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Nikkel DJ, Kaur R, Wetmore SD. How Can One Metal Power Nucleic Acid Phosphodiester Bond Cleavage by a Nuclease? Multiscale Computational Studies Highlight a Diverse Mechanistic Landscape. J Phys Chem B 2025; 129:3-18. [PMID: 39720842 DOI: 10.1021/acs.jpcb.4c05875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2024]
Abstract
Despite the remarkable resistance of the nucleic acid phosphodiester backbone to degradation affording genetic stability, the P-O bond must be broken during DNA repair and RNA metabolism, among many other critical cellular processes. Nucleases are powerful enzymes that can enhance the uncatalyzed rate of phosphodiester bond cleavage by up to ∼1017-fold. Despite the most well accepted hydrolysis mechanism involving two metals (MA2+ to activate a water nucleophile and MB2+ to stabilize the leaving group), experimental evidence suggests that some nucleases can use a single metal to facilitate the chemical step, a controversial concept in the literature. The present perspective uses the case studies of four nucleases (I-PpoI, APE1, and bacterial and human EndoV) to highlight how computational approaches ranging from quantum mechanical (QM) cluster models to molecular dynamics (MD) simulations and combined quantum mechanics-molecular mechanics (QM/MM) calculations can reveal the atomic level details necessary to understand how a nuclease can use a single metal to facilitate this difficult chemistry. The representative nucleases showcase how different amino acid residues (e.g., histidine, aspartate) can fulfill the role of the first metal (MA2+) in the two-metal-mediated mechanisms. Nevertheless, differences in active site architectures afford diversity in the single-metal-mediated mechanism in terms of the metal-substrate coordination, the role of the metal, and the identities of the general acid and base. The greater understanding of the catalytic mechanisms of nucleases obtained from the body of work reviewed can be used to further explore the progression of diseases associated with nuclease (mis)activity and the development of novel nuclease applications such as disease diagnostics, gene engineering, and therapeutics.
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Affiliation(s)
- Dylan J Nikkel
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, Canada T1K 3M4
| | - Rajwinder Kaur
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, Canada T1K 3M4
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, Canada T1K 3M4
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Kaur R, Nikkel DJ, Wetmore SD. Mechanism of Nucleic Acid Phosphodiester Bond Cleavage by Human Endonuclease V: MD and QM/MM Calculations Reveal a Versatile Metal Dependence. J Phys Chem B 2024; 128:9455-9469. [PMID: 39359137 DOI: 10.1021/acs.jpcb.4c05846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2024]
Abstract
Human endonuclease V (EndoV) catalytically removes deaminated nucleobases by cleaving the phosphodiester bond as part of RNA metabolism. Despite being implicated in several diseases (cancers, cardiovascular diseases, and neurological disorders) and potentially being a useful tool in biotechnology, details of the human EndoV catalytic pathway remain unclear due to limited experimental information beyond a crystal structure of the apoenzyme and select mutational data. Since a mechanistic understanding is critical for further deciphering the central roles and expanding applications of human EndoV in medicine and biotechnology, molecular dynamics (MD) simulations and quantum mechanics/molecular mechanics (QM/MM) calculations were used to unveil the atomistic details of the catalytic pathway. Due to controversies surrounding the number of metals required for nuclease activity, enzyme-substrate models with different numbers of active site metals and various metal-substrate binding configurations were built based on structural data for other nucleases. Subsequent MD simulations revealed the structure and stability of the human EndoV-substrate complex for a range of active site metal binding architectures. Four unique pathways were then characterized using QM/MM that vary in metal number (one versus two) and modes of substrate coordination [direct versus indirect (water-mediated)], with several mechanisms being fully consistent with experimental structural, kinetic, and mutational data for related nucleases, including members of the EndoV family. Beyond uncovering key roles for several active site amino acids (D240 and K155), our calculations highlight that while one metal is essential for human EndoV activity, the enzyme can benefit from using two metals due to the presence of two suitable metal binding sites. By directly comparing one- versus two-metal-mediated P-O bond cleavage reactions within the confines of the same active site, our work brings a fresh perspective to the "number of metals" controversy.
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Affiliation(s)
- Rajwinder Kaur
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge T1K 3M4, Alberta, Canada
| | - Dylan J Nikkel
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge T1K 3M4, Alberta, Canada
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge T1K 3M4, Alberta, Canada
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Chang C, Zhou G, Gao Y. Observing one-divalent-metal-ion-dependent and histidine-promoted His-Me family I-PpoI nuclease catalysis in crystallo. eLife 2024; 13:RP99960. [PMID: 39141555 PMCID: PMC11325842 DOI: 10.7554/elife.99960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/16/2024] Open
Abstract
Metal-ion-dependent nucleases play crucial roles in cellular defense and biotechnological applications. Time-resolved crystallography has resolved catalytic details of metal-ion-dependent DNA hydrolysis and synthesis, uncovering the essential roles of multiple metal ions during catalysis. The histidine-metal (His-Me) superfamily nucleases are renowned for binding one divalent metal ion and requiring a conserved histidine to promote catalysis. Many His-Me family nucleases, including homing endonucleases and Cas9 nuclease, have been adapted for biotechnological and biomedical applications. However, it remains unclear how the single metal ion in His-Me nucleases, together with the histidine, promotes water deprotonation, nucleophilic attack, and phosphodiester bond breakage. By observing DNA hydrolysis in crystallo with His-Me I-PpoI nuclease as a model system, we proved that only one divalent metal ion is required during its catalysis. Moreover, we uncovered several possible deprotonation pathways for the nucleophilic water. Interestingly, binding of the single metal ion and water deprotonation are concerted during catalysis. Our results reveal catalytic details of His-Me nucleases, which is distinct from multi-metal-ion-dependent DNA polymerases and nucleases.
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Affiliation(s)
- Caleb Chang
- Department of Biosciences, Rice UniversityHoustonUnited States
| | - Grace Zhou
- Department of Biosciences, Rice UniversityHoustonUnited States
| | - Yang Gao
- Department of Biosciences, Rice UniversityHoustonUnited States
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Chang C, Zhou G, Gao Y. Observing one-divalent-metal-ion dependent and histidine-promoted His-Me family I-PpoI nuclease catalysis in crystallo. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.02.592236. [PMID: 38746211 PMCID: PMC11092635 DOI: 10.1101/2024.05.02.592236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Metal-ion-dependent nucleases play crucial roles in cellular defense and biotechnological applications. Time-resolved crystallography has resolved catalytic details of metal-ion-dependent DNA hydrolysis and synthesis, uncovering the essential roles of multiple metal ions during catalysis. The histidine-metal (His-Me) superfamily nucleases are renowned for binding one divalent metal ion and requiring a conserved histidine to promote catalysis. Many His-Me family nucleases, including homing endonucleases and Cas9 nuclease, have been adapted for biotechnological and biomedical applications. However, it remains unclear how the single metal ion in His-Me nucleases, together with the histidine, promotes water deprotonation, nucleophilic attack, and phosphodiester bond breakage. By observing DNA hydrolysis in crystallo with His-Me I-PpoI nuclease as a model system, we proved that only one divalent metal ion is required during its catalysis. Moreover, we uncovered several possible deprotonation pathways for the nucleophilic water. Interestingly, binding of the single metal ion and water deprotonation are concerted during catalysis. Our results reveal catalytic details of His-Me nucleases, which is distinct from multi-metal-ion-dependent DNA polymerases and nucleases.
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Affiliation(s)
- Caleb Chang
- Department of Biosciences, Rice University, Houston, Texas, 77005, USA
| | - Grace Zhou
- Department of Biosciences, Rice University, Houston, Texas, 77005, USA
| | - Yang Gao
- Department of Biosciences, Rice University, Houston, Texas, 77005, USA
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5
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Kaur R, Frederickson A, Wetmore SD. Elucidation of the catalytic mechanism of a single-metal dependent homing endonuclease using QM and QM/MM approaches: the case study of I- PpoI. Phys Chem Chem Phys 2024; 26:8919-8931. [PMID: 38426850 DOI: 10.1039/d3cp06201e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
Homing endonucleases (HEs) are highly specific DNA cleaving enzymes, with I-PpoI having been suggested to use a single metal to accelerate phosphodiester bond cleavage. Although an I-PpoI mechanism has been proposed based on experimental structural data, no consensus has been reached regarding the roles of the metal or key active site amino acids. This study uses QM cluster and QM/MM calculations to provide atomic-level details of the I-PpoI catalytic mechanism. Minimal QM cluster and large-scale QM/MM models demonstrate that the experimentally-proposed pathway involving direct Mg2+ coordination to the substrate coupled with leaving group protonation through a metal-activated water is not feasible due to an inconducive I-PpoI active site alignment. Despite QM cluster models of varying size uncovering a pathway involving leaving group protonation by a metal-activated water, indirect (water-mediated) metal coordination to the substrate is required to afford this pathway, which renders this mechanism energetically infeasible. Instead, QM cluster models reveal that the preferred pathway involves direct Mg2+-O3' coordination to stabilize the charged substrate and assist leaving group departure, while H98 activates the water nucleophile. These calculations also underscore that both catalytic residues that directly interact with the substrate and secondary amino acids that position or stabilize these residues are required for efficient catalysis. QM/MM calculations on the solvated enzyme-DNA complex verify the preferred mechanism, which is fully consistent with experimental kinetic, structural, and mutational data. The fundamental understanding of the I-PpoI mechanism of action, gained from the present work can be used to further explore potential uses of this enzyme in biotechnology and medicine, and direct future computational investigations of other members of the understudied HE family.
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Affiliation(s)
- Rajwinder Kaur
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada.
| | - Angela Frederickson
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada.
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada.
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Kaur R, Wetmore SD. Is Metal Stabilization of the Leaving Group Required or Can Lysine Facilitate Phosphodiester Bond Cleavage in Nucleic Acids? A Computational Study of EndoV. J Chem Inf Model 2024; 64:944-959. [PMID: 38253321 DOI: 10.1021/acs.jcim.3c01775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Endonuclease V (EndoV) is a single-metal-dependent enzyme that repairs deaminated DNA nucleobases in cells by cleaving the phosphodiester bond, and this enzyme has proven to be a powerful tool in biotechnology and medicine. The catalytic mechanism used by EndoV must be understood to design new disease detection and therapeutic solutions and further exploit the enzyme in interdisciplinary applications. This study has used a mixed molecular dynamics (MD) and quantum mechanics/molecular mechanics (QM/MM) approach to compare eight distinct catalytic pathways and provides the first proposed mechanism for bacterial EndoV. The calculations demonstrate that mechanisms involving either direct or indirect metal coordination to the leaving group of the substrate previously proposed for other nucleases are unlikely for EndoV, regardless of the general base (histidine, aspartate, and substrate phosphate moiety). Instead, distinct catalytic pathways are characterized for EndoV that involve K139 stabilizing the leaving group, a metal-coordinated water stabilizing the transition structure, and either H214 or a substrate phosphate group activating the water nucleophile. In silico K139A and H214A mutational results support the newly proposed roles of these residues. Although this is a previously unseen combination of general base, general acid, and metal-binding architecture for a one-metal-dependent endonuclease, our proposed catalytic mechanisms are fully consistent with experimental kinetic, structural, and mutational data. In addition to substantiating a growing body of literature, suggesting that one metal is enough to catalyze P-O bond cleavage in nucleic acids, this new fundamental understanding of the catalytic function will promote the exploration of new and improved applications of EndoV.
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Affiliation(s)
- Rajwinder Kaur
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
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7
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Maghsoud Y, Jayasinghe-Arachchige VM, Kumari P, Cisneros GA, Liu J. Leveraging QM/MM and Molecular Dynamics Simulations to Decipher the Reaction Mechanism of the Cas9 HNH Domain to Investigate Off-Target Effects. J Chem Inf Model 2023; 63:6834-6850. [PMID: 37877218 DOI: 10.1021/acs.jcim.3c01284] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2023]
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR) technology is an RNA-guided targeted genome-editing tool using Cas family proteins. Two magnesium-dependent nuclease domains of the Cas9 enzyme, termed HNH and RuvC, are responsible for cleaving the target DNA (t-DNA) and nontarget DNA strands, respectively. The HNH domain is believed to determine the DNA cleavage activity of both endonuclease domains and is sensitive to complementary RNA-DNA base pairing. However, the underlying molecular mechanisms of CRISPR-Cas9, by which it rebukes or accepts mismatches, are poorly understood. Thus, investigation of the structure and dynamics of the catalytic state of Cas9 with either matched or mismatched t-DNA can provide insights into improving its specificity by reducing off-target cleavages. Here, we focus on a recently discovered catalytic-active form of the Streptococcus pyogenes Cas9 (SpCas9) and employ classical molecular dynamics and coupled quantum mechanics/molecular mechanics simulations to study two possible mechanisms of t-DNA cleavage reaction catalyzed by the HNH domain. Moreover, by designing a mismatched t-DNA structure called MM5 (C to G at the fifth position from the protospacer adjacent motif region), the impact of single-guide RNA (sgRNA) and t-DNA complementarity on the catalysis process was investigated. Based on these simulations, our calculated binding affinities, minimum energy paths, and analysis of catalytically important residues provide atomic-level details of the differences between matched and mismatched cleavage reactions. In addition, several residues exhibit significant differences in their catalytic roles for the two studied systems, including K253, K263, R820, K896, and K913.
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Affiliation(s)
- Yazdan Maghsoud
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Vindi M Jayasinghe-Arachchige
- Department of Pharmaceutical Sciences, University of North Texas System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, Texas 76107, United States
| | - Pratibha Kumari
- Department of Pharmaceutical Sciences, University of North Texas System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, Texas 76107, United States
| | - G Andrés Cisneros
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, Texas 75080, United States
- Department of Physics, University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Jin Liu
- Department of Pharmaceutical Sciences, University of North Texas System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, Texas 76107, United States
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8
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Antao AM, Karapurkar JK, Lee DR, Kim KS, Ramakrishna S. Disease modeling and stem cell immunoengineering in regenerative medicine using CRISPR/Cas9 systems. Comput Struct Biotechnol J 2020; 18:3649-3665. [PMID: 33304462 PMCID: PMC7710510 DOI: 10.1016/j.csbj.2020.11.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 11/16/2020] [Accepted: 11/16/2020] [Indexed: 12/14/2022] Open
Abstract
CRISPR/Cas systems are popular genome editing tools that belong to a class of programmable nucleases and have enabled tremendous progress in the field of regenerative medicine. We here outline the structural and molecular frameworks of the well-characterized type II CRISPR system and several computational tools intended to facilitate experimental designs. The use of CRISPR tools to generate disease models has advanced research into the molecular aspects of disease conditions, including unraveling the molecular basis of immune rejection. Advances in regenerative medicine have been hindered by major histocompatibility complex-human leukocyte antigen (HLA) genes, which pose a major barrier to cell- or tissue-based transplantation. Based on progress in CRISPR, including in recent clinical trials, we hypothesize that the generation of universal donor immune-engineered stem cells is now a realistic approach to tackling a multitude of disease conditions.
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Affiliation(s)
- Ainsley Mike Antao
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, South Korea
| | | | - Dong Ryul Lee
- Department of Biomedical Science, College of Life Science, CHA University, Seoul, South Korea
- CHA Stem Cell Institute, CHA University, Seoul, South Korea
| | - Kye-Seong Kim
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, South Korea
- College of Medicine, Hanyang University, Seoul, South Korea
| | - Suresh Ramakrishna
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, South Korea
- College of Medicine, Hanyang University, Seoul, South Korea
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9
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Wu CC, Lin JL, Yuan HS. Structures, Mechanisms, and Functions of His-Me Finger Nucleases. Trends Biochem Sci 2020; 45:935-946. [DOI: 10.1016/j.tibs.2020.07.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 06/30/2020] [Accepted: 07/15/2020] [Indexed: 02/06/2023]
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Park KH, Yoon SM, Song HN, Yang JH, Ryu SE, Woo EJ. Crystal structure of the mouse endonuclease G. Biochem Biophys Res Commun 2020; 526:35-40. [PMID: 32192768 DOI: 10.1016/j.bbrc.2020.03.060] [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: 03/06/2020] [Accepted: 03/10/2020] [Indexed: 10/24/2022]
Abstract
Endonuclease G (EndoG) is a mitochondrial enzyme that responds to apoptotic stimuli by translocating to the nucleus and cleaving the chromatin DNA. The molecular mechanism of EndoG still remains unknown in higher organisms. Here, we determined the crystal structure of mouse EndoG at ∼1.96 Å resolution. The EndoG shows an altered dimeric configuration in which N-terminal region of one subunit interact to the other subunit in dimer. The deletion of this region that is highly conserved in mammalian EndoGs resulted in a monomer with significantly reduced activity suggesting the association of the dimeric arrangement into the nuclease activity. Furthermore, we observed a large conformational change in the loop of the active site groove in EndoG, which corresponds to the DNA binding region. Intriguingly, EndoG dimers are linked by oxidation of the reactive cysteine 110 in this flexible loop to form a long oligomeric chain in the crystal lattice. The structural analysis and ensuing biochemical data suggest that this flexible loop region in the active site is important to the regulation of EndoG nuclease function in mouse.
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Affiliation(s)
- Kwang-Hyun Park
- Disease Target Structure Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon, 305-806, Republic of Korea
| | - Sei Mee Yoon
- Disease Target Structure Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon, 305-806, Republic of Korea
| | - Hyung Nam Song
- Disease Target Structure Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon, 305-806, Republic of Korea
| | - Joon-Hyuck Yang
- Disease Target Structure Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon, 305-806, Republic of Korea; Department of Health Informatics and Management, College of Medicine, Chungbuk National University, Cheongju, Republic of Korea
| | - Seong Eon Ryu
- Department of Bioengineering, College of Engineering, Hanyang University, Seoul, 04673, Republic of Korea.
| | - Eui-Jeon Woo
- Disease Target Structure Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon, 305-806, Republic of Korea; Department of Proteome Structural Biology, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon, 305-333, Republic of Korea.
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11
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Sun W, Yang J, Cheng Z, Amrani N, Liu C, Wang K, Ibraheim R, Edraki A, Huang X, Wang M, Wang J, Liu L, Sheng G, Yang Y, Lou J, Sontheimer EJ, Wang Y. Structures of Neisseria meningitidis Cas9 Complexes in Catalytically Poised and Anti-CRISPR-Inhibited States. Mol Cell 2019; 76:938-952.e5. [PMID: 31668930 PMCID: PMC6934045 DOI: 10.1016/j.molcel.2019.09.025] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 08/13/2019] [Accepted: 09/20/2019] [Indexed: 12/21/2022]
Abstract
High-resolution Cas9 structures have yet to reveal catalytic conformations due to HNH nuclease domain positioning away from the cleavage site. Nme1Cas9 and Nme2Cas9 are compact nucleases for in vivo genome editing. Here, we report structures of meningococcal Cas9 homologs in complex with sgRNA, dsDNA, or the AcrIIC3 anti-CRISPR protein. DNA-bound structures represent an early step of target recognition, a later HNH pre-catalytic state, the HNH catalytic state, and a cleaved-target-DNA-bound state. In the HNH catalytic state of Nme1Cas9, the active site is seen poised at the scissile phosphodiester linkage of the target strand, providing a high-resolution view of the active conformation. The HNH active conformation activates the RuvC domain. Our structures explain how Nme1Cas9 and Nme2Cas9 read distinct PAM sequences and how AcrIIC3 inhibits Nme1Cas9 activity. These structures provide insights into Cas9 domain rearrangements, guide-target engagement, cleavage mechanism, and anti-CRISPR inhibition, facilitating the optimization of these genome-editing platforms.
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Affiliation(s)
- Wei Sun
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jing Yang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Institute of Life Sciences, Jiangsu University, Zhenjiang 212013, China
| | - Zhi Cheng
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Nadia Amrani
- RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Chao Liu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kangkang Wang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Raed Ibraheim
- RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Alireza Edraki
- RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Xue Huang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Hefei National Research Center for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Min Wang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jiuyu Wang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Liang Liu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Gang Sheng
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yanhua Yang
- Institute of Life Sciences, Jiangsu University, Zhenjiang 212013, China
| | - Jizhong Lou
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Erik J Sontheimer
- RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA.
| | - Yanli Wang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Collaborative Innovation Center of Genetics and Development, Shanghai 200438, China.
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12
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Chu CH, Yen CY, Chen BW, Lin MG, Wang LH, Tang KZ, Hsiao CD, Sun YJ. Crystal structures of HpSoj-DNA complexes and the nucleoid-adaptor complex formation in chromosome segregation. Nucleic Acids Res 2019; 47:2113-2129. [PMID: 30544248 PMCID: PMC6393308 DOI: 10.1093/nar/gky1251] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 08/10/2018] [Accepted: 12/11/2018] [Indexed: 01/05/2023] Open
Abstract
ParABS, an important DNA partitioning process in chromosome segregation, includes ParA (an ATPase), ParB (a parS binding protein) and parS (a centromere-like DNA). The homologous proteins of ParA and ParB in Helicobacter pylori are HpSoj and HpSpo0J, respectively. We analyzed the ATPase activity of HpSoj and found that it is enhanced by both DNA and HpSpo0J. Crystal structures of HpSoj and its DNA complexes revealed a typical ATPase fold and that it is dimeric. DNA binding by HpSoj is promoted by ATP. The HpSoj–ATP–DNA complex non-specifically binds DNA through a continuous basic binding patch formed by lysine residues, with a single DNA-binding site. This complex exhibits a DNA-binding adept state with an active ATP-bound conformation, whereas the HpSoj–ADP–DNA complex may represent a transient DNA-bound state. Based on structural comparisons, HpSoj exhibits a similar DNA binding surface to the bacterial ParA superfamily, but the archaeal ParA superfamily exhibits distinct non-specific DNA-binding via two DNA-binding sites. We detected the HpSpo0J–HpSoj–DNA complex by electron microscopy and show that this nucleoid-adaptor complex (NAC) is formed through HpSoj and HpSpo0J interaction and parS DNA binding. NAC formation is promoted by HpSoj participation and specific parS DNA facilitation.
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Affiliation(s)
- Chen-Hsi Chu
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Cheng-Yi Yen
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Bo-Wei Chen
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
| | - Min-Guan Lin
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
| | - Lyu-Han Wang
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Kai-Zhi Tang
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Chwan-Deng Hsiao
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
| | - Yuh-Ju Sun
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 300, Taiwan
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13
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Pseudomonas aeruginosa Requires the DNA-Specific Endonuclease EndA To Degrade Extracellular Genomic DNA To Disperse from the Biofilm. J Bacteriol 2019; 201:JB.00059-19. [PMID: 30988033 DOI: 10.1128/jb.00059-19] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 04/08/2019] [Indexed: 01/16/2023] Open
Abstract
The dispersion of biofilms is an active process resulting in the release of planktonic cells from the biofilm structure. While much is known about the process of dispersion cue perception and the subsequent modulation of the c-di-GMP pool, little is known about subsequent events resulting in the release of cells from the biofilm. Given that dispersion coincides with void formation and an overall erosion of the biofilm structure, we asked whether dispersion involves degradation of the biofilm matrix. Here, we focused on extracellular genomic DNA (eDNA) due to its almost universal presence in the matrix of biofilm-forming species. We identified two probable nucleases, endA and eddB, and eddA encoding a phosphatase that were significantly increased in transcript abundance in dispersed cells. However, only inactivation of endA but not eddA or eddB impaired dispersion by Pseudomonas aeruginosa biofilms in response to glutamate and nitric oxide (NO). Heterologously produced EndA was found to be secreted and active in degrading genomic DNA. While endA inactivation had little effect on biofilm formation and the presence of eDNA in biofilms, eDNA degradation upon induction of dispersion was impaired. In contrast, induction of endA expression coincided with eDNA degradation and resulted in biofilm dispersion. Thus, released cells demonstrated a hyperattaching phenotype but remained as resistant to tobramycin as biofilm cells from which they egress, indicating EndA-dispersed cells adopted some but not all of the phenotypes associated with dispersed cells. Our findings indicate for the first time a role of DNase EndA in dispersion and suggest weakening of the biofilm matrix is a requisite for biofilm dispersion.IMPORTANCE The finding that exposure to DNase I impairs biofilm formation or leads to the dispersal of early stage biofilms has led to the realization of extracellular genomic DNA (eDNA) as a structural component of the biofilm matrix. However, little is known about the contribution of intrinsic DNases to the weakening of the biofilm matrix and dispersion of established biofilms. Here, we demonstrate for the first time that nucleases are induced in dispersed Pseudomonas aeruginosa cells and are essential to the dispersion response and that degradation of matrix eDNA by endogenously produced/secreted EndA is required for P. aeruginosa biofilm dispersion. Our findings suggest that dispersing cells mediate their active release from the biofilm matrix via the induction of nucleases.
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14
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Genna V, Marcia M, De Vivo M. A Transient and Flexible Cation-π Interaction Promotes Hydrolysis of Nucleic Acids in DNA and RNA Nucleases. J Am Chem Soc 2019; 141:10770-10776. [PMID: 31251587 DOI: 10.1021/jacs.9b03663] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Metal-dependent DNA and RNA nucleases are enzymes that cleave nucleic acids with great efficiency and precision. These enzyme-mediated hydrolytic reactions are fundamental for the replication, repair, and storage of genetic information within the cell. Here, extensive classical and quantum-based free-energy molecular simulations show that a cation-π interaction is transiently formed in situ at the metal core of Bacteriophage-λ Exonuclease (Exo-λ), during catalysis. This noncovalent interaction (Lys131-Tyr154) triggers nucleophile activation for nucleotide excision. Then, our simulations also show the oscillatory dynamics and swinging of the newly formed cation-π dyad, whose conformational change may favor proton release from the cationic Lys131 to the bulk solution, thus restoring the precatalytic protonation state in Exo-λ. Altogether, we report on the novel mechanistic character of cation-π interactions for catalysis. Structural and bioinformatic analyses support that flexible orientation and transient formation of mobile cation-π interactions may represent a common catalytic strategy to promote nucleic acid hydrolysis in DNA and RNA nucleases.
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Affiliation(s)
- Vito Genna
- Laboratory of Molecular Modeling and Drug Discovery , Istituto Italiano di Tecnologia , Via Morego 30 , 16163 , Genoa , Italy
| | - Marco Marcia
- European Molecular Biology Laboratory (EMBL) Grenoble , 71 Avenue des Martyrs , Grenoble 38042 , France
| | - Marco De Vivo
- Laboratory of Molecular Modeling and Drug Discovery , Istituto Italiano di Tecnologia , Via Morego 30 , 16163 , Genoa , Italy
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15
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Yoon H, Zhao LN, Warshel A. Exploring the Catalytic Mechanism of Cas9 Using Information Inferred from Endonuclease VII. ACS Catal 2019; 9:1329-1336. [PMID: 34046245 PMCID: PMC8153514 DOI: 10.1021/acscatal.8b04324] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Elucidating the nature of the gene editing mechanism of CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) is an important task in view of the role of this breakthrough to the advancement of human medicine. In particular, it is crucial to understand the catalytic mechanism of Cas9 (one of the CRISPR associated proteins) and its role in confirming accurate editing. Thus, we focus in this work on an attempt to analyze the catalytic mechanism of Cas9. Considering the absence of detailed structural information on the active form of Cas9, we use an empirical valence bond (EVB) which is calibrated on the closely related mechanism of T4 endonuclease VII. The calibrated EVB is then used in studying the reaction of Cas9, while trying several structural models. It is found that the catalytic activation requires a large conformational change, where K848 or other positively charged group moves from a relatively large distance toward the scissile phosphate. This conformational change leads to the change in position of the Mg2+ ion and to a major reduction in the activation barrier for the catalytic reaction. Our finding provides an important clue on the nature of the catalytic activation of CAS9 and thus should help in elucidating a key aspect of the gene editing process. For example, the approach used here should be effective in exploring the nature of off target activation and its relationship to the energetics of the unwinding process. This strategy may offer ways to improve the selectivity of Cas9.
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Affiliation(s)
- Hanwool Yoon
- Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Ave, Los Angeles, California 90089-1062, United States
| | - Li Na Zhao
- Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Ave, Los Angeles, California 90089-1062, United States
| | - Arieh Warshel
- Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Ave, Los Angeles, California 90089-1062, United States
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16
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New Nuclease from Extremely Psychrophilic Microorganism Psychromonas ingrahamii 37: Identification and Characterization. Mol Biotechnol 2018; 61:122-133. [PMID: 30539415 DOI: 10.1007/s12033-018-0142-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Nucleases are an important group of hydrolases that degrade nucleic acids, with broad spectrum of applications in science and industry. In this paper, we report the identification and characterization of the nuclease from extremely psychrophilic bacterium Psychromonas ingrahamii that grows exponentially at 5 °C, but may also grow at even lower temperatures (down to - 12 °C). The putative endonuclease I gene, identified in the genome of P. ingrahamii, was cloned and expressed in Pichia pastoris. The recombinant protein was purified and its nucleolytic features were studied. The new enzyme, named by us as PinNuc, displays the features characteristic for the nonselective endonucleases, and has the ability to degrade different forms of nucleic acids. It is very active at room temperature in low ion-strength buffer and in the presence of low concentrations of magnesium ions. The enzyme, which possesses six cysteine residues, the most likely all engaged in disulphide bridges, is active only in oxidized form, and can be efficiently inactivated by the addition of low amounts of a reducing agent. According to our knowledge, it is the first nuclease, belonging to endonuclease I family, isolated from such extremely psychrophilic organism.
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17
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Binnenkade L, Kreienbaum M, Thormann KM. Characterization of ExeM, an Extracellular Nuclease of Shewanella oneidensis MR-1. Front Microbiol 2018; 9:1761. [PMID: 30123203 PMCID: PMC6085458 DOI: 10.3389/fmicb.2018.01761] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 07/13/2018] [Indexed: 01/08/2023] Open
Abstract
Bacterial extracellular nucleases have multiple functions in processes as diverse as nutrient acquisition, natural transformation, biofilm formation, or defense against neutrophil extracellular traps (NETs). Here we explored the properties of ExeM in Shewanella oneidensis MR-1, an extracellular nuclease, which is widely conserved among species of Shewanella, Vibrio, Aeromonas, and others. In S. oneidensis, ExeM is crucial for normal biofilm formation. In vitro activity measurements on heterologously produced ExeM revealed that this enzyme is a sugar-unspecific endonuclease, which requires Ca2+ and Mg2+/Mn2+ as co-factors for full activity. ExeM was almost exclusively localized to the cytoplasmic membrane fraction, even when a putative C-terminal membrane anchor was deleted. In contrast, ExeM was not detected in medium supernatants. Based on the results we hypothesize that ExeM predominantly interacts with DNA in close proximity to the cell, e.g., to promote biofilm formation and defense against NETs, or to control uptake of DNA.
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Affiliation(s)
- Lucas Binnenkade
- Institute for Microbiology and Molecular Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Maximilian Kreienbaum
- Institute for Microbiology and Molecular Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Kai M Thormann
- Institute for Microbiology and Molecular Biology, Justus Liebig University Giessen, Giessen, Germany
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18
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Price MN, Wetmore KM, Waters RJ, Callaghan M, Ray J, Liu H, Kuehl JV, Melnyk RA, Lamson JS, Suh Y, Carlson HK, Esquivel Z, Sadeeshkumar H, Chakraborty R, Zane GM, Rubin BE, Wall JD, Visel A, Bristow J, Blow MJ, Arkin AP, Deutschbauer AM. Mutant phenotypes for thousands of bacterial genes of unknown function. Nature 2018; 557:503-509. [PMID: 29769716 DOI: 10.1038/s41586-018-0124-0] [Citation(s) in RCA: 343] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 04/09/2018] [Indexed: 01/25/2023]
Abstract
One-third of all protein-coding genes from bacterial genomes cannot be annotated with a function. Here, to investigate the functions of these genes, we present genome-wide mutant fitness data from 32 diverse bacteria across dozens of growth conditions. We identified mutant phenotypes for 11,779 protein-coding genes that had not been annotated with a specific function. Many genes could be associated with a specific condition because the gene affected fitness only in that condition, or with another gene in the same bacterium because they had similar mutant phenotypes. Of the poorly annotated genes, 2,316 had associations that have high confidence because they are conserved in other bacteria. By combining these conserved associations with comparative genomics, we identified putative DNA repair proteins; in addition, we propose specific functions for poorly annotated enzymes and transporters and for uncharacterized protein families. Our study demonstrates the scalability of microbial genetics and its utility for improving gene annotations.
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Affiliation(s)
- Morgan N Price
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Kelly M Wetmore
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - R Jordan Waters
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Mark Callaghan
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jayashree Ray
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Hualan Liu
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jennifer V Kuehl
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ryan A Melnyk
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jacob S Lamson
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Yumi Suh
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Hans K Carlson
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Zuelma Esquivel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Harini Sadeeshkumar
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Romy Chakraborty
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Grant M Zane
- Department of Biochemistry, University of Missouri, Columbia, MO, USA
| | - Benjamin E Rubin
- Division of Biological Sciences, University of California, San Diego, CA, USA
| | - Judy D Wall
- Department of Biochemistry, University of Missouri, Columbia, MO, USA
| | - Axel Visel
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,School of Natural Sciences, University of California, Merced, CA, USA
| | - James Bristow
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Matthew J Blow
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Adam P Arkin
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. .,Department of Bioengineering, University of California, Berkeley, CA, USA.
| | - Adam M Deutschbauer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. .,Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.
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19
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Anton T, Karg E, Bultmann S. Applications of the CRISPR/Cas system beyond gene editing. Biol Methods Protoc 2018; 3:bpy002. [PMID: 32161796 PMCID: PMC6994046 DOI: 10.1093/biomethods/bpy002] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 02/28/2018] [Accepted: 04/03/2018] [Indexed: 12/26/2022] Open
Abstract
Since the discovery of the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated system (Cas) as a tool for gene editing a plethora of locus-specific as well as genome-wide approaches have been developed that allow efficient and reproducible manipulation of genomic sequences. However, the seemingly unbound potential of CRISPR/Cas does not stop with its utilization as a site-directed nuclease. Mutations in its catalytic centers render Cas9 (dCas9) a universal recruitment platform that can be utilized to control transcription, visualize DNA sequences, investigate in situ proteome compositions and manipulate epigenetic modifications at user-defined genomic loci. In this review, we give a comprehensive introduction and overview of the development, improvement and application of recent dCas9-based approaches.
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Affiliation(s)
- Tobias Anton
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), LMU Munich, 82152 Martinsried, Germany
| | - Elisabeth Karg
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), LMU Munich, 82152 Martinsried, Germany
| | - Sebastian Bultmann
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), LMU Munich, 82152 Martinsried, Germany
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20
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Baslé A, Hewitt L, Koh A, Lamb HK, Thompson P, Burgess JG, Hall MJ, Hawkins AR, Murray H, Lewis RJ. Crystal structure of NucB, a biofilm-degrading endonuclease. Nucleic Acids Res 2018; 46:473-484. [PMID: 29165717 PMCID: PMC5758888 DOI: 10.1093/nar/gkx1170] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 11/13/2017] [Indexed: 01/23/2023] Open
Abstract
Bacterial biofilms are a complex architecture of cells that grow on moist interfaces, and are held together by a molecular glue of extracellular proteins, sugars and nucleic acids. Biofilms are particularly problematic in human healthcare as they can coat medical implants and are thus a potential source of disease. The enzymatic dispersal of biofilms is increasingly being developed as a new strategy to treat this problem. Here, we have characterized NucB, a biofilm-dispersing nuclease from a marine strain of Bacillus licheniformis, and present its crystal structure together with the biochemistry and a mutational analysis required to confirm its active site. Taken together, these data support the categorization of NucB into a unique subfamily of the ββα metal-dependent non-specific endonucleases. Understanding the structure and function of NucB will facilitate its future development into an anti-biofilm therapeutic agent.
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Affiliation(s)
- Arnaud Baslé
- Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Lorraine Hewitt
- Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Alan Koh
- Centre for Bacterial Cell Biology, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4AX, UK
| | - Heather K Lamb
- Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Paul Thompson
- Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - J Grant Burgess
- Marine Biology, School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Michael J Hall
- Chemistry, School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Alastair R Hawkins
- Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Heath Murray
- Centre for Bacterial Cell Biology, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4AX, UK
| | - Richard J Lewis
- Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK,To whom correspondence should be addressed. Tel: +44 191 208 5482;
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21
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Wang Y, Jia P, Sharif R, Li Z, Li Y, Chen P. High-Level Production of DNA-Specific Endonuclease AsEndI with Synonymous Codon and its Potential Utilization for Removing DNA Contamination. Appl Biochem Biotechnol 2017; 185:641-654. [PMID: 29250754 DOI: 10.1007/s12010-017-2672-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 11/30/2017] [Indexed: 12/19/2022]
Abstract
Endonuclease I is a widely distributed periplasmic or extracellular enzyme. A method for the high-level production of recombinant AsEndI (endonuclease I from Aliivibrio salmonicida) in Escherichia coli with secretion expression is investigated. The coding sequence of AsEndI gene was assembled according to the E. coli codon usage bias, and AsEndI was expressed in the periplasm of E. coli TOP10 with a C-terminal 6× His-tagged fusion. The recombinant AsEndI (His-AsEndI) was purified by Ni-NTA resin with a yield of 1.29 × 107 U from 1-L LB medium. His-AsEndI could be classified into Ca2+/Mg2+-dependent nucleases and showed highest nuclease activity to dsDNA at pH 8.0 and 37 °C. His-AsEndI is highly active in a broad range of salt concentration range up to 1.0 M with optimal NaCl concentration at 0.4 M. His-AsEndI can effectively remove DNA contamination in RNA sample or in PCR reagents to the level that cannot be detected by highly sensitive nested PCR and without adverse effects on the subsequent PCR reaction. His-AsEndI can remove DNA contamination at high salt conditions, especially for the DNA that may be shielded by DNA-binding protein at low salt conditions.
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Affiliation(s)
- Yuan Wang
- College of Life Sciences, Northwest Agriculture and Forestry University, Yangling, Shaanxi, 712100, China
| | - Peng Jia
- College of Life Sciences, Northwest Agriculture and Forestry University, Yangling, Shaanxi, 712100, China
| | - Rahat Sharif
- College of Horticulture, Northwest Agriculture and Forestry University, Yangling, Shaanxi, 712100, China
| | - Zhengchen Li
- College of Life Sciences, Northwest Agriculture and Forestry University, Yangling, Shaanxi, 712100, China
| | - Yuhong Li
- College of Horticulture, Northwest Agriculture and Forestry University, Yangling, Shaanxi, 712100, China.
| | - Peng Chen
- College of Life Sciences, Northwest Agriculture and Forestry University, Yangling, Shaanxi, 712100, China.
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22
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Jablonska J, Matelska D, Steczkiewicz K, Ginalski K. Systematic classification of the His-Me finger superfamily. Nucleic Acids Res 2017; 45:11479-11494. [PMID: 29040665 PMCID: PMC5714182 DOI: 10.1093/nar/gkx924] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 09/29/2017] [Indexed: 02/06/2023] Open
Abstract
The His-Me finger endonucleases, also known as HNH or ββα-metal endonucleases, form a large and diverse protein superfamily. The His-Me finger domain can be found in proteins that play an essential role in cells, including genome maintenance, intron homing, host defense and target offense. Its overall structural compactness and non-specificity make it a perfectly-tailored pathogenic module that participates on both sides of inter- and intra-organismal competition. An extremely low sequence similarity across the superfamily makes it difficult to identify and classify new His-Me fingers. Using state-of-the-art distant homology detection methods, we provide an updated and systematic classification of His-Me finger proteins. In this work, we identified over 100 000 proteins and clustered them into 38 groups, of which three groups are new and cannot be found in any existing public domain database of protein families. Based on an analysis of sequences, structures, domain architectures, and genomic contexts, we provide a careful functional annotation of the poorly characterized members of this superfamily. Our results may inspire further experimental investigations that should address the predicted activity and clarify the potential substrates, to provide more detailed insights into the fundamental biological roles of these proteins.
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Affiliation(s)
- Jagoda Jablonska
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Dorota Matelska
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Kamil Steczkiewicz
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Krzysztof Ginalski
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland
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23
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Oliva C, Sánchez-Murcia PA, Rico E, Bravo A, Menéndez M, Gago F, Jiménez-Ruiz A. Structure-based domain assignment in Leishmania infantum EndoG: characterization of a pH-dependent regulatory switch and a C-terminal extension that largely dictates DNA substrate preferences. Nucleic Acids Res 2017; 45:9030-9045. [PMID: 28911117 PMCID: PMC5587815 DOI: 10.1093/nar/gkx629] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 07/11/2017] [Indexed: 11/28/2022] Open
Abstract
Mitochondrial endonuclease G from Leishmania infantum (LiEndoG) participates in the degradation of double-stranded DNA (dsDNA) during parasite cell death and is catalytically inactive at a pH of 8.0 or above. The presence, in the primary sequence, of an acidic amino acid-rich insertion exclusive to trypanosomatids and its spatial position in a homology-built model of LiEndoG led us to postulate that this peptide stretch might act as a pH sensor for self-inhibition. We found that a LiEndoG variant lacking residues 145–180 is indeed far more active than its wild-type counterpart at pH values >7.0. In addition, we discovered that (i) LiEndoG exists as a homodimer, (ii) replacement of Ser211 in the active-site SRGH motif with the canonical aspartate from the DRGH motif of other nucleases leads to a catalytically deficient enzyme, (iii) the activity of the S211D variant can be restored upon the concomitant replacement of Ala247 with Arg and (iv) a C-terminal extension is responsible for the observed preferential cleavage of single-stranded DNA (ssDNA) and ssDNA–dsDNA junctions. Taken together, our results support the view that LiEndoG is a multidomain molecular machine whose nuclease activity can be subtly modulated or even abrogated through architectural changes brought about by environmental conditions and interaction with other binding partners.
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MESH Headings
- Amino Acid Sequence
- Amino Acid Substitution
- Catalytic Domain
- Cloning, Molecular
- DNA Cleavage
- DNA, Protozoan/chemistry
- DNA, Protozoan/genetics
- DNA, Protozoan/metabolism
- DNA, Single-Stranded/chemistry
- DNA, Single-Stranded/genetics
- DNA, Single-Stranded/metabolism
- Endodeoxyribonucleases/chemistry
- Endodeoxyribonucleases/genetics
- Endodeoxyribonucleases/metabolism
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Gene Expression
- Hydrogen-Ion Concentration
- Kinetics
- Leishmania infantum/chemistry
- Leishmania infantum/enzymology
- Models, Molecular
- Nucleic Acid Conformation
- Protein Binding
- Protein Conformation, alpha-Helical
- Protein Conformation, beta-Strand
- Protein Interaction Domains and Motifs
- Protein Multimerization
- Protozoan Proteins/chemistry
- Protozoan Proteins/genetics
- Protozoan Proteins/metabolism
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- Sequence Alignment
- Sequence Deletion
- Sequence Homology, Amino Acid
- Structure-Activity Relationship
- Substrate Specificity
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Affiliation(s)
- Cristina Oliva
- Departamento de Biología de Sistemas, Universidad de Alcalá, E-28805 Alcalá de Henares, Madrid, Spain
| | - Pedro A. Sánchez-Murcia
- Departamento de Ciencias Biomédicas y “Unidad Asociada IQM-CSIC”, Universidad de Alcalá, E-28805 Alcalá de Henares, Madrid, Spain
| | - Eva Rico
- Departamento de Biología de Sistemas, Universidad de Alcalá, E-28805 Alcalá de Henares, Madrid, Spain
| | - Ana Bravo
- Departamento de Ciencias Biomédicas y “Unidad Asociada IQM-CSIC”, Universidad de Alcalá, E-28805 Alcalá de Henares, Madrid, Spain
| | - Margarita Menéndez
- Instituto de Química Física Rocasolano, Consejo Superior de Investigaciones Científicas (CSIC), E-28006 Madrid, Spain
| | - Federico Gago
- Departamento de Ciencias Biomédicas y “Unidad Asociada IQM-CSIC”, Universidad de Alcalá, E-28805 Alcalá de Henares, Madrid, Spain
- To whom correspondence should be addressed. Tel: +34 918 855 109; Fax: +34 918 854 585; . Correspondence may also be addressed to Federico Gago. Tel: +34 918 854 514; Fax: +34 918 854 591;
| | - Antonio Jiménez-Ruiz
- Departamento de Biología de Sistemas, Universidad de Alcalá, E-28805 Alcalá de Henares, Madrid, Spain
- To whom correspondence should be addressed. Tel: +34 918 855 109; Fax: +34 918 854 585; . Correspondence may also be addressed to Federico Gago. Tel: +34 918 854 514; Fax: +34 918 854 591;
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25
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Flenker KS, Burghardt EL, Dutta N, Burns WJ, Grover JM, Kenkel EJ, Weaver TM, Mills J, Kim H, Huang L, Owczarzy R, Musselman CA, Behlke MA, Ford B, McNamara JO. Rapid Detection of Urinary Tract Infections via Bacterial Nuclease Activity. Mol Ther 2017; 25:1353-1362. [PMID: 28391960 DOI: 10.1016/j.ymthe.2017.03.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Revised: 03/07/2017] [Accepted: 03/08/2017] [Indexed: 12/27/2022] Open
Abstract
Rapid and accurate bacterial detection methods are needed for clinical diagnostic, water, and food testing applications. The wide diversity of bacterial nucleases provides a rich source of enzymes that could be exploited as signal amplifying biomarkers to enable rapid, selective detection of bacterial species. With the exception of the use of micrococcal nuclease activity to detect Staphylococcus aureus, rapid methods that detect bacterial pathogens via their nuclease activities have not been developed. Here, we identify endonuclease I as a robust biomarker for E. coli and develop a rapid ultrasensitive assay that detects its activity. Comparison of nuclease activities of wild-type and nuclease-knockout E. coli clones revealed that endonuclease I is the predominant DNase in E. coli lysates. Endonuclease I is detectable by immunoblot and activity assays in uropathogenic E. coli strains. A rapid assay that detects endonuclease I activity in patient urine with an oligonucleotide probe exhibited substantially higher sensitivity for urinary tract infections than that reported for rapid urinalysis methods. The 3 hr turnaround time is much shorter than that of culture-based methods, thereby providing a means for expedited administration of appropriate antimicrobial therapy. We suggest this approach could address various unmet needs for rapid detection of E. coli.
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Affiliation(s)
- Katie S Flenker
- Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Elliot L Burghardt
- Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Nirmal Dutta
- Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - William J Burns
- Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Julia M Grover
- Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Elizabeth J Kenkel
- Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Tyler M Weaver
- Department of Biochemistry, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - James Mills
- Department of Psychiatry, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Hyeon Kim
- University of Iowa Research Foundation, University of Iowa, Iowa City, IA 52242, USA
| | - Lingyan Huang
- Integrated DNA Technologies (IDT), Coralville, IA 52241, USA
| | | | - Catherine A Musselman
- Department of Biochemistry, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Mark A Behlke
- Integrated DNA Technologies (IDT), Coralville, IA 52241, USA
| | - Bradley Ford
- Department of Pathology, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - James O McNamara
- Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA.
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26
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Zhang L, Xu D, Huang Y, Zhu X, Rui M, Wan T, Zheng X, Shen Y, Chen X, Ma K, Gong Y. Structural and functional characterization of deep-sea thermophilic bacteriophage GVE2 HNH endonuclease. Sci Rep 2017; 7:42542. [PMID: 28211904 PMCID: PMC5304195 DOI: 10.1038/srep42542] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 01/10/2017] [Indexed: 01/26/2023] Open
Abstract
HNH endonucleases in bacteriophages play a variety of roles in the phage lifecycle as key components of phage DNA packaging machines. The deep-sea thermophilic bacteriophage Geobacillus virus E2 (GVE2) encodes an HNH endonuclease (GVE2 HNHE). Here, the crystal structure of GVE2 HNHE is reported. This is the first structural study of a thermostable HNH endonuclease from a thermophilic bacteriophage. Structural comparison reveals that GVE2 HNHE possesses a typical ββα-metal fold and Zn-finger motif similar to those of HNH endonucleases from other bacteriophages, apart from containing an extra α-helix, suggesting conservation of these enzymes among bacteriophages. Biochemical analysis suggests that the alanine substitutions of the conserved residues (H93, N109 and H118) in the HNH motif of GVE2 HNHE abolished 94%, 60% and 83% of nicking activity, respectively. Compared to the wild type enzyme, the H93A mutant displayed almost the same conformation while the N108A and H118A mutants had different conformations. In addition, the wild type enzyme was more thermostable than the mutants. In the presence of Mn2+ or Zn2+, the wild type enzyme displayed distinct DNA nicking patterns. However, high Mn2+ concentrations were needed for the N109A and H118A mutants to nick DNA while Zn2+ inactivated their nicking activity.
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Affiliation(s)
- Likui Zhang
- Marine Science & Technology Institute Department of Environmental Science and Engineering, Yangzhou University, China
- State Key Laboratory of Microbial Technology, Shandong University, China
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Dandan Xu
- Institute of Health Sciences and School of Life Science, Anhui University, Hefei, Anhui 230601, China
| | - Yanchao Huang
- Marine Science & Technology Institute Department of Environmental Science and Engineering, Yangzhou University, China
| | - Xinyuan Zhu
- Marine Science & Technology Institute Department of Environmental Science and Engineering, Yangzhou University, China
| | - Mianwen Rui
- Marine Science & Technology Institute Department of Environmental Science and Engineering, Yangzhou University, China
| | - Ting Wan
- Marine Science & Technology Institute Department of Environmental Science and Engineering, Yangzhou University, China
| | - Xin Zheng
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, China
| | - Yulong Shen
- State Key Laboratory of Microbial Technology, Shandong University, China
| | - Xiangdong Chen
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Kesen Ma
- Department of Biology, University of Waterloo, Canada
| | - Yong Gong
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, China
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27
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Batebi H, Imhof P. Phosphodiester hydrolysis computed for cluster models of enzymatic active sites. Theor Chem Acc 2016. [DOI: 10.1007/s00214-016-2020-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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28
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Lin JLJ, Wu CC, Yang WZ, Yuan HS. Crystal structure of endonuclease G in complex with DNA reveals how it nonspecifically degrades DNA as a homodimer. Nucleic Acids Res 2016; 44:10480-10490. [PMID: 27738134 PMCID: PMC5137453 DOI: 10.1093/nar/gkw931] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 10/05/2016] [Accepted: 10/07/2016] [Indexed: 01/20/2023] Open
Abstract
Endonuclease G (EndoG) is an evolutionarily conserved mitochondrial protein in eukaryotes that digests nucleus chromosomal DNA during apoptosis and paternal mitochondrial DNA during embryogenesis. Under oxidative stress, homodimeric EndoG becomes oxidized and converts to monomers with diminished nuclease activity. However, it remains unclear why EndoG has to function as a homodimer in DNA degradation. Here, we report the crystal structure of the Caenorhabditis elegans EndoG homologue, CPS-6, in complex with single-stranded DNA at a resolution of 2.3 Å. Two separate DNA strands are bound at the ββα-metal motifs in the homodimer with their nucleobases pointing away from the enzyme, explaining why CPS-6 degrades DNA without sequence specificity. Two obligatory monomeric CPS-6 mutants (P207E and K131D/F132N) were constructed, and they degrade DNA with diminished activity due to poorer DNA-binding affinity as compared to wild-type CPS-6. Moreover, the P207E mutant exhibits predominantly 3′-to-5′ exonuclease activity, indicating a possible endonuclease to exonuclease activity change. Thus, the dimer conformation of CPS-6 is essential for maintaining its optimal DNA-binding and endonuclease activity. Compared to other non-specific endonucleases, which are usually monomeric enzymes, EndoG is a unique dimeric endonuclease, whose activity hence can be modulated by oxidation to induce conformational changes.
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Affiliation(s)
- Jason L J Lin
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, ROC
| | - Chyuan-Chuan Wu
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, ROC
| | - Wei-Zen Yang
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, ROC
| | - Hanna S Yuan
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, ROC .,Graduate Institute of Biochemistry and Molecular Biology, National Taiwan University, Taiwan 10048, ROC
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29
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Moon AF, Krahn JM, Lu X, Cuneo MJ, Pedersen LC. Structural characterization of the virulence factor Sda1 nuclease from Streptococcus pyogenes. Nucleic Acids Res 2016; 44:3946-57. [PMID: 26969731 PMCID: PMC4856990 DOI: 10.1093/nar/gkw143] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 02/25/2016] [Indexed: 11/22/2022] Open
Abstract
Infection by Group A Streptococcus pyogenes (GAS) is a leading cause of severe invasive disease in humans, including streptococcal toxic shock syndrome and necrotizing fasciitis. GAS infections lead to nearly 163,000 annual deaths worldwide. Hypervirulent strains of S. pyogenes have evolved a plethora of virulence factors that aid in disease—by promoting bacterial adhesion to host cells, subsequent invasion of deeper tissues and blocking the immune system's attempts to eradicate the infection. Expression and secretion of the extracellular nuclease Sda1 is advantageous for promoting bacterial dissemination throughout the host organism, and evasion of the host's innate immune response. Here we present two crystal structures of Sda1, as well as biochemical studies to address key structural features and surface residues involved in DNA binding and catalysis. In the active site, Asn211 is observed to directly chelate a hydrated divalent metal ion and Arg124, on the putative substrate binding loop, likely stabilizes the transition state during phosphodiester bond cleavage. These structures provide a foundation for rational drug design of small molecule inhibitors to be used in prevention of invasive streptococcal disease.
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Affiliation(s)
- Andrea F Moon
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Juno M Krahn
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Xun Lu
- Spallation Neutron Source, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Matthew J Cuneo
- Spallation Neutron Source, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Lars C Pedersen
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
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30
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Machnicka MA, Kaminska KH, Dunin-Horkawicz S, Bujnicki JM. Phylogenomics and sequence-structure-function relationships in the GmrSD family of Type IV restriction enzymes. BMC Bioinformatics 2015; 16:336. [PMID: 26493560 PMCID: PMC4619093 DOI: 10.1186/s12859-015-0773-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 10/13/2015] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND GmrSD is a modification-dependent restriction endonuclease that specifically targets and cleaves glucosylated hydroxymethylcytosine (glc-HMC) modified DNA. It is encoded either as two separate single-domain GmrS and GmrD proteins or as a single protein carrying both domains. Previous studies suggested that GmrS acts as endonuclease and NTPase whereas GmrD binds DNA. METHODS In this work we applied homology detection, sequence conservation analysis, fold recognition and homology modeling methods to study sequence-structure-function relationships in the GmrSD restriction endonucleases family. We also analyzed the phylogeny and genomic context of the family members. RESULTS Results of our comparative genomics study show that GmrS exhibits similarity to proteins from the ParB/Srx fold which can have both NTPase and nuclease activity. In contrast to the previous studies though, we attribute the nuclease activity also to GmrD as we found it to contain the HNH endonuclease motif. We revealed residues potentially important for structure and function in both domains. Moreover, we found that GmrSD systems exist predominantly as a fused, double-domain form rather than as a heterodimer and that their homologs are often encoded in regions enriched in defense and gene mobility-related elements. Finally, phylogenetic reconstructions of GmrS and GmrD domains revealed that they coevolved and only few GmrSD systems appear to be assembled from distantly related GmrS and GmrD components. CONCLUSIONS Our study provides insight into sequence-structure-function relationships in the yet poorly characterized family of Type IV restriction enzymes. Comparative genomics allowed to propose possible role of GmrD domain in the function of the GmrSD enzyme and possible active sites of both GmrS and GmrD domains. Presented results can guide further experimental characterization of these enzymes.
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Affiliation(s)
- Magdalena A Machnicka
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109, Warsaw, Poland
| | - Katarzyna H Kaminska
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109, Warsaw, Poland
| | - Stanislaw Dunin-Horkawicz
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109, Warsaw, Poland
| | - Janusz M Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109, Warsaw, Poland. .,Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, ul. Umultowska 89, PL-61-614, Poznan, Poland.
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31
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de Buhr N, Stehr M, Neumann A, Naim HY, Valentin-Weigand P, von Köckritz-Blickwede M, Baums CG. Identification of a novel DNase of Streptococcus suis (EndAsuis) important for neutrophil extracellular trap degradation during exponential growth. MICROBIOLOGY-SGM 2015; 161:838-50. [PMID: 25667008 DOI: 10.1099/mic.0.000040] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 01/27/2015] [Indexed: 12/25/2022]
Abstract
The porcine and human pathogen Streptococcus suis induces and degrades neutrophil extracellular traps (NETs) in vitro. In this study, we investigated the working hypothesis that NET degradation is mediated not only by the known secreted S. suis nuclease A (SsnA) but also by a so-far undescribed putative endonuclease A of S. suis (designated EndAsuis) homologous to the pneumococcal endonuclease A (EndA). Comparative analysis was conducted to identify differences in localization, expression and function of EndAsuis and SsnA. In contrast to ssnA, endAsuis RNA expression was not substantially different during exponential and stationary growth. Modelling of the 3D structure confirmed a putative DRGH-motif-containing ββα-metal finger catalytic core in EndAsuis. Accordingly, nuclease activity of recombinant EndAsuis with a point-mutated H165 was rescued through imidazol treatment. In accordance with a putative membrane anchor, nuclease activity caused by endAsuis was not detectable in the supernatant. Importantly, endAsuis determined nuclease activity of S. suis prominently during exponential growth. This activity depended on the presence of Mg(2+) but, in contrast to SsnA activity, not on Ca(2+). A pH of 5.4 did not inhibit endAsuis-encoded nuclease activity during exponential growth. NET degradation of S. suis harvested during exponential growth was significantly attenuated in the endAsuis mutant. In contrast to SsnA, mutagenesis of endAsuis did not result in a significantly higher susceptibility against the antimicrobial effect mediated by NETs. As degradation of bacterial DNA caused by S. suis depended on ssnA and endAsuis, further functions of both factors in the host-pathogen interaction might be envisioned.
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Affiliation(s)
- Nicole de Buhr
- Institute for Microbiology, Department of Infectious Diseases, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Matthias Stehr
- Institute for Microbiology, Department of Infectious Diseases, University of Veterinary Medicine Hannover, Hannover, Germany LIONEX Diagnostics and Therapeutics GmbH, Braunschweig, Germany
| | - Ariane Neumann
- Department of Physiological Chemistry, Department of Infectious Diseases, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Hassan Y Naim
- Department of Physiological Chemistry, Department of Infectious Diseases, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Peter Valentin-Weigand
- Institute for Microbiology, Department of Infectious Diseases, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Maren von Köckritz-Blickwede
- Department of Physiological Chemistry, Department of Infectious Diseases, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Christoph G Baums
- Institute for Microbiology, Department of Infectious Diseases, University of Veterinary Medicine Hannover, Hannover, Germany Institute for Bacteriology and Mycology, Centre for Infectious Diseases, College of Veterinary Medicine, University of Leipzig, Leipzig, Germany
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32
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Benrezkallah D, Dauchez M, Krallafa A. Molecular dynamics of the salt dependence of a cold-adapted enzyme: endonuclease I. J Biomol Struct Dyn 2015; 33:2511-21. [DOI: 10.1080/07391102.2014.1002007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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33
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Moon AF, Gaudu P, Pedersen LC. Structural characterization of the virulence factor nuclease A from Streptococcus agalactiae. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:2937-49. [PMID: 25372684 PMCID: PMC4220975 DOI: 10.1107/s1399004714019725] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 09/01/2014] [Indexed: 12/28/2022]
Abstract
The group B pathogen Streptococcus agalactiae commonly populates the human gut and urogenital tract, and is a major cause of infection-based mortality in neonatal infants and in elderly or immunocompromised adults. Nuclease A (GBS_NucA), a secreted DNA/RNA nuclease, serves as a virulence factor for S. agalactiae, facilitating bacterial evasion of the human innate immune response. GBS_NucA efficiently degrades the DNA matrix component of neutrophil extracellular traps (NETs), which attempt to kill and clear invading bacteria during the early stages of infection. In order to better understand the mechanisms of DNA substrate binding and catalysis of GBS_NucA, the high-resolution structure of a catalytically inactive mutant (H148G) was solved by X-ray crystallography. Several mutants on the surface of GBS_NucA which might influence DNA substrate binding and catalysis were generated and evaluated using an imidazole chemical rescue technique. While several of these mutants severely inhibited nuclease activity, two mutants (K146R and Q183A) exhibited significantly increased activity. These structural and biochemical studies have greatly increased our understanding of the mechanism of action of GBS_NucA in bacterial virulence and may serve as a foundation for the structure-based drug design of antibacterial compounds targeted to S. agalactiae.
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Affiliation(s)
- Andrea F. Moon
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Philippe Gaudu
- INRA, UMR1319 Micalis, Domaine de Vilvert, Jouy-en-Josas, France; AgroParisTech, UMR Micalis, Jouy-en-Josas, France
| | - Lars C. Pedersen
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
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34
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Németh E, Körtvélyesi T, Thulstrup PW, Christensen HEM, Kožíšek M, Nagata K, Czene A, Gyurcsik B. Fine tuning of the catalytic activity of colicin E7 nuclease domain by systematic N-terminal mutations. Protein Sci 2014; 23:1113-22. [PMID: 24895333 DOI: 10.1002/pro.2497] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 05/20/2014] [Accepted: 05/29/2014] [Indexed: 11/11/2022]
Abstract
The nuclease domain of colicin E7 (NColE7) promotes the nonspecific cleavage of nucleic acids at its C-terminal HNH motif. Interestingly, the deletion of four N-terminal residues (446-449 NColE7 = KRNK) resulted in complete loss of the enzyme activity. R447A mutation was reported to decrease the nuclease activity, but a detailed analysis of the role of the highly positive and flexible N-terminus is still missing. Here, we present the study of four mutants, with a decreased activity in the following order: NColE7 >> KGNK > KGNG ∼ GGNK > GGNG. At the same time, the folding, the metal-ion, and the DNA-binding affinity were unaffected by the mutations as revealed by linear and circular dichroism spectroscopy, isothermal calorimetric titrations, and gel mobility shift experiments. Semiempirical quantum chemical calculations and molecular dynamics simulations revealed that K446, K449, and/or the N-terminal amino group are able to approach the active centre in the absence of the other positively charged residues. The results suggested a complex role of the N-terminus in the catalytic process that could be exploited in the design of a controlled nuclease.
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Affiliation(s)
- Eszter Németh
- Department of Inorganic and Analytical Chemistry, University of Szeged, 6720, Szeged, Hungary; Department of Physical Chemistry and Material Sciences, University of Szeged, 6720, Szeged, Hungary
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35
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Nishimasu H, Ran FA, Hsu PD, Konermann S, Shehata SI, Dohmae N, Ishitani R, Zhang F, Nureki O. Crystal structure of Cas9 in complex with guide RNA and target DNA. Cell 2014; 156:935-49. [PMID: 24529477 PMCID: PMC4139937 DOI: 10.1016/j.cell.2014.02.001] [Citation(s) in RCA: 1351] [Impact Index Per Article: 122.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Revised: 02/02/2014] [Accepted: 02/02/2014] [Indexed: 12/26/2022]
Abstract
The CRISPR-associated endonuclease Cas9 can be targeted to specific genomic loci by single guide RNAs (sgRNAs). Here, we report the crystal structure of Streptococcus pyogenes Cas9 in complex with sgRNA and its target DNA at 2.5 Å resolution. The structure revealed a bilobed architecture composed of target recognition and nuclease lobes, accommodating the sgRNA:DNA heteroduplex in a positively charged groove at their interface. Whereas the recognition lobe is essential for binding sgRNA and DNA, the nuclease lobe contains the HNH and RuvC nuclease domains, which are properly positioned for cleavage of the complementary and noncomplementary strands of the target DNA, respectively. The nuclease lobe also contains a carboxyl-terminal domain responsible for the interaction with the protospacer adjacent motif (PAM). This high-resolution structure and accompanying functional analyses have revealed the molecular mechanism of RNA-guided DNA targeting by Cas9, thus paving the way for the rational design of new, versatile genome-editing technologies.
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Affiliation(s)
- Hiroshi Nishimasu
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo, Tokyo 113-0032, Japan; JST, PRESTO, 2-11-16 Yayoi, Bunkyo, Tokyo 113-0032, Japan
| | - F Ann Ran
- Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA; McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Patrick D Hsu
- Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA; McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Silvana Konermann
- Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA; McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Soraya I Shehata
- Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA; McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Naoshi Dohmae
- Biomolecular Characterization Team and CREST/JST, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Ryuichiro Ishitani
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo, Tokyo 113-0032, Japan
| | - Feng Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA; McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Osamu Nureki
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo, Tokyo 113-0032, Japan.
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36
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Das A, Chakrabarti J, Ghosh M. Thermodynamics of interfacial changes in a protein–protein complex. ACTA ACUST UNITED AC 2014; 10:437-45. [DOI: 10.1039/c3mb70249a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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37
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Czene A, Tóth E, Németh E, Otten H, Poulsen JCN, Christensen HEM, Rulíšek L, Nagata K, Larsen S, Gyurcsik B. A new insight into the zinc-dependent DNA-cleavage by the colicin E7 nuclease: a crystallographic and computational study. Metallomics 2014; 6:2090-9. [DOI: 10.1039/c4mt00195h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The crystal structure of a colicin E7 metallonuclease mutant complemented by QM/MM calculations suggests an alternative catalytic mechanism of Zn2+-containing HNH nucleases.
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Affiliation(s)
- Anikó Czene
- MTA-SZTE Bioinorganic Chemistry Research Group
- H-6720 Szeged, Hungary
| | - Eszter Tóth
- Department of Inorganic and Analytical Chemistry
- University of Szeged
- H-6720 Szeged, Hungary
| | - Eszter Németh
- Department of Inorganic and Analytical Chemistry
- University of Szeged
- H-6720 Szeged, Hungary
| | - Harm Otten
- Department of Chemistry
- University of Copenhagen
- 2100 Copenhagen, Denmark
| | | | | | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- 166 10 Prague 6, Czech Republic
| | - Kyosuke Nagata
- Nagata Special Laboratory
- Faculty of Medicine
- University of Tsukuba
- Tsukuba 305-8575, Japan
| | - Sine Larsen
- Department of Chemistry
- University of Copenhagen
- 2100 Copenhagen, Denmark
| | - Béla Gyurcsik
- MTA-SZTE Bioinorganic Chemistry Research Group
- H-6720 Szeged, Hungary
- Department of Inorganic and Analytical Chemistry
- University of Szeged
- H-6720 Szeged, Hungary
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38
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Xu SY, Kuzin AP, Seetharaman J, Gutjahr A, Chan SH, Chen Y, Xiao R, Acton TB, Montelione GT, Tong L. Structure determination and biochemical characterization of a putative HNH endonuclease from Geobacter metallireducens GS-15. PLoS One 2013; 8:e72114. [PMID: 24039739 PMCID: PMC3765158 DOI: 10.1371/journal.pone.0072114] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Accepted: 07/12/2013] [Indexed: 01/07/2023] Open
Abstract
The crystal structure of a putative HNH endonuclease, Gmet_0936 protein from Geobacter metallireducens GS-15, has been determined at 2.6 Å resolution using single-wavelength anomalous dispersion method. The structure contains a two-stranded anti-parallel β-sheet that are surrounded by two helices on each face, and reveals a Zn ion bound in each monomer, coordinated by residues Cys38, Cys41, Cys73, and Cys76, which likely plays an important structural role in stabilizing the overall conformation. Structural homologs of Gmet_0936 include Hpy99I endonuclease, phage T4 endonuclease VII, and other HNH endonucleases, with these enzymes sharing 15-20% amino acid sequence identity. An overlay of Gmet_0936 and Hpy99I structures shows that most of the secondary structure elements, catalytic residues as well as the zinc binding site (zinc ribbon) are conserved. However, Gmet_0936 lacks the N-terminal domain of Hpy99I, which mediates DNA binding as well as dimerization. Purified Gmet_0936 forms dimers in solution and a dimer of the protein is observed in the crystal, but with a different mode of dimerization as compared to Hpy99I. Gmet_0936 and its N77H variant show a weak DNA binding activity in a DNA mobility shift assay and a weak Mn²⁺-dependent nicking activity on supercoiled plasmids in low pH buffers. The preferred substrate appears to be acid and heat-treated DNA with AP sites, suggesting Gmet_0936 may be a DNA repair enzyme.
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Affiliation(s)
- Shuang-yong Xu
- New England Biolabs, Inc. Research Department, Ipswich, Massachusetts, United States of America
- * E-mail: (SX); (LT)
| | - Alexandre P. Kuzin
- Department of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, New York, United States of America
| | - Jayaraman Seetharaman
- Department of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, New York, United States of America
| | - Alice Gutjahr
- New England Biolabs, Inc. Research Department, Ipswich, Massachusetts, United States of America
| | - Siu-Hong Chan
- New England Biolabs, Inc. Research Department, Ipswich, Massachusetts, United States of America
| | - Yang Chen
- Department of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, New York, United States of America
| | - Rong Xiao
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers University, Department of Biochemistry, Robert Wood Johnson Medical School, Northeast Structural Genomics Consortium, Piscataway, New Jersey, United States of America
| | - Thomas B. Acton
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers University, Department of Biochemistry, Robert Wood Johnson Medical School, Northeast Structural Genomics Consortium, Piscataway, New Jersey, United States of America
| | - Gaetano T. Montelione
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers University, Department of Biochemistry, Robert Wood Johnson Medical School, Northeast Structural Genomics Consortium, Piscataway, New Jersey, United States of America
| | - Liang Tong
- Department of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, New York, United States of America
- * E-mail: (SX); (LT)
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39
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Lambert C, Sockett RE. Nucleases in Bdellovibrio bacteriovorus contribute towards efficient self-biofilm formation and eradication of preformed prey biofilms. FEMS Microbiol Lett 2013; 340:109-16. [PMID: 23297829 PMCID: PMC3593177 DOI: 10.1111/1574-6968.12075] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 01/02/2013] [Indexed: 11/30/2022] Open
Abstract
Bdellovibrio bacteriovorus are predatory bacteria that burrow into prey bacteria and degrade their cell contents, including DNA and RNA, to grow. Their genome encodes diverse nucleases, some with potential export sequences. Transcriptomic analysis determined two candidate-predicted nuclease genes (bd1244, bd1934) upregulated upon contact with prey, which we hypothesised, may be involved in prey nucleic acid degradation. RT-PCR on total RNA from across the predatory cycle confirmed that the transcription of these genes peaks shortly after prey cell invasion, around the time that prey DNA is being degraded. We deleted bd1244 and bd1934 both singly and together and investigated their role in predation of prey cells and biofilms. Surprisingly, we found that the nuclease-mutant strains could still prey upon planktonic bacteria as efficiently as wild type and still degraded the prey genomic DNA. The Bdellovibrio nuclease mutants were less efficient at (self-) biofilm formation, and surprisingly, they showed enhanced predatory clearance of preformed prey cell biofilms relative to wild-type Bdellovibrio.
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Affiliation(s)
- Carey Lambert
- Centre for Genetics and Genomics, School of Biology, Queen's Medical Centre, University of Nottingham, Nottingham, UK
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40
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Tsutakawa SE, Shin DS, Mol CD, Izumi T, Arvai AS, Mantha AK, Szczesny B, Ivanov IN, Hosfield DJ, Maiti B, Pique ME, Frankel KA, Hitomi K, Cunningham RP, Mitra S, Tainer JA. Conserved structural chemistry for incision activity in structurally non-homologous apurinic/apyrimidinic endonuclease APE1 and endonuclease IV DNA repair enzymes. J Biol Chem 2013; 288:8445-8455. [PMID: 23355472 DOI: 10.1074/jbc.m112.422774] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Non-coding apurinic/apyrimidinic (AP) sites in DNA form spontaneously and as DNA base excision repair intermediates are the most common toxic and mutagenic in vivo DNA lesion. For repair, AP sites must be processed by 5' AP endonucleases in initial stages of base repair. Human APE1 and bacterial Nfo represent the two conserved 5' AP endonuclease families in the biosphere; they both recognize AP sites and incise the phosphodiester backbone 5' to the lesion, yet they lack similar structures and metal ion requirements. Here, we determined and analyzed crystal structures of a 2.4 Å resolution APE1-DNA product complex with Mg(2+) and a 0.92 Å Nfo with three metal ions. Structural and biochemical comparisons of these two evolutionarily distinct enzymes characterize key APE1 catalytic residues that are potentially functionally similar to Nfo active site components, as further tested and supported by computational analyses. We observe a magnesium-water cluster in the APE1 active site, with only Glu-96 forming the direct protein coordination to the Mg(2+). Despite differences in structure and metal requirements of APE1 and Nfo, comparison of their active site structures surprisingly reveals strong geometric conservation of the catalytic reaction, with APE1 catalytic side chains positioned analogously to Nfo metal positions, suggesting surprising functional equivalence between Nfo metal ions and APE1 residues. The finding that APE1 residues are positioned to substitute for Nfo metal ions is supported by the impact of mutations on activity. Collectively, the results illuminate the activities of residues, metal ions, and active site features for abasic site endonucleases.
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Affiliation(s)
| | - David S Shin
- Scripps Research Institute, La Jolla, California 92037
| | | | - Tadahide Izumi
- University of Kentucky, Lexington, Kentucky 40536; University of Texas Medical Branch, Galveston, Texas 77555
| | | | - Anil K Mantha
- University of Texas Medical Branch, Galveston, Texas 77555
| | | | | | | | | | - Mike E Pique
- Scripps Research Institute, La Jolla, California 92037
| | | | - Kenichi Hitomi
- Lawrence Berkeley National Laboratory, Berkeley, California 94720; Scripps Research Institute, La Jolla, California 92037; Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | | | - Sankar Mitra
- University of Texas Medical Branch, Galveston, Texas 77555
| | - John A Tainer
- Lawrence Berkeley National Laboratory, Berkeley, California 94720; Scripps Research Institute, La Jolla, California 92037.
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41
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Czene A, Németh E, Zóka IG, Jakab-Simon NI, Körtvélyesi T, Nagata K, Christensen HEM, Gyurcsik B. The role of the N-terminal loop in the function of the colicin E7 nuclease domain. J Biol Inorg Chem 2013; 18:309-21. [DOI: 10.1007/s00775-013-0975-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Accepted: 12/31/2012] [Indexed: 01/10/2023]
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42
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Dickey TH, McKercher MA, Wuttke DS. Nonspecific recognition is achieved in Pot1pC through the use of multiple binding modes. Structure 2013; 21:121-132. [PMID: 23201273 PMCID: PMC3545015 DOI: 10.1016/j.str.2012.10.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Revised: 10/26/2012] [Accepted: 10/26/2012] [Indexed: 01/07/2023]
Abstract
Pot1 is the protein responsible for binding to and protecting the 3' single-stranded DNA (ssDNA) overhang at most eukaryotic telomeres. Here, we present the crystal structure of one of the two oligonucleotide/oligosaccharide-binding folds (Pot1pC) that make up the ssDNA-binding domain in S. pombe Pot1. Comparison with the homologous human domain reveals unexpected structural divergence in the mode of ligand binding that explains the differing ligand requirements between species. Despite the presence of apparently base-specific hydrogen bonds, Pot1pC is able to bind a wide range of ssDNA sequences with thermodynamic equivalence. To address how Pot1pC binds ssDNA with little to no specificity, multiple structures of Pot1pC bound to noncognate ssDNA ligands were solved. These structures reveal that this promiscuity is implemented through new binding modes that thermodynamically compensate for base-substitutions through alternate stacking interactions and new H-bonding networks.
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43
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Zhukhlistova NE, Balaev VV, Lyashenko AV, Lashkov AA. Structural aspects of catalytic mechanisms of endonucleases and their binding to nucleic acids. CRYSTALLOGR REP+ 2012. [DOI: 10.1134/s1063774512030236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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44
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Functional specificity of extracellular nucleases of Shewanella oneidensis MR-1. Appl Environ Microbiol 2012; 78:4400-11. [PMID: 22492434 DOI: 10.1128/aem.07895-11] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacterial species such as Shewanella oneidensis MR-1 require extracellular nucleolytic activity for the utilization of extracellular DNA (eDNA) as a source of nutrients and for the turnover of eDNA as a structural matrix component during biofilm formation. We have previously characterized two extracellular nucleases of S. oneidensis MR-1, ExeM and ExeS. Although both are involved in biofilm formation, they are not specifically required for the utilization of eDNA as a nutrient. Here we identified and characterized EndA, a third extracellular nuclease of Shewanella. The heterologously overproduced and purified protein was highly active and rapidly degraded linear and supercoiled DNAs of various origins. Divalent metal ions (Mg(2+) or Mn(2+)) were required for function. endA is cotranscribed with phoA, an extracellular phosphatase, and is not upregulated upon phosphostarvation. Deletion of endA abolished both extracellular degradation of DNA by S. oneidensis MR-1 and the ability to use eDNA as a sole source of phosphorus. PhoA is not strictly required for the exploitation of eDNA as a nutrient. The activity of EndA prevents the formation of large cell aggregates during planktonic growth. However, in contrast to the findings for ExeM, endA deletion had only minor effects on biofilm formation. The findings strongly suggest that the extracellular nucleases of S. oneidensis exert specific functions required under different conditions.
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45
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Lin JLJ, Nakagawa A, Lin CL, Hsiao YY, Yang WZ, Wang YT, Doudeva LG, Skeen-Gaar RR, Xue D, Yuan HS. Structural insights into apoptotic DNA degradation by CED-3 protease suppressor-6 (CPS-6) from Caenorhabditis elegans. J Biol Chem 2012; 287:7110-20. [PMID: 22223640 PMCID: PMC3293555 DOI: 10.1074/jbc.m111.316075] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2011] [Revised: 12/30/2011] [Indexed: 11/06/2022] Open
Abstract
Endonuclease G (EndoG) is a mitochondrial protein that traverses to the nucleus and participates in chromosomal DNA degradation during apoptosis in yeast, worms, flies, and mammals. However, it remains unclear how EndoG binds and digests DNA. Here we show that the Caenorhabditis elegans CPS-6, a homolog of EndoG, is a homodimeric Mg(2+)-dependent nuclease, binding preferentially to G-tract DNA in the optimum low salt buffer at pH 7. The crystal structure of CPS-6 was determined at 1.8 Å resolution, revealing a mixed αβ topology with the two ββα-metal finger nuclease motifs located distantly at the two sides of the dimeric enzyme. A structural model of the CPS-6-DNA complex suggested a positively charged DNA-binding groove near the Mg(2+)-bound active site. Mutations of four aromatic and basic residues: Phe(122), Arg(146), Arg(156), and Phe(166), in the protein-DNA interface significantly reduced the DNA binding and cleavage activity of CPS-6, confirming that these residues are critical for CPS-6-DNA interactions. In vivo transformation rescue experiments further showed that the reduced DNase activity of CPS-6 mutants was positively correlated with its diminished cell killing activity in C. elegans. Taken together, these biochemical, structural, mutagenesis, and in vivo data reveal a molecular basis of how CPS-6 binds and hydrolyzes DNA to promote cell death.
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Affiliation(s)
- Jason L. J. Lin
- From the Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Akihisa Nakagawa
- the Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado 80309
| | - Chia Liang Lin
- From the Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
- the Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 30013, Taiwan, and
| | - Yu-Yuan Hsiao
- From the Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Wei-Zen Yang
- From the Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Yi-Ting Wang
- From the Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Lyudmila G. Doudeva
- From the Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Riley Robert Skeen-Gaar
- the Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado 80309
| | - Ding Xue
- the Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado 80309
| | - Hanna S. Yuan
- From the Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
- the Graduate Institute of Biochemistry and Molecular Biology, National Taiwan University, Taipei 10617, Taiwan
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46
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Midon M, Gimadutdinow O, Meiss G, Friedhoff P, Pingoud A. Chemical Rescue of Active Site Mutants of S. pneumoniae Surface Endonuclease EndA and Other Nucleases of the HNH Family by Imidazole. Chembiochem 2012; 13:713-21. [DOI: 10.1002/cbic.201100775] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2011] [Indexed: 11/08/2022]
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47
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The binding process of a nonspecific enzyme with DNA. Biophys J 2011; 101:1139-47. [PMID: 21889451 DOI: 10.1016/j.bpj.2011.07.016] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2011] [Revised: 06/20/2011] [Accepted: 07/05/2011] [Indexed: 11/22/2022] Open
Abstract
Protein-DNA recognition of a nonspecific complex is modeled to understand the nature of the transient encounter states. We consider the structural and energetic features and the role of water in the DNA grooves in the process of protein-DNA recognition. Here we have used the nuclease domain of colicin E7 (N-ColE7) from Escherichia coli in complex with a 12-bp DNA duplex as the model system to consider how a protein approaches, encounters, and associates with DNA. Multiscale simulation studies using Brownian dynamics and molecular-dynamics simulations were performed to provide the binding process on multiple length- and timescales. We define the encounter states and identified the spatial and orientational aspects. For the molecular length-scales, we used molecular-dynamics simulations. Several intermediate binding states were found, which have different positions and orientations of protein around DNA including major and minor groove orientations. The results show that the contact number and the hydrated interfacial area are measures that facilitate better understanding of sequence-independent protein-DNA binding landscapes and pathways.
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48
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Sharma A, Jenkins KR, Héroux A, Bowman GD. Crystal structure of the chromodomain helicase DNA-binding protein 1 (Chd1) DNA-binding domain in complex with DNA. J Biol Chem 2011; 286:42099-42104. [PMID: 22033927 PMCID: PMC3234930 DOI: 10.1074/jbc.c111.294462] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Revised: 10/20/2011] [Indexed: 11/06/2022] Open
Abstract
Chromatin remodelers are ATP-dependent machines that dynamically alter the chromatin packaging of eukaryotic genomes by assembling, sliding, and displacing nucleosomes. The Chd1 chromatin remodeler possesses a C-terminal DNA-binding domain that is required for efficient nucleosome sliding and believed to be essential for sensing the length of DNA flanking the nucleosome core. The structure of the Chd1 DNA-binding domain was recently shown to consist of a SANT and SLIDE domain, analogous to the DNA-binding domain of the ISWI family, yet the details of how Chd1 recognized DNA were not known. Here we present the crystal structure of the Saccharomyces cerevisiae Chd1 DNA-binding domain in complex with a DNA duplex. The bound DNA duplex is straight, consistent with the preference exhibited by the Chd1 DNA-binding domain for extranucleosomal DNA. Comparison of this structure with the recently solved ISW1a DNA-binding domain bound to DNA reveals that DNA lays across each protein at a distinct angle, yet contacts similar surfaces on the SANT and SLIDE domains. In contrast to the minor groove binding seen for Isw1 and predicted for Chd1, the SLIDE domain of the Chd1 DNA-binding domain contacts the DNA major groove. The majority of direct contacts with the phosphate backbone occur only on one DNA strand, suggesting that Chd1 may not strongly discriminate between major and minor grooves.
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Affiliation(s)
- Amit Sharma
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218
| | - Katherine R Jenkins
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218
| | - Annie Héroux
- Biology Department, Brookhaven National Laboratory, Upton, New York 11973
| | - Gregory D Bowman
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218.
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49
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Bueren-Calabuig JA, Coderch C, Rico E, Jiménez-Ruiz A, Gago F. Mechanistic insight into the catalytic activity of ββα-metallonucleases from computer simulations: Vibrio vulnificus periplasmic nuclease as a test case. Chembiochem 2011; 12:2615-22. [PMID: 22114054 DOI: 10.1002/cbic.201100485] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2011] [Indexed: 11/08/2022]
Abstract
Using information from wild-type and mutant Vibrio vulnificus nuclease (Vvn) and I-PpoI homing endonuclease co-crystallized with different oligodeoxynucleotides, we have built the complex of Vvn with a DNA octamer and carried out a series of simulations to dissect the catalytic mechanism of this metallonuclease in a stepwise fashion. The distinct roles played in the reaction by individual active site residues, the metal cation and water molecules have been clarified by using a combination of classical molecular dynamics simulations and quantum mechanical calculations. Our results strongly support the most parsimonious catalytic mechanism, namely one in which a single water molecule from bulk solvent is used to cleave the phosphodiester bond and protonate the 3'-hydroxylate leaving group.
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Affiliation(s)
- Juan A Bueren-Calabuig
- Department of Pharmacology, Universidad de Alcalá, 28871 Alcalá de Henares, Madrid, Spain
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50
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Korczynska JE, Turkenburg JP, Taylor EJ. The structural characterization of a prophage-encoded extracellular DNase from Streptococcus pyogenes. Nucleic Acids Res 2011; 40:928-38. [PMID: 21948797 PMCID: PMC3258162 DOI: 10.1093/nar/gkr789] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The pathogenic bacterium Group A Streptococcus pyogenes produces several extracellular DNases that have been shown to facilitate invasive infection by evading the human host immune system. DNases degrade the chromatin in neutrophil extracellular traps, enabling the bacterium to evade neutrophil capture. Spd1 is a type I, nonspecific ββα/metal-dependent nuclease from Streptococcus pyogenes, which is encoded by the SF370.1 prophage and is likely to be expressed as a result of prophage induction. We present here the X-ray structure of this DNase in the wild-type and Asn145Ala mutant form. Through structural and sequence alignments as well as mutagenesis studies, we have identified the key residues His121, Asn145 and Glu164, which are crucial for Spd1 nucleolytic activity and shown the active site constellation. Our wild-type structure alludes to the possibility of a catalytically blocked dimeric form of the protein. We have investigated the multimeric nature of Spd1 using size-exclusion chromatography with multi-angle light scattering (SEC-MALLS) in the presence and absence of the divalent metal ion Mg(2+), which suggests that Spd1 exists in a monomeric form in solution.
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Affiliation(s)
- Justyna E Korczynska
- Department of Chemistry, Structural Biology Laboratory, The University of York, YO10 5YW, UK
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