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Kędzierska-Mieszkowska S, Kędzierska B, Potrykus K. LIC_12757 from the pathogenic spirochaete Leptospira interrogans encodes an autoregulated ECF σ E-type factor. Vet Microbiol 2024; 293:110092. [PMID: 38615476 DOI: 10.1016/j.vetmic.2024.110092] [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: 01/07/2024] [Revised: 03/19/2024] [Accepted: 04/11/2024] [Indexed: 04/16/2024]
Abstract
ECF (extracytoplasmic function) σ factors, members of the σ70-family, are the largest class of alternative σ factors which are stimulated in the presence of specific signals and direct RNA polymerase to transcribe a defined subset of genes. Thanks to them, bacterial pathogens can effectively reprogram their gene expression and, consequently, survive in the host and establish infection in a relatively short time. The number of ECF σ factors encoded within bacterial genomes is different depending on a given species and it reflects the likelihood that these bacteria will encounter harsh environmental conditions. The genome of L. interrogans, a zoonotic pathogen responsible for leptospirosis, is predicted to encode 11 ECF σE-type factors, but none of them have been characterized biochemically to date and their functions are still unknown. Here, we focused on one of the leptospiral ECF σ factors, namely LIC_12757, which was previously found to be up-regulated at elevated temperatures and may be related to the expression of clpB encoding an important L. interrogans virulence factor. We report cloning of the coding sequence of the LIC_12757 gene, its expression with the pET system and biochemical characterization of LIC_12757. By performing EMSA and in vitro transcription assays, we provide strong evidence that LIC_12757 indeed functions as a transcriptional factor that enables RNA polymerase to bind to the specific σE-type promoter and to initiate transcription. Interestingly, we demonstrate that LIC_12757 is autoregulated at the transcriptional level. Our study is a first step towards determining key aspects of LIC_12757 function in pathogenic Leptospira.
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Affiliation(s)
| | - Barbara Kędzierska
- Department of Bacterial Molecular Genetics, Faculty of Biology, University of Gdańsk, Gdańsk 80-308, Poland
| | - Katarzyna Potrykus
- Department of Bacterial Molecular Genetics, Faculty of Biology, University of Gdańsk, Gdańsk 80-308, Poland
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2
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Patel L, Ailloud F, Suerbaum S, Josenhans C. Single-base resolution quantitative genome methylation analysis in the model bacterium Helicobacter pylori by enzymatic methyl sequencing (EM-Seq) reveals influence of strain, growth phase, and methyl homeostasis. BMC Biol 2024; 22:125. [PMID: 38807090 PMCID: PMC11134628 DOI: 10.1186/s12915-024-01921-1] [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: 01/14/2024] [Accepted: 05/16/2024] [Indexed: 05/30/2024] Open
Abstract
BACKGROUND Bacterial epigenetics is a rapidly expanding research field. DNA methylation by diverse bacterial methyltransferases (MTases) contributes to genomic integrity and replication, and many recent studies extended MTase function also to global transcript regulation and phenotypic variation. Helicobacter pylori is currently one of those bacterial species which possess the highest number and the most variably expressed set of DNA MTases. Next-generation sequencing technologies can directly detect DNA base methylation. However, they still have limitations in their quantitative and qualitative performance, in particular for cytosine methylation. RESULTS As a complementing approach, we used enzymatic methyl sequencing (EM-Seq), a technology recently established that has not yet been fully evaluated for bacteria. Thereby, we assessed quantitatively, at single-base resolution, whole genome cytosine methylation for all methylated cytosine motifs in two different H. pylori strains and isogenic MTase mutants. EM-Seq reliably detected both m5C and m4C methylation. We demonstrated that three different active cytosine MTases in H. pylori provide considerably different levels of average genome-wide single-base methylation, in contrast to isogenic mutants which completely lost specific motif methylation. We found that strain identity and changed environmental conditions, such as growth phase and interference with methyl donor homeostasis, significantly influenced quantitative global and local genome-wide methylation in H. pylori at specific motifs. We also identified significantly hyper- or hypo-methylated cytosines, partially linked to overlapping MTase target motifs. Notably, we revealed differentially methylated cytosines in genome-wide coding regions under conditions of methionine depletion, which can be linked to transcript regulation. CONCLUSIONS This study offers new knowledge on H. pylori global and local genome-wide methylation and establishes EM-Seq for quantitative single-site resolution analyses of bacterial cytosine methylation.
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Affiliation(s)
- Lubna Patel
- Max von Pettenkofer Institute, Chair for Medical Microbiology, Faculty of Medicine, LMU Munich, Pettenkoferstr. 9a, 80336, Munich, Germany
| | - Florent Ailloud
- Max von Pettenkofer Institute, Chair for Medical Microbiology, Faculty of Medicine, LMU Munich, Pettenkoferstr. 9a, 80336, Munich, Germany
| | - Sebastian Suerbaum
- Max von Pettenkofer Institute, Chair for Medical Microbiology, Faculty of Medicine, LMU Munich, Pettenkoferstr. 9a, 80336, Munich, Germany
| | - Christine Josenhans
- Max von Pettenkofer Institute, Chair for Medical Microbiology, Faculty of Medicine, LMU Munich, Pettenkoferstr. 9a, 80336, Munich, Germany.
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3
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Nguyen VN, Ho TT, Doan TD, Le NQK. Using a hybrid neural network architecture for DNA sequence representation: A study on N 4-methylcytosine sites. Comput Biol Med 2024; 178:108664. [PMID: 38875905 DOI: 10.1016/j.compbiomed.2024.108664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 05/11/2024] [Accepted: 05/26/2024] [Indexed: 06/16/2024]
Abstract
N4-methylcytosine (4mC) is a modified form of cytosine found in DNA, contributing to epigenetic regulation. It exists in various genomes, including the Rosaceae family encompassing significant fruit crops like apples, cherries, and roses. Previous investigations have examined the distribution and functional implications of 4mC sites within the Rosaceae genome, focusing on their potential roles in gene expression regulation, environmental adaptation, and evolution. This research aims to improve the accuracy of predicting 4mC sites within the genome of Fragaria vesca, a Rosaceae plant species. Building upon the original 4mc-w2vec method, which combines word embedding processing and a convolutional neural network (CNN), we have incorporated additional feature encoding techniques and leveraged pre-trained natural language processing (NLP) models with different deep learning architectures including different forms of CNN, recurrent neural networks (RNN) and long short-term memory (LSTM). Our assessments have shown that the best model is derived from a CNN model using fastText encoding. This model demonstrates enhanced performance, achieving a sensitivity of 0.909, specificity of 0.77, and accuracy of 0.879 on an independent dataset. Furthermore, our model surpasses previously published works on the same dataset, thus showcasing its superior predictive capabilities.
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Affiliation(s)
- Van-Nui Nguyen
- University of Information and Communication Technology, Thai Nguyen University, Thai Nguyen, Viet Nam
| | - Trang-Thi Ho
- Department of Computer Science and Information Engineering, TamKang University, New Taipei, 251301, Taiwan
| | - Thu-Dung Doan
- International Degree Program in Animal Vaccine Technology, International College, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Nguyen Quoc Khanh Le
- Professional Master Program in Artificial Intelligence in Medicine, College of Medicine, Taipei Medical University, Taipei, 110, Taiwan; Research Center for Artificial Intelligence in Medicine, Taipei Medical University, Taipei, 110, Taiwan; AIBioMed Research Group, Taipei Medical University, Taipei, 110, Taiwan; Translational Imaging Research Center, Taipei Medical University Hospital, Taipei, 110, Taiwan.
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4
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Giraud-Gatineau A, Nieves C, Harrison LB, Benaroudj N, Veyrier FJ, Picardeau M. Evolutionary insights into the emergence of virulent Leptospira spirochetes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.02.587687. [PMID: 38617210 PMCID: PMC11014503 DOI: 10.1101/2024.04.02.587687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Pathogenic Leptospira are spirochete bacteria which cause leptospirosis, a re-emerging zoonotic disease of global importance. Here, we use a recently described lineage of environmental-adapted leptospires, which are evolutionarily the closest relatives of the highly virulent Leptospira species, to explore the key phenotypic traits and genetic determinants of Leptospira virulence. Through a comprehensive approach integrating phylogenomic comparisons with in vitro and in vivo phenotyping studies, we show that the evolution towards pathogenicity is associated with both a decrease of the ability to survive in the environment and the acquisition of strategies that enable successful host colonization. This includes the evasion of the human complement system and the adaptations to avoid activation of the innate immune cells. Moreover, our analysis reveals specific genetic determinants that have undergone positive selection during the course of evolution in Leptospira, contributing directly to virulence and host adaptation as demonstrated by gain-of-function and knock-down studies. Taken together, our findings define a new vision on Leptospira pathogenicity, identifying virulence attributes associated with clinically relevant species, and provide insights into the evolution and emergence of these life-threatening pathogens.
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Affiliation(s)
| | - Cecilia Nieves
- Bacterial Symbionts Evolution, Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique, Université du Québec, Laval, QC, Canada
| | - Luke B. Harrison
- Bacterial Symbionts Evolution, Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique, Université du Québec, Laval, QC, Canada
| | - Nadia Benaroudj
- Institut Pasteur, Université Paris Cité, Biology of Spirochetes Unit, Paris, France
| | - Frédéric J. Veyrier
- Bacterial Symbionts Evolution, Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique, Université du Québec, Laval, QC, Canada
| | - Mathieu Picardeau
- Institut Pasteur, Université Paris Cité, Biology of Spirochetes Unit, Paris, France
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5
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Ding Y, Zhao L, Wang G, Shi Y, Guo G, Liu C, Chen Z, Coker OO, She J, Yu J. PacBio sequencing of human fecal samples uncovers the DNA methylation landscape of 22 673 gut phages. Nucleic Acids Res 2023; 51:12140-12149. [PMID: 37904586 PMCID: PMC10711547 DOI: 10.1093/nar/gkad977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 10/03/2023] [Accepted: 10/18/2023] [Indexed: 11/01/2023] Open
Abstract
Gut phages have an important impact on human health. Methylation plays key roles in DNA recognition, gene expression regulation and replication for phages. However, the DNA methylation landscape of gut phages is largely unknown. Here, with PacBio sequencing (2120×, 4785 Gb), we detected gut phage methylation landscape based on 22 673 gut phage genomes, and presented diverse methylation motifs and methylation differences in genomic elements. Moreover, the methylation rate of phages was associated with taxonomy and host, and N6-methyladenine methylation rate was higher in temperate phages than in virulent phages, suggesting an important role for methylation in phage-host interaction. In particular, 3543 (15.63%) phage genomes contained restriction-modification system, which could aid in evading clearance by the host. This study revealed the DNA methylation landscape of gut phage and its potential roles, which will advance the understanding of gut phage survival and human health.
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Affiliation(s)
- Yanqiang Ding
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK-Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Liuyang Zhao
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK-Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Guoping Wang
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK-Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Yu Shi
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK-Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Gang Guo
- Center for Gut Microbiome Research, Department of Surgery, Med-X Institute, Department of High Talent, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Changan Liu
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK-Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Zigui Chen
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Olabisi Oluwabukola Coker
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK-Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Junjun She
- Center for Gut Microbiome Research, Department of Surgery, Med-X Institute, Department of High Talent, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Jun Yu
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK-Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
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Kędzierska-Mieszkowska S. Sigma factors of RNA polymerase in the pathogenic spirochaete Leptospira interrogans, the causative agent of leptospirosis. FASEB J 2023; 37:e23163. [PMID: 37688587 DOI: 10.1096/fj.202300252rrr] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 07/13/2023] [Accepted: 08/14/2023] [Indexed: 09/11/2023]
Abstract
The aim of this review is to summarize the current knowledge on the role of σ factors in a highly invasive spirochaete Leptospira interrogans responsible for leptospirosis that affects many mammals, including humans. This disease has a significant impact on public health and the economy worldwide. In bacteria, σ factors are the key regulators of gene expression at the transcriptional level and therefore play an important role in bacterial adaptative response to different environmental stimuli. These factors form a holoenzyme with the RNA polymerase core enzyme and then direct it to specific promoters, which results in turning on selected genes. Most bacteria possess several different σ factors that enable them to maintain basal gene expression, as well as to regulate gene expression in response to specific environmental signals. Recent comparative genomics and in silico genome-wide analyses have revealed that the L. interrogans genome, consisting of two circular chromosomes, encodes a total of 14 σ factors. Among them, there is one putative housekeeping σ70 -like factor, and three types of alternative σ factors, i.e., one σ54 , one σ28 and 11 putative ECF (extracytoplasmic function) σE -type factors. Here, characteristics of these putative σ factors and their possible role in the L. interrogans gene regulation (especially in this pathogen's adaptive response to various environmental conditions, an important determinant of leptospiral virulence), are presented.
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7
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Gao WL, Fang JL, Zhu CY, Xu WF, Lyu ZY, Chan XA, Zhao QW, Li YQ. Identification and Characterization of a New Regulator, TagR, for Environmental Stress Resistance Based on the DNA Methylome of Streptomyces roseosporus. Microbiol Spectr 2023; 11:e0038023. [PMID: 37154757 PMCID: PMC10269677 DOI: 10.1128/spectrum.00380-23] [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: 01/24/2023] [Accepted: 04/10/2023] [Indexed: 05/10/2023] Open
Abstract
DNA methylation is a defense that microorganisms use against extreme environmental stress, and improving resistance against environmental stress is essential for industrial actinomycetes. However, research on strain optimization utilizing DNA methylation for breakthroughs is rare. Based on DNA methylome analysis and KEGG pathway assignment in Streptomyces roseosporus, we discovered an environmental stress resistance regulator, TagR. A series of in vivo and in vitro experiments identified TagR as a negative regulator, and it is the first reported regulator of the wall teichoic acid (WTA) ABC transport system. Further study showed that TagR had a positive self-regulatory loop and m4C methylation in the promoter improved its expression. The ΔtagR mutant exhibited better hyperosmotic resistance and higher decanoic acid tolerance than the wild type, which led to a 100% increase in the yield of daptomycin. Moreover, enhancing the expression of the WTA transporter resulted in better osmotic stress resistance in Streptomyces lividans TK24, indicating the potential for wide application of the TagR-WTA transporter regulatory pathway. This research confirmed the feasibility and effectiveness of mining regulators of environmental stress resistance based on the DNA methylome, characterized the mechanism of TagR, and improved the resistance and daptomycin yield of strains. Furthermore, this research provides a new perspective on the optimization of industrial actinomycetes. IMPORTANCE This study established a novel strategy for screening regulators of environmental stress resistance based on the DNA methylome and discovered a new regulator, TagR. The TagR-WTA transporter regulatory pathway improved the resistance and antibiotic yield of strains and has the potential for wide application. Our research provides a new perspective on the optimization and reconstruction of industrial actinomycetes.
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Affiliation(s)
- Wen-Li Gao
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Institute of Pharmaceutical Biotechnology, Hangzhou, China
| | - Jiao-Le Fang
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Institute of Pharmaceutical Biotechnology, Hangzhou, China
| | - Chen-Yang Zhu
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Institute of Pharmaceutical Biotechnology, Hangzhou, China
| | - Wei-Feng Xu
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Institute of Pharmaceutical Biotechnology, Hangzhou, China
| | - Zhong-Yuan Lyu
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Institute of Pharmaceutical Biotechnology, Hangzhou, China
| | - Xin-Ai Chan
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Institute of Pharmaceutical Biotechnology, Hangzhou, China
| | - Qing-Wei Zhao
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, China
| | - Yong-Quan Li
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Institute of Pharmaceutical Biotechnology, Hangzhou, China
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8
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Nishimura M, Tanaka T, Murata S, Miyabe A, Ishige T, Kawasaki K, Yokoyama M, Hashimoto N, Yamagata K, Nagano H, Tojo-Nishimura S, Matsushita K. Extension of bacterial rDNA sequencing for simultaneous methylation detection and its application in microflora analysis. Sci Rep 2023; 13:5731. [PMID: 37029177 PMCID: PMC10082018 DOI: 10.1038/s41598-023-28706-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 01/23/2023] [Indexed: 04/09/2023] Open
Abstract
Although polymerase chain reaction (PCR) amplification and sequencing of the bacterial 16S rDNA region has numerous scientific applications, it does not provide DNA methylation information. Herein, we propose a simple extension for bisulfite sequencing to investigate 5-methylcytosine residues in the bacterial 16S rDNA region from clinical isolates or flora. Multiple displacement amplification without DNA denaturation was used to preferentially pre-amplify single-stranded bacterial DNA after bisulfite conversion. Following the pre-amplification, the 16S rDNA region was analyzed using nested bisulfite PCR and sequencing, enabling the simultaneous identification of DNA methylation status and sequence data. We used this approach (termed sm16S rDNA PCR/sequencing) to identify novel methylation sites and a methyltransferase (M. MmnI) in Morganella morganii and different methylation motifs among Enterococcus faecalis strains from small volumes of clinical specimens. Further, our analysis suggested that M. MmnI may be correlated to erythromycin resistance. Thus, sm16S rDNA PCR/sequencing is a useful extension method for analyzing the DNA methylation of 16S rDNA regions in a microflora, providing additional information not provided by conventional PCR. Given the relationship between DNA methylation status and drug resistance in bacteria, we believe this technique can be effectively applied in clinical sample testing.
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Affiliation(s)
- Motoi Nishimura
- Division of Laboratory Medicine, Clinical Genetics and Proteomics, Chiba University Hospital, Chiba, Japan.
| | - Tomoaki Tanaka
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba, Japan
- Research Institute of Disaster Medicine, Chiba University, Chiba, Japan
| | - Syota Murata
- Division of Laboratory Medicine, Clinical Genetics and Proteomics, Chiba University Hospital, Chiba, Japan
| | - Akiko Miyabe
- Division of Laboratory Medicine, Clinical Genetics and Proteomics, Chiba University Hospital, Chiba, Japan
| | - Takayuki Ishige
- Division of Laboratory Medicine, Clinical Genetics and Proteomics, Chiba University Hospital, Chiba, Japan
| | - Kenji Kawasaki
- Division of Laboratory Medicine, Clinical Genetics and Proteomics, Chiba University Hospital, Chiba, Japan
| | - Masataka Yokoyama
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Naoko Hashimoto
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba, Japan
- Research Institute of Disaster Medicine, Chiba University, Chiba, Japan
| | - Kazuyuki Yamagata
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Hidekazu Nagano
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Satomi Tojo-Nishimura
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Kazuyuki Matsushita
- Division of Laboratory Medicine, Clinical Genetics and Proteomics, Chiba University Hospital, Chiba, Japan
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Yang S, Yang Z, Yang J. 4mCBERT: A computing tool for the identification of DNA N4-methylcytosine sites by sequence- and chemical-derived information based on ensemble learning strategies. Int J Biol Macromol 2023; 231:123180. [PMID: 36646347 DOI: 10.1016/j.ijbiomac.2023.123180] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 11/26/2022] [Accepted: 12/30/2022] [Indexed: 01/15/2023]
Abstract
N4-methylcytosine (4mC) is an important DNA chemical modification pattern which is a new methylation modification discovered in recent years and plays critical roles in gene expression regulation, defense against invading genetic elements, genomic imprinting, and so on. Identifying 4mC site from DNA sequence segment contributes to discovering more novel modification patterns. In this paper, we present a model called 4mCBERT that encodes DNA sequence segments by sequence characteristics including one-hot, electron-ion interaction pseudopotential, nucleotide chemical property, word2vec and chemical information containing physicochemical properties (PCP), chemical bidirectional encoder representations from transformers (chemical BERT) and employs ensemble learning framework to develop a prediction model. PCP and chemical BERT features are firstly constructed and applied to predict 4mC sites and show positive contributions to identifying 4mC. For the Matthew's Correlation Coefficient, 4mCBERT significantly outperformed other state-of-the-art models on six independent benchmark datasets including A. thaliana, C. elegans, D. melanogaster, E. coli, G. Pickering, and G. subterraneous by 4.32 % to 24.39 %, 2.52 % to 31.65 %, 2 % to 16.49 %, 6.63 % to 35.15, 8.59 % to 61.85 %, and 8.45 % to 34.45 %. Moreover, 4mCBERT is designed to allow users to predict 4mC sites and retrain 4mC prediction models. In brief, 4mCBERT shows higher performance on six benchmark datasets by incorporating sequence- and chemical-driven information and is available at http://cczubio.top/4mCBERT and https://github.com/abcair/4mCBERT.
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Affiliation(s)
- Sen Yang
- School of Computer Science and Artificial Intelligence, Aliyun School of Big Data, School of Software, Changzhou 213164, China; The Affiliated Changzhou No 2 People's Hospital of Nanjing Medical University, Changzhou 213164, China.
| | - Zexi Yang
- School of Computer Science and Artificial Intelligence, Aliyun School of Big Data, School of Software, Changzhou 213164, China
| | - Jun Yang
- School of Educational Sciences, Yili Normal University, Yining 835000, China
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10
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Cheah HL, Ahmed SA, Tang TH. Transcription start site mapping and small RNA profiling of Leptospira biflexa serovar Patoc. World J Microbiol Biotechnol 2023; 39:104. [PMID: 36808011 DOI: 10.1007/s11274-023-03540-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 02/03/2023] [Indexed: 02/23/2023]
Abstract
Leptospirosis is an emerging zoonotic disease caused by bacterial species of the genus Leptospira. However, the regulatory mechanisms and pathways underlying the adaptation of pathogenic and non-pathogenic Leptospira spp. in different environmental conditions remain elusive. Leptospira biflexa is a non-pathogenic species of Leptospira that lives exclusively in a natural environment. It is an ideal model not only for exploring molecular mechanisms underlying the environmental survival of Leptospira species but also for identifying virulence factors unique to Leptospira's pathogenic species. In this study, we aim to establish the transcription start site (TSS) landscape and the small RNA (sRNA) profile of L. biflexa serovar Patoc grown to exponential and stationary phases via differential RNA-seq (dRNA-seq) and small RNA-seq (sRNA-seq) analyses, respectively. Our dRNA-seq analysis uncovered a total of 2726 TSSs, which are also used to identify other elements, e.g., promoter and untranslated regions (UTRs). Besides, our sRNA-seq analysis revealed a total of 603 sRNA candidates, comprising 16 promoter-associated sRNAs, 184 5'UTR-derived sRNAs, 230 true intergenic sRNAs, 136 5'UTR-antisense sRNAs, and 130 open reading frame (ORF)-antisense sRNAs. In summary, these findings reflect the transcriptional complexity of L. biflexa serovar Patoc under different growth conditions and help to facilitate our understanding of regulatory networks in L. biflexa. To the best of our knowledge, this is the first study reporting the TSS landscape of L. biflexa. The TSS and sRNA landscapes of L. biflexa can also be compared with its pathogenic counterparts, e.g., L. borgpetersenii and L. interrogans, to identify features contributing to their environmental survival and virulence.
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Affiliation(s)
- Hong-Leong Cheah
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia
| | - Siti Aminah Ahmed
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia
| | - Thean-Hock Tang
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia.
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11
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Fang JL, Gao WL, Xu WF, Lyu ZY, Ma L, Luo S, Chen XA, Mao XM, Li YQ. m4C DNA methylation regulates biosynthesis of daptomycin in Streptomyces roseosporus L30. Synth Syst Biotechnol 2022; 7:1013-1023. [PMID: 35801092 PMCID: PMC9240718 DOI: 10.1016/j.synbio.2022.06.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 06/09/2022] [Accepted: 06/09/2022] [Indexed: 11/18/2022] Open
Affiliation(s)
- Jiao-Le Fang
- Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, 310058, PR China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, 310058, Hangzhou, PR China
| | - Wen-Li Gao
- Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, 310058, PR China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, 310058, Hangzhou, PR China
| | - Wei-Feng Xu
- Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, 310058, PR China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, 310058, Hangzhou, PR China
| | - Zhong-Yuan Lyu
- Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, 310058, PR China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, 310058, Hangzhou, PR China
| | - Lie Ma
- Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, 310058, PR China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, 310058, Hangzhou, PR China
| | - Shuai Luo
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, 310058, Hangzhou, PR China
| | - Xin-Ai Chen
- Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, 310058, PR China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, 310058, Hangzhou, PR China
| | - Xu-Ming Mao
- Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, 310058, PR China
| | - Yong-Quan Li
- Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, 310058, PR China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, 310058, Hangzhou, PR China
- Corresponding author. Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, 310058, PR China.
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12
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Breckell GL, Silander OK. Growth condition-dependent differences in methylation imply transiently differentiated DNA methylation states in Escherichia coli. G3 (BETHESDA, MD.) 2022; 13:6858946. [PMID: 36454087 PMCID: PMC9911048 DOI: 10.1093/g3journal/jkac310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 09/14/2022] [Accepted: 09/28/2022] [Indexed: 12/05/2022]
Abstract
DNA methylation in bacteria frequently serves as a simple immune system, allowing recognition of DNA from foreign sources, such as phages or selfish genetic elements. However, DNA methylation also affects other cell phenotypes in a heritable manner (i.e. epigenetically). While there are several examples of methylation affecting transcription in an epigenetic manner in highly localized contexts, it is not well-established how frequently methylation serves a more general epigenetic function over larger genomic scales. To address this question, here we use Oxford Nanopore sequencing to profile DNA modification marks in three natural isolates of Escherichia coli. We first identify the DNA sequence motifs targeted by the methyltransferases in each strain. We then quantify the frequency of methylation at each of these motifs across the entire genome in different growth conditions. We find that motifs in specific regions of the genome consistently exhibit high or low levels of methylation. Furthermore, we show that there are replicable and consistent differences in methylated regions across different growth conditions. This suggests that during growth, E. coli transiently differentiate into distinct methylation states that depend on the growth state, raising the possibility that measuring DNA methylation alone can be used to infer bacterial growth states without additional information such as transcriptome or proteome data. These results show the utility of using Oxford Nanopore sequencing as an economic means to infer DNA methylation status. They also provide new insights into the dynamics of methylation during bacterial growth and provide evidence of differentiated cell states, a transient analog to what is observed in the differentiation of cell types in multicellular organisms.
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Affiliation(s)
- Georgia L Breckell
- Corresponding author: School of Natural and Sciences, Massey University, Auckland 0745, New Zealand. ; Corresponding author: School of Natural and Sciences, Massey University, Auckland 0745, New Zealand. Present address: Ministry for Primary Industries, Auckland 2022, New Zealand
| | - Olin K Silander
- Corresponding author: School of Natural and Sciences, Massey University, Auckland 0745, New Zealand. ; Corresponding author: School of Natural and Sciences, Massey University, Auckland 0745, New Zealand. Present address: Ministry for Primary Industries, Auckland 2022, New Zealand
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13
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Surdel MC, Hahn BL, Anderson PN, Coburn J. Heterologous production of the adhesin LIC13411 from pathogenic Leptospira facilitates binding of non-pathogenic Leptospira in vitro and in vivo. Front Cell Infect Microbiol 2022; 12:917963. [PMID: 35937702 PMCID: PMC9354625 DOI: 10.3389/fcimb.2022.917963] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 06/27/2022] [Indexed: 01/19/2023] Open
Abstract
Leptospirosis is an important cause of morbidity and mortality worldwide. Disease severity ranges from asymptomatic colonization to widespread hemorrhage and multiorgan dysfunction. The causative agents, Leptospira spp., are zoonotic Gram-negative spirochetes. One important step in pathogenesis is binding of bacterial adhesins to host components. Previously our laboratory identified two L. interrogans candidate adhesins, LIC11574 and LIC13411, that bind to VE-cadherin in vitro. In the current study, we demonstrate the ability of two strains of pathogenic L. interrogans to disrupt the localization of VE-cadherin, a protein important to maintaining inter-endothelial junctions. Purified MBP-LIC11574 and MBP-LIC13411 bind human dermal microvascular endothelial cells in a pattern reminiscent of VE-cadherin, but do not disrupt VE-cadherin localization. Genes encoding the candidate adhesins from pathogenic Leptospira were cloned in an overexpression vector and introduced into non-pathogenic L. biflexa, creating gain-of-function strains producing LIC11574 or LIC13411. Protein production and localization to the outer membrane were confirmed by Triton X-114 fractionation. Although these strains do not disrupt VE-cadherin localization, production of LIC13411 increases binding of non-pathogenic Leptospira to human endothelial cells and specifically to VE-cadherin. In a short-term murine model of infection, LIC13411 production led to increased burdens of the non-pathogen in the lung, liver, kidney, and bladder. These data confirm the role of LIC13411 as an adhesin in Leptospira spp. and implicate it in dissemination to multiple organs. Importantly, anti-adhesin therapy has been shown to have many benefits over classical antibiotics. Taken together, this work provides novel insight into the pathogenesis of Leptospira spp. and identifies LIC13411 as a potential prophylactic and therapeutic target.
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Affiliation(s)
- Matthew C. Surdel
- Department of Medicine, Division of Infectious Diseases, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Beth L. Hahn
- Department of Medicine, Division of Infectious Diseases, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Phillip N. Anderson
- Department of Medicine, Division of Infectious Diseases, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Jenifer Coburn
- Department of Medicine, Division of Infectious Diseases, Medical College of Wisconsin, Milwaukee, WI, United States,Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, United States,*Correspondence: Jenifer Coburn,
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14
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Surdel MC, Anderson PN, Hahn BL, Coburn J. Hematogenous dissemination of pathogenic and non-pathogenic Leptospira in a short-term murine model of infection. Front Cell Infect Microbiol 2022; 12:917962. [PMID: 35923802 PMCID: PMC9339599 DOI: 10.3389/fcimb.2022.917962] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 06/27/2022] [Indexed: 01/19/2023] Open
Abstract
Leptospirosis is an emerging zoonosis caused by pathogenic Leptospira spp. Because rodents are natural hosts of Leptospira, rodent models of pathogenesis have been limited, but are valuable to understand infection in reservoir animals even in the absence of disease. Mouse models of infection provide advantages due to genetic tractability, so developing murine models of Leptospira infection is crucial for further understanding the biology of this organism. Previously our laboratory developed a short-term murine model of Borrelia burgdorferi hematogenous dissemination to investigate the role of adhesion proteins on bacterial survival and dissemination within a host. Here we adapt this model to Leptospira. C3H/HeJ mice are anesthetized, inoculated intravenously, and then bacteria are allowed to circulate for up to twenty-four hours. Mice are euthanized, perfused with saline, and tissues are harvested for culture and DNA purification. Bacterial burdens are determined by quantitative PCR. Reproducible burdens of bacteria were found in tissues upon inoculation with pathogens and non-pathogens, demonstrating the utility of this model to probe different Leptospira species and strains. Pathogenic L. interrogans has a significantly higher burden in blood, liver, kidney, and bladder at one-hour post-inoculation when compared to non-pathogenic L. biflexa. Colonization of the kidney is essential to the life cycle of pathogenic Leptospira in nature. Measurable burdens of non-pathogenic L. biflexa were found in numerous organs and live leptospires were recovered from blood samples for at least three hours post-inoculation, contrary to the previous belief that non-pathogenic leptospires are rapidly cleared. This short-term murine model of Leptospira hematogenous dissemination will allow for the interrogation of virulence factors potentially important for tissue colonization and evasion of host defenses, and represents a novel animal model for investigating determinants of Leptospira infection.
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Affiliation(s)
- Matthew C. Surdel
- Department of Medicine, Division of Infectious Diseases, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Phillip N. Anderson
- Department of Medicine, Division of Infectious Diseases, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Beth L. Hahn
- Department of Medicine, Division of Infectious Diseases, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Jenifer Coburn
- Department of Medicine, Division of Infectious Diseases, Medical College of Wisconsin, Milwaukee, WI, United States,Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, United States,*Correspondence: Jenifer Coburn,
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15
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Terrazas-Salgado L, García-Gasca A, Betancourt-Lozano M, Llera-Herrera R, Alvarado-Cruz I, Yáñez-Rivera B. Epigenetic Transgenerational Modifications Induced by Xenobiotic Exposure in Zebrafish. Front Cell Dev Biol 2022; 10:832982. [PMID: 35281093 PMCID: PMC8914061 DOI: 10.3389/fcell.2022.832982] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 01/21/2022] [Indexed: 11/23/2022] Open
Abstract
Zebrafish (Danio rerio) is a well-established vertebrate model in ecotoxicology research that responds to a wide range of xenobiotics such as pesticides, drugs, and endocrine-disrupting compounds. The epigenome can interact with the environment and transform internal and/or external signals into phenotypic responses through changes in gene transcription. Environmental exposures can also generate epigenetic variations in offspring even by indirect exposure. In this review, we address the advantages of using zebrafish as an experimental animal model to study transgenerational epigenetic processes upon exposure to xenobiotics. We focused mostly on DNA methylation, although studies on post-translational modifications of histones, and non-coding RNAs related to xenobiotic exposure in zebrafish are also discussed. A revision of the methods used to study epigenetic changes in zebrafish revealed the relevance and reproducibility for epigenetics-related research. PubMed and Google Scholar databases were consulted for original research articles published from 2013 to date, by using six keywords: zebrafish, epigenetics, exposure, parental, transgenerational, and F2. From 499 articles identified, 92 were considered, of which 14 were selected as included F2 and epigenetic mechanisms. Current knowledge regarding the effect of xenobiotics on DNA methylation, histone modifications, and changes in non-coding RNAs expressed in F2 is summarized, along with key experimental design considerations to characterize transgenerational effects.
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Affiliation(s)
| | | | | | - Raúl Llera-Herrera
- Instituto de Ciencias del Mar y Limnología—Unidad Académica Mazatlán, Universidad Nacional Autónoma de México, Mazatlán, Mexico
| | - Isabel Alvarado-Cruz
- Department of Cellular and Molecular Medicine, University of Arizona Cancer Center, Tucson, AZ, United States
| | - Beatriz Yáñez-Rivera
- Centro de Investigación en Alimentación y Desarrollo, A. C., Mazatlán, Mexico
- Consejo Nacional de Ciencia y Tecnología, México, Mexico
- *Correspondence: Beatriz Yáñez-Rivera,
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16
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Xiong J, Wang P, Shao WX, Li G, Ding JH, Xie NB, Wang M, Cheng QY, Xie C, Feng YQ, Ci W, Yuan BF. Genome-wide mapping of N4-methylcytosine at single-base resolution by APOBEC3A-mediated deamination sequencing. Chem Sci 2022; 13:9960-9972. [PMID: 36128236 PMCID: PMC9430668 DOI: 10.1039/d2sc02446b] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 08/04/2022] [Indexed: 12/15/2022] Open
Abstract
N4-methylcytosine (4mC) is a natural DNA modification occurring in thermophiles and plays important roles in restriction-modification (R-M) systems in bacterial genomes. However, the precise location and sequence context of 4mC in the whole genome are limited. In this study, we developed an APOBEC3A-mediated deamination sequencing (4mC-AMD-seq) method for genome-wide mapping of 4mC at single-base resolution. In the 4mC-AMD-seq method, cytosine and 5-methylcytosine (5mC) are deaminated by APOBEC3A (A3A) protein to generate uracil and thymine, both of which are read as thymine in sequencing, while 4mC is resistant to deamination and therefore read as cytosine. Thus, the readouts of cytosines from sequencing could manifest the original 4mC sites in genomes. With the 4mC-AMD-seq method, we achieved the genome-wide mapping of 4mC in Deinococcus radiodurans (D. radiodurans). In addition, we confirmed that 4mC, but not 5mC, was the major modification in the D. radiodurans genome. We identified 1586 4mC sites in the genome of D. radiodurans, among which 564 sites were located in the CCGCGG motif. The average methylation levels in the CCGCGG motif and non-CCGCGG sequence were 70.0% and 22.8%, respectively. We envision that the 4mC-AMD-seq method will facilitate the investigation of 4mC functions, including the 4mC-involved R-M systems, in uncharacterized but potentially useful strains. Genome-wide mapping of N4-methylcytosine (4mC) at single-base resolution with APOBEC3A-mediated deamination sequencing (4mC-AMD-seq).![]()
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Affiliation(s)
- Jun Xiong
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, School of Public Health, Wuhan University, Wuhan 430071, China
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China
- Cancer Precision Diagnosis and Treatment and Translational Medicine Hubei Engineering Research Center, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Ping Wang
- Key Laboratory of Genomics and Precision Medicine, China National Center for Bioinformation, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wen-Xuan Shao
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, School of Public Health, Wuhan University, Wuhan 430071, China
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Gaojie Li
- Key Laboratory of Genomics and Precision Medicine, China National Center for Bioinformation, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiang-Hui Ding
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, School of Public Health, Wuhan University, Wuhan 430071, China
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Neng-Bin Xie
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, School of Public Health, Wuhan University, Wuhan 430071, China
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Min Wang
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, School of Public Health, Wuhan University, Wuhan 430071, China
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Qing-Yun Cheng
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, School of Public Health, Wuhan University, Wuhan 430071, China
| | - Conghua Xie
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, School of Public Health, Wuhan University, Wuhan 430071, China
- Cancer Precision Diagnosis and Treatment and Translational Medicine Hubei Engineering Research Center, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yu-Qi Feng
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, School of Public Health, Wuhan University, Wuhan 430071, China
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Weimin Ci
- Key Laboratory of Genomics and Precision Medicine, China National Center for Bioinformation, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bi-Feng Yuan
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, School of Public Health, Wuhan University, Wuhan 430071, China
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China
- Cancer Precision Diagnosis and Treatment and Translational Medicine Hubei Engineering Research Center, Zhongnan Hospital of Wuhan University, Wuhan, China
- Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, China
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17
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Phoka T, Fule L, Da Fonseca JP, Cokelaer T, Picardeau M, Patarakul K. Investigating the role of the carbon storage regulator A (CsrA) in Leptospira spp. PLoS One 2021; 16:e0260981. [PMID: 34898610 PMCID: PMC8668096 DOI: 10.1371/journal.pone.0260981] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 11/20/2021] [Indexed: 01/08/2023] Open
Abstract
Carbon Storage Regulator A (CsrA) is a well-characterized post-transcriptional global regulator that plays a critical role in response to environmental changes in many bacteria. CsrA has been reported to regulate several metabolic pathways, motility, biofilm formation, and virulence-associated genes. The role of csrA in Leptospira spp., which are able to survive in different environmental niches and infect a wide variety of reservoir hosts, has not been characterized. To investigate the role of csrA as a gene regulator in Leptospira, we generated a L. biflexa csrA deletion mutant (ΔcsrA) and csrA overexpressing Leptospira strains. The ΔcsrA L. biflexa displayed poor growth under starvation conditions. RNA sequencing revealed that in rich medium only a few genes, including the gene encoding the flagellar filament protein FlaB3, were differentially expressed in the ΔcsrA mutant. In contrast, 575 transcripts were differentially expressed when csrA was overexpressed in L. biflexa. Electrophoretic mobility shift assay (EMSA) confirmed the RNA-seq data in the ΔcsrA mutant, showing direct binding of recombinant CsrA to flaB3 mRNA. In the pathogen L. interrogans, we were not able to generate a csrA mutant. We therefore decided to overexpress csrA in L. interrogans. In contrast to the overexpressing strain of L. biflexa, the overexpressing L. interrogans strain had poor motility on soft agar. The overexpressing strain of L. interrogans also showed significant upregulation of the flagellin flaB1, flaB2, and flaB4. The interaction of L. interrogans rCsrA and flaB4 was confirmed by EMSA. Our results demonstrated that CsrA may function as a global regulator in Leptospira spp. under certain conditions that cause csrA overexpression. Interestingly, the mechanisms of action and gene targets of CsrA may be different between non-pathogenic and pathogenic Leptospira strains.
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Affiliation(s)
- Theerapat Phoka
- Medical Microbiology, Interdisciplinary and International Program, Graduate School, Chulalongkorn University, Bangkok, Thailand
| | - Lenka Fule
- Institut Pasteur, Biology of Spirochetes Unit, French National Reference Centre for Leptospirosis, Paris, France
| | - Juliana Pipoli Da Fonseca
- Plate-forme Technologique Biomics, Centre de Ressources et Recherches Technologiques (C2RT), Institut Pasteur, Paris, France
| | - Thomas Cokelaer
- Plate-forme Technologique Biomics, Centre de Ressources et Recherches Technologiques (C2RT), Institut Pasteur, Paris, France
- Hub de Bioinformatique et Biostatistique – Département Biologie Computationnelle, Institut Pasteur, Paris, France
| | - Mathieu Picardeau
- Institut Pasteur, Biology of Spirochetes Unit, French National Reference Centre for Leptospirosis, Paris, France
| | - Kanitha Patarakul
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Pathumwan, Bangkok, Thailand
- Chula Vaccine Research Center (Chula VRC), Center of Excellence in Vaccine Research and Development, Chulalongkorn University, Bangkok, Thailand
- * E-mail: ,
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18
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Mohammadi MM, Bavi O. DNA sequencing: an overview of solid-state and biological nanopore-based methods. Biophys Rev 2021; 14:99-110. [PMID: 34840616 PMCID: PMC8609259 DOI: 10.1007/s12551-021-00857-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 10/14/2021] [Indexed: 12/23/2022] Open
Abstract
The field of sequencing is a topic of significant interest since its emergence and has become increasingly important over time. Impressive achievements have been obtained in this field, especially in relations to DNA and RNA sequencing. Since the first achievements by Sanger and colleagues in the 1950s, many sequencing techniques have been developed, while others have disappeared. DNA sequencing has undergone three generations of major evolution. Each generation has its own specifications that are mentioned briefly. Among these generations, nanopore sequencing has its own exciting characteristics that have been given more attention here. Among pioneer technologies being used by the third-generation techniques, nanopores, either biological or solid-state, have been experimentally or theoretically extensively studied. All sequencing technologies have their own advantages and disadvantages, so nanopores are not free from this general rule. It is also generally pointed out what research has been done to overcome the obstacles. In this review, biological and solid-state nanopores are elaborated on, and applications of them are also discussed briefly.
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Affiliation(s)
- Mohammad M Mohammadi
- Department of Mechanical and Aerospace Engineering, Shiraz University of Technology, Shiraz, 71557-13876 Iran
| | - Omid Bavi
- Department of Mechanical and Aerospace Engineering, Shiraz University of Technology, Shiraz, 71557-13876 Iran
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19
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Dorado G, Gálvez S, Rosales TE, Vásquez VF, Hernández P. Analyzing Modern Biomolecules: The Revolution of Nucleic-Acid Sequencing - Review. Biomolecules 2021; 11:1111. [PMID: 34439777 PMCID: PMC8393538 DOI: 10.3390/biom11081111] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/12/2021] [Accepted: 07/23/2021] [Indexed: 02/06/2023] Open
Abstract
Recent developments have revolutionized the study of biomolecules. Among them are molecular markers, amplification and sequencing of nucleic acids. The latter is classified into three generations. The first allows to sequence small DNA fragments. The second one increases throughput, reducing turnaround and pricing, and is therefore more convenient to sequence full genomes and transcriptomes. The third generation is currently pushing technology to its limits, being able to sequence single molecules, without previous amplification, which was previously impossible. Besides, this represents a new revolution, allowing researchers to directly sequence RNA without previous retrotranscription. These technologies are having a significant impact on different areas, such as medicine, agronomy, ecology and biotechnology. Additionally, the study of biomolecules is revealing interesting evolutionary information. That includes deciphering what makes us human, including phenomena like non-coding RNA expansion. All this is redefining the concept of gene and transcript. Basic analyses and applications are now facilitated with new genome editing tools, such as CRISPR. All these developments, in general, and nucleic-acid sequencing, in particular, are opening a new exciting era of biomolecule analyses and applications, including personalized medicine, and diagnosis and prevention of diseases for humans and other animals.
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Affiliation(s)
- Gabriel Dorado
- Dep. Bioquímica y Biología Molecular, Campus Rabanales C6-1-E17, Campus de Excelencia Internacional Agroalimentario (ceiA3), Universidad de Córdoba, 14071 Córdoba, Spain
| | - Sergio Gálvez
- Dep. Lenguajes y Ciencias de la Computación, Boulevard Louis Pasteur 35, Universidad de Málaga, 29071 Málaga, Spain;
| | - Teresa E. Rosales
- Laboratorio de Arqueobiología, Avda. Universitaria s/n, Universidad Nacional de Trujillo, 13011 Trujillo, Peru;
| | - Víctor F. Vásquez
- Centro de Investigaciones Arqueobiológicas y Paleoecológicas Andinas Arqueobios, Martínez de Companón 430-Bajo 100, Urbanización San Andres, 13088 Trujillo, Peru;
| | - Pilar Hernández
- Instituto de Agricultura Sostenible (IAS), Consejo Superior de Investigaciones Científicas (CSIC), Alameda del Obispo s/n, 14080 Córdoba, Spain;
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20
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Payelleville A, Brillard J. Novel Identification of Bacterial Epigenetic Regulations Would Benefit From a Better Exploitation of Methylomic Data. Front Microbiol 2021; 12:685670. [PMID: 34054792 PMCID: PMC8160106 DOI: 10.3389/fmicb.2021.685670] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 04/22/2021] [Indexed: 12/21/2022] Open
Abstract
DNA methylation can be part of epigenetic mechanisms, leading to cellular subpopulations with heterogeneous phenotypes. While prokaryotic phenotypic heterogeneity is of critical importance for a successful infection by several major pathogens, the exact mechanisms involved in this phenomenon remain unknown in many cases. Powerful sequencing tools have been developed to allow the detection of the DNA methylated bases at the genome level, and they have recently been extensively applied on numerous bacterial species. Some of these tools are increasingly used for metagenomics analysis but only a limited amount of the available methylomic data is currently being exploited. Because newly developed tools now allow the detection of subpopulations differing in their genome methylation patterns, it is time to emphasize future strategies based on a more extensive use of methylomic data. This will ultimately help to discover new epigenetic gene regulations involved in bacterial phenotypic heterogeneity, including during host-pathogen interactions.
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Affiliation(s)
- Amaury Payelleville
- DGIMI, INRAE, Univ. Montpellier, Montpellier, France.,Cellular and Molecular Microbiology, Faculté des Sciences, Université Libre de Bruxelles, Gosselies, Belgium
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