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Boyd BM, James I, Johnson KP, Weiss RB, Bush SE, Clayton DH, Dale C. Stochasticity, determinism, and contingency shape genome evolution of endosymbiotic bacteria. Nat Commun 2024; 15:4571. [PMID: 38811551 PMCID: PMC11137140 DOI: 10.1038/s41467-024-48784-2] [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: 07/06/2023] [Accepted: 05/10/2024] [Indexed: 05/31/2024] Open
Abstract
Evolution results from the interaction of stochastic and deterministic processes that create a web of historical contingency, shaping gene content and organismal function. To understand the scope of this interaction, we examine the relative contributions of stochasticity, determinism, and contingency in shaping gene inactivation in 34 lineages of endosymbiotic bacteria, Sodalis, found in parasitic lice, Columbicola, that are independently undergoing genome degeneration. Here we show that the process of genome degeneration in this system is largely deterministic: genes involved in amino acid biosynthesis are lost while those involved in providing B-vitamins to the host are retained. In contrast, many genes encoding redundant functions, including components of the respiratory chain and DNA repair pathways, are subject to stochastic loss, yielding historical contingencies that constrain subsequent losses. Thus, while selection results in functional convergence between symbiont lineages, stochastic mutations initiate distinct evolutionary trajectories, generating diverse gene inventories that lack the functional redundancy typically found in free-living relatives.
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Affiliation(s)
- Bret M Boyd
- Center for Biological Data Science, Virginia Commonwealth University, Richmond, VA, US.
| | - Ian James
- School of Biological Sciences, University of Utah, Salt Lake City, UT, US
| | - Kevin P Johnson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL, US
| | - Robert B Weiss
- Department of Human Genetics, University of Utah, Salt Lake City, UT, US
| | - Sarah E Bush
- School of Biological Sciences, University of Utah, Salt Lake City, UT, US
| | - Dale H Clayton
- School of Biological Sciences, University of Utah, Salt Lake City, UT, US
| | - Colin Dale
- School of Biological Sciences, University of Utah, Salt Lake City, UT, US
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2
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Gao L, Shi W, Xia X. Genomic Plasticity of Acid-Tolerant Phenotypic Evolution in Acetobacter pasteurianus. Appl Biochem Biotechnol 2023; 195:6003-6019. [PMID: 36738389 DOI: 10.1007/s12010-023-04353-9] [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] [Accepted: 01/10/2023] [Indexed: 02/05/2023]
Abstract
Acetic acid bacteria have a remarkable capacity to cope with elevated concentrations of cytotoxic acetic acid in their fermentation environment. In particular, the high-level acetate tolerance of Acetobacter pasteurianus that occurs in vinegar industrial settings must be constantly selected for. However, the improved acetic acid tolerance is rapidly lost without a selection pressure. To understand genetic and molecular biology of this acquired acetic acid tolerance in A. pasteurianus, we evolved three strains A. pasteurianus CICIM B7003, CICIM B7003-02, and ATCC 33,445 over 960 generations (4 months) in two initial acetic acids of 20 g·L-1 and 30 g·L-1, respectively. An acetic acid-adapted strain M20 with significantly improved specific growth rate of 0.159 h-1 and acid productivity of 1.61 g·L-1·h-1 was obtained. Comparative genome analysis of six evolved strains revealed that the genetic variations of adaptation were mainly focused on lactate metabolism, membrane proteins, transcriptional regulators, transposases, replication, and repair system. Among of these, lactate dehydrogenase, acetolactate synthase, glycosyltransferase, ABC transporter ATP-binding protein, two-component regulatory systems, the type II toxin-antitoxin system (RelE/RelB/StbE), exodeoxyribonuclease III, type I restriction endonuclease, tRNA-uridine 2-sulfurtransferase, and transposase might collaboratively contribute to the improved acetic acid tolerance in A. pasteurianus strains. The balance between repair factors and transposition variations might be the basis for genomic plasticity of A. pasteurianus strains, allowing the survival of populations and their offspring in acetic acid stress fluctuations. These observations provide important insights into the nature of acquired acetic acid tolerance phenotype and lay a foundation for future genetic manipulation of these strains.
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Affiliation(s)
- Ling Gao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, People's Republic of China
| | - Wei Shi
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, People's Republic of China
| | - Xiaole Xia
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, People's Republic of China.
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Geng B, Liu S, Chen Y, Wu Y, Wang Y, Zhou X, Li H, Li M, Yang S. A plasmid-free Zymomonas mobilis mutant strain reducing reactive oxygen species for efficient bioethanol production using industrial effluent of xylose mother liquor. Front Bioeng Biotechnol 2022; 10:1110513. [PMID: 36619397 PMCID: PMC9816438 DOI: 10.3389/fbioe.2022.1110513] [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: 11/28/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022] Open
Abstract
Genome minimization is an effective way for industrial chassis development. In this study, Zymomonas mobilis ZMNP, a plasmid-free mutant strain of Z. mobilis ZM4 with four native plasmids deleted, was constructed using native type I-F CRISPR-Cas system. Cell growth of ZMNP under different temperatures and industrial effluent of xylose mother liquor were examined to investigate the impact of native plasmid removal. Despite ZMNP grew similarly as ZM4 under different temperatures, ZMNP had better xylose mother liquor utilization than ZM4. In addition, genomic, transcriptomic, and proteomic analyses were applied to unravel the molecular changes between ZM4 and ZMNP. Whole-genome resequencing result indicated that an S267P mutation in the C-terminal of OxyR, a peroxide-sensing transcriptional regulator, probably alters the transcription initiation of antioxidant genes for stress responses. Transcriptomic and proteomic studies illustrated that the reason that ZMNP utilized the toxic xylose mother liquor better than ZM4 was probably due to the upregulation of genes in ZMNP involving in stress responses as well as cysteine biosynthesis to accelerate the intracellular ROS detoxification and nucleic acid damage repair. This was further confirmed by lower ROS levels in ZMNP compared to ZM4 in different media supplemented with furfural or ethanol. The upregulation of stress response genes due to the OxyR mutation to accelerate ROS detoxification and DNA/RNA repair not only illustrates the underlying mechanism of the robustness of ZMNP in the toxic xylose mother liquor, but also provides an idea for the rational design of synthetic inhibitor-tolerant microorganisms for economic lignocellulosic biochemical production.
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Affiliation(s)
- Binan Geng
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, School of Life Sciences, Hubei University, Wuhan, China
| | - Shuyi Liu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, School of Life Sciences, Hubei University, Wuhan, China
| | - Yunhao Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, School of Life Sciences, Hubei University, Wuhan, China
| | - Yalun Wu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, School of Life Sciences, Hubei University, Wuhan, China
| | - Yi Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, School of Life Sciences, Hubei University, Wuhan, China
| | - Xuan Zhou
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, School of Life Sciences, Hubei University, Wuhan, China
| | - Han Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, School of Life Sciences, Hubei University, Wuhan, China
| | - Mian Li
- Zhejiang Huakang Pharmaceutical Co., Ltd., Quzhou, Zhejiang, China
| | - Shihui Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, School of Life Sciences, Hubei University, Wuhan, China,*Correspondence: Shihui Yang,
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Liu TC, Guo KW, Chu JW, Hsiao YY. Understanding APE1 cellular functions by the structural preference of exonuclease activities. Comput Struct Biotechnol J 2021; 19:3682-3691. [PMID: 34285771 PMCID: PMC8258793 DOI: 10.1016/j.csbj.2021.06.036] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 06/21/2021] [Accepted: 06/22/2021] [Indexed: 12/17/2022] Open
Abstract
Mammalian apurinic/apyrimidinic (AP) endonuclease 1 (APE1) has versatile enzymatic functions, including redox, endonuclease, and exonuclease activities. APE1 is thus broadly associated with pathways in DNA repair, cancer cell growth, and drug resistance. Unlike its AP site-specific endonuclease activity in Base excision repair (BER), the 3′-5′ exonucleolytic cleavage of APE1 using the same active site exhibits complex substrate selection patterns, which are key to the biological functions. This work aims to integrate molecular structural information and biocatalytic properties to deduce the substrate recognition mechanism of APE1 as an exonuclease and make connection to its diverse functionalities in the cell. In particular, an induced space-filling model emerges in which a bridge-like structure is formed by Arg177 and Met270 (RM bridge) upon substrate binding, causing the active site to adopt a long and narrow product pocket for hosting the leaving group of an AP site or the 3′-end nucleotide. Rather than distinguishing bases as other exonucleases, the hydrophobicity and steric hindrance due to the APE1 product pocket provides selectivity for substrate structures, such as matched or mismatched blunt-ended dsDNA, recessed dsDNA, gapped dsDNA, and nicked dsDNA with 3′-end overhang shorter than 2 nucleotides. These dsDNAs are similar to the native substrates in BER proofreading, BER for trinucleotide repeats (TNR), Nucleotide incision repair (NIR), DNA single-strand breaks (SSB), SSB with damaged bases, and apoptosis. Integration of in vivo studies, in vitro biochemical assays, and structural analysis is thus essential for linking the APE1 exonuclease activity to the specific roles in cellular functions.
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Affiliation(s)
- Tung-Chang Liu
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan.,Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan 30068, Taiwan
| | - Kai-Wei Guo
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan.,Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan 30068, Taiwan
| | - Jhih-Wei Chu
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan.,Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan 30068, Taiwan.,Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu, 30068, Taiwan.,Center For Intelligent Drug Systems and Smart Bio-devices (IDSB), National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Yu-Yuan Hsiao
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan.,Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan 30068, Taiwan.,Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu, 30068, Taiwan.,Center For Intelligent Drug Systems and Smart Bio-devices (IDSB), National Yang Ming Chiao Tung University, Hsinchu, Taiwan.,Drug Development and Value Creation Research Center, Center for Cancer Research, Kaohsiung Medical University, Kaohsiung, Taiwan
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5
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Srivastava PN, Narwal SK, Mishra S. Mitochondrial apurinic/apyrimidinic endonuclease Apn1 is not critical for the completion of the Plasmodium berghei life cycle. DNA Repair (Amst) 2021; 101:103078. [PMID: 33711786 DOI: 10.1016/j.dnarep.2021.103078] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/22/2021] [Accepted: 02/24/2021] [Indexed: 12/14/2022]
Abstract
Mitochondrion is an essential organelle in malaria parasite and its DNA must be maintained for optimal function during its complex life cycle. Base excision repair is one of the major pathways by which this is achieved. Apurinic/apyrimidinic (AP) endonucleases are important components of this pathway as they create a nick at the 5'-phosphodiester bond in the AP site and generate free 5'-phosphate and 3'-hydroxyl groups. Two class II AP endonucleases (Apn1 and Ape1) have been annotated in the Plasmodium berghei genome. Using reverse genetic approaches, we provide direct evidence that Apn1 is exclusively localized to the mitochondria of P. berghei. Surprisingly, our gene deletion study revealed a completely dispensable role of Apn1 for the entirety of the P. berghei life cycle. Apn1- parasites were found to successfully grow in the blood. They were transmitted normally to the mosquito midguts and salivary glands. Sporozoites obtained from the salivary glands were infective and achieved similar patency as WT. Our results help emphasize the non-availability of this enzyme as a plausible drug target. We also emphasize the importance of genetic validation of antimalarial drug targets before furthering them down the drug discovery pipeline.
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Affiliation(s)
- Pratik Narain Srivastava
- Division of Molecular Parasitology and Immunology, CSIR-Central Drug Research Institute, Lucknow, 226031, India
| | - Sunil Kumar Narwal
- Division of Molecular Parasitology and Immunology, CSIR-Central Drug Research Institute, Lucknow, 226031, India
| | - Satish Mishra
- Division of Molecular Parasitology and Immunology, CSIR-Central Drug Research Institute, Lucknow, 226031, India; Academy of Scientific and Innovative Research, Ghaziabad, India.
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6
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Liu X, Wu Y, Wu X, Zhao JX. A graphene oxide-based fluorescence assay for the sensitive detection of DNA exonuclease enzymatic activity. Analyst 2020; 144:6231-6239. [PMID: 31552930 DOI: 10.1039/c9an01283d] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The 3'-5' exonuclease enzyme plays a dominant role in multiple pivotal physiological activities, such as DNA replication and repair processes. In this study, we designed a sensitive graphene oxide (GO)-based probe for the detection of exonuclease enzymatic activity. In the absence of Exo III, the strong π-π interaction between the fluorophore-tagged DNA and GO causes the efficient fluorescence quenching via a fluorescence resonance energy transfer (FRET). In contrast, in the presence of Exo III, the fluorophore-tagged 3'-hydroxyl termini of the DNA probe was digested by Exo III to set the fluorophore free from adsorption when GO was introduced, causing an inefficient fluorescence quenching. As a result, the fluorescence intensity of the sensor was found to be proportional to the concentration of Exo III; towards the detection of Exo III, this simple GO-based probe demonstrated a highly sensitive and selective linear response in the low detection range from 0.01 U mL-1 to 0.5 U mL-1 and with the limit of detection (LOD) of 0.001 U mL-1. Compared with other fluorescent probes, this assay exhibited superior sensitivity and selectivity in both buffer and fetal bovine serum samples, in addition to being cost effective and having a simple setup.
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Affiliation(s)
- Xiao Liu
- Department of Chemistry, University of North Dakota, Grand Forks, ND 58202, USA.
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7
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Zhang Y, Matsuzaka T, Yano H, Furuta Y, Nakano T, Ishikawa K, Fukuyo M, Takahashi N, Suzuki Y, Sugano S, Ide H, Kobayashi I. Restriction glycosylases: involvement of endonuclease activities in the restriction process. Nucleic Acids Res 2017; 45:1392-1403. [PMID: 28180312 PMCID: PMC5388411 DOI: 10.1093/nar/gkw1250] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 11/23/2016] [Accepted: 12/12/2016] [Indexed: 11/18/2022] Open
Abstract
All restriction enzymes examined are phosphodiesterases generating 3΄-OH and 5΄-P ends, but one restriction enzyme (restriction glycosylase) excises unmethylated bases from its recognition sequence. Whether its restriction activity involves endonucleolytic cleavage remains unclear. One report on this enzyme, R.PabI from a hyperthermophile, ascribed the breakage to high temperature while another showed its weak AP lyase activity generates atypical ends. Here, we addressed this issue in mesophiles. We purified R.PabI homologs from Campylobacter coli (R.CcoLI) and Helicobacter pylori (R.HpyAXII) and demonstrated their DNA cleavage, DNA glycosylase and AP lyase activities in vitro at 37°C. The AP lyase activity is more coupled with glycosylase activity in R.CcoLI than in R.PabI. R.CcoLI/R.PabI expression caused restriction of incoming bacteriophage/plasmid DNA and endogenous chromosomal DNA within Escherichia coli at 37°C. The R.PabI-mediated restriction was promoted by AP endonuclease action in vivo or in vitro. These results reveal the role of endonucleolytic DNA cleavage in restriction and yet point to diversity among the endonucleases. The cleaved ends are difficult to repair in vivo, which may indicate their biological significance. These results support generalization of the concept of restriction–modification system to the concept of self-recognizing epigenetic system, which combines any epigenetic labeling and any DNA damaging.
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Affiliation(s)
- Yingbiao Zhang
- Department of Computational Biology and Medical Sciences (formerly Department of Medical Genome Sciences), Graduate School of Frontier Sciences, University of Tokyo, Tokyo 108-8639, Japan
| | - Tomoyuki Matsuzaka
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University Higashi-Hiroshima 739-8526, Japan
| | - Hirokazu Yano
- Department of Computational Biology and Medical Sciences (formerly Department of Medical Genome Sciences), Graduate School of Frontier Sciences, University of Tokyo, Tokyo 108-8639, Japan
- Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo 108-8639, Japan
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan
| | - Yoshikazu Furuta
- Department of Computational Biology and Medical Sciences (formerly Department of Medical Genome Sciences), Graduate School of Frontier Sciences, University of Tokyo, Tokyo 108-8639, Japan
- Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo 108-8639, Japan
| | - Toshiaki Nakano
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University Higashi-Hiroshima 739-8526, Japan
| | - Ken Ishikawa
- National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Masaki Fukuyo
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
| | - Noriko Takahashi
- Department of Computational Biology and Medical Sciences (formerly Department of Medical Genome Sciences), Graduate School of Frontier Sciences, University of Tokyo, Tokyo 108-8639, Japan
- Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo 108-8639, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences (formerly Department of Medical Genome Sciences), Graduate School of Frontier Sciences, University of Tokyo, Tokyo 108-8639, Japan
| | - Sumio Sugano
- Department of Computational Biology and Medical Sciences (formerly Department of Medical Genome Sciences), Graduate School of Frontier Sciences, University of Tokyo, Tokyo 108-8639, Japan
| | - Hiroshi Ide
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University Higashi-Hiroshima 739-8526, Japan
| | - Ichizo Kobayashi
- Department of Computational Biology and Medical Sciences (formerly Department of Medical Genome Sciences), Graduate School of Frontier Sciences, University of Tokyo, Tokyo 108-8639, Japan
- Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo 108-8639, Japan
- Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan
- Faculty of Medicine, Kyorin University, Mitaka, Tokyo 181-8611, Japan
- Institut for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette 91198, France
- Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru 560 064, India
- To whom correspondence should be addressed. Tel: +81 90 2487 7510; ; ;
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Kurth D, Belfiore C, Gorriti MF, Cortez N, Farias ME, Albarracín VH. Genomic and proteomic evidences unravel the UV-resistome of the poly-extremophile Acinetobacter sp. Ver3. Front Microbiol 2015; 6:328. [PMID: 25954258 PMCID: PMC4406064 DOI: 10.3389/fmicb.2015.00328] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 04/01/2015] [Indexed: 12/20/2022] Open
Abstract
Ultraviolet radiation can damage biomolecules, with detrimental or even lethal effects for life. Even though lower wavelengths are filtered by the ozone layer, a significant amount of harmful UV-B and UV-A radiation reach Earth's surface, particularly in high altitude environments. high-altitude Andean lakes (HAALs) are a group of disperse shallow lakes and salterns, located at the Dry Central Andes region in South America at altitudes above 3,000 m. As it is considered one of the highest UV-exposed environments, HAAL microbes constitute model systems to study UV-resistance mechanisms in environmental bacteria at various complexity levels. Herein, we present the genome sequence of Acinetobacter sp. Ver3, a gammaproteobacterium isolated from Lake Verde (4,400 m), together with further experimental evidence supporting the phenomenological observations regarding this bacterium ability to cope with increased UV-induced DNA damage. Comparison with the genomes of other Acinetobacter strains highlighted a number of unique genes, such as a novel cryptochrome. Proteomic profiling of UV-exposed cells identified up-regulated proteins such as a specific cytoplasmic catalase, a putative regulator, and proteins associated to amino acid and protein synthesis. Down-regulated proteins were related to several energy-generating pathways such as glycolysis, beta-oxidation of fatty acids, and electronic respiratory chain. To the best of our knowledge, this is the first report on a genome from a polyextremophilic Acinetobacter strain. From the genomic and proteomic data, an "UV-resistome" was defined, encompassing the genes that would support the outstanding UV-resistance of this strain.
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Affiliation(s)
- Daniel Kurth
- Laboratorio de Investigaciones Microbiologicas Lagunas Andinas, Centro Científico Tecnológico, Planta Piloto de Procesos Industriales Microbiológicos - Consejo Nacional de Investigaciones Científicas y Técnicas, San Miguel de Tucumán Argentina
| | - Carolina Belfiore
- Laboratorio de Investigaciones Microbiologicas Lagunas Andinas, Centro Científico Tecnológico, Planta Piloto de Procesos Industriales Microbiológicos - Consejo Nacional de Investigaciones Científicas y Técnicas, San Miguel de Tucumán Argentina
| | - Marta F Gorriti
- Laboratorio de Investigaciones Microbiologicas Lagunas Andinas, Centro Científico Tecnológico, Planta Piloto de Procesos Industriales Microbiológicos - Consejo Nacional de Investigaciones Científicas y Técnicas, San Miguel de Tucumán Argentina
| | - Néstor Cortez
- Centro Científico Tecnológico, IBR - CONICET, Universidad Nacional de Rosario Rosario, Argentina
| | - María E Farias
- Laboratorio de Investigaciones Microbiologicas Lagunas Andinas, Centro Científico Tecnológico, Planta Piloto de Procesos Industriales Microbiológicos - Consejo Nacional de Investigaciones Científicas y Técnicas, San Miguel de Tucumán Argentina
| | - Virginia H Albarracín
- Laboratorio de Investigaciones Microbiologicas Lagunas Andinas, Centro Científico Tecnológico, Planta Piloto de Procesos Industriales Microbiológicos - Consejo Nacional de Investigaciones Científicas y Técnicas, San Miguel de Tucumán Argentina ; Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán, San Miguel de Tucumán Argentina
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Dyakonova ES, Koval VV, Lomzov AA, Ishchenko AA, Fedorova OS. The role of His-83 of yeast apurinic/apyrimidinic endonuclease Apn1 in catalytic incision of abasic sites in DNA. Biochim Biophys Acta Gen Subj 2015; 1850:1297-309. [PMID: 25766873 DOI: 10.1016/j.bbagen.2015.03.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 02/16/2015] [Accepted: 03/04/2015] [Indexed: 10/23/2022]
Abstract
BACKGROUND The apurinic/apyrimidinic (AP) endonuclease Apn1 from Saccharomyces cerevisiae is a key enzyme involved in the base excision repair (BER) at the cleavage stage of abasic sites (AP sites) in DNA. The crystal structure of Apn1 from S. cerevisiae is unresolved. Based on its high amino acid homology to Escherichia coli Endo IV, His-83 is believed to coordinate one of three Zn2+ ions in Apn1's active site similar to His-69 in Endo IV. Substituting His-83 with Ala is proposed to decrease the AP endonuclease activity of Apn1 owing to weak coordination of Zn2+ ions involved in enzymatic catalysis. METHODS The kinetics of recognition, binding, and incision of DNA substrates with the H83A Apn1 mutant was investigated. The stopped-flow method detecting fluorescence intensity changes of 2-aminopurine (2-aPu) was used to monitor the conformational dynamics of DNA at pre-steady-state conditions. RESULTS We found substituting His-83 with Ala influenced catalytic complex formation and further incision of the damaged DNA strand. The H83A Apn1 catalysis depends not only on the location of the mismatch relative to the abasic site in DNA, but also on the nature of damage. CONCLUSIONS We consider His-83 properly coordinates the active site Zn2+ ion playing a crucial role in catalytic incision stage. Our data prove suppressed enzymatic activity of H83A Apn1 results from the reduced number of active site Zn2+ ions. GENERAL SIGNIFICANCE Our study provides insights into mechanistic specialty of AP site repair by yeast AP endonuclease Apn1 of Endo IV family, which members are not found in mammals, but are present in many microorganisms. The results will provide useful guidelines for design of new anti-fungal and anti-malarial agents.
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Affiliation(s)
- Elena S Dyakonova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentyev Ave., 8, Novosibirsk, 630090, Russian Federation
| | - Vladimir V Koval
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentyev Ave., 8, Novosibirsk, 630090, Russian Federation; Novosibirsk State University, Pirogov St., 2, Novosibirsk, 630090, Russian Federation
| | - Alexander A Lomzov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentyev Ave., 8, Novosibirsk, 630090, Russian Federation; Novosibirsk State University, Pirogov St., 2, Novosibirsk, 630090, Russian Federation
| | - Alexander A Ishchenko
- Groupe «Réparation de l'ADN», Université Paris-Sud XI, UMR8200 CNRS, Institut Gustave Roussy, Villejuif Cedex F-94805, France
| | - Olga S Fedorova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentyev Ave., 8, Novosibirsk, 630090, Russian Federation; Novosibirsk State University, Pirogov St., 2, Novosibirsk, 630090, Russian Federation.
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10
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Cadet J, Douki T, Ravanat JL. Oxidatively generated damage to cellular DNA by UVB and UVA radiation. Photochem Photobiol 2014; 91:140-55. [PMID: 25327445 DOI: 10.1111/php.12368] [Citation(s) in RCA: 197] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2014] [Accepted: 10/09/2014] [Indexed: 12/13/2022]
Abstract
This review article focuses on a critical survey of the main available information on the UVB and UVA oxidative reactions to cellular DNA as the result of direct interactions of UV photons, photosensitized pathways and biochemical responses including inflammation and bystander effects. UVA radiation appears to be much more efficient than UVB in inducing oxidatively generated damage to the bases and 2-deoxyribose moieties of DNA in isolated cells and skin. The UVA-induced generation of 8-oxo-7,8-dihydroguanine is mostly rationalized in terms of selective guanine oxidation by singlet oxygen generated through type II photosensitization mechanism. In addition, hydroxyl radical whose formation may be accounted for by metal-catalyzed Haber-Weiss reactions subsequent to the initial generation of superoxide anion radical contributes in a minor way to the DNA degradation. This leads to the formation of both oxidized purine and pyrimidine bases together with DNA single-strand breaks at the exclusion, however, of direct double-strand breaks. No evidence has been provided so far for the implication of delayed oxidative degradation pathways of cellular DNA. In that respect putative characteristic UVA-induced DNA damage could include single and more complex lesions arising from one-electron oxidation of the guanine base together with aldehyde adducts to amino-substituted nucleobases.
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Affiliation(s)
- Jean Cadet
- University Grenoble Alpes, INAC, Grenoble, France; CEA, INAC, Grenoble, France; Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, Canada
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11
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Leesukon P, Wirathorn W, Chuchue T, Charoenlap N, Mongkolsuk S. The selectable antibiotic marker, tetA(C), increases Pseudomonas aeruginosa susceptibility to the herbicide/superoxide generator, paraquat. Arch Microbiol 2013; 195:671-4. [PMID: 23907582 DOI: 10.1007/s00203-013-0913-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Revised: 07/11/2013] [Accepted: 07/15/2013] [Indexed: 11/29/2022]
Affiliation(s)
- Panithi Leesukon
- Molecular Medicine Graduate Program, Faculty of Science, Mahidol University, Bangkok, Thailand
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12
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Couvé S, Ishchenko AA, Fedorova OS, Ramanculov EM, Laval J, Saparbaev M. Direct DNA Lesion Reversal and Excision Repair in Escherichia coli. EcoSal Plus 2013; 5. [PMID: 26442931 DOI: 10.1128/ecosalplus.7.2.4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2012] [Indexed: 06/05/2023]
Abstract
Cellular DNA is constantly challenged by various endogenous and exogenous genotoxic factors that inevitably lead to DNA damage: structural and chemical modifications of primary DNA sequence. These DNA lesions are either cytotoxic, because they block DNA replication and transcription, or mutagenic due to the miscoding nature of the DNA modifications, or both, and are believed to contribute to cell lethality and mutagenesis. Studies on DNA repair in Escherichia coli spearheaded formulation of principal strategies to counteract DNA damage and mutagenesis, such as: direct lesion reversal, DNA excision repair, mismatch and recombinational repair and genotoxic stress signalling pathways. These DNA repair pathways are universal among cellular organisms. Mechanistic principles used for each repair strategies are fundamentally different. Direct lesion reversal removes DNA damage without need for excision and de novo DNA synthesis, whereas DNA excision repair that includes pathways such as base excision, nucleotide excision, alternative excision and mismatch repair, proceeds through phosphodiester bond breakage, de novo DNA synthesis and ligation. Cell signalling systems, such as adaptive and oxidative stress responses, although not DNA repair pathways per se, are nevertheless essential to counteract DNA damage and mutagenesis. The present review focuses on the nature of DNA damage, direct lesion reversal, DNA excision repair pathways and adaptive and oxidative stress responses in E. coli.
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Gomes MR, Guimarães ACR, de Miranda AB. Specific and nonhomologous isofunctional enzymes of the genetic information processing pathways as potential therapeutical targets for tritryps. Enzyme Res 2011; 2011:543912. [PMID: 21808726 PMCID: PMC3145330 DOI: 10.4061/2011/543912] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2011] [Revised: 03/22/2011] [Accepted: 05/05/2011] [Indexed: 12/03/2022] Open
Abstract
Leishmania major, Trypanosoma brucei, and Trypanosoma cruzi (Tritryps) are unicellular protozoa that cause leishmaniasis, sleeping sickness and Chagas' disease, respectively. Most drugs against them were discovered through the screening of large numbers of compounds against whole parasites. Nonhomologous isofunctional enzymes (NISEs) may present good opportunities for the identification of new putative drug targets because, though sharing the same enzymatic activity, they possess different three-dimensional structures thus allowing the development of molecules against one or other isoform. From public data of the Tritryps' genomes, we reconstructed the Genetic Information Processing Pathways (GIPPs). We then used AnEnPi to look for the presence of these enzymes between Homo sapiens and Tritryps, as well as specific enzymes of the parasites. We identified three candidates (ECs 3.1.11.2 and 6.1.1.-) in these pathways that may be further studied as new therapeutic targets for drug development against these parasites.
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Affiliation(s)
- Monete Rajão Gomes
- Laboratório de Biologia Computacional e Sistemas, Instituto Oswaldo Cruz/FIOCRUZ, 21045-900 Rio de Janeiro, RJ, Brazil
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14
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Pinto AV, Deodato EL, Cardoso JS, Oliveira EF, Machado SL, Toma HK, Leitão AC, de Pádula M. Enzymatic recognition of DNA damage induced by UVB-photosensitized titanium dioxide and biological consequences in Saccharomyces cerevisiae: evidence for oxidatively DNA damage generation. Mutat Res 2010; 688:3-11. [PMID: 20167226 DOI: 10.1016/j.mrfmmm.2010.02.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2009] [Revised: 01/27/2010] [Accepted: 02/09/2010] [Indexed: 11/17/2022]
Abstract
Although titanium dioxide (TiO(2)) has been considered to be biologically inert, finding use in cosmetics, paints and food colorants, recent reports have demonstrated that when TiO(2) is attained by UVA radiation oxidative genotoxic and cytotoxic effects are observed in living cells. However, data concerning TiO(2)-UVB association is poor, even if UVB radiation represents a major environmental carcinogen. Herein, we investigated DNA damage, repair and mutagenesis induced by TiO(2) associated with UVB irradiation in vitro and in vivo using Saccharomyces cerevisiae model. It was found that TiO(2) plus UVB treatment in plasmid pUC18 generated, in addition to cyclobutane pyrimidine dimers (CPDs), specific damage to guanine residues, such as 8-oxo-7,8-dihydroguanine (8-oxoG) and 2,6-diamino-4-hydroxy-5-formamidopyrimidine (FapyG), which are characteristic oxidatively generated lesions. In vivo experiments showed that, although the presence of TiO(2) protects yeast cells from UVB cytotoxicity, high mutation frequencies are observed in the wild-type (WT) and in an ogg1 strain (deficient in 8-oxoG and FapyG repair). Indeed, after TiO(2) plus UVB treatment, induced mutagenesis was drastically enhanced in ogg1 cells, indicating that mutagenic DNA lesions are repaired by the Ogg1 protein. This effect could be attenuated by the presence of metallic ion chelators: neocuproine or dipyridyl, which partially block oxidatively generated damage occurring via Fenton reactions. Altogether, the results indicate that TiO(2) plus UVB potentates UVB oxidatively generated damage to DNA, possibly via Fenton reactions involving the production of DNA base damage, such as 8-oxo-7,8-dihydroguanine.
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Affiliation(s)
- A Viviana Pinto
- Laboratório de Diagnóstico Molecular e Hematologia, Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Centro de Ciências da Saúde - Ilha do Fundão, CEP 21941-540, Rio de Janeiro, Brazil.
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15
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Shin JH, Lee HW, Kim SM, Kim J. Proteomic analysis of Acinetobacter baumannii in biofilm and planktonic growth mode. J Microbiol 2010; 47:728-35. [PMID: 20127467 DOI: 10.1007/s12275-009-0158-y] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2009] [Accepted: 07/08/2009] [Indexed: 01/12/2023]
Abstract
Recently, multidrug-resistant clinical isolates of Acinetobacter baumannii have been found to have a high capacity to form biofilm. It is well known that bacterial cells within biofilms are highly resistant to antibiotics, UV light, acid exposure, dehydration, and phagocytosis in comparison to their planktonic counterparts, which suggests that the cells in a biofilm have altered metabolic activity. To determine which proteins are up-regulated in A. baumannii biofilm cells, we performed a proteomic analysis. A clinical isolate of A. baumannii 1656-2, which was characterized to have a high biofilm forming ability, was cultivated under biofilm and planktonic conditions. Outer membrane enriched A. baumannii 1656-2 proteins were separated by two-dimensional (2-D) gel electrophoresis and the differentially expressed proteins were identified by MALDI-TOF mass spectrometry. The proteins up-regulated or expressed only in biofilm cells of A. baumannii are categorized as follows: (i) proteins processing environmental information such as the outer membrane receptor protein involved in mostly Fe transport, a sensor histidine kinase/response regulator, and diguanylate cyclase (PAS-GGEDF-EAL domain); (ii) proteins involved in metabolism such as NAD-linked malate dehydrogenase, nucleoside-diphosphate sugar epimerase, putative GalE, ProFAR isomerase, and N-acetylmuramoyl-L: -alanine amidase; (iii) bacterial antibiotic resistance related proteins; and (iv) proteins related to gene repair such as exodeoxyribonuclease III and GidA. This proteomic analysis provides a fundamental platform for further studies to reveal the role of biofilm in the persistence and tolerance of A. baumannii.
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Affiliation(s)
- Ji-Hyun Shin
- Department of Microbiology, Kyungpook National University, School of Medicine, Daegu 700-422, Republic of Korea
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Dos Vultos T, Mestre O, Tonjum T, Gicquel B. DNA repair inMycobacterium tuberculosisrevisited. FEMS Microbiol Rev 2009; 33:471-87. [DOI: 10.1111/j.1574-6976.2009.00170.x] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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17
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Pang BCM, Cheung BKK. One-step generation of degraded DNA by UV irradiation. Anal Biochem 2007; 360:163-5. [PMID: 17113560 DOI: 10.1016/j.ab.2006.10.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2006] [Accepted: 10/02/2006] [Indexed: 10/24/2022]
Affiliation(s)
- B C M Pang
- Forensic Science Division, Hong Kong Government Laboratory, Homantin Government Offices, 88 Chung Hau Street, Kowloon, Hong Kong SAR, China.
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