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Colautti A, Comi G, Peterlunger E, Iacumin L. Ancient Roman bacterium against current issues: strain Aquil_B6, Paenisporosarcina quisquiliarum, or Psychrobacillus psychrodurans? Microbiol Spectr 2023; 11:e0068623. [PMID: 37975675 PMCID: PMC10714998 DOI: 10.1128/spectrum.00686-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 10/08/2023] [Indexed: 11/19/2023] Open
Abstract
IMPORTANCE Since 1988, through the United States government's founding, the National Center for Biotechnology Information (NCBI) has provided an invaluable service to scientific advancement. The universality and total freedom of use if on the one hand allow the use of this database on a global level by all researchers for their valuable work, on the other hand, it has the disadvantage of making it difficult to check the correctness of all the materials present. It is, therefore, of fundamental importance for the correctness and ethics of research to improve the databases at our disposal, identifying and amending the critical issues. This work aims to provide the scientific community with a new sequence for the type strain Paenisporosarcina quisquiliarum SK 55 and broaden the knowledge of the Psychrobacillus psychrodurans species, in particular, considering the ancient strain Aquil_B6 found in an ancient Roman amphora.
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Affiliation(s)
- Andrea Colautti
- Department of Agricultural, Food, Environmental and Animal Science, University of Udine, Udine, Italy
| | - Giuseppe Comi
- Department of Agricultural, Food, Environmental and Animal Science, University of Udine, Udine, Italy
| | - Enrico Peterlunger
- Department of Agricultural, Food, Environmental and Animal Science, University of Udine, Udine, Italy
| | - Lucilla Iacumin
- Department of Agricultural, Food, Environmental and Animal Science, University of Udine, Udine, Italy
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Ott F, Rabe KS, Niemeyer CM, Gygli G. Toward Reproducible Enzyme Modeling with Isothermal Titration Calorimetry. ACS Catal 2021. [DOI: 10.1021/acscatal.1c02076] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Felix Ott
- Institute for Biological Interfaces (IBG 1), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Kersten S. Rabe
- Institute for Biological Interfaces (IBG 1), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Christof M. Niemeyer
- Institute for Biological Interfaces (IBG 1), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Gudrun Gygli
- Institute for Biological Interfaces (IBG 1), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
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Abstract
Cold-active enzymes increase their catalytic efficiency at low-temperature, introducing structural flexibility at or near the active sites. Inevitably, this feat seems to be accompanied by lower thermal stability. These characteristics have made cold-active enzymes into attractive targets for the industrial applications, since they could reduce the energy cost in the reaction, attenuate side-reactions, and simply be inactivated. In addition, the increased structural flexibility could result in broad substrate specificity for various non-native substrates, which is called substrate promiscuity. In this perspective, we deal with a less addressed aspect of cold-active enzymes, substrate promiscuity, which has enormous potential for semi-synthesis or enzymatic modification of fine chemicals and drugs. Further structural and directed-evolutional studies on substrate promiscuity of cold-active enzymes will provide a new workhorse in white biotechnology.
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Pote S, Kachhap S, Mank NJ, Daneshian L, Klapper V, Pye S, Arnette AK, Shimizu LS, Borowski T, Chruszcz M. Comparative structural and mechanistic studies of 4-hydroxy-tetrahydrodipicolinate reductases from Mycobacterium tuberculosis and Vibrio vulnificus. Biochim Biophys Acta Gen Subj 2020; 1865:129750. [PMID: 32980502 DOI: 10.1016/j.bbagen.2020.129750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 09/20/2020] [Accepted: 09/21/2020] [Indexed: 10/23/2022]
Abstract
BACKGROUND The products of the lysine biosynthesis pathway, meso-diaminopimelate and lysine, are essential for bacterial survival. This paper focuses on the structural and mechanistic characterization of 4-hydroxy-tetrahydrodipicolinate reductase (DapB), which is one of the enzymes from the lysine biosynthesis pathway. DapB catalyzes the conversion of (2S, 4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate (HTPA) to 2,3,4,5-tetrahydrodipicolinate in an NADH/NADPH dependent reaction. Genes coding for DapBs were identified as essential for many pathogenic bacteria, and therefore DapB is an interesting new target for the development of antibiotics. METHODS We have combined experimental and computational approaches to provide novel insights into mechanism of the DapB catalyzed reaction. RESULTS Structures of DapBs originating from Mycobacterium tuberculosis and Vibrio vulnificus in complexes with NAD+, NADP+, as well as with inhibitors, were determined and described. The structures determined by us, as well as currently available structures of DapBs from other bacterial species, were compared and used to elucidate a mechanism of reaction catalyzed by this group of enzymes. Several different computational methods were used to provide a detailed description of a plausible reaction mechanism. CONCLUSIONS This is the first report presenting the detailed mechanism of reaction catalyzed by DapB. GENERAL SIGNIFICANCE Structural data in combination with information on the reaction mechanism provide a background for development of DapB inhibitors, including transition-state analogues.
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Affiliation(s)
- Swanandi Pote
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
| | - Sangita Kachhap
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, 30-239 Krakow, Poland
| | - Nicholas J Mank
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
| | - Leily Daneshian
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
| | - Vincent Klapper
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
| | - Sarah Pye
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
| | - Amy K Arnette
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
| | - Linda S Shimizu
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
| | - Tomasz Borowski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, 30-239 Krakow, Poland
| | - Maksymilian Chruszcz
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA.
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Lee CW, Park SH, Koh HY, Jeong CS, Hwang J, Lee SG, Youn UJ, Lee CS, Park HH, Kim HJ, Park H, Lee JH. Crystal structure of a transcription factor, GerE (PaGerE), from spore-forming bacterium Paenisporosarcina sp. TG-14. Biochem Biophys Res Commun 2019; 513:374-379. [PMID: 30967265 DOI: 10.1016/j.bbrc.2019.04.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 04/03/2019] [Indexed: 11/28/2022]
Abstract
In cold and harsh environments such as glaciers and sediments in ice cores, microbes can survive by forming spores. Spores are composed of a thick coat protein, which protects against external factors such as heat-shock, high salinity, and nutrient deficiency. GerE is a key transcription factor involved in spore coat protein expression in the mother cell during sporulation. GerE regulates transcription during the late sporulation stage by directly binding to the promoter of cotB gene. Here, we report the crystal structure of PaGerE at 2.09 Å resolution from Paenisporosarcina sp. TG-14, which was isolated from the Taylor glacier. The PaGerE structure is composed of four α-helices and adopts a helix-turn-helix architecture with 68 amino acid residues. Based on our DNA binding analysis, the PaGerE binds to the promoter region of CotB to affect protein expression. Additionally, our structural comparison studies suggest that DNA binding by PaGerE causes a conformational change in the α4-helix region, which may strongly induce dimerization of PaGerE.
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Affiliation(s)
- Chang Woo Lee
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, 21990, Republic of Korea
| | - Sun-Ha Park
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, 21990, Republic of Korea
| | - Hye Yeon Koh
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, 21990, Republic of Korea
| | - Chang Sook Jeong
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, 21990, Republic of Korea; Department of Polar Sciences, University of Science and Technology, Incheon, 21990, Republic of Korea
| | - Jisub Hwang
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, 21990, Republic of Korea; Department of Polar Sciences, University of Science and Technology, Incheon, 21990, Republic of Korea
| | - Sung Gu Lee
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, 21990, Republic of Korea; Department of Polar Sciences, University of Science and Technology, Incheon, 21990, Republic of Korea
| | - Ui Joung Youn
- Division of Life Sciences, Korea Polar Research Institute, Incheon, 21990, Republic of Korea
| | - Chang Sup Lee
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Hyun Ho Park
- College of Pharmacy, Chung-Ang University, 84 Heukseok-ro, Dongjak, Seoul, 06974, Republic of Korea
| | - Hak Jun Kim
- Department of Chemistry, Pukyong National University, 45 Yongso-ro, Busan, 48513, Republic of Korea
| | - Hyun Park
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, 21990, Republic of Korea; Department of Polar Sciences, University of Science and Technology, Incheon, 21990, Republic of Korea
| | - Jun Hyuck Lee
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, 21990, Republic of Korea; Department of Polar Sciences, University of Science and Technology, Incheon, 21990, Republic of Korea.
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Pote S, Pye SE, Sheahan TE, Gawlicka-Chruszcz A, Majorek KA, Chruszcz M. 4-Hydroxy-tetrahydrodipicolinate reductase from Neisseria gonorrhoeae - structure and interactions with coenzymes and substrate analog. Biochem Biophys Res Commun 2018; 503:1993-1999. [PMID: 30093108 PMCID: PMC6192261 DOI: 10.1016/j.bbrc.2018.07.147] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 07/30/2018] [Indexed: 01/07/2023]
Abstract
Neisseria gonorrhoeae, an obligate human pathogen, is a leading cause of communicable diseases globally. Due to rapid development of drug resistance, the rate of successfully curing gonococcal infections is rapidly decreasing. Hence, research is being directed toward finding alternative drugs or drug targets to help eradicate these infections. 4-Hydroxy-tetrahydrodipicolinate reductase (DapB), an important enzyme in the meso-diaminopimelate pathway, is a promising target for the development of new antibiotics. This manuscript describes the first structure of DapB from N. gonorrhoeae determined at 1.85 Å. This enzyme uses NAD(P)H as cofactor. Details of the interactions of the enzyme with its cofactors and a substrate analog/inhibitor are discussed. A large scale bioinformatics analysis of DapBs' sequences is also described.
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Affiliation(s)
- Swanandi Pote
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
| | - Sarah E. Pye
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
| | - Tyler E. Sheahan
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
| | - Anna Gawlicka-Chruszcz
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
| | - Karolina A. Majorek
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
| | - Maksymilian Chruszcz
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
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