1
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Gao J, Zhu Y, Zhang R, Xu J, Zhou R, Di M, Zhang D, Liang W, Zhou X, Ren X, Li H, Yang Y. Isolation and Characterization of a Novel Phage against Vibrio alginolyticus Belonging to a New Genus. Int J Mol Sci 2024; 25:9132. [PMID: 39201817 PMCID: PMC11354583 DOI: 10.3390/ijms25169132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Revised: 08/16/2024] [Accepted: 08/21/2024] [Indexed: 09/03/2024] Open
Abstract
Vibrio alginolyticus causes substantial economic losses in the aquaculture industry. With the rise of multidrug-resistant Vibrio strains, phages present a promising solution. Here, a novel lytic Vibrio phage, vB_ValC_RH2G (RH2G), that efficiently infects the pathogenic strain V. alginolyticus ATCC 17749T, was isolated from mixed wastewater from an aquatic market in Xiamen, China. Transmission electron microscopy revealed that RH2G has the morphology of Siphoviruses, featuring an icosahedral head (73 ± 2 nm diameter) and long noncontractile tail (142 ± 4 nm). A one-step growth experiment showed that RH2G had a short latent period (10 min) and a burst size of 48 phage particles per infected cell. Additionally, RH2G was highly species-specific and was relatively stable at 4-55 °C and pH 4-10. A genomic analysis showed that RH2G has a 116,749 bp double-stranded DNA genome with 43.76% GC content. The intergenomic similarity between the genome sequence of RH2G and other phages recorded in the GenBank database was below 38.8%, suggesting that RH2G represents a new genus. RH2G did not exhibit any virulence or resistance genes. Its rapid lysis capacity, lytic activity, environmental resilience, and genetic safety suggested that RH2G may be a safe candidate for phage therapy in combatting vibriosis in aquaculture settings.
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Affiliation(s)
- Jie Gao
- Jiangsu Institute of Marine Resources Development, Jiangsu Ocean University, Lianyungang 222005, China; (J.G.); (J.X.); (D.Z.)
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University (Xiang’an), Xiamen 361005, China
| | - Yuang Zhu
- Jiangsu Institute of Marine Resources Development, Jiangsu Ocean University, Lianyungang 222005, China; (J.G.); (J.X.); (D.Z.)
| | - Rui Zhang
- Institute for Advanced Study, Shenzhen University, Shenzhen 518061, China;
| | - Juntian Xu
- Jiangsu Institute of Marine Resources Development, Jiangsu Ocean University, Lianyungang 222005, China; (J.G.); (J.X.); (D.Z.)
| | - Runjie Zhou
- State Key Laboratory of Trophic Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China;
- Centre for Regional Oceans, Department of Ocean Science and Technology, Faculty of Science and Technology, University of Macau, Macau 999078, China
| | - Meiqi Di
- Jiangsu Institute of Marine Resources Development, Jiangsu Ocean University, Lianyungang 222005, China; (J.G.); (J.X.); (D.Z.)
| | - Di Zhang
- Jiangsu Institute of Marine Resources Development, Jiangsu Ocean University, Lianyungang 222005, China; (J.G.); (J.X.); (D.Z.)
- Guangxi Key Laboratory of Beibu Gulf Marine Resources, Environment and Sustainable Development/Ministry of Natural Resources, Beihai 536000, China
| | - Wenxin Liang
- Jiangsu Institute of Marine Resources Development, Jiangsu Ocean University, Lianyungang 222005, China; (J.G.); (J.X.); (D.Z.)
| | - Xing Zhou
- Jiangsu Institute of Marine Resources Development, Jiangsu Ocean University, Lianyungang 222005, China; (J.G.); (J.X.); (D.Z.)
| | - Xing Ren
- Guangxi Key Laboratory of Beibu Gulf Marine Resources, Environment and Sustainable Development/Ministry of Natural Resources, Beihai 536000, China
| | - Huifang Li
- Jiangsu Institute of Marine Resources Development, Jiangsu Ocean University, Lianyungang 222005, China; (J.G.); (J.X.); (D.Z.)
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University (Xiang’an), Xiamen 361005, China
| | - Yunlan Yang
- Institute for Advanced Study, Shenzhen University, Shenzhen 518061, China;
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2
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Stolar T, Pearce BK, Etter M, Truong KN, Ostojić T, Krajnc A, Mali G, Rossi B, Molčanov K, Lončarić I, Meštrović E, Užarević K, Grisanti L. Base-pairing of uracil and 2,6-diaminopurine: from cocrystals to photoreactivity. iScience 2024; 27:109894. [PMID: 38783999 PMCID: PMC11112615 DOI: 10.1016/j.isci.2024.109894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 12/18/2023] [Accepted: 05/01/2024] [Indexed: 05/25/2024] Open
Abstract
We show that the non-canonical nucleobase 2,6-diaminopurine (D) spontaneously base pairs with uracil (U) in water and the solid state without the need to be attached to the ribose-phosphate backbone. Depending on the reaction conditions, D and U assemble in thermodynamically stable hydrated and anhydrated D-U base-paired cocrystals. Under UV irradiation, an aqueous solution of D-U base-pair undergoes photochemical degradation, while a pure aqueous solution of U does not. Our simulations suggest that D may trigger the U photodimerization and show that complementary base-pairing modifies the photochemical properties of nucleobases, which might have implications for prebiotic chemistry.
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Affiliation(s)
- Tomislav Stolar
- Ruđer Bošković Institute, Bijenička c. 54, 10000 Zagreb, Croatia
- Federal Institute for Materials Research and Testing (BAM), Richard-Willstätter-Straße 11, 12489 Berlin, Germany
| | - Ben K.D. Pearce
- Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA
| | - Martin Etter
- Deutsches Elektronen-Synchrotron (DESY), Notkestraße 85, 22607 Hamburg, Germany
| | - Khai-Nghi Truong
- Rigaku Europe SE, Hugenottenallee 167, 63263 Neu-Isenburg, Germany
| | - Tea Ostojić
- Ruđer Bošković Institute, Bijenička c. 54, 10000 Zagreb, Croatia
| | - Andraž Krajnc
- National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Gregor Mali
- National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Barbara Rossi
- Elettra Sincrotrone Trieste, Strada Statale 14 km 163.5, 34149 Trieste, Italy
| | | | - Ivor Lončarić
- Ruđer Bošković Institute, Bijenička c. 54, 10000 Zagreb, Croatia
| | - Ernest Meštrović
- Faculty of Chemical Engineering and Technology, University of Zagreb, Trg Marka Marulića 19, 10000 Zagreb, Croatia
| | | | - Luca Grisanti
- Ruđer Bošković Institute, Bijenička c. 54, 10000 Zagreb, Croatia
- National Research Council - Materials Foundry Institute (CNR-IOM) c/o SISSA (International School for Advanced Studies), Via Bonomea 265, 34136 Trieste, Italy
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3
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Jia X, Fang Z, Kim SC, Ding D, Zhou L, Szostak JW. Diaminopurine in Nonenzymatic RNA Template Copying. J Am Chem Soc 2024; 146:15897-15907. [PMID: 38818863 PMCID: PMC11177312 DOI: 10.1021/jacs.4c02560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 05/07/2024] [Accepted: 05/22/2024] [Indexed: 06/01/2024]
Abstract
In the RNA World before the emergence of an RNA polymerase, nonenzymatic template copying would have been essential for the transmission of genetic information. However, the products of chemical copying with the canonical nucleotides (A, U, C, and G) are heavily biased toward the incorporation of G and C, which form a more stable base pair than A and U. We therefore asked whether replacing adenine (A) with diaminopurine (D) might lead to more efficient and less biased nonenzymatic template copying by making a stronger version of the A:U pair. As expected, primer extension substrates containing D bound to U in the template more tightly than substrates containing A. However, primer extension with D exhibited elevated reaction rates on a C template, leading to concerns about fidelity. Our crystallographic studies revealed the nature of the D:C mismatch by showing that D can form a wobble-type base pair with C. We then asked whether competition with G would decrease the mismatched primer extension. We performed nonenzymatic primer extension with all four activated nucleotides on randomized RNA templates containing all four letters and used deep sequencing to analyze the products. We found that the DUCG genetic system exhibited a more even product distribution and a lower mismatch frequency than the canonical AUCG system. Furthermore, primer extension is greatly reduced following all mismatches, including the D:C mismatch. Our study suggests that D deserves further attention for its possible role in the RNA World and as a potentially useful component of artificial nonenzymatic RNA replication systems.
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Affiliation(s)
- Xiwen Jia
- Department
of Chemistry and Chemical Biology, Harvard
University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
- Department
of Molecular Biology and Center for Computational and Integrative
Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
- Howard
Hughes Medical Institute, Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Ziyuan Fang
- Howard
Hughes Medical Institute, Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Seohyun Chris Kim
- Department
of Chemistry and Chemical Biology, Harvard
University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
- Department
of Molecular Biology and Center for Computational and Integrative
Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
- Department
of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Dian Ding
- Department
of Chemistry and Chemical Biology, Harvard
University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
- Department
of Molecular Biology and Center for Computational and Integrative
Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
| | - Lijun Zhou
- Department
of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Penn
Institute
for RNA Innovation, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Jack W. Szostak
- Howard
Hughes Medical Institute, Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
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4
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Wang B, Bradley KM, Kim MJ, Laos R, Chen C, Gerloff DL, Manfio L, Yang Z, Benner SA. Enzyme-assisted high throughput sequencing of an expanded genetic alphabet at single base resolution. Nat Commun 2024; 15:4057. [PMID: 38744910 PMCID: PMC11094070 DOI: 10.1038/s41467-024-48408-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 04/29/2024] [Indexed: 05/16/2024] Open
Abstract
With just four building blocks, low sequence information density, few functional groups, poor control over folding, and difficulties in forming compact folds, natural DNA and RNA have been disappointing platforms from which to evolve receptors, ligands, and catalysts. Accordingly, synthetic biology has created "artificially expanded genetic information systems" (AEGIS) to add nucleotides, functionality, and information density. With the expected improvements seen in AegisBodies and AegisZymes, the task for synthetic biologists shifts to developing for expanded DNA the same analytical tools available to natural DNA. Here we report one of these, an enzyme-assisted sequencing of expanded genetic alphabet (ESEGA) method to sequence six-letter AEGIS DNA. We show how ESEGA analyses this DNA at single base resolution, and applies it to optimized conditions for six-nucleotide PCR, assessing the fidelity of various DNA polymerases, and extending this to AEGIS components with functional groups. This supports the renewed exploitation of expanded DNA alphabets in biotechnology.
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Affiliation(s)
- Bang Wang
- Foundation for Applied Molecular Evolution, Alachua, FL, USA
- Department of Chemistry, University of Florida, Gainesville, FL, USA
| | | | | | - Roberto Laos
- Foundation for Applied Molecular Evolution, Alachua, FL, USA
| | - Cen Chen
- Foundation for Applied Molecular Evolution, Alachua, FL, USA
| | | | - Luran Manfio
- Foundation for Applied Molecular Evolution, Alachua, FL, USA
| | - Zunyi Yang
- Foundation for Applied Molecular Evolution, Alachua, FL, USA.
- Firebird Biomolecular Sciences, LLC, Alachua, FL, USA.
| | - Steven A Benner
- Foundation for Applied Molecular Evolution, Alachua, FL, USA.
- Firebird Biomolecular Sciences, LLC, Alachua, FL, USA.
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5
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Xun G, Zhu Z, Singh N, Lu J, Jain PK, Zhao H. Harnessing noncanonical crRNA for highly efficient genome editing. Nat Commun 2024; 15:3823. [PMID: 38714643 PMCID: PMC11076584 DOI: 10.1038/s41467-024-48012-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 04/18/2024] [Indexed: 05/10/2024] Open
Abstract
The CRISPR-Cas12a system is more advantageous than the widely used CRISPR-Cas9 system in terms of specificity and multiplexibility. However, its on-target editing efficiency is typically much lower than that of the CRISPR-Cas9 system. Here we improved its on-target editing efficiency by simply incorporating 2-aminoadenine (base Z, which alters canonical Watson-Crick base pairing) into the crRNA to increase the binding affinity between crRNA and its complementary DNA target. The resulting CRISPR-Cas12a (named zCRISPR-Cas12a thereafter) shows an on-target editing efficiency comparable to that of the CRISPR-Cas9 system but with much lower off-target effects than the CRISPR-Cas9 system in mammalian cells. In addition, zCRISPR-Cas12a can be used for precise gene knock-in and highly efficient multiplex genome editing. Overall, the zCRISPR-Cas12a system is superior to the CRISPR-Cas9 system, and our simple crRNA engineering strategy may be extended to other CRISPR-Cas family members as well as their derivatives.
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Affiliation(s)
- Guanhua Xun
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Champaign, IL, 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL, 61801, USA
| | - Zhixin Zhu
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL, 61801, USA
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Champaign, IL, 61801, USA
| | - Nilmani Singh
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL, 61801, USA
| | - Jingxia Lu
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Champaign, IL, 61801, USA
| | - Piyush K Jain
- Department of Chemical Engineering, University of Florida, Gainesville, FL, 32611, USA
| | - Huimin Zhao
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Champaign, IL, 61801, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL, 61801, USA.
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Champaign, IL, 61801, USA.
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6
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Chen S, Lai W, Wang H. Recent advances in high-performance liquid chromatography tandem mass spectrometry techniques for analysis of DNA damage and epigenetic modifications. MUTATION RESEARCH. GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2024; 896:503755. [PMID: 38821674 DOI: 10.1016/j.mrgentox.2024.503755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 03/25/2024] [Accepted: 03/26/2024] [Indexed: 06/02/2024]
Abstract
Environmental exposure would cause DNA damage and epigenetic modification changes, potentially resulting in physiological dysfunction, thereby triggering diseases and even cancer. DNA damage and epigenetic modifications are thus promising biomarkers for environmental exposures and disease states. Benefiting from its high sensitivity and accuracy, high-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) is considered the "gold standard technique" for investigating epigenetic DNA modifications. This review summarizes the recent advancements of UHPLC-MS/MS-based technologies for DNA damage and epigenetic modifications analysis, mainly focusing on the innovative methods developed for UHPLC-MS/MS-related pretreatment technologies containing efficient genomic DNA digestion and effective removal of the inorganic salt matrix, and the new strategies for improving detection sensitivity of liquid chromatography-mass spectrometry. Moreover, we also summarized the novel hyphenated techniques of the advanced UHPLC-MS/MS coupled with other separation and analysis methods for the measurement of DNA damage and epigenetic modification changes in special regions and fragments of chromosomes.
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Affiliation(s)
- Shaokun Chen
- The State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Weiyi Lai
- The State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
| | - Hailin Wang
- The State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Institute of Environment and Health, Institute for Advanced Study, UCAS, Hangzhou 310000, China
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7
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Kang S, Liu Q, Zhang J, Zhang Y, Qi H. 2,6-diaminopurine (Z)-containing toehold probes improve genotyping sensitivity. Biotechnol Bioeng 2024; 121:1384-1393. [PMID: 38151965 DOI: 10.1002/bit.28642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 12/15/2023] [Accepted: 12/15/2023] [Indexed: 12/29/2023]
Abstract
2,6-diaminopurine (Z), a naturally occurring noncanonical nucleotide base found in bacteriophages, enhances DNA hybridization by forming three hydrogen bonds with thymine (T). These distinct biochemical characteristics make it particularly valuable in applications that rely on the thermodynamics of DNA hybridization. However, the practical use of Z-containing oligos is limited by their high production cost and the challenges associated with their synthesis. Here, we developed an efficient and cost-effective approach to synthesize Z-containing oligos of high quality based on an isothermal strand displacement reaction. These newly synthesized Z-oligos are then employed as toehold-blockers in an isothermal genotyping assay designed to detect rare single nucleotide variations (SNV). When compared with their counterparts containing the standard adenine (A) base, the Z-containing blockers significantly enhance the accuracy of identifying SNV. Overall, our innovative methodology in the synthesis of Z-containing oligos, which can also be used to incorporate other unconventional and unnatural bases into oligonucleotides, is anticipated to be adopted for diverse applications, including genotyping, biosensing, and gene therapy.
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Affiliation(s)
- Shaohua Kang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
| | - Qian Liu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
| | - Jie Zhang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
| | - Yan Zhang
- New Cornerstone Science Laboratory, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Hao Qi
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
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8
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Ortiz-Rodríguez LA, Caldero-Rodríguez NE, Seth SK, Díaz-González K, Crespo-Hernández CE. Electronic relaxation mechanism of 9-methyl-2,6-diaminopurine and 2,6-diaminopurine-2'-deoxyribose in solution. Photochem Photobiol 2024; 100:393-403. [PMID: 38018292 DOI: 10.1111/php.13887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 10/16/2023] [Accepted: 11/05/2023] [Indexed: 11/30/2023]
Abstract
Prolonged ultraviolet exposure results in the formation of cyclobutane pyrimidine dimers (CPDs) in RNA. Consequently, prebiotic photolesion repair mechanisms should have played an important role in the maintenance of the structural integrity of primitive nucleic acids. 2,6-Diaminopurine is a prebiotic nucleobase that repairs CPDs with high efficiency when incorporated into polymers. We investigate the electronic deactivation pathways of 2,6-diaminopurine-2'-deoxyribose and 9-methyl-2,6-diaminopurine in acetonitrile and aqueous solution to shed light on the photophysical and excited state properties of the 2,6-diaminopurine chromophore. Evidence is presented that both are photostable compounds exhibiting similar deactivation mechanisms upon the population of the S1 (ππ* La ) state at 290 nm. The mechanism involves deactivation through the C2- and C6-reaction coordinates and >99% of the excited state population decays through nonradiative pathways involving two conical intersections with the ground state. The radiative and nonradiative lifetimes are longer in aqueous solution compared to acetonitrile. While τ1 is similar in both derivatives, τ2 is ca. 1.5-fold longer in 2,6-diaminopurine-2'-deoxyribose due to a more efficient trapping in the S1 (ππ* La ) minimum. Therefore, 2,6-diaminopurine could have accumulated in significant quantities during prebiotic times to be incorporated into non-canonical RNA and play a significant role in its photoprotection.
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Affiliation(s)
| | | | - Sourav Kanti Seth
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio, USA
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9
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Gate G, Williams A, Boldissar S, Šponer J, Szabla R, de Vries M. The tautomer-specific excited state dynamics of 2,6-diaminopurine using resonance-enhanced multiphoton ionization and quantum chemical calculations. Photochem Photobiol 2024; 100:404-418. [PMID: 38124372 DOI: 10.1111/php.13897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 10/25/2023] [Accepted: 11/14/2023] [Indexed: 12/23/2023]
Abstract
2,6-Diaminopurine (2,6-dAP) is an alternative nucleobase that potentially played a role in prebiotic chemistry. We studied its excited state dynamics in the gas phase by REMPI, IR-UV hole burning, and ps pump-probe spectroscopy and performed quantum chemical calculations at the SCS-ADC(2) level of theory to interpret the experimental results. We found the 9H tautomer to have a small barrier to ultrafast relaxation via puckering of its 6-membered ring. The 7H tautomer has a larger barrier to reach a conical intersection and also has a sizable triplet yield. These results are discussed relative to other purines, for which 9H tautomerization appears to be more photostable than 7H and homosubstituted purines appear to be less photostable than heterosubstituted or singly substituted purines.
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Affiliation(s)
- Gregory Gate
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California, USA
| | - Ann Williams
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California, USA
| | - Samuel Boldissar
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California, USA
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacky University Olomouc, Olomouc-Holice, Czech Republic
| | - Rafal Szabla
- Institute of Advanced Materials, Faculty of Chemistry, Wrocław University of Science and Technology, Wrocław, Poland
| | - Mattanjah de Vries
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California, USA
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10
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Gao S, Guan H, Bloomer H, Wich D, Song D, Khirallah J, Ye Z, Zhao Y, Chen M, Xu C, Liu L, Xu Q. Harnessing non-Watson-Crick's base pairing to enhance CRISPR effectors cleavage activities and enable gene editing in mammalian cells. Proc Natl Acad Sci U S A 2024; 121:e2308415120. [PMID: 38150477 PMCID: PMC10786293 DOI: 10.1073/pnas.2308415120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 11/21/2023] [Indexed: 12/29/2023] Open
Abstract
Genomic DNA of the cyanophage S-2L virus is composed of 2-aminoadenine (Z), thymine (T), guanine (G), and cytosine (C), forming the genetic alphabet ZTGC, which violates Watson-Crick base pairing rules. The Z-base has an extra amino group on the two position that allows the formation of a third hydrogen bond with thymine in DNA strands. Here, we explored and expanded applications of this non-Watson-Crick base pairing in protein expression and gene editing. Both ZTGC-DNA (Z-DNA) and ZUGC-RNA (Z-RNA) produced in vitro show detectable compatibility and can be decoded in mammalian cells, including Homo sapiens cells. Z-crRNA can guide CRISPR-effectors SpCas9 and LbCas12a to cleave specific DNA through non-Watson-Crick base pairing and boost cleavage activities compared to A-crRNA. Z-crRNA can also allow for efficient gene and base editing in human cells. Together, our results help pave the way for potential strategies for optimizing DNA or RNA payloads for gene editing therapeutics and give insights to understanding the natural Z-DNA genome.
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Affiliation(s)
- Shuliang Gao
- Department of Biomedical Engineering, Tufts University, Medford, MA02155
| | - Huiwen Guan
- Department of Biomedical Engineering, Tufts University, Medford, MA02155
| | - Hanan Bloomer
- Department of Biomedical Engineering, Tufts University, Medford, MA02155
| | - Douglas Wich
- Department of Biomedical Engineering, Tufts University, Medford, MA02155
| | - Donghui Song
- Department of Biomedical Engineering, Tufts University, Medford, MA02155
| | - Jennifer Khirallah
- Department of Biomedical Engineering, Tufts University, Medford, MA02155
| | - Zhongfeng Ye
- Department of Biomedical Engineering, Tufts University, Medford, MA02155
| | - Yu Zhao
- Department of Biomedical Engineering, Tufts University, Medford, MA02155
| | - Mengting Chen
- Department of Biomedical Engineering, Tufts University, Medford, MA02155
| | - Chutian Xu
- Department of Biomedical Engineering, Tufts University, Medford, MA02155
| | - Lihan Liu
- Department of Biomedical Engineering, Tufts University, Medford, MA02155
| | - Qiaobing Xu
- Department of Biomedical Engineering, Tufts University, Medford, MA02155
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11
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Yudkina AV, Endutkin AV, Diatlova EA, Zharkov DO. A non-canonical nucleotide from viral genomes interferes with the oxidative DNA damage repair system. DNA Repair (Amst) 2024; 133:103605. [PMID: 38042029 DOI: 10.1016/j.dnarep.2023.103605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 09/09/2023] [Accepted: 11/15/2023] [Indexed: 12/04/2023]
Abstract
Oxidative damage is a major source of genomic instability in all organisms with the aerobic metabolism. 8-Oxoguanine (8-oxoG), an abundant oxidized purine, is mutagenic and must be controlled by a dedicated DNA repair system (GO system) that prevents G:C→T:A transversions through an easily formed 8-oxoG:A mispair. In some forms, the GO system is present in nearly all cellular organisms. However, recent studies uncovered many instances of viruses possessing non-canonical nucleotides in their genomes. The features of genome damage and maintenance in such cases of alternative genetic chemistry remain barely explored. In particular, 2,6-diaminopurine (Z nucleotide) completely substitutes for A in the genomes of some bacteriophages, which have evolved pathways for dZTP synthesis and specialized polymerases that prefer dZTP over dATP. Here we address the ability of the GO system enzymes to cope with oxidative DNA damage in the presence of Z in DNA. DNA polymerases of two different structural families (Klenow fragment and RB69 polymerase) were able to incorporate dZMP opposite to 8-oxoG in the template, as well as 8-oxodGMP opposite to Z in the template. Fpg, a 8-oxoguanine-DNA glycosylase that discriminates against 8-oxoG:A mispairs, also did not remove 8-oxoG from 8-oxoG:Z mispairs. However, MutY, a DNA glycosylase that excises A from pairs with 8-oxoG, had a significantly lower activity on Z:8-oxoG mispairs. Similar preferences were observed for Fpg and MutY from different bacterial species (Escherichia coli, Staphylococcus aureus and Lactococcus lactis). Overall, the relaxed control of 8-oxoG in the presence of the Z nucleotide may be a source of additional mutagenesis in the genomes of bacteriophages or bacteria that have survived the viral invasion.
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Affiliation(s)
- Anna V Yudkina
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk 630090, Russia; Novosibirsk State University, 2 Pirogova St., Novosibirsk 630090, Russia
| | - Anton V Endutkin
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk 630090, Russia
| | - Evgeniia A Diatlova
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk 630090, Russia
| | - Dmitry O Zharkov
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk 630090, Russia; Novosibirsk State University, 2 Pirogova St., Novosibirsk 630090, Russia.
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12
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Zhang M, Singh N, Ehmann ME, Zheng L, Zhao H. Incorporation of noncanonical base Z yields modified mRNA with minimal immunogenicity and improved translational capacity in mammalian cells. iScience 2023; 26:107739. [PMID: 37720088 PMCID: PMC10504480 DOI: 10.1016/j.isci.2023.107739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 07/18/2023] [Accepted: 08/23/2023] [Indexed: 09/19/2023] Open
Abstract
Chemically modified mRNAs hold great potential for therapeutic applications in vivo. Currently, the base modification scheme largely preserves the canonical Watson-Crick base pairing, thus missing one mode of mRNA modulation by altering its secondary structure. Here we report the incorporation of base Z (2-aminoadenine) into mRNA to create Z-mRNA with improved translational capacity, decreased cytotoxicity, and drastically reduced immunogenicity compared to the unmodified mRNA in mammalian cells. In particular, the A-to-Z substitution renders modified mRNAs less immunogenic than the state-of-the-art base modification N1-methylpseudouridine (m1ψ) in mouse embryonic fibroblast cells. As a proof of concept, we developed a Z-mRNA-based vaccine against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Antigen-encoding Z-mRNA elicited substantial humoral and cellular immune responses in vivo in mice, albeit with relatively lower efficacy than the state-of-the-art m1ψ-mRNA. Z-mRNA expands the scope of mRNA base modifications toward noncanonical bases and could offer an advantageous platform for mRNA-based therapeutics where minimal immunogenicity is desired.
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Affiliation(s)
- Meng Zhang
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Nilmani Singh
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Mary Elisabeth Ehmann
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Lining Zheng
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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13
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Pallan PS, Lybrand TP, Rozners E, Abramov M, Schepers G, Eremeeva E, Herdewijn P, Egli M. Conformational Morphing by a DNA Analogue Featuring 7-Deazapurines and 5-Halogenpyrimidines and the Origins of Adenine-Tract Geometry. Biochemistry 2023; 62:2854-2867. [PMID: 37694722 PMCID: PMC11062489 DOI: 10.1021/acs.biochem.3c00327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Several efforts are currently directed at the creation and cellular implementation of alternative genetic systems composed of pairing components that are orthogonal to the natural dA/dT and dG/dC base pairs. In an alternative approach, Watson-Crick-type pairing is conserved, but one or all of the four letters of the A, C, G, and T alphabet are substituted by modified components. Thus, all four nucleobases were altered to create halogenated deazanucleic acid (DZA): dA was replaced by 7-deaza-2'-deoxyadenosine (dzA), dG by 7-deaza-2'-deoxyguanosine (dzG), dC by 5-fluoro-2'-deoxycytidine (FdC), and dT by 5-chloro-2'-deoxyuridine (CldU). This base-pairing system was previously shown to retain function in Escherichia coli. Here, we analyze the stability, hydration, structure, and dynamics of a DZA Dickerson-Drew Dodecamer (DDD) of sequence 5'-FdC-dzG-FdC-dzG-dzA-dzA-CldU-CldU-FdC-dzG-FdC-dzG-3'. Contrary to similar stabilities of DDD and DZA-DDD, osmotic stressing revealed a dramatic loss of hydration for the DZA-DDD relative to that for the DDD. The parent DDD 5'-d(CGCGAATTCGCG)-3' features an A-tract, a run of adenosines uninterrupted by a TpA step, and exhibits a hallmark narrow minor groove. Crystal structures─in the presence of RNase H─and MD simulations show increased conformational plasticity ("morphing") of DZA-DDD relative to that of the DDD. The narrow dzA-tract minor groove in one structure widens to resemble that in canonical B-DNA in a second structure. These changes reflect an indirect consequence of altered DZA major groove electrostatics (less negatively polarized compared to that in DNA) and hydration (reduced compared to that in DNA). Therefore, chemical modifications outside the minor groove that lead to collapse of major groove electrostatics and hydration can modulate A-tract geometry.
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Affiliation(s)
- Pradeep S Pallan
- School of Medicine, Department of Biochemistry, and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Terry P Lybrand
- Department of Chemistry and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Eriks Rozners
- Department of Chemistry, Binghamton University, Binghamton, New York 13902, United States
| | - Mikhail Abramov
- Laboratory of Medicinal Chemistry, KU Leuven, Rega Institute for Medical Research, Minderbroedersstraat 10, Leuven 3000, Belgium
| | - Guy Schepers
- Laboratory of Medicinal Chemistry, KU Leuven, Rega Institute for Medical Research, Minderbroedersstraat 10, Leuven 3000, Belgium
| | - Elena Eremeeva
- Laboratory of Medicinal Chemistry, KU Leuven, Rega Institute for Medical Research, Minderbroedersstraat 10, Leuven 3000, Belgium
| | - Piet Herdewijn
- Laboratory of Medicinal Chemistry, KU Leuven, Rega Institute for Medical Research, Minderbroedersstraat 10, Leuven 3000, Belgium
| | - Martin Egli
- School of Medicine, Department of Biochemistry, and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232, United States
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14
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Zhou Y, Wei Y, Jiang L, Jiao X, Zhang Y. Anaerobic phloroglucinol degradation by Clostridium scatologenes. mBio 2023; 14:e0109923. [PMID: 37341492 PMCID: PMC10470551 DOI: 10.1128/mbio.01099-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 05/05/2023] [Indexed: 06/22/2023] Open
Abstract
Polyphenols are abundant in nature, and their anaerobic biodegradation by gut and soil bacteria is a topic of great interest. The O2 requirement of phenol oxidases is thought to explain the microbial inertness of phenolic compounds in anoxic environments, such as peatlands, termed the enzyme latch hypothesis. A caveat of this model is that certain phenols are known to be degraded by strict anaerobic bacteria, although the biochemical basis for this process is incompletely understood. Here, we report the discovery and characterization of a gene cluster in the environmental bacterium Clostridium scatologenes for the degradation phloroglucinol (1,3,5-trihydroxybenzene), a key intermediate in the anaerobic degradation of flavonoids and tannins, which constitute the most abundant polyphenols in nature. The gene cluster encodes the key C-C cleavage enzyme dihydrophloroglucinol cyclohydrolase, as well as (S)-3-hydroxy-5-oxo-hexanoate dehydrogenase and triacetate acetoacetate-lyase, which enable phloroglucinol to be utilized as a carbon and energy source. Bioinformatics studies revealed the presence of this gene cluster in phylogenetically and metabolically diverse gut and environmental bacteria, with potential impacts on human health and carbon preservation in peat soils and other anaerobic environmental niches. IMPORTANCE This study provides novel insights into the microbiota's anaerobic metabolism of phloroglucinol, a critical intermediate in the degradation of polyphenols in plants. Elucidation of this anaerobic pathway reveals enzymatic mechanisms for the degradation of phloroglucinol into short-chain fatty acids and acetyl-CoA, which are used as a carbon and energy source for bacterium growth. Bioinformatics studies suggested the prevalence of this pathway in phylogenetically and metabolically diverse gut and environmental bacteria, with potential impacts on carbon preservation in peat soils and human gut health.
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Affiliation(s)
- Yan Zhou
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu Province, China
| | - Yifeng Wei
- Singapore Institute of Food and Biotechnology Innovation, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Li Jiang
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Xinan Jiao
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu Province, China
| | - Yan Zhang
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
- Department of Chemistry, Tianjin University, Tianjin, China
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15
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Wang H, Ren L, Liang Y, Zheng K, Guo R, Liu Y, Wang Z, Han Y, Zhang X, Shao H, Sung YY, Mok WJ, Wong LL, McMinn A, Wang M. Psychrobacter Phage Encoding an Antibiotics Resistance Gene Represents a Novel Caudoviral Family. Microbiol Spectr 2023; 11:e0533522. [PMID: 37272818 PMCID: PMC10434257 DOI: 10.1128/spectrum.05335-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 05/07/2023] [Indexed: 06/06/2023] Open
Abstract
Psychrobacter is an important bacterial genus that is widespread in Antarctic and marine environments. However, to date, only two complete Psychrobacter phage sequences have been deposited in the NCBI database. Here, the novel Psychrobacter phage vB_PmaS_Y8A, infecting Psychrobacter HM08A, was isolated from sewage in the Qingdao area, China. The morphology of vB_PmaS_Y8A was characterized by transmission electron microscopy, revealing an icosahedral head and long tail. The genomic sequence of vB_PmaS_Y8A is linear, double-stranded DNA with a length of 40,226 bp and 44.1% G+C content, and encodes 69 putative open reading frames. Two auxiliary metabolic genes (AMGs) were identified, encoding phosphoadenosine phosphosulfate reductase and MarR protein. The first AMG uses thioredoxin as an electron donor for the reduction of phosphoadenosine phosphosulfate to phosphoadenosine phosphate. MarR regulates multiple antibiotic resistance mechanisms in Escherichia coli and is rarely found in viruses. No tRNA genes were identified and no lysogeny-related feature genes were detected. However, many similar open reading frames (ORFs) were found in the host genome, which may indicate that Y8A also has a lysogenic stage. Phylogenetic analysis based on the amino acid sequences of whole genomes and comparative genomic analysis indicate that vB_PmaS_Y8A contains a novel genomic architecture similar only to that of Psychrobacter phage pOW20-A, although at a low similarity. vB_PmaS_Y8A represents a new family-level virus cluster with 22 metagenomic assembled viral genomes, here named Minviridae. IMPORTANCE Although Psychrobacter is a well-known and important bacterial genus that is widespread in Antarctic and marine environments, genetic characterization of its phages is still rare. This study describes a novel Psychrobacter phage containing an uncharacterized antibiotic resistance gene and representing a new virus family, Minviridae. The characterization provided here will bolster current understanding of genomes, diversity, evolution, and phage-host interactions in Psychrobacter populations.
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Affiliation(s)
- Hongmin Wang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Linyi Ren
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Yantao Liang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
| | - Kaiyang Zheng
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Ruizhe Guo
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Yundan Liu
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Ziyue Wang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Ying Han
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Xinran Zhang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Hongbing Shao
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
| | - Yeong Yik Sung
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Terengganu, Malaysia
| | - Wen Jye Mok
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Terengganu, Malaysia
| | - Li Lian Wong
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Terengganu, Malaysia
| | - Andrew McMinn
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, Australia
| | - Min Wang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
- Haide College, Ocean University of China, Qingdao, China
- The Affiliated Hospital of Qingdao University, Qingdao, China
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16
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Tong Y, Wu X, Liu Y, Chen H, Zhou Y, Jiang L, Li M, Zhao S, Zhang Y. Alternative Z-genome biosynthesis pathway shows evolutionary progression from Archaea to phage. Nat Microbiol 2023:10.1038/s41564-023-01410-1. [PMID: 37308591 DOI: 10.1038/s41564-023-01410-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 05/11/2023] [Indexed: 06/14/2023]
Abstract
Many bacteriophages evade bacterial immune recognition by substituting adenine with 2,6-diaminopurine (Z) in their genomes. The Z-genome biosynthetic pathway involves PurZ that belongs to the PurA (adenylosuccinate synthetase) family and bears particular similarity to archaeal PurA. However, how the transition of PurA to PurZ occurred during evolution is not clear; recapturing this process may shed light on the origin of Z-containing phages. Here we describe the computer-guided identification and biochemical characterization of a naturally existing PurZ variant, PurZ0, which uses guanosine triphosphate as the phosphate donor rather than the ATP used by PurZ. The atomic resolution structure of PurZ0 reveals a guanine nucleotide binding pocket highly analogous to that of archaeal PurA. Phylogenetic analyses suggest PurZ0 as an intermediate during the evolution of archaeal PurA to phage PurZ. Maintaining the balance of different purines necessitates further evolvement of guanosine triphosphate-using PurZ0 to ATP-using PurZ in adaptation to Z-genome life.
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Affiliation(s)
- Yang Tong
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
- Frontiers Science Center for Synthetic Biology, Ministry of Education, Tianjin University, Tianjin, China
- Key Laboratory of Systems Bioengineering, Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Department of Chemistry, Tianjin University, Tianjin, China
| | - Xinying Wu
- iHuman Institute, ShanghaiTech University, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Yang Liu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Huiyu Chen
- iHuman Institute, ShanghaiTech University, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Yan Zhou
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Li Jiang
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China.
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China.
| | - Suwen Zhao
- iHuman Institute, ShanghaiTech University, Shanghai, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
| | - Yan Zhang
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China.
- Frontiers Science Center for Synthetic Biology, Ministry of Education, Tianjin University, Tianjin, China.
- Key Laboratory of Systems Bioengineering, Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.
- Department of Chemistry, Tianjin University, Tianjin, China.
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17
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Czernecki D, Nourisson A, Legrand P, Delarue M. Reclassification of family A DNA polymerases reveals novel functional subfamilies and distinctive structural features. Nucleic Acids Res 2023; 51:4488-4507. [PMID: 37070157 PMCID: PMC10201439 DOI: 10.1093/nar/gkad242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 03/07/2023] [Accepted: 03/24/2023] [Indexed: 04/19/2023] Open
Abstract
Family A DNA polymerases (PolAs) form an important and well-studied class of extant polymerases participating in DNA replication and repair. Nonetheless, despite the characterization of multiple subfamilies in independent, dedicated works, their comprehensive classification thus far is missing. We therefore re-examine all presently available PolA sequences, converting their pairwise similarities into positions in Euclidean space, separating them into 19 major clusters. While 11 of them correspond to known subfamilies, eight had not been characterized before. For every group, we compile their general characteristics, examine their phylogenetic relationships and perform conservation analysis in the essential sequence motifs. While most subfamilies are linked to a particular domain of life (including phages), one subfamily appears in Bacteria, Archaea and Eukaryota. We also show that two new bacterial subfamilies contain functional enzymes. We use AlphaFold2 to generate high-confidence prediction models for all clusters lacking an experimentally determined structure. We identify new, conserved features involving structural alterations, ordered insertions and an apparent structural incorporation of a uracil-DNA glycosylase (UDG) domain. Finally, genetic and structural analyses of a subset of T7-like phages indicate a splitting of the 3'-5' exo and pol domains into two separate genes, observed in PolAs for the first time.
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Affiliation(s)
- Dariusz Czernecki
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Unit of Architecture and Dynamics of Biological Macromolecules, 75015 Paris, France
- Sorbonne Université, Collège Doctoral, ED 515, 75005 Paris, France
| | - Antonin Nourisson
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Unit of Architecture and Dynamics of Biological Macromolecules, 75015 Paris, France
- Sorbonne Université, Collège Doctoral, ED 515, 75005 Paris, France
| | - Pierre Legrand
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Unit of Architecture and Dynamics of Biological Macromolecules, 75015 Paris, France
- Synchrotron SOLEIL, L’Orme des Merisiers, 91190 Saint-Aubin, France
| | - Marc Delarue
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Unit of Architecture and Dynamics of Biological Macromolecules, 75015 Paris, France
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18
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Zhu X, Li Z, Tong Y, Chen L, Sun T, Zhang W. From natural to artificial cyanophages: Current progress and application prospects. ENVIRONMENTAL RESEARCH 2023; 223:115428. [PMID: 36746205 DOI: 10.1016/j.envres.2023.115428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 02/01/2023] [Accepted: 02/03/2023] [Indexed: 06/18/2023]
Abstract
The over proliferation of harmful cyanobacteria and their cyanotoxins resulted in damaged aquatic ecosystem, polluted drinking water and threatened human health. Cyanophages are a kind of viruses that exclusively infect cyanobacteria, which is considered as a potential strategy to deal with cyanobacterial blooms. Nevertheless, the infecting host range and/or lysis efficiency of natural cyanophages is limited, rising the necessity of constructing non-natural cyanophages via artificial modification, design and synthesis to expand their host range and/or efficiency. The paper firstly reviewed representative cyanophages such as P60 with a short latent period of 1.5 h and S-CBS1 having a burst size up to 200 PFU/cell. To explore the in-silico design principles, we critically summarized the interactions between cyanophages and the hosts, indicating modifying the recognized receptors, enhancing the adsorption ability, changing the lysogeny and excluding the defense of hosts are important for artificial cyanophages. The research progress of synthesizing artificial cyanophages were summarized subsequently, raising the importance of developing genetic manipulation technologies and their rescue strategies in the future. Meanwhile, Large-scale preparation of cyanophages for bloom control is a big challenge. The application prospects of artificial cyanophages besides cyanobacteria bloom control like adaptive evolution and phage therapy were discussed at last. The review will promote the design, synthesis and application of cyanophages for cyanobacteria blooms, which may provide new insights for the related water pollution control and ensuring hydrosphere security.
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Affiliation(s)
- Xiaofei Zhu
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, PR China; Frontier Science Center for Synthetic Biology & Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin, 300072, PR China
| | - Zipeng Li
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300072, China
| | - Yindong Tong
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300072, China
| | - Lei Chen
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, PR China; Frontier Science Center for Synthetic Biology & Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin, 300072, PR China.
| | - Tao Sun
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, PR China; Frontier Science Center for Synthetic Biology & Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin, 300072, PR China; Center for Biosafety Research and Strategy, Tianjin University, Tianjin, 300072, PR China.
| | - Weiwen Zhang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, PR China; Frontier Science Center for Synthetic Biology & Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin, 300072, PR China; Center for Biosafety Research and Strategy, Tianjin University, Tianjin, 300072, PR China
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19
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Thomas CA, Craig JM, Hoshika S, Brinkerhoff H, Huang JR, Abell SJ, Kim HC, Franzi MC, Carrasco JD, Kim HJ, Smith DC, Gundlach JH, Benner SA, Laszlo AH. Assessing Readability of an 8-Letter Expanded Deoxyribonucleic Acid Alphabet with Nanopores. J Am Chem Soc 2023; 145:8560-8568. [PMID: 37036666 DOI: 10.1021/jacs.3c00829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
Abstract
Chemists have now synthesized new kinds of DNA that add nucleotides to the four standard nucleotides (guanine, adenine, cytosine, and thymine) found in standard Terran DNA. Such "artificially expanded genetic information systems" are today used in molecular diagnostics; to support directed evolution to create medically useful receptors, ligands, and catalysts; and to explore issues related to the early evolution of life. Further applications are limited by the inability to directly sequence DNA containing nonstandard nucleotides. Nanopore sequencing is well-suited for this purpose, as it does not require enzymatic synthesis, amplification, or nucleotide modification. Here, we take the first steps to realize nanopore sequencing of an 8-letter "hachimoji" expanded DNA alphabet by assessing its nanopore signal range using the MspA (Mycobacterium smegmatis porin A) nanopore. We find that hachimoji DNA exhibits a broader signal range in nanopore sequencing than standard DNA alone and that hachimoji single-base substitutions are distinguishable with high confidence. Because nanopore sequencing relies on a molecular motor to control the motion of DNA, we then assessed the compatibility of the Hel308 motor enzyme with nonstandard nucleotides by tracking the translocation of single Hel308 molecules along hachimoji DNA, monitoring the enzyme kinetics and premature enzyme dissociation from the DNA. We find that Hel308 is compatible with hachimoji DNA but dissociates more frequently when walking over C-glycoside nucleosides, compared to N-glycosides. C-glycocide nucleosides passing a particular site within Hel308 induce a higher likelihood of dissociation. This highlights the need to optimize nanopore sequencing motors to handle different glycosidic bonds. It may also inform designs of future alternative DNA systems that can be sequenced with existing motors and pores.
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Affiliation(s)
- Christopher A Thomas
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
| | - Jonathan M Craig
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
| | - Shuichi Hoshika
- Foundation for Applied Molecular Evolution, Alachua, Florida 32615, United States
| | - Henry Brinkerhoff
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
| | - Jesse R Huang
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
| | - Sarah J Abell
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
| | - Hwanhee C Kim
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
| | - Michaela C Franzi
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
| | - Jessica D Carrasco
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
| | - Hyo-Joong Kim
- Foundation for Applied Molecular Evolution, Alachua, Florida 32615, United States
| | - Drew C Smith
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
| | - Jens H Gundlach
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
| | - Steven A Benner
- Foundation for Applied Molecular Evolution, Alachua, Florida 32615, United States
| | - Andrew H Laszlo
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
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20
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Yuan X, Huang Z, Zhu Z, Zhang J, Wu Q, Xue L, Wang J, Ding Y. Recent advances in phage defense systems and potential overcoming strategies. Biotechnol Adv 2023; 65:108152. [PMID: 37037289 DOI: 10.1016/j.biotechadv.2023.108152] [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: 12/23/2022] [Revised: 04/05/2023] [Accepted: 04/06/2023] [Indexed: 04/12/2023]
Abstract
Bacteriophages are effective in the prevention and control of bacteria, and many phage products have been permitted and applied in the field. Because bacteriophages are expected to replace other antimicrobial agents like antibiotics, the antibacterial effect of bacteriophage has attracted widespread attention. Recently, the diversified defense systems discovered in the target host have become potential threats to the continued effective application of phages. Therefore, a systematic summary and in-depth illustration of the interaction between phages and bacteria is conducive to the development of this biological control approach. In this review, we introduce different defense systems in bacteria against phages and emphasize newly discovered defense mechanisms in recent years. Additionally, we draw attention to the striking resemblance between defense system genes and antibiotic resistance genes, which raises concerns about the potential transfer of phage defense systems within bacterial populations and its future impact on phage efficacy. Thus, attention should be given to the effects of phage defense genes in practical applications. This article is not exhaustive, but strategies to overcome phage defense systems are also discussed to further promote more efficient use of phages.
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Affiliation(s)
- Xiaoming Yuan
- State Key Laboratory of Applied Microbiology Southern China, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Safety and Health, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; Department of Food Science & Engineering, Jinan University, Guangzhou 510632, China
| | - Zhichao Huang
- State Key Laboratory of Applied Microbiology Southern China, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Safety and Health, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; Department of Food Science & Engineering, Jinan University, Guangzhou 510632, China
| | - Zhenjun Zhu
- Department of Food Science & Engineering, Jinan University, Guangzhou 510632, China
| | - Jumei Zhang
- State Key Laboratory of Applied Microbiology Southern China, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Safety and Health, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Qingping Wu
- State Key Laboratory of Applied Microbiology Southern China, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Safety and Health, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Liang Xue
- State Key Laboratory of Applied Microbiology Southern China, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Safety and Health, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Juan Wang
- State Key Laboratory of Applied Microbiology Southern China, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Safety and Health, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; College of Food Science, South China Agricultural University, Guangzhou 510432, China.
| | - Yu Ding
- Department of Food Science & Engineering, Jinan University, Guangzhou 510632, China.
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21
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Nielsen TK, Forero-Junco LM, Kot W, Moineau S, Hansen LH, Riber L. Detection of nucleotide modifications in bacteria and bacteriophages: Strengths and limitations of current technologies and software. Mol Ecol 2023; 32:1236-1247. [PMID: 36052951 DOI: 10.1111/mec.16679] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 08/25/2022] [Accepted: 08/30/2022] [Indexed: 11/27/2022]
Abstract
RNA and DNA modifications occur in eukaryotes and prokaryotes, as well as in their viruses, and serve a wide range of functions, from gene regulation to nucleic acid protection. Although the first nucleotide modification was discovered almost 100 years ago, new and unusual modifications are still being described. Nucleotide modifications have also received more attention lately because of their increased significance, but also because new sequencing approaches have eased their detection. Chiefly, third generation sequencing platforms PacBio and Nanopore offer direct detection of modified bases by measuring deviations of the signals. These unusual modifications are especially prevalent in bacteriophage genomes, the viruses of bacteria, where they mostly appear to protect DNA against degradation from host nucleases. In this Opinion article, we highlight and discuss current approaches to detect nucleotide modifications, including hardwares and softwares, and look onward to future applications, especially for studying unusual, rare, or complex genome modifications in bacteriophages. The ability to distinguish between several types of nucleotide modifications may even shed new light on metagenomic studies.
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Affiliation(s)
- Tue Kjaergaard Nielsen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | | | - Witold Kot
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Sylvain Moineau
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec, Quebec, Canada
| | - Lars Hestbjerg Hansen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Leise Riber
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
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22
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Sun Q, Shen L, Zhang BL, Yu J, Wei F, Sun Y, Chen W, Wang S. Advance on Engineering of Bacteriophages by Synthetic Biology. Infect Drug Resist 2023; 16:1941-1953. [PMID: 37025193 PMCID: PMC10072152 DOI: 10.2147/idr.s402962] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 03/16/2023] [Indexed: 04/03/2023] Open
Abstract
Since bacteriophages (phages) were firstly reported at the beginning of the 20th century, the study on them experiences booming-fading-emerging with discovery and overuse of antibiotics. Although they are the hotspots for therapy of antibiotic-resistant strains nowadays, natural phage applications encounter some challenges such as limited host range and bacterial resistance to phages. Synthetic biology, one of the most dramatic directions in the recent 20-years study of microbiology, has generated numerous methods and tools and has contributed a lot to understanding phage evolution, engineering modification, and controlling phage-bacteria interactions. In order to better modify and apply phages by using synthetic biology techniques in the future, in this review, we comprehensively introduce various strategies on engineering or modification of phage genome and rebooting of recombinant phages, summarize the recent researches and potential directions of phage synthetic biology, and outline the current application of engineered phages in practice.
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Affiliation(s)
- Qingqing Sun
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, Provincial Key Laboratory of Biotechnology of Shaanxi Province, the College of Life Sciences, Northwest University, Xi’an, 710069, People’s Republic of China
| | - Lixin Shen
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, Provincial Key Laboratory of Biotechnology of Shaanxi Province, the College of Life Sciences, Northwest University, Xi’an, 710069, People’s Republic of China
| | - Bai-Ling Zhang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, 330006, People’s Republic of China
| | - Jiaoyang Yu
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, Provincial Key Laboratory of Biotechnology of Shaanxi Province, the College of Life Sciences, Northwest University, Xi’an, 710069, People’s Republic of China
- Clinical Research Center, the Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, 210003, People’s Republic of China
| | - Fu Wei
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, Provincial Key Laboratory of Biotechnology of Shaanxi Province, the College of Life Sciences, Northwest University, Xi’an, 710069, People’s Republic of China
| | - Yanmei Sun
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, Provincial Key Laboratory of Biotechnology of Shaanxi Province, the College of Life Sciences, Northwest University, Xi’an, 710069, People’s Republic of China
| | - Wei Chen
- Clinical Research Center, the Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, 210003, People’s Republic of China
- The Clinical Infectious Disease Center of Nanjing, Nanjing, 210003, People’s Republic of China
- Correspondence: Wei Chen; Shiwei Wang, Email ;
| | - Shiwei Wang
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, Provincial Key Laboratory of Biotechnology of Shaanxi Province, the College of Life Sciences, Northwest University, Xi’an, 710069, People’s Republic of China
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23
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McQuaid K, Pipier A, Cardin C, Monchaud D. Interactions of small molecules with DNA junctions. Nucleic Acids Res 2022; 50:12636-12656. [PMID: 36382400 PMCID: PMC9825177 DOI: 10.1093/nar/gkac1043] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 10/13/2022] [Accepted: 10/23/2022] [Indexed: 11/17/2022] Open
Abstract
The four natural DNA bases (A, T, G and C) associate in base pairs (A=T and G≡C), allowing the attached DNA strands to assemble into the canonical double helix of DNA (or duplex-DNA, also known as B-DNA). The intrinsic supramolecular properties of nucleobases make other associations possible (such as base triplets or quartets), which thus translates into a diversity of DNA structures beyond B-DNA. To date, the alphabet of DNA structures is ripe with approximately 20 letters (from A- to Z-DNA); however, only a few of them are being considered as key players in cell biology and, by extension, valuable targets for chemical biology intervention. In the present review, we summarise what is known about alternative DNA structures (what are they? When, where and how do they fold?) and proceed to discuss further about those considered nowadays as valuable therapeutic targets. We discuss in more detail the molecular tools (ligands) that have been recently developed to target these structures, particularly the three- and four-way DNA junctions, in order to intervene in the biological processes where they are involved. This new and stimulating chemical biology playground allows for devising innovative strategies to fight against genetic diseases.
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Affiliation(s)
- Kane T McQuaid
- Department of Chemistry, University of Reading, Whiteknights, Reading RG6 6AD, UK
| | - Angélique Pipier
- Institut de Chimie Moléculaire de l’Université de Bourgogne (ICMUB), CNRS UMR 6302, UBFC Dijon, 21078 Dijon, France
| | - Christine J Cardin
- Department of Chemistry, University of Reading, Whiteknights, Reading RG6 6AD, UK
| | - David Monchaud
- Institut de Chimie Moléculaire de l’Université de Bourgogne (ICMUB), CNRS UMR 6302, UBFC Dijon, 21078 Dijon, France
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24
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Peters DL, Harris G, Davis CM, Dennis JJ, Chen W. Bacteriophage Isolation, Purification, and Characterization Techniques Against Ubiquitous Opportunistic Pathogens. Curr Protoc 2022; 2:e594. [PMID: 36383057 DOI: 10.1002/cpz1.594] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Healthcare-associated infection with "ESKAPE" pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) is a global health crisis due to their extensive intrinsic antibiotic resistance and the ability to quickly acquire resistance determinants. Alternative treatment options are required to combat this crisis, and one possibility is the use of bacteriophages, or viruses that strictly infect the pathogenic bacteria. Currently, there is a renaissance in research and development into the use of phages to target multi-, extensively, and pan-resistant bacterial infections in humans, known as phage therapy. Using A. baumannii as an example, this article describes the isolation and purification of bacteriophages from sewage and soil samples, as well as general methods used in phage research such as precipitation of phages using polyethylene glycol, host range analysis, single-cell burst size determination, DNA extraction, and restriction fragment length polymorphism analysis. © 2022 National Research Council Canada. Current Protocols © 2022 Wiley Periodicals LLC. Reproduced with the permission of the Minister of Innovation, Science, and Industry. Basic Protocol 1: Isolation of bacteriophages against A. baumannii from sewage samples Alternate Protocol 1: Isolation of bacteriophages against A. baumannii from soil samples Support Protocol 1: Titering a bacteriophage stock Basic Protocol 2: Purification of phage to an axenic working stock Support Protocol 2: Liquid propagation of bacteriophage Basic Protocol 3: Host range analysis using the spot plate method Basic Protocol 4: Single burst size analysis Alternate Protocol 2: One-step growth curve Basic Protocol 5: Precipitation of bacteriophage using PEG 6000 Basic Protocol 6: DNA extraction from dsDNA bacteriophages Basic Protocol 7: Restriction fragment length polymorphism analysis of novel phage genomes.
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Affiliation(s)
- Danielle L Peters
- Human Health Therapeutics (HHT), National Research Council Canada, Ottawa, Ontario, Canada
| | - Greg Harris
- Human Health Therapeutics (HHT), National Research Council Canada, Ottawa, Ontario, Canada
| | - Carly M Davis
- Human Health Therapeutics (HHT), National Research Council Canada, Ottawa, Ontario, Canada
- Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Jonathan J Dennis
- Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Wangxue Chen
- Human Health Therapeutics (HHT), National Research Council Canada, Ottawa, Ontario, Canada
- Department of Biology, Brock University, St. Catharines, Ontario, Canada
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25
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Abstract
In this article, the evolution of viruses is analyzed in terms of their complexity. It is shown that the evolution of viruses is a partially directed process. The participation of viruses and mobile genetic elements in the evolution of other organisms by integration into the genome is also an a priori directed process. The high variability of genomes (including the genes of antibodies), which differs by orders of magnitude for various viruses and their hosts, is not a random process but is the result of the action of a molecular genetic control system. Herein, a model of partially directed evolution of viruses is proposed. Throughout the life cycle of viruses, there is an interaction of complex biologically important molecules that cannot be explained on the basis of classic laws. The interaction of a virus with a cell is essentially a quantum event, including selective long-range action. Such an interaction can be interpreted as the "remote key-lock" principle. In this article, a model of the interaction of biologically important viral molecules with cellular molecules based on nontrivial quantum interactions is proposed. Experiments to test the model are also proposed.
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26
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Špaček J, Benner SA. Agnostic Life Finder (ALF) for Large-Scale Screening of Martian Life During In Situ Refueling. ASTROBIOLOGY 2022; 22:1255-1263. [PMID: 35796703 DOI: 10.1089/ast.2021.0070] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Before the first humans depart for Mars in the next decade, hundreds of tons of martian water-ice must be harvested to produce propellant for the return vehicle, a process known as in situ resource utilization (ISRU). We describe here an instrument, the Agnostic Life Finder (ALF), that is an inexpensive life-detection add-on to ISRU. ALF exploits a well-supported view that informational genetic biopolymers in life in water must have two structural features: (1) Informational biopolymers must carry a repeating charge; they must be polyelectrolytes. (2) Their building blocks must fit into an aperiodic crystal structure; the building blocks must be size-shape regular. ALF exploits the first structural feature to extract polyelectrolytes from ∼10 cubic meters of mined martian water by applying a voltage gradient perpendicularly to the water's flow. This gradient diverts polyelectrolytes from the flow toward their respective electrodes (polyanions to the anode, polycations to the cathode), where they are captured in cartridges before they encounter the electrodes. There, they can later be released to analyze their building blocks, for example, by mass spectrometry or nanopore. Upstream, martian cells holding martian informational polyelectrolytes are disrupted by ultrasound. To manage the (unknown) conductivity of the water due to the presence of salts, the mined water is preconditioned by electrodialysis using porous membranes. ALF uses only resources and technology that must already be available for ISRU. Thus, life detection is easily and inexpensively integrated into SpaceX or NASA ISRU missions.
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Affiliation(s)
- Jan Špaček
- Firebird Biomolecular Sciences, LLC, Alachua, Florida, USA
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27
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Hoshika S, Shukla MS, Benner SA, Georgiadis MM. Visualizing "Alternative Isoinformational Engineered" DNA in A- and B-Forms at High Resolution. J Am Chem Soc 2022; 144:15603-15611. [PMID: 35969672 DOI: 10.1021/jacs.2c05255] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A fundamental property of DNA built from four informational nucleotide units (GCAT) is its ability to adopt different helical forms within the context of the Watson-Crick pair. Well-characterized examples include A-, B-, and Z-DNA. For this study, we created an isoinformational biomimetic polymer, built (like standard DNA) from four informational "letters", but with the building blocks being artificial. This ALternative Isoinformational ENgineered (ALIEN) DNA was hypothesized to support two nucleobase pairs, the P:Z pair matching 2-amino-imidazo-[1,2a]-1,3,5-triazin-[8H]-4-one with 6-amino-3-5-nitro-1H-pyridin-2-one and the B:S pair matching 6-amino-4-hydroxy-5-1H-purin-2-one with 3-methyl-6-amino-pyrimidin-2-one. We report two structures of ALIEN DNA duplexes at 1.2 Å resolution and a third at 1.65 Å. All of these are built from a single self-complementary sequence (5'-CTSZZPBSBSZPPBAG) that includes 12 consecutive ALIEN nucleotides. We characterized the helical, nucleobase pair, and dinucleotide step parameters of ALIEN DNA in these structures. In addition to showing that ALIEN pairs retain basic Watson-Crick pairing geometry, two of the ALIEN DNA structures are characterized as A-form DNA and one as B-form DNA. We identified parameters that map differences effecting the transition between the two helical forms; these same parameters distinguish helical forms of isoinformational natural DNA. Collectively, our analyses suggest that ALIEN DNA retains essential structural features of natural DNA, not only its information density and Watson-Crick pairing but also its ability to adopt two canonical forms.
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Affiliation(s)
- Shuichi Hoshika
- Foundation for Molecular Evolution, 13709 Progress Boulevard, No. 7, Alachua, Florida 32615, United States
| | - Madhura S Shukla
- Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, 635 Barnhill Dr., Indianapolis, Indiana 46202, United States
| | - Steven A Benner
- Foundation for Molecular Evolution, 13709 Progress Boulevard, No. 7, Alachua, Florida 32615, United States
| | - Millie M Georgiadis
- Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, 635 Barnhill Dr., Indianapolis, Indiana 46202, United States
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28
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Zhao F, Wei Y, Wang X, Zhou Y, Tong Y, Ang EL, Liu S, Zhao H, Zhang Y. Enzymatic Synthesis of the Unnatural Nucleotide 2'-Deoxyisoguanosine 5'-Monophosphate. Chembiochem 2022; 23:e202200295. [PMID: 35959532 DOI: 10.1002/cbic.202200295] [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: 05/24/2022] [Revised: 08/05/2022] [Indexed: 11/05/2022]
Abstract
Naturally occurring DNA contains four canonical bases, forming two Watson-Crick base pairs (adenine-thymine, guanine-cytosine). Efforts over the past decades have led to the development of several unnatural base pairs, enabling the synthesis of unnatural DNA with an expanded genetic alphabet. The engineering of organisms capable of de novo biosynthesis of unnatural DNA would have significant technological and philosophical implications, but remains a challenge. Here we report the enzymatic conversion of 2'-deoxyxanthosine 5'-monophosphate (dXMP) into deoxyisoguanosine monophosphate (dBMP), a precursor of the unnatural isoguanine-isocytosine base pair. The reaction is catalyzed by the bacteriophage enzyme PurZ and bacterial PurB, and is a key addition to the toolbox for de novo biosynthesis of unnatural DNA.
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Affiliation(s)
- Fuping Zhao
- Tianjin University, School of Pharmacology Science and Technology, CHINA
| | - Yifeng Wei
- Agency for Science Technology and Research, Singapore Institute of Food and Biotechnology Innovation, SINGAPORE
| | - Xinyu Wang
- Tianjin University, School of Pharmacology Science and Technology, CHINA
| | - Yan Zhou
- Tianjin University, School of Pharmacology Science and Technology, CHINA
| | - Yang Tong
- Tianjin University, School of Pharmacology Science and Technology, CHINA
| | - Ee Lui Ang
- Agency for Science Technology and Research, Singapore Institute of Food and Biotechnology Innovation, SINGAPORE
| | - Shengnan Liu
- Tianjin University, Institute of Molecular Plus, CHINA
| | - Huimin Zhao
- Agency for Science Technology and Research, Singapore Institute of Food and Biotechnology Innovation, SINGAPORE
| | - Yan Zhang
- Tianjin University, School of Pharmaceutical Science and Technology, Office 417-4, 92 Weijin Rd, Nankai District, 300072, Tianjin, CHINA
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29
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Casjens SR, Davidson AR, Grose JH. The small genome, virulent, non-contractile tailed bacteriophages that infect Enterobacteriales hosts. Virology 2022; 573:151-166. [DOI: 10.1016/j.virol.2022.06.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 05/07/2022] [Accepted: 06/01/2022] [Indexed: 11/25/2022]
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30
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Tan Y, You C, Park J, Kim HS, Guo S, Schärer OD, Wang Y. Transcriptional Perturbations of 2,6-Diaminopurine and 2-Aminopurine. ACS Chem Biol 2022; 17:1672-1676. [PMID: 35700389 DOI: 10.1021/acschembio.2c00369] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
2,6-Diaminopurine (Z) is a naturally occurring adenine (A) analog that bacteriophages employ in place of A in their genetic alphabet. Recent discoveries of biogenesis pathways of Z in bacteriophages have stimulated substantial research interest in this DNA modification. Here, we systematically examined the effects of Z on the efficiency and fidelity of DNA transcription. Our results showed that Z exhibited no mutagenic yet substantial inhibitory effects on transcription mediated by purified T7 RNA polymerase and by human RNA polymerase II in HeLa nuclear extracts and in human cells. A structurally related adenine analog, 2-aminopurine (2AP), strongly blocked T7 RNA polymerase but did not impede human RNA polymerase II in vitro or in human cells, where no mutant transcript could be detected. The lack of mutagenic consequence and the presence of a strong blockage effect of Z on transcription suggest a role of Z in transcriptional regulation. Z is also subjected to removal by transcription-coupled nucleotide-excision repair (TC-NER), but not global-genome NER in human cells. Our findings provide new insight into the effects of Z on transcription and its potential biological functions.
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Affiliation(s)
| | | | - Jiyeong Park
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
| | - Hyun Suk Kim
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
| | | | - Orlando D Schärer
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea.,Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
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31
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Kminek G, Benardini JN, Brenker FE, Brooks T, Burton AS, Dhaniyala S, Dworkin JP, Fortman JL, Glamoclija M, Grady MM, Graham HV, Haruyama J, Kieft TL, Koopmans M, McCubbin FM, Meyer MA, Mustin C, Onstott TC, Pearce N, Pratt LM, Sephton MA, Siljeström S, Sugahara H, Suzuki S, Suzuki Y, van Zuilen M, Viso M. COSPAR Sample Safety Assessment Framework (SSAF). ASTROBIOLOGY 2022; 22:S186-S216. [PMID: 35653292 DOI: 10.1089/ast.2022.0017] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The Committee on Space Research (COSPAR) Sample Safety Assessment Framework (SSAF) has been developed by a COSPAR appointed Working Group. The objective of the sample safety assessment would be to evaluate whether samples returned from Mars could be harmful for Earth's systems (e.g., environment, biosphere, geochemical cycles). During the Working Group's deliberations, it became clear that a comprehensive assessment to predict the effects of introducing life in new environments or ecologies is difficult and practically impossible, even for terrestrial life and certainly more so for unknown extraterrestrial life. To manage expectations, the scope of the SSAF was adjusted to evaluate only whether the presence of martian life can be excluded in samples returned from Mars. If the presence of martian life cannot be excluded, a Hold & Critical Review must be established to evaluate the risk management measures and decide on the next steps. The SSAF starts from a positive hypothesis (there is martian life in the samples), which is complementary to the null-hypothesis (there is no martian life in the samples) typically used for science. Testing the positive hypothesis includes four elements: (1) Bayesian statistics, (2) subsampling strategy, (3) test sequence, and (4) decision criteria. The test sequence capability covers self-replicating and non-self-replicating biology and biologically active molecules. Most of the investigations associated with the SSAF would need to be carried out within biological containment. The SSAF is described in sufficient detail to support planning activities for a Sample Receiving Facility (SRF) and for preparing science announcements, while at the same time acknowledging that further work is required before a detailed Sample Safety Assessment Protocol (SSAP) can be developed. The three major open issues to be addressed to optimize and implement the SSAF are (1) setting a value for the level of assurance to effectively exclude the presence of martian life in the samples, (2) carrying out an analogue test program, and (3) acquiring relevant contamination knowledge from all Mars Sample Return (MSR) flight and ground elements. Although the SSAF was developed specifically for assessing samples from Mars in the context of the currently planned NASA-ESA MSR Campaign, this framework and the basic safety approach are applicable to any other Mars sample return mission concept, with minor adjustments in the execution part related to the specific nature of the samples to be returned. The SSAF is also considered a sound basis for other COSPAR Planetary Protection Category V, restricted Earth return missions beyond Mars. It is anticipated that the SSAF will be subject to future review by the various MSR stakeholders.
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Affiliation(s)
- Gerhard Kminek
- European Space Agency, Mars Exploration Group, Noordwijk, The Netherlands
| | - James N Benardini
- NASA Headquarters, Office of Planetary Protection, Washington, DC, USA
| | - Frank E Brenker
- Goethe University, Department of Geoscience, Frankfurt, Germany
| | - Timothy Brooks
- UK Health Security Agency, Rare & Imported Pathogens Laboratory, Salisbury, UK
| | - Aaron S Burton
- NASA Johnson Space Center, Astromaterials Research and Exploration Science Division, Houston, Texas, USA
| | - Suresh Dhaniyala
- Clarkson University, Department of Mechanical and Aeronautical Engineering, Potsdam, New York, USA
| | - Jason P Dworkin
- NASA Goddard Space Flight Center, Solar System Exploration Division, Greenbelt, Maryland, USA
| | - Jeffrey L Fortman
- Security Programs, Engineering Biology Research Consortium, Emeryville, USA
| | - Mihaela Glamoclija
- Rutgers University, Department of Earth and Environmental Sciences, Newark, New Jersey, USA
| | - Monica M Grady
- The Open University, Faculty of Science, Technology, Engineering & Mathematics, Milton Keynes, UK
| | - Heather V Graham
- NASA Goddard Space Flight Center, Astrochemistry Laboratory, Greenbelt, Maryland, USA
| | - Junichi Haruyama
- Japan Aerospace Exploration Agency (JAXA), Institute of Space and Astronautical Science (ISAS), Chofu, Tokyo, Japan
| | - Thomas L Kieft
- New Mexico Institute of Mining and Technology, Biology Department, Socorro, New Mexico, USA
| | - Marion Koopmans
- Erasmus University Medical Centre, Department of Viroscience, Rotterdam, The Netherlands
| | - Francis M McCubbin
- NASA Johnson Space Center, Astromaterials Research and Exploration Science Division, Houston, Texas, USA
| | - Michael A Meyer
- NASA Headquarters, Planetary Science Division, Washington, DC, USA
| | | | - Tullis C Onstott
- Princeton University, Department of Geosciences, Princeton, New Jersey, USA
| | - Neil Pearce
- London School of Hygiene & Tropical Medicine, Department of Medical Statistics, London, UK
| | - Lisa M Pratt
- Indiana University Bloomington, Earth and Atmospheric Sciences, Emeritus, Bloomington, Indiana, USA
| | - Mark A Sephton
- Imperial College London, Department of Earth Science & Engineering, London, UK
| | - Sandra Siljeström
- RISE, Research Institutes of Sweden, Department of Methodology, Textiles and Medical Technology, Stockholm, Sweden
| | - Haruna Sugahara
- Japan Aerospace Exploration Agency (JAXA), Institute of Space and Astronautical Science, Sagamihara Kanagawa, Japan
| | - Shino Suzuki
- Japan Aerospace Exploration Agency (JAXA), Institute of Space and Astronautical Science, Sagamihara Kanagawa, Japan
| | - Yohey Suzuki
- University of Tokyo, Graduate School of Science, Tokyo, Japan
| | - Mark van Zuilen
- Université de Paris, Institut de Physique du Globe de Paris, Paris, France
- European Institute for Marine Studies (IUEM), CNRS-UMR6538 Laboratoire Geo-Ocean, Plouzané, France
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32
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Kaminski PA. [A family of bacteriophages uses an expanded genetic alphabet]. Med Sci (Paris) 2022; 38:374-380. [PMID: 35485898 DOI: 10.1051/medsci/2022041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Bacteriophage genomes are the richest source of modified nucleobases of any life form. Of these, 2,6-diaminopurine (2-aminoadénine) that pairs with thymine by forming three hydrogen bonds is the only one violating Watson and Crick's base pairing. 2,6-diaminopurine (2-aminoadénine), initially found in the cyanophage S-2L, is more widespread than expected and has also been detected in bacteriophage infecting Gram-negative and Gram-positive bacteria. The biosynthetic pathway for aminoadenine containing DNA as well as the exclusion of adenine are now elucidated. This example of a natural deviation from the DNA canonical nucleotides represents only one of the possibilities explored by nature and provides a proof of concept for the synthetic biology of non-canonical nucleic acids.
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Affiliation(s)
- Pierre-Alexandre Kaminski
- Institut Pasteur, Université de Paris, CNRS UMR2001, Biologie des bactéries pathogènes à Gram-positif, F-75015, Paris, France
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Wang Z, Zhang Y, Yin Y, Liu J, Li P, Zhao Y, Bai D, Zhao H, Han X, Chen Q. High-Strength and Injectable Supramolecular Hydrogel Self-Assembled by Monomeric Nucleoside for Tooth-Extraction Wound Healing. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2108300. [PMID: 35066934 DOI: 10.1002/adma.202108300] [Citation(s) in RCA: 60] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 01/18/2022] [Indexed: 02/05/2023]
Abstract
Hydrogels with high mechanical strength and injectability have attracted extensive attention in biomedical and tissue engineering. However, endowing a hydrogel with both properties is challenging because they are generally inversely related. In this work, by constructing a multi-hydrogen-bonding system, a high-strength and injectable supramolecular hydrogel is successfully fabricated. It is constructed by the self-assembly of a monomeric nucleoside molecular gelator (2-amino-2'-fluoro-2'-deoxyadenosine (2-FA)) with distilled water/phosphate buffered saline as solvent. Its storage modulus reaches 1 MPa at a concentration of 5.0 wt%, which is the strongest supramolecular hydrogel comprising an ultralow-molecular-weight (MW < 300) gelator. Furthermore, it exhibits excellent shear-thinning injectability, and completes the sol-gel transition in seconds after injection at 37 °C. The multi-hydrogen-bonding system is essentially based on the synergistic interactions between the double NH2 groups, water molecules, and 2'-F atoms. Furthermore, the 2-FA hydrogel exhibits excellent biocompatibility and antibacterial activity. When applied to rat molar extraction sockets, compared to natural healing and the commercial hemorrhage agent gelatin sponge, the 2-FA hydrogel exhibits faster degradation and induces less osteoclastic activity and inflammatory infiltration, resulting in more complete bone healing. In summary, this study provides ideas for proposing a multifunctional, high-strength, and injectable supramolecular hydrogel for various biomedical engineering applications.
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Affiliation(s)
- Zheng Wang
- State Key Laboratory of Oral Diseases National Clinical Research Center for Oral Diseases Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, Med‐X Center for Materials West China Hospital of Stomatology Sichuan University Chengdu Sichuan 610041 P. R. China
| | - Yanan Zhang
- State Key Laboratory of Oral Diseases National Clinical Research Center for Oral Diseases Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, Med‐X Center for Materials West China Hospital of Stomatology Sichuan University Chengdu Sichuan 610041 P. R. China
| | - Yijia Yin
- State Key Laboratory of Oral Diseases National Clinical Research Center for Oral Diseases Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, Med‐X Center for Materials West China Hospital of Stomatology Sichuan University Chengdu Sichuan 610041 P. R. China
| | - Jiang Liu
- State Key Laboratory of Oral Diseases National Clinical Research Center for Oral Diseases Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, Med‐X Center for Materials West China Hospital of Stomatology Sichuan University Chengdu Sichuan 610041 P. R. China
| | - Peiran Li
- State Key Laboratory of Oral Diseases National Clinical Research Center for Oral Diseases Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, Med‐X Center for Materials West China Hospital of Stomatology Sichuan University Chengdu Sichuan 610041 P. R. China
| | - Yuxi Zhao
- State Key Laboratory of Oral Diseases National Clinical Research Center for Oral Diseases Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, Med‐X Center for Materials West China Hospital of Stomatology Sichuan University Chengdu Sichuan 610041 P. R. China
| | - Ding Bai
- State Key Laboratory of Oral Diseases National Clinical Research Center for Oral Diseases Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, Med‐X Center for Materials West China Hospital of Stomatology Sichuan University Chengdu Sichuan 610041 P. R. China
| | - Hang Zhao
- State Key Laboratory of Oral Diseases National Clinical Research Center for Oral Diseases Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, Med‐X Center for Materials West China Hospital of Stomatology Sichuan University Chengdu Sichuan 610041 P. R. China
| | - Xianglong Han
- State Key Laboratory of Oral Diseases National Clinical Research Center for Oral Diseases Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, Med‐X Center for Materials West China Hospital of Stomatology Sichuan University Chengdu Sichuan 610041 P. R. China
| | - Qianming Chen
- State Key Laboratory of Oral Diseases National Clinical Research Center for Oral Diseases Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, Med‐X Center for Materials West China Hospital of Stomatology Sichuan University Chengdu Sichuan 610041 P. R. China
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Quantification of Epigenetic DNA Modifications of Subchromatin Structures by UHPLC-MS/MS. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2022. [DOI: 10.1016/j.cjac.2022.100093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Jia TZ, Nishikawa S, Fujishima K. Sequencing the Origins of Life. BBA ADVANCES 2022; 2:100049. [PMID: 37082609 PMCID: PMC10074849 DOI: 10.1016/j.bbadva.2022.100049] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 02/27/2022] [Accepted: 03/02/2022] [Indexed: 01/10/2023] Open
Abstract
One goal of origins of life research is to understand how primitive informational and catalytic biopolymers emerged and evolved. Recently, a number of sequencing techniques have been applied to analysis of replicating and evolving primitive biopolymer systems, providing a sequence-specific and high-resolution view of primitive chemical processes. Here, we review application of sequencing techniques to analysis of synthetic and primitive nucleic acids and polypeptides. This includes next-generation sequencing of primitive polymerization and evolution processes, followed by discussion of other novel biochemical techniques that could contribute to sequence analysis of primitive biopolymer driven chemical systems. Further application of sequencing to origins of life research, perhaps as a life detection technology, could provide insight into the origin and evolution of informational and catalytic biopolymers on early Earth or elsewhere.
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Affiliation(s)
- Tony Z. Jia
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
- Blue Marble Space Institute of Science, 600 1st Ave, Floor 1, Seattle, WA 98104, USA
- Corresponding author
| | - Shota Nishikawa
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8501, Japan
| | - Kosuke Fujishima
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
- Graduate School of Media and Governance, Keio University, 5322 Endo, Fujisawa-shi, Kanagawa 252-0882, Japan
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36
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Mobile CRISPR-Cas9 based anti-phage system in E. coli. Front Chem Sci Eng 2022; 16:1281-1289. [PMID: 35251747 PMCID: PMC8882345 DOI: 10.1007/s11705-022-2141-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 11/03/2021] [Indexed: 10/26/2022]
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37
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Caldero-Rodríguez NE, Ortiz-Rodríguez LA, Gonzalez AA, Crespo-Hernández CE. Photostability of 2,6-diaminopurine and its 2'-deoxyriboside investigated by femtosecond transient absorption spectroscopy. Phys Chem Chem Phys 2022; 24:4204-4211. [PMID: 35119441 DOI: 10.1039/d1cp05269a] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ultraviolet radiation (UVR) from the sun is essential for the prebiotic syntheses of nucleotides, but it can also induce photolesions such as the cyclobutane pyrimidine dimers (CPDs) to RNA or DNA oligonucleotide in prebiotic Earth. 2,6-Diaminopurine (26DAP) has been proposed to repair CPDs in high yield under prebiotic conditions and be a key component in enhancing the photostability of higher-order prebiotic DNA structures. However, its electronic relaxation pathways have not been studied, which is necessary to know whether 26DAP could have survived the intense UV fluxes of the prebiotic Earth. We investigate the electronic relaxation mechanism of both 26DAP and its 2'-deoxyribonucleoside (26DAP-d) in aqueous solution using steady-state and femtosecond transient absorption measurements that are complemented with electronic-structure calculations. The results demonstrate that both purine derivatives are significantly photostable to UVR. It is shown that upon excitation at 287 nm, the lowest energy 1ππ* state is initially populated. The population then branches following two relaxation coordinates in the 1ππ* potential energy surface, which are identified as the C2- and C6-relaxation coordinates. The population following the C6-coordinate internally converts to the ground state nonradiatively through a nearly barrierless conical intersection within 0.7 ps in 26DAP or within 1.1 ps in 26DAP-d. The population that follows the C2-relaxation coordinate decays back to the ground state by a combination of nonradiative internal conversion via a conical intersection and fluorescence emission from the 1ππ* minimum in 43 ps and 1.8 ns for the N9 and N7 tautomers of 26DAP, respectively, or in 70 ps for 26DAP-d. Fluorescence quantum yields of 0.037 and 0.008 are determined for 26DAP and 26DAP-d, respectively. Collectively, it is demonstrated that most of the excited state population in 26DAP and 26DAP-d decays back to the ground state via both nonradiative and radiative relaxation pathways. This result lends support to the idea that 26DAP could have accumulated in large enough quantities during the prebiotic era to participate in the formation of prebiotic RNA or DNA oligomers and act as a key component in the protection of the prebiotic genetic alphabet.
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Affiliation(s)
| | | | - Andres A Gonzalez
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA.
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38
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Freeland S. Undefining life's biochemistry: implications for abiogenesis. J R Soc Interface 2022; 19:20210814. [PMID: 35193384 PMCID: PMC8867283 DOI: 10.1098/rsif.2021.0814] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 01/19/2022] [Indexed: 12/22/2022] Open
Abstract
In the mid-twentieth century, multiple Nobel Prizes rewarded discoveries of a seemingly universal set of molecules and interactions that collectively defined the chemical basis for life. Twenty-first-century science knows that every detail of this Central Dogma of Molecular Biology can vary through either biological evolution, human engineering (synthetic biology) or both. Clearly the material, molecular basis of replicating, evolving entities can be different. There is far less clarity yet for what constitutes this set of possibilities. One approach to better understand the limits and scope of moving beyond life's central dogma comes from those who study life's origins. RNA, proteins and the genetic code that binds them each look like products of natural selection. This raises the question of what step(s) preceded these particular components? Answers here will clarify whether any discrete point in time or biochemical evolution will objectively merit the label of life's origin, or whether life unfolds seamlessly from the non-living universe.
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Affiliation(s)
- Stephen Freeland
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD 21250, USA
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39
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Morcinek-Orłowska J, Zdrojewska K, Węgrzyn A. Bacteriophage-Encoded DNA Polymerases-Beyond the Traditional View of Polymerase Activities. Int J Mol Sci 2022; 23:635. [PMID: 35054821 PMCID: PMC8775771 DOI: 10.3390/ijms23020635] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/28/2021] [Accepted: 01/06/2022] [Indexed: 02/04/2023] Open
Abstract
DNA polymerases are enzymes capable of synthesizing DNA. They are involved in replication of genomes of all cellular organisms as well as in processes of DNA repair and genetic recombination. However, DNA polymerases can also be encoded by viruses, including bacteriophages, and such enzymes are involved in viral DNA replication. DNA synthesizing enzymes are grouped in several families according to their structures and functions. Nevertheless, there are examples of bacteriophage-encoded DNA polymerases which are significantly different from other known enzymes capable of catalyzing synthesis of DNA. These differences are both structural and functional, indicating a huge biodiversity of bacteriophages and specific properties of their enzymes which had to evolve under certain conditions, selecting unusual properties of the enzymes which are nonetheless crucial for survival of these viruses, propagating as special kinds of obligatory parasites. In this review, we present a brief overview on DNA polymerases, and then we discuss unusual properties of different bacteriophage-encoded enzymes, such as those able to initiate DNA synthesis using the protein-priming mechanisms or even start this process without any primer, as well as able to incorporate untypical nucleotides. Apart from being extremely interesting examples of biochemical biodiversity, bacteriophage-encoded DNA polymerases can also be useful tools in genetic engineering and biotechnology.
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Affiliation(s)
- Joanna Morcinek-Orłowska
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (J.M.-O.); (K.Z.)
| | - Karolina Zdrojewska
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (J.M.-O.); (K.Z.)
| | - Alicja Węgrzyn
- Laboratory of Phage Therapy, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Kładki 24, 80-822 Gdansk, Poland
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40
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Yan YM, Chen H, Chen WL, Wang DW, Liao L, Lu Q, Cheng YX. Alkyl-modified nucleobases with 6/5/7/5 ring systems from the insect Cyclopelta parva. Org Chem Front 2022. [DOI: 10.1039/d1qo01603b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
(±)-Cyclopeltains A and B (1 and 2), two pairs of unusual alkylated adenine derivatives, were isolated from the insect Cyclopelta parva and structurally characterized.
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Affiliation(s)
- Yong-Ming Yan
- Institute for Inheritance-Based Innovation of Chinese Medicine, Marshall Laboratory of Biomedical Engineering, School of Pharmaceutical Sciences, Health Science Center, Shenzhen University, Shenzhen 518060, PR China
| | - Heng Chen
- Institute for Inheritance-Based Innovation of Chinese Medicine, Marshall Laboratory of Biomedical Engineering, School of Pharmaceutical Sciences, Health Science Center, Shenzhen University, Shenzhen 518060, PR China
| | - Wen-Long Chen
- Institute for Inheritance-Based Innovation of Chinese Medicine, Marshall Laboratory of Biomedical Engineering, School of Pharmaceutical Sciences, Health Science Center, Shenzhen University, Shenzhen 518060, PR China
| | - Dai-Wei Wang
- Institute for Inheritance-Based Innovation of Chinese Medicine, Marshall Laboratory of Biomedical Engineering, School of Pharmaceutical Sciences, Health Science Center, Shenzhen University, Shenzhen 518060, PR China
| | - Li Liao
- Institute for Inheritance-Based Innovation of Chinese Medicine, Marshall Laboratory of Biomedical Engineering, School of Pharmaceutical Sciences, Health Science Center, Shenzhen University, Shenzhen 518060, PR China
| | - Qing Lu
- Institute for Inheritance-Based Innovation of Chinese Medicine, Marshall Laboratory of Biomedical Engineering, School of Pharmaceutical Sciences, Health Science Center, Shenzhen University, Shenzhen 518060, PR China
- Guangdong Key Laboratory for Functional Substances in Medicinal Edible Resources and Healthcare Products, School of Life Sciences and Food Engineering, Hanshan Normal University, Chaozhou 521041, PR China
| | - Yong-Xian Cheng
- Institute for Inheritance-Based Innovation of Chinese Medicine, Marshall Laboratory of Biomedical Engineering, School of Pharmaceutical Sciences, Health Science Center, Shenzhen University, Shenzhen 518060, PR China
- Guangdong Key Laboratory for Functional Substances in Medicinal Edible Resources and Healthcare Products, School of Life Sciences and Food Engineering, Hanshan Normal University, Chaozhou 521041, PR China
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41
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Stolar T, Alić J, Lončarić I, Etter M, Jung D, Farha OK, Đilović I, Meštrović E, Užarević K. Sustainable solid form screening: mechanochemical control over nucleobase hydrogen-bonded organic framework polymorphism. CrystEngComm 2022. [DOI: 10.1039/d2ce00668e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The choice is yours! Liquid-assisted grinding can be used to control HOF polymorphism.
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Affiliation(s)
| | - Jasna Alić
- Ruđer Bošković Institute, Bijenička c. 54, Zagreb, Croatia
| | - Ivor Lončarić
- Ruđer Bošković Institute, Bijenička c. 54, Zagreb, Croatia
| | - Martin Etter
- Deutsches Elektronen-Synchrotron (DESY), Notkestr. 85, Hamburg, Germany
| | - Dahee Jung
- Department of Chemistry and International Institute of Nanotechnology, Northwestern University, Evanston, Illinois 60208, USA
| | - Omar K. Farha
- Department of Chemistry and International Institute of Nanotechnology, Northwestern University, Evanston, Illinois 60208, USA
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, USA
| | - Ivica Đilović
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, Zagreb, Croatia
| | - Ernest Meštrović
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, Zagreb, Croatia
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42
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Lv P, Yang Y, Li S, Tan CS, Ming D. Biological nanopore approach for single‐molecule analysis of nucleobase modifications. ELECTROCHEMICAL SCIENCE ADVANCES 2021. [DOI: 10.1002/elsa.202100119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Affiliation(s)
- Pengrui Lv
- Academy of Medical Engineering and Translational Medicine Tianjin University Tianjin China
| | - Yongyi Yang
- Academy of Medical Engineering and Translational Medicine Tianjin University Tianjin China
| | - Shuang Li
- Academy of Medical Engineering and Translational Medicine Tianjin University Tianjin China
| | - Cherie S. Tan
- Academy of Medical Engineering and Translational Medicine Tianjin University Tianjin China
| | - Dong Ming
- Academy of Medical Engineering and Translational Medicine Tianjin University Tianjin China
- Department of Biomedical Engineering College of Precision Instruments and Optoelectronics Engineering Tianjin University Tianjin China
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43
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Hutinet G, Lee YJ, de Crécy-Lagard V, Weigele PR. Hypermodified DNA in Viruses of E. coli and Salmonella. EcoSal Plus 2021; 9:eESP00282019. [PMID: 34910575 PMCID: PMC11163837 DOI: 10.1128/ecosalplus.esp-0028-2019] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 07/26/2021] [Indexed: 12/23/2022]
Abstract
The DNA in bacterial viruses collectively contains a rich, yet relatively underexplored, chemical diversity of nucleobases beyond the canonical adenine, guanine, cytosine, and thymine. Herein, we review what is known about the genetic and biochemical basis for the biosynthesis of complex DNA modifications, also called DNA hypermodifications, in the DNA of tailed bacteriophages infecting Escherichia coli and Salmonella enterica. These modifications, and their diversification, likely arose out of the evolutionary arms race between bacteriophages and their cellular hosts. Despite their apparent diversity in chemical structure, the syntheses of various hypermodified bases share some common themes. Hypermodifications form through virus-directed synthesis of noncanonical deoxyribonucleotide triphosphates, direct modification DNA, or a combination of both. Hypermodification enzymes are often encoded in modular operons reminiscent of biosynthetic gene clusters observed in natural product biosynthesis. The study of phage-hypermodified DNA provides an exciting opportunity to expand what is known about the enzyme-catalyzed chemistry of nucleic acids and will yield new tools for the manipulation and interrogation of DNA.
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Affiliation(s)
- Geoffrey Hutinet
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA
| | - Yan-Jiun Lee
- Research Department, New England Biolabs, Ipswich, Massachusetts, USA
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA
| | - Peter R. Weigele
- Research Department, New England Biolabs, Ipswich, Massachusetts, USA
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44
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Kaminski PA. Mechanisms supporting aminoadenine-based viral DNA genomes. Cell Mol Life Sci 2021; 79:51. [PMID: 34910247 PMCID: PMC11072226 DOI: 10.1007/s00018-021-04055-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/17/2021] [Accepted: 11/21/2021] [Indexed: 10/19/2022]
Abstract
Bacteriophage genomes are the richest source of modified nucleobases of any life form. Of these, 2,6 diaminopurine, which pairs with thymine by forming three hydrogen bonds violates Watson and Crick's base pairing. 2,6 diaminopurine initially found in the cyanophage S-2L is more widespread than expected and has also been detected in phage infecting Gram-negative and Gram-positive bacteria. The biosynthetic pathway for aminoadenine containing DNA as well as the exclusion of adenine are now elucidated. This example of a natural deviation from the genetic code represents only one of the possibilities explored by nature and provides a proof of concept for the synthetic biology of non-canonical nucleic acids.
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Affiliation(s)
- P A Kaminski
- Biologie des Bactéries Pathogènes à Gram-Positif, Institut Pasteur, CNRS-UMR 2001, Paris, France.
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45
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Freund N, Fürst MJLJ, Holliger P. New chemistries and enzymes for synthetic genetics. Curr Opin Biotechnol 2021; 74:129-136. [PMID: 34883451 DOI: 10.1016/j.copbio.2021.11.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 10/27/2021] [Accepted: 11/01/2021] [Indexed: 12/15/2022]
Abstract
Beyond the natural nucleic acids DNA and RNA, nucleic acid chemistry has unlocked a whole universe of modifications to their canonical chemical structure, which can in various ways modify and enhance nucleic acid function and utility for applications in biotechnology and medicine. Unlike the natural modifications of tRNA and rRNA or the epigenetic modifications in mRNA and genomic DNA, these altered chemistries are not found in nature and therefore these molecules are referred to as xeno-nucleic acids (XNAs). In this review we aim to focus specifically on recent progress in a subsection of this vast field-synthetic genetics-concerned with encoded synthesis, reverse transcription, and evolution of XNAs.
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Affiliation(s)
- Niklas Freund
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | | | - Philipp Holliger
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
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46
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Zhang R, Lai W, Wang H. Quantification of Epigenetic DNA Modifications in the Subchromatin Structure Matrix Attachment Regions by Stable Isotope Dilution UHPLC-MS/MS Analysis. Anal Chem 2021; 93:15567-15572. [PMID: 34783527 DOI: 10.1021/acs.analchem.1c04151] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To date, subchromatin structure-based quantification of epigenetic DNA modifications is limited. Matrix attachment regions (MARs), an important subchromatin structure, contain DNA elements that specifically bind chromatin to the nuclear matrix in eukaryotes and are involved in a number of diseases. Here, we exploited a high-salt extraction-based subchromatin fractionation approach for the isolation of MAR DNA and other fractions and further developed heavy stable isotope-diluted ultrahigh-performance liquid chromatography tandem mass spectrometry (UHPLC-MS/MS) for the specific quantification of epigenetic DNA modifications in the subchromatin structures. By this approach, we showed for the first time that the content of a DNA demethylation intermediate, 5-hydroxymethylcytosine (5hmdC), in MARs decreased significantly in four tested cell lines compared to the contents in genomic DNA. In particular, the content of DNA 5hmdC in the MARs of 293T cell lines decreased the most at approximately 41.09%. Together, our findings implicate that MAR DNA is less sensitive than genomic DNA to DNA demethylation.
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Affiliation(s)
- Rui Zhang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weiyi Lai
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hailin Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Institute of Environment and Health, Jianghan University, Wuhan 430056, China
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47
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Czernecki D, Hu H, Romoli F, Delarue M. Structural dynamics and determinants of 2-aminoadenine specificity in DNA polymerase DpoZ of vibriophage ϕVC8. Nucleic Acids Res 2021; 49:11974-11985. [PMID: 34751404 PMCID: PMC8599892 DOI: 10.1093/nar/gkab955] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/29/2021] [Accepted: 10/04/2021] [Indexed: 11/12/2022] Open
Abstract
All genetic information in cellular life is stored in DNA copolymers composed of four basic building blocks (ATGC-DNA). In contrast, a group of bacteriophages belonging to families Siphoviridae and Podoviridae has abandoned the usage of one of them, adenine (A), replacing it with 2-aminoadenine (Z). The resulting ZTGC-DNA is more stable than its ATGC-DNA counterpart, owing to the additional hydrogen bond present in the 2-aminoadenine:thymine (Z:T) base pair, while the additional amino group also confers resistance to the host endonucleases. Recently, two classes of replicative proteins found in ZTGC-DNA-containing phages were characterized and one of them, DpoZ from DNA polymerase A (PolA) family, was shown to possess significant Z-vs-A specificity. Here, we present the crystallographic structure of the apo form of DpoZ of vibriophage ϕVC8, composed of the 3′-5′ exonuclease and polymerase domains. We captured the enzyme in two conformations that involve the tip of the thumb subdomain and the exonuclease domain. We highlight insertions and mutations characteristic of ϕVC8 DpoZ and its close homologues. Through mutagenesis and functional assays we suggest that the preference of ϕVC8 DpoZ towards Z relies on a polymerase backtracking process, more efficient when the nascent base pair is A:T than when it is Z:T.
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Affiliation(s)
- Dariusz Czernecki
- Unit of Architecture and Dynamics of Biological Macromolecules, CNRS UMR 3528, 25-28 rue du Docteur Roux, Institut Pasteur, 75015 Paris, France.,Sorbonne Université, Collège Doctoral, ED 515, 75005 Paris, France
| | - Haidai Hu
- Unit of Architecture and Dynamics of Biological Macromolecules, CNRS UMR 3528, 25-28 rue du Docteur Roux, Institut Pasteur, 75015 Paris, France
| | - Filippo Romoli
- Unit of Architecture and Dynamics of Biological Macromolecules, CNRS UMR 3528, 25-28 rue du Docteur Roux, Institut Pasteur, 75015 Paris, France
| | - Marc Delarue
- Unit of Architecture and Dynamics of Biological Macromolecules, CNRS UMR 3528, 25-28 rue du Docteur Roux, Institut Pasteur, 75015 Paris, France
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48
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Genome and Ecology of a Novel Alteromonas Podovirus, ZP6, Representing a New Viral Genus, Mareflavirus. Microbiol Spectr 2021; 9:e0046321. [PMID: 34643440 PMCID: PMC8515928 DOI: 10.1128/spectrum.00463-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Alteromonas is a ubiquitous, abundant, copiotrophic and phytoplankton-associated marine member of the Gammaproteobacteria with a range extending from tropical waters to polar regions and including hadal zones. Here, we describe a novel Alteromonas phage, ZP6, that was isolated from surface coastal waters of Qingdao, China. ZP6 contains a linear, double-stranded, 38,080-bp DNA molecule with 50.1% G+C content and 47 putative open reading frames (ORFs). Three auxiliary metabolic genes were identified, encoding metal-dependent phosphohydrolase, diaminopurine synthetase, and nucleotide pyrophosphohydrolase. The first two ORFs facilitate the replacement of adenine (A) by diaminopurine (Z) in phage genomes and help phages to evade attack from host restriction enzymes. The nucleotide pyrophosphohydrolase enables the host cells to stop programmed cell death and improves the survival rate of the host in a nutrient-depleted environment. Phylogenetic analysis based on the amino acid sequences of whole genomes and comparative genomic analysis revealed that ZP6 is most closely related to Enhodamvirus but with low similarity (shared genes, <30%, and average nucleotide sequence identity, <65%); it is distinct from other bacteriophages. Together, these results suggest that ZP6 could represent a novel viral genus, here named Mareflavirus. Combining its ability to infect Alteromonas, its harboring of a diaminopurine genome-biosynthetic system, and its representativeness of an understudied viral group, ZP6 could be an important and novel model system for marine virus research. IMPORTANCEAlteromonas is an important symbiotic bacterium of phytoplankton, but research on its bacteriophages is still at an elementary level. Our isolation and genome characterization of a novel Alteromonas podovirus, ZP6, identified a new viral genus of podovirus, namely, Mareflavirus. The ZP6 genome, with a diaminopurine genome-biosynthetic system, is different from those of other isolated Alteromonas phages and will bring new impetus to the development of virus classification and provide important insights into novel viral sequences from metagenomic data sets.
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49
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Erickson S, Paulson J, Brown M, Hahn W, Gil J, Barron-Montenegro R, Moreno-Switt AI, Eisenberg M, Nguyen MM. Isolation and engineering of a Listeria grayi bacteriophage. Sci Rep 2021; 11:18947. [PMID: 34556683 PMCID: PMC8460666 DOI: 10.1038/s41598-021-98134-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 09/03/2021] [Indexed: 01/02/2023] Open
Abstract
The lack of bacteriophages capable of infecting the Listeria species, Listeria grayi, is academically intriguing and presents an obstacle to the development of bacteriophage-based technologies for Listeria. We describe the isolation and engineering of a novel L. grayi bacteriophage, LPJP1, isolated from farm silage. With a genome over 200,000 base pairs, LPJP1 is the first and only reported jumbo bacteriophage infecting the Listeria genus. Similar to other Gram-positive jumbo phages, LPJP1 appeared to contain modified base pairs, which complicated initial attempts to obtain genomic sequence using standard methods. Following successful sequencing with a modified approach, a recombinant of LPJP1 encoding the NanoLuc luciferase was engineered using homologous recombination. This luciferase reporter bacteriophage successfully detected 100 stationary phase colony forming units of both subspecies of L. grayi in four hours. A single log phase colony forming unit was also sufficient for positive detection in the same time period. The recombinant demonstrated complete specificity for this particular Listeria species and did not infect 150 non-L. grayi Listeria strains nor any other bacterial genus. LPJP1 is believed to be the first reported lytic bacteriophage of L. grayi as well as the only jumbo bacteriophage to be successfully engineered into a luciferase reporter.
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Affiliation(s)
- Stephen Erickson
- Laboratory Corporation of America Holdings, New Brighton, MN, 55112, USA.
| | - John Paulson
- Laboratory Corporation of America Holdings, New Brighton, MN, 55112, USA
| | - Matthew Brown
- Laboratory Corporation of America Holdings, Burlington, NC, 27215, USA
| | - Wendy Hahn
- Laboratory Corporation of America Holdings, New Brighton, MN, 55112, USA
| | - Jose Gil
- Laboratory Corporation of America Holdings, Los Angeles, CA, 90062, USA
| | - Rocío Barron-Montenegro
- Escuela de Medicina Veterinaria, Facultad de Agronomía e Ingeniería Forestal, Facultad de Ciencias Biológicas, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile.,Millennium Initiative for Collaborative Research on Bacteria Resistance (MICROB-R), Santiago, Chile
| | - Andrea I Moreno-Switt
- Escuela de Medicina Veterinaria, Facultad de Agronomía e Ingeniería Forestal, Facultad de Ciencias Biológicas, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile.,Millennium Initiative for Collaborative Research on Bacteria Resistance (MICROB-R), Santiago, Chile
| | - Marcia Eisenberg
- Laboratory Corporation of America Holdings, Burlington, NC, 27215, USA
| | - Minh M Nguyen
- Laboratory Corporation of America Holdings, New Brighton, MN, 55112, USA
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50
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Czernecki D, Bonhomme F, Kaminski PA, Delarue M. Characterization of a triad of genes in cyanophage S-2L sufficient to replace adenine by 2-aminoadenine in bacterial DNA. Nat Commun 2021; 12:4710. [PMID: 34354070 PMCID: PMC8342488 DOI: 10.1038/s41467-021-25064-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/21/2021] [Indexed: 11/09/2022] Open
Abstract
Cyanophage S-2L is known to profoundly alter the biophysical properties of its DNA by replacing all adenines (A) with 2-aminoadenines (Z), which still pair with thymines but with a triple hydrogen bond. It was recently demonstrated that a homologue of adenylosuccinate synthetase (PurZ) and a dATP triphosphohydrolase (DatZ) are two important pieces of the metabolism of 2-aminoadenine, participating in the synthesis of ZTGC-DNA. Here, we determine that S-2L PurZ can use either dATP or ATP as a source of energy, thereby also depleting the pool of nucleotides in dATP. Furthermore, we identify a conserved gene (mazZ) located between purZ and datZ genes in S-2L and related phage genomes. We show that it encodes a (d)GTP-specific diphosphohydrolase, thereby providing the substrate of PurZ in the 2-aminoadenine synthesis pathway. High-resolution crystal structures of S-2L PurZ and MazZ with their respective substrates provide a rationale for their specificities. The Z-cluster made of these three genes - datZ, mazZ and purZ - was expressed in E. coli, resulting in a successful incorporation of 2-aminoadenine in the bacterial chromosomal and plasmidic DNA. This work opens the possibility to study synthetic organisms containing ZTGC-DNA.
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Affiliation(s)
- Dariusz Czernecki
- Unit of Architecture and Dynamics of Biological Macromolecules, CNRS UMR 3528, 25-28 rue du Docteur Roux, Institut Pasteur, Paris, France
- Sorbonne Université, Collège Doctoral, ED 515, Paris, France
| | - Frédéric Bonhomme
- Unit of Epigenetic Chemical Biology, CNRS UMR 3523, 25-28 rue du Docteur Roux, Institut Pasteur, Paris, France
| | - Pierre-Alexandre Kaminski
- Unit of Biology of Pathogenic Gram-Positive Bacteria, CNRS UMR 2001, 25-28 rue du Docteur Roux, Institut Pasteur, Paris, France
| | - Marc Delarue
- Unit of Architecture and Dynamics of Biological Macromolecules, CNRS UMR 3528, 25-28 rue du Docteur Roux, Institut Pasteur, Paris, France.
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