberger JW, Alphey M, Cukier C, Duthie F, Kopec J, Liu H, Jacewicz A, Hunter WN, Naismith JH, Schneider G. The AEROPATH project targeting Pseudomonas aeruginosa: crystallographic studies for assessment of potential targets in early-stage drug discovery. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:25-34. [PMID: 23295481 PMCID: PMC3539698 DOI: 10.1107/s1744309112044739] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Accepted: 10/29/2012] [Indexed: 12/25/2022]
Abstract
Bacterial infections are increasingly difficult to treat owing to the spread of antibiotic resistance. A major concern is Gram-negative bacteria, for which the discovery of new antimicrobial drugs has been particularly scarce. In an effort to accelerate early steps in drug discovery, the EU-funded AEROPATH project aims to identify novel targets in the opportunistic pathogen Pseudomonas aeruginosa by applying a multidisciplinary approach encompassing target validation, structural characterization, assay development and hit identification from small-molecule libraries. Here, the strategies used for target selection are described and progress in protein production and structure analysis is reported. Of the 102 selected targets, 84 could be produced in soluble form and the de novo structures of 39 proteins have been determined. The crystal structures of eight of these targets, ranging from hypothetical unknown proteins to metabolic enzymes from different functional classes (PA1645, PA1648, PA2169, PA3770, PA4098, PA4485, PA4992 and PA5259), are reported here. The structural information is expected to provide a firm basis for the improvement of hit compounds identified from fragment-based and high-throughput screening campaigns.
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Affiliation(s)
- Lucille Moynie
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews KY16 9ST, Scotland
| | - Robert Schnell
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 77 Stockholm, Sweden
| | - Stephen A. McMahon
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews KY16 9ST, Scotland
| | - Tatyana Sandalova
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 77 Stockholm, Sweden
| | | | - Jason W. Schmidberger
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 77 Stockholm, Sweden
| | - Magnus Alphey
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews KY16 9ST, Scotland
| | - Cyprian Cukier
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 77 Stockholm, Sweden
| | - Fraser Duthie
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews KY16 9ST, Scotland
| | - Jolanta Kopec
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 77 Stockholm, Sweden
| | - Huanting Liu
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews KY16 9ST, Scotland
| | - Agata Jacewicz
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 77 Stockholm, Sweden
| | - William N. Hunter
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland
| | - James H. Naismith
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews KY16 9ST, Scotland
| | - Gunter Schneider
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 77 Stockholm, Sweden
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17
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Chim N, Owens CP, Contreras H, Goulding CW. Withdrawn. Infect Disord Drug Targets 2012:CDTID-EPUB-20121116-2. [PMID: 23167715 PMCID: PMC3695056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Withdrawn by the publisher.
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Affiliation(s)
- Nicholas Chim
- Department of Molecular Biology and Biochemistry, University of California, Irvine CA 92697, USA
| | - Cedric P. Owens
- Department of Molecular Biology and Biochemistry, University of California, Irvine CA 92697, USA
| | - Heidi Contreras
- Department of Molecular Biology and Biochemistry, University of California, Irvine CA 92697, USA
| | - Celia W. Goulding
- Department of Molecular Biology and Biochemistry, University of California, Irvine CA 92697, USA
- Department of Pharmaceutical Sciences, University of California, Irvine CA 92697, USA
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