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Mishra A, Chakraborty S, Jaiswal TP, Bhattacharjee S, Kesarwani S, Mishra AK, Singh SS. Untangling the adaptive strategies of thermophilic bacterium Anoxybacillus rupiensis TPH1 under low temperature. Extremophiles 2024; 28:31. [PMID: 39020126 DOI: 10.1007/s00792-024-01346-2] [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: 12/28/2023] [Accepted: 06/10/2024] [Indexed: 07/19/2024]
Abstract
The present study investigates the low temperature tolerance strategies of thermophilic bacterium Anoxybacillus rupiensis TPH1, which grows optimally at 55 °C , by subjecting it to a temperature down-shift of 10 °C (45 °C) for 4 and 6 h followed by studying its growth, morphophysiological, molecular and proteomic responses. Results suggested that although TPH1 experienced increased growth inhibition, ROS production, protein oxidation and membrane disruption after 4 h of incubation at 45 °C yet maintained its DNA integrity and cellular structure through the increased expression of DNA damage repair and cell envelop synthesizing proteins and also progressively alleviated growth inhibition by 20% within two hours i.e., 6 h, by inducing the expression of antioxidative enzymes, production of unsaturated fatty acids, capsular and released exopolysaccharides and forming biofilm along with chemotaxis proteins. Conclusively, the adaptation of Anoxybacillus rupiensis TPH1 to lower temperature is mainly mediated by the synthesis of large numbers of defense proteins and exopolysaccharide rich biofilm formation.
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Affiliation(s)
- Aditi Mishra
- Laboratory of Cyanobacterial Systematics and Stress Biology, Department of Botany, Banaras Hindu University, Varanasi, India
| | - Sindhunath Chakraborty
- Laboratory of Microbial Genetics, Department of Botany, Banaras Hindu University, Varanasi, India
| | - Tameshwar Prasad Jaiswal
- Laboratory of Cyanobacterial Systematics and Stress Biology, Department of Botany, Banaras Hindu University, Varanasi, India
| | - Samujjal Bhattacharjee
- Laboratory of Microbial Genetics, Department of Botany, Banaras Hindu University, Varanasi, India
| | - Shreya Kesarwani
- Laboratory of Cyanobacterial Systematics and Stress Biology, Department of Botany, Banaras Hindu University, Varanasi, India
| | - Arun Kumar Mishra
- Laboratory of Microbial Genetics, Department of Botany, Banaras Hindu University, Varanasi, India
| | - Satya Shila Singh
- Laboratory of Cyanobacterial Systematics and Stress Biology, Department of Botany, Banaras Hindu University, Varanasi, India.
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2
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Won C, Yim SS. Emerging methylation-based approaches in microbiome engineering. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:96. [PMID: 38987811 PMCID: PMC11238421 DOI: 10.1186/s13068-024-02529-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 06/10/2024] [Indexed: 07/12/2024]
Abstract
Bacterial epigenetics, particularly through DNA methylation, exerts significant influence over various biological processes such as DNA replication, uptake, and gene regulation in bacteria. In this review, we explore recent advances in characterizing bacterial epigenomes, accompanied by emerging strategies that harness bacterial epigenetics to elucidate and engineer diverse bacterial species with precision and effectiveness. Furthermore, we delve into the potential of epigenetic modifications to steer microbial functions and influence community dynamics, offering promising opportunities for understanding and modulating microbiomes. Additionally, we investigate the extensive diversity of DNA methyltransferases and emphasize their potential utility in the context of the human microbiome. In summary, this review highlights the potential of DNA methylation as a powerful toolkit for engineering microbiomes.
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Affiliation(s)
- Changhee Won
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Sung Sun Yim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.
- Graduate School of Engineering Biology, KAIST, Daejeon, Republic of Korea.
- KAIST Institute for BioCentury, KAIST, Daejeon, Republic of Korea.
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea.
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3
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Dong H, Wang Y, Zhi T, Guo H, Guo Y, Liu L, Yin Y, Shi J, He B, Hu L, Jiang G. Construction of protein-protein interaction network in sulfate-reducing bacteria: Unveiling of global response to Hg. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 351:124048. [PMID: 38714230 DOI: 10.1016/j.envpol.2024.124048] [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: 01/28/2024] [Revised: 04/20/2024] [Accepted: 04/23/2024] [Indexed: 05/09/2024]
Abstract
Sulfate-reducing bacteria (SRB) play pivotal roles in the biotransformation of mercury (Hg). However, unrevealed global responses of SRB to Hg have restricted our understanding of details of Hg biotransformation processes. The absence of protein-protein interaction (PPI) network under Hg stimuli has been a bottleneck of proteomic analysis for molecular mechanisms of Hg transformation. This study constructed the first comprehensive PPI network of SRB in response to Hg, encompassing 67 connected nodes, 26 independent nodes, and 121 edges, covering 93% of differentially expressed proteins from both previous studies and this study. The network suggested that proteomic changes of SRB in response to Hg occurred globally, including microbial metabolism in diverse environments, carbon metabolism, nucleic acid metabolism and translation, nucleic acid repair, transport systems, nitrogen metabolism, and methyltransferase activity, partial of which could cover the known knowledge. Antibiotic resistance was the original response revealed by this network, providing insights into of Hg biotransformation mechanisms. This study firstly provided the foundational network for a comprehensive understanding of SRB's responses to Hg, convenient for exploration of potential targets for Hg biotransformation. Furthermore, the network indicated that Hg enhances the metabolic activities and modification pathways of SRB to maintain cellular activities, shedding light on the influences of Hg on the carbon, nitrogen, and sulfur cycles at the cellular level.
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Affiliation(s)
- Hongzhe Dong
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; Sino-Danish College, University of Chinese Academy of Sciences, Beijing, 100049, China; Sino-Danish Centre for Education and Research, Beijing, 100049, China
| | - Yuchuan Wang
- Hebei Key Laboratory for Chronic Diseases, School of Basic Medical Sciences, North China University of Science and Technology, Tangshan, Hebei, 063210, China
| | - Tingting Zhi
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Hua Guo
- School of Environment, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China
| | - Yingying Guo
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Lihong Liu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Yongguang Yin
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; School of Environment, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China
| | - Jianbo Shi
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; School of Environment and Health, Jianghan University, Wuhan, 430056, China
| | - Bin He
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; School of Environment, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China
| | - Ligang Hu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; Sino-Danish College, University of Chinese Academy of Sciences, Beijing, 100049, China; Sino-Danish Centre for Education and Research, Beijing, 100049, China; School of Environment, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China.
| | - Guibin Jiang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; School of Environment, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China
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4
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Ruan S, Bourne CR. Escherichia coli cells evade inducible parE toxin expression by reducing plasmid copy number. Microbiol Spectr 2024; 12:e0397323. [PMID: 38700352 PMCID: PMC11237751 DOI: 10.1128/spectrum.03973-23] [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: 11/17/2023] [Accepted: 04/15/2024] [Indexed: 05/05/2024] Open
Abstract
Plasmids play important roles in microbial ecosystems, serving as carriers of antibiotic resistance and virulence. In the laboratory, they are essential tools for genetic manipulation and recombinant protein expression. We uncovered an intriguing survival phenotype in a fraction of the bacterial population while using plasmid-mediated arabinose-inducible gene expression to monitor the production of toxic ParE proteins. This phenotype was not correlated with changes to the plasmid sequence and could not be rescued by increasing arabinose uptake. Instead, survival correlates with a marked reduction in plasmid copy number (PCN). Reduced PCN is reproducible, not a function of the pre-existing population, and can be sequentially enriched by continual passage with induction. The reduction in PCN appears to allow mitigation of toxicity from the expression of ParE proteins while balancing the need to maintain a threshold PCN to withstand selection conditions. This indicates an adaptive cellular response to stressful conditions, likely by altering the regulation of plasmid replication. Furthermore, this survival mechanism appears to not be limited to a specific bacterial strain of Escherichia coli or ParE toxin family member, suggesting a generalized response. Finally, bacterial whole genome sequencing indicated an N845S residue substitution in DNA polymerase I, which correlates with the observed reduction in PCN and has been previously reported to impact plasmid replication. Further understanding this molecular mechanism has broader implications for this adaptive response of the dynamics of plasmid-mediated gene expression, microbial adaptation, and genetic engineering methodologies. IMPORTANCE This research has increased our understanding of how bacteria respond to the pressure from plasmid-borne toxic genes, such as those found in toxin-antitoxin systems. Surprisingly, we found that bacteria survived toxic ParE protein expression by reducing the number of these plasmids in the cells. This discovery reveals another way in which bacteria can balance toxin expression with antibiotic selection to attenuate the effects of deleterious genes. This insight is not only valuable for understanding bacterial survival strategies but may also influence the development of better tools in biotechnology, where plasmids are often used to study the functional roles of genes.
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Affiliation(s)
- Shengfeng Ruan
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
| | - Christina R. Bourne
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
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Zhou Z, Xiao C, Yin J, She J, Duan H, Liu C, Fu X, Cui F, Qi Q, Zhang Z. PSAC-6mA: 6mA site identifier using self-attention capsule network based on sequence-positioning. Comput Biol Med 2024; 171:108129. [PMID: 38342046 DOI: 10.1016/j.compbiomed.2024.108129] [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: 12/19/2023] [Revised: 02/06/2024] [Accepted: 02/06/2024] [Indexed: 02/13/2024]
Abstract
DNA N6-methyladenine (6mA) modifications play a pivotal role in the regulation of growth, development, and diseases in organisms. As a significant epigenetic marker, 6mA modifications extensively participate in the intricate regulatory networks of the genome. Hence, gaining a profound understanding of how 6mA is intricately involved in these biological processes is imperative for deciphering the gene regulatory networks within organisms. In this study, we propose PSAC-6mA (Position-self-attention Capsule-6mA), a sequence-location-based self-attention capsule network. The positional layer in the model enables positional relationship extraction and independent parameter setting for each base position, avoiding parameter sharing inherent in convolutional approaches. Simultaneously, the self-attention capsule network enhances dimensionality, capturing correlation information between capsules and achieving exceptional results in feature extraction across multiple spatial dimensions within the model. Experimental results demonstrate the superior performance of PSAC-6mA in recognizing 6mA motifs across various species.
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Affiliation(s)
- Zheyu Zhou
- School of Computer Science and Technology, Hainan University, Haikou, 570228, China
| | - Cuilin Xiao
- School of Computer Science and Technology, Hainan University, Haikou, 570228, China
| | - Jinfen Yin
- School of Computer Science and Technology, Hainan University, Haikou, 570228, China
| | - Jiayi She
- School of Computer Science and Technology, Hainan University, Haikou, 570228, China
| | - Hao Duan
- School of Computer Science and Technology, Hainan University, Haikou, 570228, China
| | - Chunling Liu
- School of Computer Science and Technology, Hainan University, Haikou, 570228, China
| | - Xiuhao Fu
- School of Computer Science and Technology, Hainan University, Haikou, 570228, China
| | - Feifei Cui
- School of Computer Science and Technology, Hainan University, Haikou, 570228, China
| | - Qi Qi
- School of Computer Science and Technology, Hainan University, Haikou, 570228, China
| | - Zilong Zhang
- School of Computer Science and Technology, Hainan University, Haikou, 570228, China.
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6
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Bonde NJ, Wood EA, Myers KS, Place M, Keck JL, Cox MM. Identification of recG genetic interactions in Escherichia coli by transposon sequencing. J Bacteriol 2023; 205:e0018423. [PMID: 38019006 PMCID: PMC10870727 DOI: 10.1128/jb.00184-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 08/07/2023] [Indexed: 11/30/2023] Open
Abstract
IMPORTANCE DNA damage and subsequent DNA repair processes are mutagenic in nature and an important driver of evolution in prokaryotes, including antibiotic resistance development. Genetic screening approaches, such as transposon sequencing (Tn-seq), have provided important new insights into gene function and genetic relationships. Here, we employed Tn-seq to gain insight into the function of the recG gene, which renders Escherichia coli cells moderately sensitive to a variety of DNA-damaging agents when they are absent. The reported recG genetic interactions can be used in combination with future screens to aid in a more complete reconstruction of DNA repair pathways in bacteria.
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Affiliation(s)
- Nina J. Bonde
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Elizabeth A. Wood
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Kevin S. Myers
- Great Lakes Bioenergy Research Center and the Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Michael Place
- Great Lakes Bioenergy Research Center and the Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - James L. Keck
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Michael M. Cox
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
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7
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Sinha D, Dasmandal T, Paul K, Yeasin M, Bhattacharjee S, Murmu S, Mishra DC, Pal S, Rai A, Archak S. MethSemble-6mA: an ensemble-based 6mA prediction server and its application on promoter region of LBD gene family in Poaceae. FRONTIERS IN PLANT SCIENCE 2023; 14:1256186. [PMID: 37877081 PMCID: PMC10591185 DOI: 10.3389/fpls.2023.1256186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 09/01/2023] [Indexed: 10/26/2023]
Abstract
The Lateral Organ Boundaries Domain (LBD) containing genes are a set of plant-specific transcription factors and are crucial for controlling both organ development and defense mechanisms as well as anthocyanin synthesis and nitrogen metabolism. It is imperative to understand how methylation regulates gene expression, through predicting methylation sites of their promoters particularly in major crop species. In this study, we developed a user-friendly prediction server for accurate prediction of 6mA sites by incorporating a robust feature set, viz., Binary Encoding of Mono-nucleotide DNA. Our model,MethSemble-6mA, outperformed other state-of-the-art tools in terms of accuracy (93.12%). Furthermore, we investigated the pattern of probable 6mA sites at the upstream promoter regions of the LBD-containing genes in Triticum aestivum and its allied species using the developed tool. On average, each selected species had four 6mA sites, and it was found that with speciation and due course of evolution in wheat, the frequency of methylation have reduced, and a few sites remain conserved. This obviously cues gene birth and gene expression alteration through methylation over time in a species and reflects functional conservation throughout evolution. Since DNA methylation is a vital event in almost all plant developmental processes (e.g., genomic imprinting and gametogenesis) along with other life processes, our findings on epigenetic regulation of LBD-containing genes have dynamic implications in basic and applied research. Additionally, MethSemble-6mA (http://cabgrid.res.in:5799/) will serve as a useful resource for a plant breeders who are interested to pursue epigenetic-based crop improvement research.
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Affiliation(s)
- Dipro Sinha
- ICAR-Indian Agricultural Statistics Research Institute, Delhi, India
- Graduate School, ICAR-Indian Agricultural Research Institute, Delhi, India
| | - Tanwy Dasmandal
- ICAR-Indian Agricultural Statistics Research Institute, Delhi, India
- Graduate School, ICAR-Indian Agricultural Research Institute, Delhi, India
- ICAR-National Bureau of Fish Genetic Resources, Lucknow, India
| | - Krishnayan Paul
- Graduate School, ICAR-Indian Agricultural Research Institute, Delhi, India
- ICAR-National Institute for Plant Biotechnology, Delhi, India
| | - Md Yeasin
- ICAR-Indian Agricultural Statistics Research Institute, Delhi, India
| | - Sougata Bhattacharjee
- Graduate School, ICAR-Indian Agricultural Research Institute, Delhi, India
- ICAR-National Institute for Plant Biotechnology, Delhi, India
- ICAR-Indian Agricultural Research Institute, Hazaribagh, Jharkhand, India
| | - Sneha Murmu
- ICAR-Indian Agricultural Statistics Research Institute, Delhi, India
| | | | - Soumen Pal
- ICAR-Indian Agricultural Statistics Research Institute, Delhi, India
| | - Anil Rai
- Indian Council of Agricultural Research, Delhi, India
| | - Sunil Archak
- ICAR-National Bureau of Plant Genetic Resources, Delhi, India
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8
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Vogelgsang L, Nisar A, Scharf SA, Rommerskirchen A, Belick D, Dilthey A, Henrich B. Characterisation of Type II DNA Methyltransferases of Metamycoplasma hominis. Microorganisms 2023; 11:1591. [PMID: 37375093 DOI: 10.3390/microorganisms11061591] [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: 03/27/2023] [Revised: 06/02/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
Bacterial virulence, persistence and defence are affected by epigenetic modifications, including DNA methylation. Solitary DNA methyltransferases modulate a variety of cellular processes and influence bacterial virulence; as part of a restriction-modification (RM) system, they act as a primitive immune system in methylating the own DNA, while unmethylated foreign DNA is restricted. We identified a large family of type II DNA methyltransferases in Metamycoplasma hominis, comprising six solitary methyltransferases and four RM systems. Motif-specific 5mC and 6mA methylations were identified with a tailored Tombo analysis on Nanopore reads. Selected motifs with methylation scores >0.5 fit with the gene presence of DAM1 and DAM2, DCM2, DCM3, and DCM6, but not for DCM1, whose activity was strain-dependent. The activity of DCM1 for CmCWGG and of both DAM1 and DAM2 for GmATC was proven in methylation-sensitive restriction and finally for recombinant rDCM1 and rDAM2 against a dam-, dcm-negative background. A hitherto unknown dcm8/dam3 gene fusion containing a (TA) repeat region of varying length was characterized within a single strain, suggesting the expression of DCM8/DAM3 phase variants. The combination of genetic, bioinformatics, and enzymatic approaches enabled the detection of a huge family of type II DNA MTases in M. hominis, whose involvement in virulence and defence can now be characterized in future work.
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Affiliation(s)
- Lars Vogelgsang
- Institute of Medical Microbiology and Hospital Hygiene, Medical Faculty of the Heinrich-Heine-University Duesseldorf, Universitätsstraße 1, 40225 Duesseldorf, Germany
| | - Azlan Nisar
- Institute of Medical Microbiology and Hospital Hygiene, Medical Faculty of the Heinrich-Heine-University Duesseldorf, Universitätsstraße 1, 40225 Duesseldorf, Germany
| | - Sebastian Alexander Scharf
- Institute of Medical Microbiology and Hospital Hygiene, Medical Faculty of the Heinrich-Heine-University Duesseldorf, Universitätsstraße 1, 40225 Duesseldorf, Germany
| | - Anna Rommerskirchen
- Institute of Medical Microbiology and Hospital Hygiene, Medical Faculty of the Heinrich-Heine-University Duesseldorf, Universitätsstraße 1, 40225 Duesseldorf, Germany
| | - Dana Belick
- Institute of Medical Microbiology and Hospital Hygiene, Medical Faculty of the Heinrich-Heine-University Duesseldorf, Universitätsstraße 1, 40225 Duesseldorf, Germany
| | - Alexander Dilthey
- Institute of Medical Microbiology and Hospital Hygiene, Medical Faculty of the Heinrich-Heine-University Duesseldorf, Universitätsstraße 1, 40225 Duesseldorf, Germany
| | - Birgit Henrich
- Institute of Medical Microbiology and Hospital Hygiene, Medical Faculty of the Heinrich-Heine-University Duesseldorf, Universitätsstraße 1, 40225 Duesseldorf, Germany
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9
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Diaz-Diaz S, Recacha E, Pulido MR, Romero-Muñoz M, de Gregorio-Iaria B, Docobo-Pérez F, Pascual A, Rodríguez-Martínez JM. Synergistic Effect of SOS Response and GATC Methylome Suppression on Antibiotic Stress Survival in Escherichia coli. Antimicrob Agents Chemother 2023; 67:e0139222. [PMID: 36802234 PMCID: PMC10019295 DOI: 10.1128/aac.01392-22] [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: 10/14/2022] [Accepted: 01/22/2023] [Indexed: 02/23/2023] Open
Abstract
The suppression of the SOS response has been shown to enhance the in vitro activity of quinolones. Furthermore, Dam-dependent base methylation has an impact on susceptibility to other antimicrobials affecting DNA synthesis. Here, we investigated the interplay between these two processes, alone and in combination, in terms of antimicrobial activity. A genetic strategy was used employing single- and double-gene mutants for the SOS response (recA gene) and the Dam methylation system (dam gene) in isogenic models of Escherichia coli both susceptible and resistant to quinolones. Regarding the bacteriostatic activity of quinolones, a synergistic sensitization effect was observed when the Dam methylation system and the recA gene were suppressed. In terms of growth, after 24 h in the presence of quinolones, the Δdam ΔrecA double mutant showed no growth or delayed growth compared to the control strain. In bactericidal terms, spot tests showed that the Δdam ΔrecA double mutant was more sensitive than the ΔrecA single mutant (about 10- to 102-fold) and the wild type (about 103- to 104-fold) in both susceptible and resistant genetic backgrounds. Differences between the wild type and the Δdam ΔrecA double mutant were confirmed by time-kill assays. The suppression of both systems, in a strain with chromosomal mechanisms of quinolone resistance, prevents the evolution of resistance. This genetic and microbiological approach demonstrated the enhanced sensitization of E. coli to quinolones by dual targeting of the recA (SOS response) and Dam methylation system genes, even in a resistant strain model.
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Affiliation(s)
- S. Diaz-Diaz
- Unidad de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen Macarena, Seville, Spain
- Departamento de Microbiología, Facultad de Medicina, Universidad de Sevilla, Seville, Spain
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen Macarena/CSIC/Universidad de Sevilla, Seville, Spain
| | - E. Recacha
- Unidad de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen Macarena, Seville, Spain
- Departamento de Microbiología, Facultad de Medicina, Universidad de Sevilla, Seville, Spain
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen Macarena/CSIC/Universidad de Sevilla, Seville, Spain
| | - Marina R. Pulido
- Departamento de Microbiología, Facultad de Medicina, Universidad de Sevilla, Seville, Spain
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen Macarena/CSIC/Universidad de Sevilla, Seville, Spain
| | - María Romero-Muñoz
- Departamento de Microbiología, Facultad de Medicina, Universidad de Sevilla, Seville, Spain
| | - B. de Gregorio-Iaria
- Departamento de Microbiología, Facultad de Medicina, Universidad de Sevilla, Seville, Spain
| | - F. Docobo-Pérez
- Departamento de Microbiología, Facultad de Medicina, Universidad de Sevilla, Seville, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen Macarena/CSIC/Universidad de Sevilla, Seville, Spain
| | - A. Pascual
- Unidad de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen Macarena, Seville, Spain
- Departamento de Microbiología, Facultad de Medicina, Universidad de Sevilla, Seville, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen Macarena/CSIC/Universidad de Sevilla, Seville, Spain
| | - J. M. Rodríguez-Martínez
- Departamento de Microbiología, Facultad de Medicina, Universidad de Sevilla, Seville, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen Macarena/CSIC/Universidad de Sevilla, Seville, Spain
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10
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Global Transcriptional Response of Escherichia coli Exposed In Situ to Different Low-Dose Ionizing Radiation Sources. mSystems 2023; 8:e0071822. [PMID: 36779725 PMCID: PMC10134817 DOI: 10.1128/msystems.00718-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2023] Open
Abstract
Characterization of biological and chemical responses to ionizing radiation by various organisms is essential for potential applications in bioremediation, alternative modes of detecting nuclear material, and national security. Escherichia coli DH10β is an optimal system to study the microbial response to low-dose ionizing radiation at the transcriptional level because it is a well-characterized model bacterium and its responses to other environmental stressors, including those to higher radiation doses, have been elucidated in prior studies. In this study, RNA sequencing with downstream transcriptomic analysis (RNA-seq) was employed to characterize the global transcriptional response of stationary-phase E. coli subjected to 239Pu, 3H (tritium), and 55Fe, at an approximate absorbed dose rate of 10 mGy day-1 for 1 day and 15 days. Differential expression analysis identified significant changes in gene expression of E. coli for both short- and long-term exposures. Radionuclide source exposure induced differential expression in E. coli of genes involved in biosynthesis pathways of nuclear envelope components, amino acids, and siderophores, transport systems such as ABC transporters and type II secretion proteins, and initiation of stress response and regulatory systems of temperature stress, the RpoS regulon, and oxidative stress. These findings provide a basic understanding of the relationship between low-dose exposure and biological effect of a model bacterium that is critical for applications in alternative nuclear material detection and bioremediation. IMPORTANCE Escherichia coli strain DH10β, a well-characterized model bacterium, was subjected to short-term (1-day) and long-term (15-day) exposures to three different in situ radiation sources comprised of radionuclides relevant to nuclear activities to induce a measurable and identifiable genetic response. We found E. coli had both common and unique responses to the three exposures studied, suggesting both dose rate- and radionuclide-specific effects. This study is the first to provide insights into the transcriptional response of a microorganism in short- and long-term exposure to continuous low-dose ionizing radiation with multiple in situ radionuclide sources and the first to examine microbial transcriptional response in stationary phase. Moreover, this work provides a basis for the development of biosensors and informing more robust dose-response relationships to support ecological risk assessment.
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11
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Tsukiyama S, Hasan MM, Kurata H. CNN6mA: Interpretable neural network model based on position-specific CNN and cross-interactive network for 6mA site prediction. Comput Struct Biotechnol J 2022; 21:644-654. [PMID: 36659917 PMCID: PMC9826936 DOI: 10.1016/j.csbj.2022.12.043] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/26/2022] [Accepted: 12/27/2022] [Indexed: 12/29/2022] Open
Abstract
N6-methyladenine (6mA) plays a critical role in various epigenetic processing including DNA replication, DNA repair, silencing, transcription, and diseases such as cancer. To understand such epigenetic mechanisms, 6 mA has been detected by high-throughput technologies on a genome-wide scale at single-base resolution, together with conventional methods such as immunoprecipitation, mass spectrometry and capillary electrophoresis, but these experimental approaches are time-consuming and laborious. To complement these problems, we have developed a CNN-based 6 mA site predictor, named CNN6mA, which proposed two new architectures: a position-specific 1-D convolutional layer and a cross-interactive network. In the position-specific 1-D convolutional layer, position-specific filters with different window sizes were applied to an inquiry sequence instead of sharing the same filters over all positions in order to extract the position-specific features at different levels. The cross-interactive network explored the relationships between all the nucleotide patterns within the inquiry sequence. Consequently, CNN6mA outperformed the existing state-of-the-art models in many species and created the contribution score vector that intelligibly interpret the prediction mechanism. The source codes and web application in CNN6mA are freely accessible at https://github.com/kuratahiroyuki/CNN6mA.git and http://kurata35.bio.kyutech.ac.jp/CNN6mA/, respectively.
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Key Words
- 6mA, N6-methyladenine
- AUCs, Area under the curves
- BERT, Bidirectional Encoder Representations from Transformers
- CNN
- CNN, Convolutional neural network
- DNA modification
- Deep learning
- Interpretable prediction
- LSTM, Long short-term memory
- MCC, Matthews correlation coefficient
- Machine learning
- N6-methyladenine
- RF, Random forest
- SMRT, Single-molecule real-time
- SN, Sensitivity
- SP, Specificity
- UMAP, Uniform manifold approximation and projection
- t-SNE, t-distributed stochastic neighbor embedding
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Affiliation(s)
- Sho Tsukiyama
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680–4 Kawazu, Iizuka, Fukuoka 820-8502, Japan
| | - Md Mehedi Hasan
- Tulane Center for Aging and Department of Medicine, Tulane University Health Sciences Center, New Orleans, LA 70112, USA
| | - Hiroyuki Kurata
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680–4 Kawazu, Iizuka, Fukuoka 820-8502, Japan,Corresponding author.
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12
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Sheng Y, Zhou M, You C, Dai X. Dynamics and biological relevance of epigenetic N6-methyladenine DNA modification in eukaryotic cells. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2021.08.109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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13
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Tsukiyama S, Hasan MM, Deng HW, Kurata H. BERT6mA: prediction of DNA N6-methyladenine site using deep learning-based approaches. Brief Bioinform 2022; 23:6539171. [PMID: 35225328 PMCID: PMC8921755 DOI: 10.1093/bib/bbac053] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/28/2022] [Accepted: 01/31/2022] [Indexed: 01/29/2023] Open
Abstract
N6-methyladenine (6mA) is associated with important roles in DNA replication, DNA repair, transcription, regulation of gene expression. Several experimental methods were used to identify DNA modifications. However, these experimental methods are costly and time-consuming. To detect the 6mA and complement these shortcomings of experimental methods, we proposed a novel, deep leaning approach called BERT6mA. To compare the BERT6mA with other deep learning approaches, we used the benchmark datasets including 11 species. The BERT6mA presented the highest AUCs in eight species in independent tests. Furthermore, BERT6mA showed higher and comparable performance with the state-of-the-art models while the BERT6mA showed poor performances in a few species with a small sample size. To overcome this issue, pretraining and fine-tuning between two species were applied to the BERT6mA. The pretrained and fine-tuned models on specific species presented higher performances than other models even for the species with a small sample size. In addition to the prediction, we analyzed the attention weights generated by BERT6mA to reveal how the BERT6mA model extracts critical features responsible for the 6mA prediction. To facilitate biological sciences, the BERT6mA online web server and its source codes are freely accessible at https://github.com/kuratahiroyuki/BERT6mA.git, respectively.
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Affiliation(s)
- Sho Tsukiyama
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka 820-8502, Japan
| | - Md Mehedi Hasan
- Tulane Center for Biomedical Informatics and Genomics, Division of Biomedical Informatics and Genomics, John W. Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Hong-Wen Deng
- Tulane Center for Biomedical Informatics and Genomics, Division of Biomedical Informatics and Genomics, John W. Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Hiroyuki Kurata
- Corresponding author: Hiroyuki Kurata, Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka 820-8502, Japan. Tel: 81-948-29-7828; E-mail:
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14
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Zhang Z, Wang L. Using Chou's 5-steps rule to identify N 6-methyladenine sites by ensemble learning combined with multiple feature extraction methods. J Biomol Struct Dyn 2022; 40:796-806. [PMID: 32948102 DOI: 10.1080/07391102.2020.1821778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
N6-methyladenine (m6A), a type of modification mostly affecting the downstream biological functions and determining the levels of gene expression, is mediated by the methylation of adenine in nucleic acids. It is also a key factor for influencing biological processes and has attracted attention as a target for treating diseases. Here, an ensemble predictor named as TL-Methy, was developed to identify m6A sites across the genome. TL-Methy is a 2-level machine learning method developed by combining the support vector machine model and multiple features extraction methods, including nucleic acid composition, di-nucleotide composition, tri-nucleotide composition, position-specific trinucleotide propensity, Bi-profile Bayes, binary encoding, and accumulated nucleotide frequency. For Homo sapiens, TL-Methy method reached the accuracy of 91.68% on jackknife test and of 92.23% on 10-fold cross validation test; For Mus musculus, TL-Methy method achieved the accuracy of 93.66% on jackknife test and of 97.07% on 10-fold cross validation test; For Saccharomyces cerevisiae, TL-Methy method obtained the accuracy of 81.57% on jackknife test and of 82.54% on 10-fold cross validation test; For rice genome, TL-Methy method achieved the accuracy of 91.87% on jackknife test and of 93.04% on 10-fold cross validation test. The results via these two test approaches demonstrated the robustness and practicality of our TL-Methy model. The TL-Methy model may be as a potential method for m6A site identification.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Zhongwang Zhang
- College of Science, Dalian Maritime University, Dalian, P.R. China
| | - Lidong Wang
- College of Science, Dalian Maritime University, Dalian, P.R. China
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15
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O’Brown ZK, Greer EL. N6-methyladenine: A Rare and Dynamic DNA Mark. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:177-210. [DOI: 10.1007/978-3-031-11454-0_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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16
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Ren J, Lee HM, Shen J, Na D. Advanced biotechnology using methyltransferase and its applications in bacteria: a mini review. Biotechnol Lett 2021; 44:33-44. [PMID: 34820721 DOI: 10.1007/s10529-021-03208-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 11/12/2021] [Indexed: 11/26/2022]
Abstract
Since prokaryotic restriction-modification (RM) systems protect the host by cleaving foreign DNA by restriction endonucleases, it is difficult to introduce engineered plasmid DNAs into newly isolated microorganisms whose RM system is not discovered. The prokaryotes also possess methyltransferases to protect their own DNA from the endonucleases. As those methyltransferases can be utilized to methylate engineered plasmid DNAs before transformation and to enhance the stability within the cells, the study on methyltransferases in newly isolated bacteria is essential for genetic engineering. Here, we introduce the mechanism of the RM system, specifically the methyltransferases and their biotechnological applications. These biotechnological strategies could facilitate plasmid DNA-based genetic engineering in bacteria strains that strongly defend against foreign DNA.
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Affiliation(s)
- Jun Ren
- Department of Biomedical Engineering, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Hyang-Mi Lee
- Department of Biomedical Engineering, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - JunHao Shen
- Department of Biomedical Engineering, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Dokyun Na
- Department of Biomedical Engineering, Chung-Ang University, Seoul, 06974, Republic of Korea.
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17
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Li X, Zhang Z, Luo X, Schrier J, Yang AD, Wu TP. The exploration of N6-deoxyadenosine methylation in mammalian genomes. Protein Cell 2021; 12:756-768. [PMID: 34405377 PMCID: PMC8464638 DOI: 10.1007/s13238-021-00866-3] [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] [Received: 03/03/2021] [Accepted: 07/12/2021] [Indexed: 11/11/2022] Open
Abstract
N6-methyladenine (N6-mA, m6dA, or 6mA), a prevalent DNA modification in prokaryotes, has recently been identified in higher eukaryotes, including mammals. Although 6mA has been well-studied in prokaryotes, the function and regulatory mechanism of 6mA in eukaryotes are still poorly understood. Recent studies indicate that 6mA can serve as an epigenetic mark and play critical roles in various biological processes, from transposable-element suppression to environmental stress response. Here, we review the significant advances in methodology for 6mA detection and major progress in understanding the regulation and function of this non-canonical DNA methylation in eukaryotes, predominantly mammals.
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Affiliation(s)
- Xuwen Li
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Zijian Zhang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Xinlong Luo
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jacob Schrier
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Andrew D Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Tao P Wu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA. .,Huffington Center on Aging, Baylor College of Medicine, Houston, TX, 77030, USA. .,Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA.
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18
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Hughes L, Roberts W, Johnson D. The impact of DNA adenine methyltransferase knockout on the development of triclosan resistance and antibiotic cross-resistance in Escherichia coli. Access Microbiol 2021; 3:acmi000178. [PMID: 33997609 PMCID: PMC8115981 DOI: 10.1099/acmi.0.000178] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 10/27/2020] [Indexed: 11/18/2022] Open
Abstract
Background DNA adenine methyltransferase (dam) has been well documented for its role in regulation of replication, mismatch repair and transposition. Recent studies have also suggested a role for dam in protection against antibiotic stress, although this is not yet fully defined. We therefore evaluated the role of dam in the development of antibiotic resistance and triclosan-associated cross-resistance. Results A significant impact on growth rate was seen in the dam knockout compared to the parental strain. Known triclosan resistance-associated mutations in fabI were seen regardless of dam status, with an additional mutation in lrhA seen in the dam knockout. The expression of multiple antibiotic resistance-associated genes was significantly different between the parent and dam knockout post-resistance induction. Reversion rate assays showed that resistance mechanisms were stable. Conclusions dam knockout had a significant effect on growth, but its role in the development of antibiotic resistance is likely confined to those antibiotics using acrAD-containing efflux pumps.
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Affiliation(s)
- Lewis Hughes
- Biomedical Sciences, Leeds Beckett University, Leeds, UK
| | - Wayne Roberts
- Biomedical Sciences, Leeds Beckett University, Leeds, UK
| | - Donna Johnson
- Biomedical Sciences, Leeds Beckett University, Leeds, UK
- *Correspondence: Donna Johnson,
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i6mA-VC: A Multi-Classifier Voting Method for the Computational Identification of DNA N6-methyladenine Sites. Interdiscip Sci 2021; 13:413-425. [PMID: 33834381 DOI: 10.1007/s12539-021-00429-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 03/26/2021] [Accepted: 03/29/2021] [Indexed: 12/14/2022]
Abstract
DNA N6-methyladenine (6 mA), as an essential component of epigenetic modification, cannot be neglected in genetic regulation mechanism. The efficient and accurate prediction of 6 mA sites is beneficial to the development of biological genetics. Biochemical experimental methods are considered to be time-consuming and laborious. Most of the established machine learning methods have a single dataset. Although some of them have achieved cross-species prediction, their results are not satisfactory. Therefore, we designed a novel statistical model called i6mA-VC to improve the accuracy for 6 mA sites. On the one hand, kmer and binary encoding are applied to extract features, and then gradient boosting decision tree (GBDT) embedded method is applied as the feature selection strategy. On the other hand, DNA sequences are represented by vectors through the feature extraction method of ring-function-hydrogen-chemical properties (RFHCP) and the feature selection strategy of ExtraTree. After fusing the two optimal features, a voting classifier based on gradient boosting decision tree (GBDT), light gradient boosting machine (LightGBM) and multilayer perceptron classifier (MLPC) is constructed for final classification and prediction. The accuracy of Rice dataset and M.musculus dataset with five-fold cross-validation are 0.888 and 0.967, respectively. The cross-species dataset is selected as independent testing dataset, and the accuracy reaches 0.848. Through rigorous experiments, it is demonstrated that the proposed predictor is convincing and applicable. The development of i6mA-VC predictor will become an effective way for the recognition of N6-methyladenine sites, and it will also be beneficial for biological geneticists to further study gene expression and DNA modification. In addition, an accessible web-server for i6mA-VC is available from http://www.zhanglab.site/ .
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20
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Conjoint expression and purification strategy for acquiring proteins with ultra-low DNA N6-methyladenine backgrounds in Escherichia coli. Biosci Rep 2021; 41:228016. [PMID: 33660764 PMCID: PMC7960888 DOI: 10.1042/bsr20203769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 03/02/2021] [Accepted: 03/03/2021] [Indexed: 11/21/2022] Open
Abstract
DNA N6-methyladenine (6mA), a kind of DNA epigenetic modification, is widespread in eukaryotes and prokaryotes. An enzyme activity study coupled with 6mA detection using ultra-high-performance liquid chromatography-quadruple mass spectrometry (UHPLC-MS/MS) is commonly applied to investigate 6mA potentially related enzymes in vitro. However, the protein expressed in a common Escherichia coli (E. coli) strain shows an extremely high 6mA background due to minute co-purified bacterial DNA, though it has been purified to remove DNA using multiple strategies. Furthermore, as occupied by DNA with abundant 6mA, the activity of 6mA-related proteins will be influenced seriously. Here, to address this issue, we for the first time construct a derivative of E. coli Rosetta (DE3) via the λRed knockout system specifically for the expression of 6mA-related enzymes. The gene dam encoding the 6mA methyltransferase (MTase) is knocked out in the newly constructed strain named LAMBS (low adenine methylation background strain). Contrasting with E. coli Rosetta (DE3), LAMBS shows an ultra-low 6mA background on the genomic DNA when analyzed by UHPLC-MS/MS. We also demonstrate an integral strategy of protein purification, coupled with the application of LAMBS. As a result, the purified protein expressed in LAMBS exhibits an ultra-low 6mA background comparing with the one expressed in E. coli Rosetta (DE3). Our integral strategy of protein expression and purification will benefit the in vitro investigation and application of 6mA-related proteins from eukaryotes, although these proteins are elusive until now.
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21
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Carter MQ, Pham A, Huynh S, Parker CT, Miller A, He X, Hu B, Chain PSG. DNA adenine methylase, not the PstI restriction-modification system, regulates virulence gene expression in Shiga toxin-producing Escherichia coli. Food Microbiol 2020; 96:103722. [PMID: 33494894 DOI: 10.1016/j.fm.2020.103722] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 12/15/2020] [Accepted: 12/22/2020] [Indexed: 01/20/2023]
Abstract
We previously reported a distinct methylome between the two Shiga toxin-producing Escherichia coli (STEC) O145:H28 strains linked to the 2010 U.S. lettuce-associated outbreak (RM13514) and the 2007 Belgium ice cream-associated outbreak (RM13516), respectively. This difference was thought to be attributed to a prophage encoded type II restriction-modification system (PstI R-M) in RM13514. Here, we characterized this PstI R-M system in comparison to DNA adenine methylase (Dam), a highly conserved enzyme in γ proteobacteria, by functional genomics. Deficiency in Dam led to a differential expression of over 1000 genes in RM13514, whereas deficiency in PstI R-M only impacted a few genes transcriptionally. Dam regulated genes involved in diverse functions, whereas PstI R-M regulated genes mostly encoding transporters and adhesins. Dam regulated a large number of genes located on prophages, pathogenicity islands, and plasmids, including Shiga toxin genes, type III secretion system (TTSS) genes, and enterohemolysin genes. Production of Stx2 in dam mutant was significantly higher than in RM13514, supporting a role of Dam in maintaining lysogeny of Stx2-prophage. However, following mitomycin C treatment, Stx2 in RM13514 was significantly higher than that of dam or PstI R-M deletion mutant, implying that both Dam and PstI R-M contributed to maximum Stx2 production.
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Affiliation(s)
- Michelle Qiu Carter
- U.S. Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Produce Safety and Microbiology Research Unit, Albany, CA, USA.
| | - Antares Pham
- U.S. Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Produce Safety and Microbiology Research Unit, Albany, CA, USA
| | - Steven Huynh
- U.S. Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Produce Safety and Microbiology Research Unit, Albany, CA, USA
| | - Craig T Parker
- U.S. Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Produce Safety and Microbiology Research Unit, Albany, CA, USA
| | - Avalon Miller
- U.S. Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Produce Safety and Microbiology Research Unit, Albany, CA, USA
| | - Xiaohua He
- U.S. Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Foodborne Toxin and Detection Research Unit, Albany, CA, USA
| | - Bin Hu
- Biosecurity and Public Health Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Patrick S G Chain
- Biosecurity and Public Health Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
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Hasan MM, Basith S, Khatun MS, Lee G, Manavalan B, Kurata H. Meta-i6mA: an interspecies predictor for identifying DNA N6-methyladenine sites of plant genomes by exploiting informative features in an integrative machine-learning framework. Brief Bioinform 2020; 22:5903398. [PMID: 32910169 DOI: 10.1093/bib/bbaa202] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 08/06/2020] [Accepted: 08/06/2020] [Indexed: 12/13/2022] Open
Abstract
DNA N6-methyladenine (6mA) represents important epigenetic modifications, which are responsible for various cellular processes. The accurate identification of 6mA sites is one of the challenging tasks in genome analysis, which leads to an understanding of their biological functions. To date, several species-specific machine learning (ML)-based models have been proposed, but majority of them did not test their model to other species. Hence, their practical application to other plant species is quite limited. In this study, we explored 10 different feature encoding schemes, with the goal of capturing key characteristics around 6mA sites. We selected five feature encoding schemes based on physicochemical and position-specific information that possesses high discriminative capability. The resultant feature sets were inputted to six commonly used ML methods (random forest, support vector machine, extremely randomized tree, logistic regression, naïve Bayes and AdaBoost). The Rosaceae genome was employed to train the above classifiers, which generated 30 baseline models. To integrate their individual strength, Meta-i6mA was proposed that combined the baseline models using the meta-predictor approach. In extensive independent test, Meta-i6mA showed high Matthews correlation coefficient values of 0.918, 0.827 and 0.635 on Rosaceae, rice and Arabidopsis thaliana, respectively and outperformed the existing predictors. We anticipate that the Meta-i6mA can be applied across different plant species. Furthermore, we developed an online user-friendly web server, which is available at http://kurata14.bio.kyutech.ac.jp/Meta-i6mA/.
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Affiliation(s)
| | - Shaherin Basith
- Department of Physiology, Ajou University School of Medicine, Republic of Korea
| | - Mst Shamima Khatun
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Japan
| | - Gwang Lee
- Department of Physiology, Ajou University School of Medicine, Republic of Korea
| | | | - Hiroyuki Kurata
- Department of Bioscience and Bioinformatics in the Kyushu Institute of Technology, Japan
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Rehman MU, Chong KT. DNA6mA-MINT: DNA-6mA Modification Identification Neural Tool. Genes (Basel) 2020; 11:E898. [PMID: 32764497 PMCID: PMC7463462 DOI: 10.3390/genes11080898] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 07/28/2020] [Accepted: 07/28/2020] [Indexed: 11/16/2022] Open
Abstract
DNA N6-methyladenine (6mA) is part of numerous biological processes including DNA repair, DNA replication, and DNA transcription. The 6mA modification sites hold a great impact when their biological function is under consideration. Research in biochemical experiments for this purpose is carried out and they have demonstrated good results. However, they proved not to be a practical solution when accessed under cost and time parameters. This led researchers to develop computational models to fulfill the requirement of modification identification. In consensus, we have developed a computational model recommended by Chou's 5-steps rule. The Neural Network (NN) model uses convolution layers to extract the high-level features from the encoded binary sequence. These extracted features were given an optimal interpretation by using a Long Short-Term Memory (LSTM) layer. The proposed architecture showed higher performance compared to state-of-the-art techniques. The proposed model is evaluated on Mus musculus, Rice, and "Combined-species" genomes with 5- and 10-fold cross-validation. Further, with access to a user-friendly web server, publicly available can be accessed freely.
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Affiliation(s)
- Mobeen Ur Rehman
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju 54896, Korea; or
- Department of Avionics Engineering, Air University, Islamabad 44000, Pakistan
| | - Kil To Chong
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju 54896, Korea; or
- Advanced Electronics and Information Research Center, Jeonbuk National University, Jeonju 54896, Korea
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24
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Epigenetic competition reveals density-dependent regulation and target site plasticity of phosphorothioate epigenetics in bacteria. Proc Natl Acad Sci U S A 2020; 117:14322-14330. [PMID: 32518115 DOI: 10.1073/pnas.2002933117] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Phosphorothioate (PT) DNA modifications-in which a nonbonding phosphate oxygen is replaced with sulfur-represent a widespread, horizontally transferred epigenetic system in prokaryotes and have a highly unusual property of occupying only a small fraction of available consensus sequences in a genome. Using Salmonella enterica as a model, we asked a question of fundamental importance: How do the PT-modifying DndA-E proteins select their GPSAAC/GPSTTC targets? Here, we applied innovative analytical, sequencing, and computational tools to discover a novel behavior for DNA-binding proteins: The Dnd proteins are "parked" at the G6mATC Dam methyltransferase consensus sequence instead of the expected GAAC/GTTC motif, with removal of the 6mA permitting extensive PT modification of GATC sites. This shift in modification sites further revealed a surprising constancy in the density of PT modifications across the genome. Computational analysis showed that GAAC, GTTC, and GATC share common features of DNA shape, which suggests that PT epigenetics are regulated in a density-dependent manner partly by DNA shape-driven target selection in the genome.
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25
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Wang HT, Xiao FH, Li GH, Kong QP. Identification of DNA N 6-methyladenine sites by integration of sequence features. Epigenetics Chromatin 2020; 13:8. [PMID: 32093759 PMCID: PMC7038560 DOI: 10.1186/s13072-020-00330-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 02/03/2020] [Indexed: 02/21/2023] Open
Abstract
Background An increasing number of nucleic acid modifications have been profiled with the development of sequencing technologies. DNA N6-methyladenine (6mA), which is a prevalent epigenetic modification, plays important roles in a series of biological processes. So far, identification of DNA 6mA relies primarily on time-consuming and expensive experimental approaches. However, in silico methods can be implemented to conduct preliminary screening to save experimental resources and time, especially given the rapid accumulation of sequencing data. Results In this study, we constructed a 6mA predictor, p6mA, from a series of sequence-based features, including physicochemical properties, position-specific triple-nucleotide propensity (PSTNP), and electron–ion interaction pseudopotential (EIIP). We performed maximum relevance maximum distance (MRMD) analysis to select key features and used the Extreme Gradient Boosting (XGBoost) algorithm to build our predictor. Results demonstrated that p6mA outperformed other existing predictors using different datasets. Conclusions p6mA can predict the methylation status of DNA adenines, using only sequence files. It may be used as a tool to help the study of 6mA distribution pattern. Users can download it from https://github.com/Konglab404/p6mA.
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Affiliation(s)
- Hao-Tian Wang
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.,Kunming Key Laboratory of Healthy Aging Study, Kunming, 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fu-Hui Xiao
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.,Kunming Key Laboratory of Healthy Aging Study, Kunming, 650223, China
| | - Gong-Hua Li
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.,Kunming Key Laboratory of Healthy Aging Study, Kunming, 650223, China
| | - Qing-Peng Kong
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China. .,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China. .,Kunming Key Laboratory of Healthy Aging Study, Kunming, 650223, China. .,KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, 650223, China.
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26
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Cai J, Wang D, Chen R, Niu Y, Ye X, Su R, Xiao G, Wei L. A Bioinformatics Tool for the Prediction of DNA N6-Methyladenine Modifications Based on Feature Fusion and Optimization Protocol. Front Bioeng Biotechnol 2020; 8:502. [PMID: 32582654 PMCID: PMC7287168 DOI: 10.3389/fbioe.2020.00502] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 04/29/2020] [Indexed: 01/04/2023] Open
Abstract
DNA N6-methyladenine (6mA) is closely involved with various biological processes. Identifying the distributions of 6mA modifications in genome-scale is of great significance to in-depth understand the functions. In recent years, various experimental and computational methods have been proposed for this purpose. Unfortunately, existing methods cannot provide accurate and fast 6mA prediction. In this study, we present 6mAPred-FO, a bioinformatics tool that enables researchers to make predictions based on sequences only. To sufficiently capture the characteristics of 6mA sites, we integrate the sequence-order information with nucleotide positional specificity information for feature encoding, and further improve the feature representation capacity by analysis of variance-based feature optimization protocol. The experimental results show that using this feature protocol, we can significantly improve the predictive performance. Via further feature analysis, we found that the sequence-order information and positional specificity information are complementary to each other, contributing to the performance improvement. On the other hand, the improvement is also due to the use of the feature optimization protocol, which is capable of effectively capturing the most informative features from the original feature space. Moreover, benchmarking comparison results demonstrate that our 6mAPred-FO outperforms several existing predictors. Finally, we establish a web-server that implements the proposed method for convenience of researchers' use, which is currently available at http://server.malab.cn/6mAPred-FO.
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Affiliation(s)
- Jianhua Cai
- Fujian Provincial Key Laboratory of Information Processing and Intelligent Control, College of Computer and Control Engineering, Minjiang University, Fuzhou, China
- College of Mathematics and Computer Science, Fuzhou University, Fuzhou, China
| | - Donghua Wang
- Department of General Surgery, Heilongjiang Province Land Reclamation Headquarters General Hospital, Harbin, China
| | - Riqing Chen
- College of Computer and Information Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuzhen Niu
- Fujian Provincial Key Laboratory of Information Processing and Intelligent Control, College of Computer and Control Engineering, Minjiang University, Fuzhou, China
| | - Xiucai Ye
- Department of Computer Science, University of Tsukuba, Tsukuba, Japan
| | - Ran Su
- College of Intelligence and Computing, Tianjin University, Tianjin, China
| | - Guobao Xiao
- Fujian Provincial Key Laboratory of Information Processing and Intelligent Control, College of Computer and Control Engineering, Minjiang University, Fuzhou, China
- *Correspondence: Guobao Xiao
| | - Leyi Wei
- Fujian Provincial Key Laboratory of Information Processing and Intelligent Control, College of Computer and Control Engineering, Minjiang University, Fuzhou, China
- School of Software, Shandong University, Jinan, China
- Leyi Wei
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27
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Yu H, Dai Z. SNNRice6mA: A Deep Learning Method for Predicting DNA N6-Methyladenine Sites in Rice Genome. Front Genet 2019; 10:1071. [PMID: 31681441 PMCID: PMC6797597 DOI: 10.3389/fgene.2019.01071] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 10/04/2019] [Indexed: 01/08/2023] Open
Abstract
DNA N6-methyladenine (6mA) is an important epigenetic modification, which is involved in many biology regulation processes. An accurate and reliable method for 6mA identification can help us gain a better insight into the regulatory mechanism of the modification. Although many experimental techniques have been proposed to identify 6mA sites genome-wide, these techniques are time consuming and laborious. Recently, several machine learning methods have been developed to identify 6mA sites genome-wide. However, there is room for the improvement on their performance for predicting 6mA sites in rice genome. In this paper, we developed a simple and lightweight deep learning model to identify DNA 6mA sites in rice genome. Our model needs no prior knowledge of 6mA or manually crafted sequence feature. We built our model based on two rice 6mA benchmark datasets. Our method got an average prediction accuracy of ∼93% and ∼92% on the two datasets we used. We compared our method with existing 6mA prediction tools. The comparison results show that our model outperforms the state-of-the-art methods.
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Affiliation(s)
- Haitao Yu
- School of Data and Computer Science, Sun Yat-Sen University, Guangzhou, China
| | - Zhiming Dai
- School of Data and Computer Science, Sun Yat-Sen University, Guangzhou, China.,Guangdong Province Key Laboratory of Big Data Analysis and Processing, Sun Yat-Sen University, Guangzhou, China
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28
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Frasca M, Bianchi NC. Multitask Protein Function Prediction through Task Dissimilarity. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2019; 16:1550-1560. [PMID: 28328509 DOI: 10.1109/tcbb.2017.2684127] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Automated protein function prediction is a challenging problem with distinctive features, such as the hierarchical organization of protein functions and the scarcity of annotated proteins for most biological functions. We propose a multitask learning algorithm addressing both issues. Unlike standard multitask algorithms, which use task (protein functions) similarity information as a bias to speed up learning, we show that dissimilarity information enforces separation of rare class labels from frequent class labels, and for this reason is better suited for solving unbalanced protein function prediction problems. We support our claim by showing that a multitask extension of the label propagation algorithm empirically works best when the task relatedness information is represented using a dissimilarity matrix as opposed to a similarity matrix. Moreover, the experimental comparison carried out on three model organism shows that our method has a more stable performance in both "protein-centric" and "function-centric" evaluation settings.
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29
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Abstract
DNA modifications are a major form of epigenetic regulation that eukaryotic cells utilize in concert with histone modifications. While much work has been done elucidating the role of 5-methylcytosine over the past several decades, only recently has it been recognized that N(6)-methyladenine (N6-mA) is present in quantifiable and biologically active levels in the DNA of eukaryotic cells. Unlike prokaryotes which utilize N6-mA to recognize "self" from "foreign" DNA, eukaryotes have been found to use N6-mA in varying ways, from regulating transposable elements to gene regulation in response to hypoxia and stress. In this review, we examine the current state of the N6-mA in research field, and the current understanding of the biochemical mechanisms which deposit and remove N6-mA from the eukaryotic genome.
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Affiliation(s)
- Myles H Alderman
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Andrew Z Xiao
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT, 06520, USA.
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30
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Abstract
Bacteria frequently encounter low concentrations of antibiotics. Active antibiotics are commonly detected in soil and water at concentrations much below lethal concentration. Although sub-MICs of antibiotics do not kill bacteria, they can have a major impact on bacterial populations by contributing to the development of antibiotic resistance through mutations in originally sensitive bacteria or acquisition of DNA from resistant bacteria. It was shown that concentrations as low as 100-fold below the MIC can actually lead to the selection of antibiotic-resistant cells. We seek to understand how bacterial cells react to such antibiotic concentrations using E. coli, the Gram-negative bacterial paradigm, and V. cholerae, the causative agent of cholera. Our findings shed light on the processes triggered at the DNA level by antibiotics targeting translation, how damage occurs, and what the bacterial strategies are to respond to such DNA damage. We have previously identified Vibrio cholerae mutants in which the stress response to subinhibitory concentrations of aminoglycoside is altered. One gene identified, VC1636, encodes a putative DNA/RNA helicase, recently named RadD in Escherichia coli. Here we combined extensive genetic characterization and high-throughput approaches in order to identify partners and molecular mechanisms involving RadD. We show that double-strand DNA breaks (DSBs) are formed upon subinhibitory tobramycin treatment in the absence of radD and recBCD and that formation of these DSBs can be overcome by RNase H1 overexpression. Loss of RNase H1, or of the transcription-translation coupling factor EF-P, is lethal in the radD deletion mutant. We propose that R-loops are formed upon sublethal aminoglycoside treatment, leading to the formation of DSBs that can be repaired by the RecBCD homologous recombination pathway, and that RadD counteracts such R-loop accumulation. We discuss how R-loops that can occur upon translation-transcription uncoupling could be the link between tobramycin treatment and DNA break formation.
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31
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Chen W, Lv H, Nie F, Lin H. i6mA-Pred: identifying DNA N6-methyladenine sites in the rice genome. Bioinformatics 2019; 35:2796-2800. [DOI: 10.1093/bioinformatics/btz015] [Citation(s) in RCA: 156] [Impact Index Per Article: 31.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Revised: 12/12/2018] [Accepted: 01/05/2019] [Indexed: 01/10/2023] Open
Abstract
Abstract
Motivation
DNA N6-methyladenine (6mA) is associated with a wide range of biological processes. Since the distribution of 6mA site in the genome is non-random, accurate identification of 6mA sites is crucial for understanding its biological functions. Although experimental methods have been proposed for this regard, they are still cost-ineffective for detecting 6mA site in genome-wide scope. Therefore, it is desirable to develop computational methods to facilitate the identification of 6mA site.
Results
In this study, a computational method called i6mA-Pred was developed to identify 6mA sites in the rice genome, in which the optimal nucleotide chemical properties obtained by the using feature selection technique were used to encode the DNA sequences. It was observed that the i6mA-Pred yielded an accuracy of 83.13% in the jackknife test. Meanwhile, the performance of i6mA-Pred was also superior to other methods.
Availability and implementation
A user-friendly web-server, i6mA-Pred is freely accessible at http://lin-group.cn/server/i6mA-Pred.
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Affiliation(s)
- Wei Chen
- Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - Hao Lv
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Fulei Nie
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - Hao Lin
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
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32
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Uğur S, Akçelik N, Yüksel FN, Taşkale Karatuğ N, Akçelik M. Effects of dam and seqA genes on biofilm and pellicle formation in Salmonella. Pathog Glob Health 2018; 112:368-377. [PMID: 30433856 PMCID: PMC6300737 DOI: 10.1080/20477724.2018.1539803] [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] [Indexed: 10/27/2022] Open
Abstract
In this study, the effects of dam and seqA genes on the formation of pellicle and biofilm was determined using five different Salmonella serovars S. Group C1 (DMC2 encoded), S. Typhimurium (DMC4 encoded), S. Virchow (DMC11 encoded), S. Enteritidis (DMC22 encoded), and S. Montevideo (DMC89 encoded). dam and seqA mutants in Salmonella serovars were performed by the single step lambda red recombination method. The mutants obtained were examined according to the properties of biofilm on the polystyrene surfaces and the pellicle formation on the liquid medium. As a result of these investigations, it was determined that the biofilm formation properties on polystyrene surfaces decreased significantly (p < 0.05) in all tested dam and seqA mutants, while the pellicle formation properties were lost in the liquid medium. When pBAD24 vector, containing the dam and seqA genes cloned behind the inducible arabinose promoter, transduced into dam and seqA mutant strains, it was determined that the biofilm formation properties on the polystyrene surfaces reached to the natural strains' level in all mutant strains. Also, the pellicle formation ability was regained in the liquid media. All these data demonstrate that dam and seqA genes play an important role in the formation of biofilm and pellicle structures in Salmonella serovars.
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Affiliation(s)
- Sinem Uğur
- Department of Biology, Faculty of Science, Ankara University, Ankara, Turkey
| | - Nefise Akçelik
- Institute of Biotechnology, Ankara University, Ankara, Turkey
| | | | | | - Mustafa Akçelik
- Department of Biology, Faculty of Science, Ankara University, Ankara, Turkey
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33
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Yoon KJ, Vissers C, Ming GL, Song H. Epigenetics and epitranscriptomics in temporal patterning of cortical neural progenitor competence. J Cell Biol 2018; 217:1901-1914. [PMID: 29666150 PMCID: PMC5987727 DOI: 10.1083/jcb.201802117] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 04/05/2018] [Accepted: 04/06/2018] [Indexed: 12/12/2022] Open
Abstract
Yoon et al. review epigenetic and epitranscriptomic mechanisms that regulate the lineage specification of neural progenitor cells in the developing brain. During embryonic brain development, neural progenitor/stem cells (NPCs) sequentially give rise to different subtypes of neurons and glia via a highly orchestrated process. To accomplish the ordered generation of distinct progenies, NPCs go through multistep transitions of their developmental competence. The molecular mechanisms driving precise temporal coordination of these transitions remains enigmatic. Epigenetic regulation, including changes in chromatin structures, DNA methylation, and histone modifications, has been extensively investigated in the context of cortical neurogenesis. Recent studies of chemical modifications on RNA, termed epitranscriptomics, have also revealed their critical roles in neural development. In this review, we discuss advances in understanding molecular regulation of the sequential lineage specification of NPCs in the embryonic mammalian brain with a focus on epigenetic and epitranscriptomic mechanisms. In particular, the discovery of lineage-specific gene transcripts undergoing rapid turnover in NPCs suggests that NPC developmental fate competence is determined much earlier, before the final cell division, and is more tightly controlled than previously appreciated. We discuss how multiple regulatory systems work in harmony to coordinate NPC behavior and summarize recent findings in the context of a model of epigenetic and transcriptional prepatterning to explain NPC developmental competence.
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Affiliation(s)
- Ki-Jun Yoon
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA
| | - Caroline Vissers
- The Biochemistry, Cellular and Molecular Biology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Guo-Li Ming
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA.,The Biochemistry, Cellular and Molecular Biology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD.,Department of Cell and Developmental Biology, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA.,Institute for Regenerative Medicine, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA
| | - Hongjun Song
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA .,The Biochemistry, Cellular and Molecular Biology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD.,Department of Cell and Developmental Biology, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA.,Institute for Regenerative Medicine, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA.,The Epigenetics Institute, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA
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34
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Feng P, Yang H, Ding H, Lin H, Chen W, Chou KC. iDNA6mA-PseKNC: Identifying DNA N 6-methyladenosine sites by incorporating nucleotide physicochemical properties into PseKNC. Genomics 2018; 111:96-102. [PMID: 29360500 DOI: 10.1016/j.ygeno.2018.01.005] [Citation(s) in RCA: 188] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 12/24/2017] [Accepted: 01/07/2018] [Indexed: 11/29/2022]
Abstract
N6-methyladenine (6mA) is one kind of post-replication modification (PTM or PTRM) occurring in a wide range of DNA sequences. Accurate identification of its sites will be very helpful for revealing the biological functions of 6mA, but it is time-consuming and expensive to determine them by experiments alone. Unfortunately, so far, no bioinformatics tool is available to do so. To fill in such an empty area, we have proposed a novel predictor called iDNA6mA-PseKNC that is established by incorporating nucleotide physicochemical properties into Pseudo K-tuple Nucleotide Composition (PseKNC). It has been observed via rigorous cross-validations that the predictor's sensitivity (Sn), specificity (Sp), accuracy (Acc), and stability (MCC) are 93%, 100%, 96%, and 0.93, respectively. For the convenience of most experimental scientists, a user-friendly web server for iDNA6mA-PseKNC has been established at http://lin-group.cn/server/iDNA6mA-PseKNC, by which users can easily obtain their desired results without the need to go through the complicated mathematical equations involved.
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Affiliation(s)
- Pengmian Feng
- Hebei Province Key Laboratory of Occupational Health and Safety for Coal Industry, School of Public Health, North China University of Science and Technology, Tangshan 063000, China
| | - Hui Yang
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Hui Ding
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Hao Lin
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China; Gordon Life Science Institute, Boston, MA 02478, USA.
| | - Wei Chen
- Department of Physics, School of Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Tangshan 063000, China; Gordon Life Science Institute, Boston, MA 02478, USA.
| | - Kuo-Chen Chou
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China; Gordon Life Science Institute, Boston, MA 02478, USA.
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35
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Beauchamp JM, Leveque RM, Dawid S, DiRita VJ. Methylation-dependent DNA discrimination in natural transformation of Campylobacter jejuni. Proc Natl Acad Sci U S A 2017; 114:E8053-E8061. [PMID: 28855338 PMCID: PMC5617262 DOI: 10.1073/pnas.1703331114] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Campylobacter jejuni, a leading cause of bacterial gastroenteritis, is naturally competent. Like many competent organisms, C. jejuni restricts the DNA that can be used for transformation to minimize undesirable changes in the chromosome. Although C. jejuni can be transformed by C. jejuni-derived DNA, it is poorly transformed by the same DNA propagated in Escherichia coli or produced with PCR. Our work indicates that methylation plays an important role in marking DNA for transformation. We have identified a highly conserved DNA methyltransferase, which we term Campylobacter transformation system methyltransferase (ctsM), which methylates an overrepresented 6-bp sequence in the chromosome. DNA derived from a ctsM mutant transforms C. jejuni significantly less well than DNA derived from ctsM+ (parental) cells. The ctsM mutation itself does not affect transformation efficiency when parental DNA is used, suggesting that CtsM is important for marking transforming DNA, but not for transformation itself. The mutant has no growth defect, arguing against ongoing restriction of its own DNA. We further show that E. coli plasmid and PCR-derived DNA can efficiently transform C. jejuni when only a subset of the CtsM sites are methylated in vitro. A single methylation event 1 kb upstream of the DNA involved in homologous recombination is sufficient to transform C. jejuni, whereas otherwise identical unmethylated DNA is not. Methylation influences DNA uptake, with a slight effect also seen on DNA binding. This mechanism of DNA discrimination in C. jejuni is distinct from the DNA discrimination described in other competent bacteria.
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Affiliation(s)
- Jessica M Beauchamp
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI; 48109
| | - Rhiannon M Leveque
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI; 48824
| | - Suzanne Dawid
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI; 48109
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI 48109
| | - Victor J DiRita
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI; 48824;
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36
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Cairns J, Frickel J, Jalasvuori M, Hiltunen T, Becks L. Genomic evolution of bacterial populations under coselection by antibiotics and phage. Mol Ecol 2017; 26:1848-1859. [DOI: 10.1111/mec.13950] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 10/06/2016] [Accepted: 11/28/2016] [Indexed: 12/25/2022]
Affiliation(s)
- Johannes Cairns
- Department of Food and Environmental Sciences / Microbiology and Biotechnology; University of Helsinki; P.O. Box 65 00014 Helsinki Finland
| | - Jens Frickel
- Department of Evolutionary Ecology / Community Dynamics Group; Max Planck Institute for Evolutionary Biology; August Thienemann Street 2 24306 Plön Germany
| | - Matti Jalasvuori
- Department of Biological and Environmental Science / Centre of Excellence in Biological Interactions; University of Jyväskylä; P.O. Box 35 Jyväskylä 40014 Finland
| | - Teppo Hiltunen
- Department of Food and Environmental Sciences / Microbiology and Biotechnology; University of Helsinki; P.O. Box 65 00014 Helsinki Finland
| | - Lutz Becks
- Department of Evolutionary Ecology / Community Dynamics Group; Max Planck Institute for Evolutionary Biology; August Thienemann Street 2 24306 Plön Germany
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37
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Gorrell R, Kwok T. The Helicobacter pylori Methylome: Roles in Gene Regulation and Virulence. Curr Top Microbiol Immunol 2017; 400:105-127. [PMID: 28124151 DOI: 10.1007/978-3-319-50520-6_5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The methylome is defined as a map of DNA methylation patterns at single-base resolution. DNA methylation in bacteria was first discovered as a function of restriction-modification (R-M) systems. R-M systems in Helicobacter pylori, like those in other bacteria, are important host-specificity determinants that provide protection against foreign DNA. Moreover, the gene regulatory role of the methyltransferase (Mtase) unit of various Helicobacter pylori R-M systems is being increasingly recognized. Recent advances in the application of single-molecule real-time (SMRT) DNA sequencing to analyse DNA methylation have revealed for the first time comprehensive pictures of the genome-wide distribution of methylation sites in various strains of H. pylori. The methylomic data published so far have not only confirmed the significant inter-strain diversity of H. pylori Mtases and their DNA methylation profiles, but also identified numerous novel Mtase target recognition sites. The precise knowledge of the nucleotide sequence of Mtase recognition sites and their distribution within the H. pylori genome will in turn enable researchers to more readily test hypotheses on how H. pylori Mtases function to orchestrate gene regulation and/or modulate virulence. Methylomic studies hold promise for providing a deeper understanding into the roles of H. pylori Mtase and R-M systems in the physiology, epigenetics and possibly also pathogenesis of this important human pathogen. Consequently, the knowledge gained will provide crucial insights into the potential application of H. pylori methylomes as novel biomarkers for the prediction of disease outcome and/or antibiotic susceptibility.
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Affiliation(s)
- Rebecca Gorrell
- Infection and Immunity, and Cancer Programs, Monash Biomedicine Discovery Institute, Clayton, Australia.,Department of Biochemistry and Molecular Biology, Monash University, Clayton, 3800, Australia.,Department of Microbiology, Monash University, Clayton, 3800, Australia
| | - Terry Kwok
- Infection and Immunity, and Cancer Programs, Monash Biomedicine Discovery Institute, Clayton, Australia. .,Department of Biochemistry and Molecular Biology, Monash University, Clayton, 3800, Australia. .,Department of Microbiology, Monash University, Clayton, 3800, Australia.
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38
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Adhikari S, Curtis PD. DNA methyltransferases and epigenetic regulation in bacteria. FEMS Microbiol Rev 2016; 40:575-91. [PMID: 27476077 DOI: 10.1093/femsre/fuw023] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/30/2016] [Indexed: 12/21/2022] Open
Abstract
Epigenetics is a change in gene expression that is heritable without a change in DNA sequence itself. This phenomenon is well studied in eukaryotes, particularly in humans for its role in cellular differentiation, X chromosome inactivation and diseases like cancer. However, comparatively little is known about epigenetic regulation in bacteria. Bacterial epigenetics is mainly present in the form of DNA methylation where DNA methyltransferases add methyl groups to nucleotides. This review focuses on two methyltransferases well characterized for their roles in gene regulation: Dam and CcrM. Dam methyltransferase in Escherichia coli is important for expression of certain genes such as the pap operon, as well as other cellular processes like DNA replication initiation and DNA repair. In Caulobacter crescentus and other Alphaproteobacteria, the methyltransferase CcrM is cell cycle regulated and is involved in the cell-cycle-dependent regulation of several genes. The diversity of regulatory targets as well as regulatory mechanisms suggests that gene regulation by methylation could be a widespread and potent method of regulation in bacteria.
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Affiliation(s)
- Satish Adhikari
- Department of Biology, University of Mississippi, University, MS 38677, USA
| | - Patrick D Curtis
- Department of Biology, University of Mississippi, University, MS 38677, USA
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39
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Stephenson SAM, Brown PD. Epigenetic Influence of Dam Methylation on Gene Expression and Attachment in Uropathogenic Escherichia coli. Front Public Health 2016; 4:131. [PMID: 27446897 PMCID: PMC4921776 DOI: 10.3389/fpubh.2016.00131] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 06/09/2016] [Indexed: 11/13/2022] Open
Abstract
Urinary tract infections (UTI) are among the most frequently encountered infections in clinical practice globally. Predominantly a burden among female adults and infants, UTIs primarily caused by uropathogenic Escherichia coli (UPEC) results in high morbidity and fiscal health strains. During pathogenesis, colonization of the urinary tract via fimbrial adhesion to mucosal cells is the most critical point in infection and has been linked to DNA methylation. Furthermore, with continuous exposure to antibiotics as the standard therapeutic strategy, UPEC has evolved to become highly adaptable in circumventing the effect of antimicrobial agents and host defenses. Hence, the need for alternative treatment strategies arises. Since differential DNA methylation is observed as a critical precursor to virulence in various pathogenic bacteria, this body of work sought to assess the influence of the DNA adenine methylase (dam) gene on gene expression and cellular adhesion in UPEC and its potential as a therapeutic target. To monitor the influence of dam on attachment and FQ resistance, selected UPEC dam mutants created via one-step allelic exchange were transformed with cloned qnrA and dam complement plasmid for comparative analysis of growth rate, antimicrobial susceptibility, biofilm formation, gene expression, and mammalian cell attachment. The absence of DNA methylation among dam mutants was apparent. Varying deficiencies in cell growth, antimicrobial resistance and biofilm formation, alongside low-level increases in gene expression (recA and papI), and adherence to HEK-293 and HTB-9 mammalian cells were also detected as a factor of SOS induction to result in increased mutability. Phenotypic characteristics of parental strains were restored in dam complement strains. Dam's vital role in DNA methylation and gene expression in local UPEC isolates was confirmed. Similarly to dam-deficient Enterohemorrhagic E. coli (EHEC), these findings suggest unsuccessful therapeutic use of Dam inhibitors against UPEC or dam-deficient UPEC strains as attenuated live vaccines. However, further investigations are necessary to determine the post-transcriptional influence of dam on the regulatory network of virulence genes central to pathogenesis.
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Affiliation(s)
| | - Paul D Brown
- Department of Basic Medical Sciences, Faculty of Medical Sciences, University of West Indies , Jamaica
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40
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Shin JE, Lin C, Lim HN. Horizontal transfer of DNA methylation patterns into bacterial chromosomes. Nucleic Acids Res 2016; 44:4460-71. [PMID: 27084942 PMCID: PMC4872104 DOI: 10.1093/nar/gkw230] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2016] [Accepted: 03/29/2016] [Indexed: 12/21/2022] Open
Abstract
Horizontal gene transfer (HGT) is the non-inherited acquisition of novel DNA sequences. HGT is common and important in bacteria because it enables the rapid generation of new phenotypes such as antibiotic resistance. Here we show that in vivo and in vitro DNA methylation patterns can be horizontally transferred into bacterial chromosomes to program cell phenotypes. The experiments were performed using a synthetic system in Escherichia coli where different DNA methylation patterns within the cis-regulatory sequence of the agn43 gene turn on or off a fluorescent reporter (CFP). With this system we demonstrated that DNA methylation patterns not only accompany the horizontal transfer of genes into the bacterial cytoplasm but can be transferred into chromosomes by: (i) bacteriophage P1 transduction; and (ii) transformation of extracellular synthetic DNA. We also modified the experimental system by replacing CFP with the SgrS small RNA, which regulates glucose and methyl α-D-glucoside uptake, and showed that horizontally acquired DNA methylation patterns can increase or decrease cell fitness. That is, horizontally acquired DNA methylation patterns can result in the selection for and against cells that have HGT. Findings from these proof-of-concept experiments have applications in synthetic biology and potentially broad implications for bacterial adaptation and evolution.
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Affiliation(s)
- Jung-Eun Shin
- Department of Integrative Biology, University of California Berkeley, CA 94720-3140, USA
| | - Chris Lin
- Department of Integrative Biology, University of California Berkeley, CA 94720-3140, USA
| | - Han N Lim
- Department of Integrative Biology, University of California Berkeley, CA 94720-3140, USA
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41
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Ronda C, Pedersen LE, Sommer MOA, Nielsen AT. CRMAGE: CRISPR Optimized MAGE Recombineering. Sci Rep 2016; 6:19452. [PMID: 26797514 PMCID: PMC4726160 DOI: 10.1038/srep19452] [Citation(s) in RCA: 151] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 12/14/2015] [Indexed: 12/23/2022] Open
Abstract
A bottleneck in metabolic engineering and systems biology approaches is the lack of efficient genome engineering technologies. Here, we combine CRISPR/Cas9 and λ Red recombineering based MAGE technology (CRMAGE) to create a highly efficient and fast method for genome engineering of Escherichia coli. Using CRMAGE, the recombineering efficiency was between 96.5% and 99.7% for gene recoding of three genomic targets, compared to between 0.68% and 5.4% using traditional recombineering. For modulation of protein synthesis (small insertion/RBS substitution) the efficiency was increased from 6% to 70%. CRMAGE can be multiplexed and enables introduction of at least two mutations in a single round of recombineering with similar efficiencies. PAM-independent loci were targeted using degenerate codons, thereby making it possible to modify any site in the genome. CRMAGE is based on two plasmids that are assembled by a USER-cloning approach enabling quick and cost efficient gRNA replacement. CRMAGE furthermore utilizes CRISPR/Cas9 for efficient plasmid curing, thereby enabling multiple engineering rounds per day. To facilitate the design process, a web-based tool was developed to predict both the λ Red oligos and the gRNAs. The CRMAGE platform enables highly efficient and fast genome editing and may open up promising prospective for automation of genome-scale engineering.
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Affiliation(s)
- Carlotta Ronda
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Allé 6, 2970 Hørsholm, Denmark
| | - Lasse Ebdrup Pedersen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Allé 6, 2970 Hørsholm, Denmark
| | - Morten O. A. Sommer
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Allé 6, 2970 Hørsholm, Denmark
| | - Alex Toftgaard Nielsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Allé 6, 2970 Hørsholm, Denmark
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42
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O'Brown ZK, Greer EL. N6-Methyladenine: A Conserved and Dynamic DNA Mark. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 945:213-246. [PMID: 27826841 DOI: 10.1007/978-3-319-43624-1_10] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Chromatin, consisting of deoxyribonucleic acid (DNA) wrapped around histone proteins, facilitates DNA compaction and allows identical DNA codes to confer many different cellular phenotypes. This biological versatility is accomplished in large part by posttranslational modifications to histones and chemical modifications to DNA. These modifications direct the cellular machinery to expand or compact specific chromatin regions and mark regions of the DNA as important for cellular functions. While each of the four bases that make up DNA can be modified (Iyer et al. 2011), this chapter will focus on methylation of the sixth position on adenines (6mA), as this modification has been poorly characterized in recently evolved eukaryotes, but shows promise as a new conserved layer of epigenetic regulation. 6mA was previously thought to be restricted to unicellular organisms, but recent work has revealed its presence in metazoa. Here, we will briefly describe the history of 6mA, examine its evolutionary conservation, and evaluate the current methods for detecting 6mA. We will discuss the enzymes that bind and regulate this mark and finally examine known and potential functions of 6mA in eukaryotes.
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Affiliation(s)
- Zach Klapholz O'Brown
- Division of Newborn Medicine, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA, 02115, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - Eric Lieberman Greer
- Division of Newborn Medicine, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA, 02115, USA. .,Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA.
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Abstract
The DNA of Escherichia coli contains 19,120 6-methyladenines and 12,045 5-methylcytosines in addition to the four regular bases, and these are formed by the postreplicative action of three DNA methyltransferases. The majority of the methylated bases are formed by the Dam and Dcm methyltransferases encoded by the dam (DNA adenine methyltransferase) and dcm (DNA cytosine methyltransferase) genes. Although not essential, Dam methylation is important for strand discrimination during the repair of replication errors, controlling the frequency of initiation of chromosome replication at oriC, and the regulation of transcription initiation at promoters containing GATC sequences. In contrast, there is no known function for Dcm methylation, although Dcm recognition sites constitute sequence motifs for Very Short Patch repair of T/G base mismatches. In certain bacteria (e.g., Vibrio cholerae, Caulobacter crescentus) adenine methylation is essential, and, in C. crescentus, it is important for temporal gene expression, which, in turn, is required for coordinating chromosome initiation, replication, and division. In practical terms, Dam and Dcm methylation can inhibit restriction enzyme cleavage, decrease transformation frequency in certain bacteria, and decrease the stability of short direct repeats and are necessary for site-directed mutagenesis and to probe eukaryotic structure and function.
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44
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Horton JR, Zhang X, Blumenthal RM, Cheng X. Structures of Escherichia coli DNA adenine methyltransferase (Dam) in complex with a non-GATC sequence: potential implications for methylation-independent transcriptional repression. Nucleic Acids Res 2015; 43:4296-308. [PMID: 25845600 PMCID: PMC4417163 DOI: 10.1093/nar/gkv251] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Revised: 11/21/2014] [Accepted: 03/11/2015] [Indexed: 12/31/2022] Open
Abstract
DNA adenine methyltransferase (Dam) is widespread and conserved among the γ-proteobacteria. Methylation of the Ade in GATC sequences regulates diverse bacterial cell functions, including gene expression, mismatch repair and chromosome replication. Dam also controls virulence in many pathogenic Gram-negative bacteria. An unexplained and perplexing observation about Escherichia coli Dam (EcoDam) is that there is no obvious relationship between the genes that are transcriptionally responsive to Dam and the promoter-proximal presence of GATC sequences. Here, we demonstrate that EcoDam interacts with a 5-base pair non-cognate sequence distinct from GATC. The crystal structure of a non-cognate complex allowed us to identify a DNA binding element, GTYTA/TARAC (where Y = C/T and R = A/G). This element immediately flanks GATC sites in some Dam-regulated promoters, including the Pap operon which specifies pyelonephritis-associated pili. In addition, Dam interacts with near-cognate GATC sequences (i.e. 3/4-site ATC and GAT). Taken together, these results imply that Dam, in addition to being responsible for GATC methylation, could also function as a methylation-independent transcriptional repressor.
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Affiliation(s)
- John R Horton
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Xing Zhang
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Robert M Blumenthal
- Department of Medical Microbiology and Immunology and Program in Bioinformatics, The University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA
| | - Xiaodong Cheng
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
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Mismatch repair at stop codons is directed independent of GATC methylation on the Escherichia coli chromosome. Sci Rep 2014; 4:7346. [PMID: 25475788 PMCID: PMC5376664 DOI: 10.1038/srep07346] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 11/19/2014] [Indexed: 12/03/2022] Open
Abstract
The mismatch repair system (MMR) corrects replication errors that escape proofreading. Previous studies on extrachromosomal DNA in Escherichia coli suggested that MMR uses hemimethylated GATC sites to identify the newly synthesized strand. In this work we asked how the distance of GATC sites and their methylation status affect the occurrence of single base substitutions on the E. coli chromosome. As a reporter system we used a lacZ gene containing an early TAA stop codon. We found that occurrence of point mutations at this stop codon is unaffected by GATC sites located more than 115 base pairs away. However, a GATC site located about 50 base pairs away resulted in a decreased mutation rate. This effect was independent of Dam methylation. The reversion rate of the stop codon increased only slightly in dam mutants compared to mutL and mutS mutants. We suggest that unlike on extrachromosomal DNA, GATC methylation is not the only strand discrimination signal for MMR on the E. coli chromosome.
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Youssef M, Al-Omair M, Picksley S. Genetic characterization of Escherichia coli RecN protein as a member of SMC family of proteins. ARAB J CHEM 2014. [DOI: 10.1016/j.arabjc.2011.02.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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47
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Baharoglu Z, Mazel D. Influence of very short patch mismatch repair on SOS inducing lesions after aminoglycoside treatment in Escherichia coli. Res Microbiol 2014; 165:476-80. [PMID: 24946128 DOI: 10.1016/j.resmic.2014.05.039] [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: 03/21/2014] [Revised: 05/22/2014] [Accepted: 05/28/2014] [Indexed: 10/25/2022]
Abstract
Low concentrations of aminoglycosides induce the SOS response in Vibrio cholerae but not in Escherichia coli. In order to determine whether a specific factor present in E. coli prevents this induction, we developed a genetic screen where only SOS inducing mutants are viable. We identified the vsr gene coding for the Vsr protein of the very short patch mismatch repair (VSPR) pathway. The effect of mismatch repair (MMR) mutants was also studied. We propose that lesions formed upon aminoglycoside treatment are preferentially repaired by VSPR without SOS induction in E. coli and by MMR when VSPR is impaired.
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Affiliation(s)
- Zeynep Baharoglu
- Institut Pasteur, Unité Plasticité du Génome Bactérien, Département Génomes et Génétique, 25 rue du docteur Roux, 75015 Paris, France; CNRS, UMR3525, Paris, France.
| | - Didier Mazel
- Institut Pasteur, Unité Plasticité du Génome Bactérien, Département Génomes et Génétique, 25 rue du docteur Roux, 75015 Paris, France; CNRS, UMR3525, Paris, France
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48
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Gonzalez D, Kozdon JB, McAdams HH, Shapiro L, Collier J. The functions of DNA methylation by CcrM in Caulobacter crescentus: a global approach. Nucleic Acids Res 2014; 42:3720-35. [PMID: 24398711 PMCID: PMC3973325 DOI: 10.1093/nar/gkt1352] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
DNA methylation is involved in a diversity of processes in bacteria, including maintenance of genome integrity and regulation of gene expression. Here, using Caulobacter crescentus as a model, we exploit genome-wide experimental methods to uncover the functions of CcrM, a DNA methyltransferase conserved in most Alphaproteobacteria. Using single molecule sequencing, we provide evidence that most CcrM target motifs (GANTC) switch from a fully methylated to a hemi-methylated state when they are replicated, and back to a fully methylated state at the onset of cell division. We show that DNA methylation by CcrM is not required for the control of the initiation of chromosome replication or for DNA mismatch repair. By contrast, our transcriptome analysis shows that >10% of the genes are misexpressed in cells lacking or constitutively over-expressing CcrM. Strikingly, GANTC methylation is needed for the efficient transcription of dozens of genes that are essential for cell cycle progression, in particular for DNA metabolism and cell division. Many of them are controlled by promoters methylated by CcrM and co-regulated by other global cell cycle regulators, demonstrating an extensive cross talk between DNA methylation and the complex regulatory network that controls the cell cycle of C. crescentus and, presumably, of many other Alphaproteobacteria.
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Affiliation(s)
- Diego Gonzalez
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, CH 1015, Switzerland, Department of Developmental Biology, Stanford University, CA 94305, USA and Department of Chemistry, Stanford University, CA 94305, USA
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Val ME, Kennedy SP, Soler-Bistué AJ, Barbe V, Bouchier C, Ducos-Galand M, Skovgaard O, Mazel D. Fuse or die: how to survive the loss of Dam inVibrio cholerae. Mol Microbiol 2014; 91:665-78. [DOI: 10.1111/mmi.12483] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/04/2013] [Indexed: 11/26/2022]
Affiliation(s)
- Marie-Eve Val
- Department of Genomes and Genetics; Institut Pasteur; F-75015 Paris France
- CNRS; UMR3525 F-75015 Paris France
| | | | - Alfonso J. Soler-Bistué
- Department of Genomes and Genetics; Institut Pasteur; F-75015 Paris France
- CNRS; UMR3525 F-75015 Paris France
| | | | | | - Magaly Ducos-Galand
- Department of Genomes and Genetics; Institut Pasteur; F-75015 Paris France
- CNRS; UMR3525 F-75015 Paris France
| | - Ole Skovgaard
- Department of Science, Systems and Models; Roskilde University; DK-4000 Roskilde Denmark
| | - Didier Mazel
- Department of Genomes and Genetics; Institut Pasteur; F-75015 Paris France
- CNRS; UMR3525 F-75015 Paris France
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50
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Exploring the roles of DNA methylation in the metal-reducing bacterium Shewanella oneidensis MR-1. J Bacteriol 2013; 195:4966-74. [PMID: 23995632 DOI: 10.1128/jb.00935-13] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We performed whole-genome analyses of DNA methylation in Shewanella oneidensis MR-1 to examine its possible role in regulating gene expression and other cellular processes. Single-molecule real-time (SMRT) sequencing revealed extensive methylation of adenine (N6mA) throughout the genome. These methylated bases were located in five sequence motifs, including three novel targets for type I restriction/modification enzymes. The sequence motifs targeted by putative methyltranferases were determined via SMRT sequencing of gene knockout mutants. In addition, we found that S. oneidensis MR-1 cultures grown under various culture conditions displayed different DNA methylation patterns. However, the small number of differentially methylated sites could not be directly linked to the much larger number of differentially expressed genes under these conditions, suggesting that DNA methylation is not a major regulator of gene expression in S. oneidensis MR-1. The enrichment of methylated GATC motifs in the origin of replication indicates that DNA methylation may regulate genome replication in a manner similar to that seen in Escherichia coli. Furthermore, comparative analyses suggest that many Gammaproteobacteria, including all members of the Shewanellaceae family, may also utilize DNA methylation to regulate genome replication.
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