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Wang S, Tian R, Bi Y, Meng F, Zhang R, Wang C, Wang D, Liu L, Zhang B. A review of distribution and functions of extracellular DNA in the environment and wastewater treatment systems. CHEMOSPHERE 2024; 359:142264. [PMID: 38714248 DOI: 10.1016/j.chemosphere.2024.142264] [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: 02/18/2024] [Revised: 04/23/2024] [Accepted: 05/04/2024] [Indexed: 05/09/2024]
Abstract
Extracellular DNA refers to DNA fragments existing outside the cell, originating from various cell release mechanisms, including active secretion, cell lysis, and phage-mediated processes. Extracellular DNA serves as a vital environmental biomarker, playing crucial ecological and environmental roles in water bodies. This review is summarized the mechanisms of extracellular DNA release, including pathways involving cell lysis, extracellular vesicles, and type IV secretion systems. Then, the extraction and detection methods of extracellular DNA from water, soil, and biofilm are described and analyzed. Finally, we emphasize the role of extracellular DNA in microbial community systems, including its significant contributions to biofilm formation, biodiversity through horizontal gene transfer, and electron transfer processes. This review offers a comprehensive insight into the sources, distribution, functions, and impacts of extracellular DNA within aquatic environments, aiming to foster further exploration and understanding of extracellular DNA dynamics in aquatic environments as well as other environments.
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Affiliation(s)
- Shaopo Wang
- School of Environmental and Municipal Engineering, Tianjin Chengjian University, Jinjing Road 26, Tianjin, 300384, China; Tianjin Key Laboratory of Aquatic Science and Technology, Jinjing Road 26, Tianjin, China
| | - Ruimin Tian
- School of Environmental and Municipal Engineering, Tianjin Chengjian University, Jinjing Road 26, Tianjin, 300384, China; Tianjin Key Laboratory of Aquatic Science and Technology, Jinjing Road 26, Tianjin, China
| | - Yanmeng Bi
- School of Environmental and Municipal Engineering, Tianjin Chengjian University, Jinjing Road 26, Tianjin, 300384, China; Tianjin Key Laboratory of Aquatic Science and Technology, Jinjing Road 26, Tianjin, China
| | - Fansheng Meng
- School of Environmental and Municipal Engineering, Tianjin Chengjian University, Jinjing Road 26, Tianjin, 300384, China; Tianjin Key Laboratory of Aquatic Science and Technology, Jinjing Road 26, Tianjin, China
| | - Rui Zhang
- School of Environmental and Municipal Engineering, Tianjin Chengjian University, Jinjing Road 26, Tianjin, 300384, China; Tianjin Key Laboratory of Aquatic Science and Technology, Jinjing Road 26, Tianjin, China
| | - Chenchen Wang
- School of Environmental and Municipal Engineering, Tianjin Chengjian University, Jinjing Road 26, Tianjin, 300384, China; Tianjin Key Laboratory of Aquatic Science and Technology, Jinjing Road 26, Tianjin, China
| | - Dong Wang
- School of Environmental and Municipal Engineering, Tianjin Chengjian University, Jinjing Road 26, Tianjin, 300384, China; Tianjin Key Laboratory of Aquatic Science and Technology, Jinjing Road 26, Tianjin, China
| | - Lingjie Liu
- School of Environmental and Municipal Engineering, Tianjin Chengjian University, Jinjing Road 26, Tianjin, 300384, China; Tianjin Key Laboratory of Aquatic Science and Technology, Jinjing Road 26, Tianjin, China.
| | - Bo Zhang
- Tianjin Eco-City Water Investment and Construction Co. Ltd, Hexu Road 276, Tianjin, 300467, China
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Filgueiras JPC, Zámocký M, Turchetto-Zolet AC. Unraveling the evolutionary origin of the P5CS gene: a story of gene fusion and horizontal transfer. Front Mol Biosci 2024; 11:1341684. [PMID: 38693917 PMCID: PMC11061531 DOI: 10.3389/fmolb.2024.1341684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 03/25/2024] [Indexed: 05/03/2024] Open
Abstract
The accumulation of proline in response to the most diverse types of stress is a widespread defense mechanism. In prokaryotes, fungi, and certain unicellular eukaryotes (green algae), the first two reactions of proline biosynthesis occur through two distinct enzymes, γ-glutamyl kinase (GK E.C. 2.7.2.11) and γ-glutamyl phosphate reductase (GPR E.C. 1.2.1.41), encoded by two different genes, ProB and ProA, respectively. Plants, animals, and a few unicellular eukaryotes carry out these reactions through a single bifunctional enzyme, the Δ1-pyrroline-5-carboxylate synthase (P5CS), which has the GK and GPR domains fused. To better understand the origin and diversification of the P5CS gene, we use a robust phylogenetic approach with a broad sampling of the P5CS, ProB and ProA genes, including species from all three domains of life. Our results suggest that the collected P5CS genes have arisen from a single fusion event between the ProA and ProB gene paralogs. A peculiar fusion event occurred in an ancestral eukaryotic lineage and was spread to other lineages through horizontal gene transfer. As for the diversification of this gene family, the phylogeny of the P5CS gene in plants shows that there have been multiple independent processes of duplication and loss of this gene, with the duplications being related to old polyploidy events.
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Affiliation(s)
- João Pedro Carmo Filgueiras
- Graduate Program in Genetics and Molecular Biology, Department of Genetics, Institute of Biosciences, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Marcel Zámocký
- Laboratory of Phylogenomic Ecology, Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Andreia Carina Turchetto-Zolet
- Graduate Program in Genetics and Molecular Biology, Department of Genetics, Institute of Biosciences, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
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3
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Gucwa K, Wons E, Wisniewska A, Jakalski M, Dubiak Z, Kozlowski LP, Mruk I. Lethal perturbation of an Escherichia coli regulatory network is triggered by a restriction-modification system's regulator and can be mitigated by excision of the cryptic prophage Rac. Nucleic Acids Res 2024; 52:2942-2960. [PMID: 38153127 PMCID: PMC11014345 DOI: 10.1093/nar/gkad1234] [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: 06/09/2023] [Revised: 12/08/2023] [Accepted: 12/13/2023] [Indexed: 12/29/2023] Open
Abstract
Bacterial gene regulatory networks orchestrate responses to environmental challenges. Horizontal gene transfer can bring in genes with regulatory potential, such as new transcription factors (TFs), and this can disrupt existing networks. Serious regulatory perturbations may even result in cell death. Here, we show the impact on Escherichia coli of importing a promiscuous TF that has adventitious transcriptional effects within the cryptic Rac prophage. A cascade of regulatory network perturbations occurred on a global level. The TF, a C regulatory protein, normally controls a Type II restriction-modification system, but in E. coli K-12 interferes with expression of the RacR repressor gene, resulting in de-repression of the normally-silent Rac ydaT gene. YdaT is a prophage-encoded TF with pleiotropic effects on E. coli physiology. In turn, YdaT alters expression of a variety of bacterial regulons normally controlled by the RcsA TF, resulting in deficient lipopolysaccharide biosynthesis and cell division. At the same time, insufficient RacR repressor results in Rac DNA excision, halting Rac gene expression due to loss of the replication-defective Rac prophage. Overall, Rac induction appears to counteract the lethal toxicity of YdaT. We show here that E. coli rewires its regulatory network, so as to minimize the adverse regulatory effects of the imported C TF. This complex set of interactions may reflect the ability of bacteria to protect themselves by having robust mechanisms to maintain their regulatory networks, and/or suggest that regulatory C proteins from mobile operons are under selection to manipulate their host's regulatory networks for their own benefit.
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Affiliation(s)
- Katarzyna Gucwa
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Ewa Wons
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Aleksandra Wisniewska
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Marcin Jakalski
- 3P-Medicine Laboratory, Medical University of Gdansk, Debinki 7, 80-211 Gdansk, Poland
| | - Zuzanna Dubiak
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Lukasz Pawel Kozlowski
- Institute of Informatics, Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Banacha 2, 02-097 Warsaw, Poland
| | - Iwona Mruk
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
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Lyu B, Song Q. The intricate relationship of G-Quadruplexes and bacterial pathogenicity islands. eLife 2024; 12:RP91985. [PMID: 38391174 PMCID: PMC10942614 DOI: 10.7554/elife.91985] [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: 02/24/2024] Open
Abstract
The dynamic interplay between guanine-quadruplex (G4) structures and pathogenicity islands (PAIs) represents a captivating area of research with implications for understanding the molecular mechanisms underlying pathogenicity. This study conducted a comprehensive analysis of a large-scale dataset from reported 89 pathogenic strains of bacteria to investigate the potential interactions between G4 structures and PAIs. G4 structures exhibited an uneven and non-random distribution within the PAIs and were consistently conserved within the same pathogenic strains. Additionally, this investigation identified positive correlations between the number and frequency of G4 structures and the GC content across different genomic features, including the genome, promoters, genes, tRNA, and rRNA regions, indicating a potential relationship between G4 structures and the GC-associated regions of the genome. The observed differences in GC content between PAIs and the core genome further highlight the unique nature of PAIs and underlying factors, such as DNA topology. High-confidence G4 structures within regulatory regions of Escherichia coli were identified, modulating the efficiency or specificity of DNA integration events within PAIs. Collectively, these findings pave the way for future research to unravel the intricate molecular mechanisms and functional implications of G4-PAI interactions, thereby advancing our understanding of bacterial pathogenicity and the role of G4 structures in pathogenic diseases.
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Affiliation(s)
- Bo Lyu
- Division of Plant Science and Technology, University of MissouriColumbiaUnited States
| | - Qisheng Song
- Division of Plant Science and Technology, University of MissouriColumbiaUnited States
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Peng M, Lin W, Zhou A, Jiang Z, Zhou F, Wang Z. High genetic diversity and different type VI secretion systems in Enterobacter species revealed by comparative genomics analysis. BMC Microbiol 2024; 24:26. [PMID: 38238664 PMCID: PMC10797944 DOI: 10.1186/s12866-023-03164-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 12/18/2023] [Indexed: 01/22/2024] Open
Abstract
The human-pathogenic Enterobacter species are widely distributed in diverse environmental conditions, however, the understanding of the virulence factors and genetic variations within the genus is very limited. In this study, we performed comparative genomics analysis of 49 strains originated from diverse niches and belonged to eight Enterobacter species, in order to further understand the mechanism of adaption to the environment in Enterobacter. The results showed that they had an open pan-genome and high genomic diversity which allowed adaptation to distinctive ecological niches. We found the number of secretion systems was the highest among various virulence factors in these Enterobacter strains. Three types of T6SS gene clusters including T6SS-A, T6SS-B and T6SS-C were detected in most Enterobacter strains. T6SS-A and T6SS-B shared 13 specific core genes, but they had different gene structures, suggesting they probably have different biological functions. Notably, T6SS-C was restricted to E. cancerogenus. We detected a T6SS gene cluster, highly similar to T6SS-C (91.2%), in the remote related Citrobacter rodenitum, suggesting that this unique gene cluster was probably acquired by horizontal gene transfer. The genomes of Enterobacter strains possess high genetic diversity, limited number of conserved core genes, and multiple copies of T6SS gene clusters with differentiated structures, suggesting that the origins of T6SS were not by duplication instead by independent acquisition. These findings provide valuable information for better understanding of the functional features of Enterobacter species and their evolutionary relationships.
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Affiliation(s)
- Mu Peng
- Hubei Key Laboratory of Biological Resources Protection and Utilization, Hubei Minzu University, Enshi, China.
- College of Biological and Food Engineering, College of Biological and Food Engineering, Hubei Minzu University, Hubei Minzu University, No. 39 Xueyuan Street, Enshi, 445000, China.
| | - Weiyuan Lin
- College of Biological and Food Engineering, College of Biological and Food Engineering, Hubei Minzu University, Hubei Minzu University, No. 39 Xueyuan Street, Enshi, 445000, China
| | - Aifen Zhou
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Zhihui Jiang
- College of Biological and Food Engineering, College of Biological and Food Engineering, Hubei Minzu University, Hubei Minzu University, No. 39 Xueyuan Street, Enshi, 445000, China
| | - Fangzhen Zhou
- College of Biological and Food Engineering, College of Biological and Food Engineering, Hubei Minzu University, Hubei Minzu University, No. 39 Xueyuan Street, Enshi, 445000, China
| | - Zhiyong Wang
- College of Biological and Food Engineering, College of Biological and Food Engineering, Hubei Minzu University, Hubei Minzu University, No. 39 Xueyuan Street, Enshi, 445000, China.
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Densi A, Iyer RS, Bhat PJ. Synonymous and Nonsynonymous Substitutions in Dictyostelium discoideum Ammonium Transporter amtA Are Necessary for Functional Complementation in Saccharomyces cerevisiae. Microbiol Spectr 2023; 11:e0384722. [PMID: 36840598 PMCID: PMC10100761 DOI: 10.1128/spectrum.03847-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 01/24/2023] [Indexed: 02/24/2023] Open
Abstract
Ammonium transporters are present in all three domains of life. They have undergone extensive horizontal gene transfer (HGT), gene duplication, and functional diversification and therefore offer an excellent paradigm to study protein evolution. We attempted to complement a mep1Δmep2Δmep3Δ strain of Saccharomyces cerevisiae (triple-deletion strain), which otherwise cannot grow on ammonium as a sole nitrogen source at concentrations of <3 mM, with amtA of Dictyostelium discoideum, an orthologue of S. cerevisiae MEP2. We observed that amtA did not complement the triple-deletion strain of S. cerevisiae for growth on low-ammonium medium. We isolated two mutant derivatives of amtA (amtA M1 and amtA M2) from a PCR-generated mutant plasmid library that complemented the triple-deletion strain of S. cerevisiae. amtA M1 bears three nonsynonymous and two synonymous substitutions, which are necessary for its functionality. amtA M2 bears two nonsynonymous substitutions and one synonymous substitution, all of which are necessary for functionality. Interestingly, AmtA M1 transports ammonium but does not confer methylamine toxicity, while AmtA M2 transports ammonium and confers methylamine toxicity, demonstrating functional diversification. Preliminary biochemical analyses indicated that the mutants differ in their conformations as well as their mechanisms of ammonium transport. These intriguing results clearly point out that protein evolution cannot be fathomed by studying nonsynonymous and synonymous substitutions in isolation. The above-described observations have significant implications for various facets of biological processes and are discussed in detail. IMPORTANCE Functional diversification following gene duplication is one of the major driving forces of protein evolution. While the role of nonsynonymous substitutions in the functional diversification of proteins is well recognized, knowledge of the role of synonymous substitutions in protein evolution is in its infancy. Using functional complementation, we isolated two functional alleles of the D. discoideum ammonium transporter gene (amtA), which otherwise does not function in S. cerevisiae as an ammonium transporters. One of them is an ammonium transporter, while the other is an ammonium transporter that also confers methylammonium (ammonium analogue) toxicity, suggesting functional diversification. Surprisingly, both alleles require a combination of synonymous and nonsynonymous substitutions for their functionality. These results bring out a hitherto-unknown pathway of protein evolution and pave the way for not only understanding protein evolution but also interpreting single nucleotide polymorphisms (SNPs).
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Affiliation(s)
- Asha Densi
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Revathi S. Iyer
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Paike Jayadeva Bhat
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
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Genomics, Transcriptomics, and Metabolomics Reveal That Minimal Modifications in the Host Are Crucial for the Compensatory Evolution of ColE1-Like Plasmids. mSphere 2022; 7:e0018422. [PMID: 36416553 PMCID: PMC9769657 DOI: 10.1128/msphere.00184-22] [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] [Indexed: 11/24/2022] Open
Abstract
Plasmid-mediated antimicrobial resistance is one of the major threats to public health worldwide. The mechanisms involved in the plasmid/host coadaptation are still poorly characterized, and their understanding is crucial to comprehend the genesis and evolution of multidrug-resistant bacteria. With this purpose, we designed an experimental evolution using Haemophilus influenzae RdKW20 as the model strain carrying the ColE1-like plasmid pB1000. Five H. influenzae populations adapted previously to the culture conditions were transformed with pB1000 and subsequently evolved to compensate for the plasmid-associated fitness cost. Afterward, we performed an integrative multiomic analysis combining genomics, transcriptomics, and metabolomics to explore the molecular mechanisms involved in the compensatory evolution of the plasmid. Our results demonstrate that minimal modifications in the host are responsible for plasmid adaptation. Among all of them, the most enriched process was amino acid metabolism, especially those pathways related to serine, tryptophan, and arginine, eventually related to the genesis and resolution of plasmid dimers. Additional rearrangements occurred during the plasmid adaptation, such as an overexpression of the ribonucleotide reductases and metabolic modifications within specific membrane phospholipids. All these findings demonstrate that the plasmid compensation occurs through the combination of diverse host-mediated mechanisms, of which some are beyond genomic and transcriptomic modifications. IMPORTANCE The ability of bacteria to horizontally transfer genetic material has turned antimicrobial resistance into one of the major sanitary crises of the 21st century. Plasmid conjugation is considered the main mechanism responsible for the mobilization of resistance genes, and its understanding is crucial to tackle this crisis. It is generally accepted that the acquisition and maintenance of mobile genetic elements entail a fitness cost to its host, which is susceptible to be alleviated through a coadaptation process or compensatory evolution. Notwithstanding, despite recent major efforts, the underlying mechanisms involved in this adaptation remain poorly characterized. Analyzing the plasmid/host coadaptation from a multiomic perspective sheds light on the physiological processes involved in the compensation, providing a new understanding on the genesis and evolution of plasmid-mediated antimicrobial-resistant bacteria.
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Hao C, Dewar AE, West SA, Ghoul M. Gene transferability and sociality do not correlate with gene connectivity. Proc Biol Sci 2022; 289:20221819. [PMID: 36448285 PMCID: PMC9709509 DOI: 10.1098/rspb.2022.1819] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
The connectivity of a gene, defined as the number of interactions a gene's product has with other genes' products, is a key characteristic of a gene. In prokaryotes, the complexity hypothesis predicts that genes which undergo more frequent horizontal transfer will be less connected than genes which are only very rarely transferred. We tested the role of horizontal gene transfer, and other potentially important factors, by examining the connectivity of chromosomal and plasmid genes, across 134 diverse prokaryotic species. We found that (i) genes on plasmids were less connected than genes on chromosomes; (ii) connectivity of plasmid genes was not correlated with plasmid mobility; and (iii) the sociality of genes (cooperative or private) was not correlated with gene connectivity.
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Affiliation(s)
- Chunhui Hao
- Department of Biology, University of Oxford, Oxford OX1 3SZ, UK
| | - Anna E. Dewar
- Department of Biology, University of Oxford, Oxford OX1 3SZ, UK
| | - Stuart A. West
- Department of Biology, University of Oxford, Oxford OX1 3SZ, UK
| | - Melanie Ghoul
- Department of Biology, University of Oxford, Oxford OX1 3SZ, UK
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Eissler Y, Castillo-Reyes A, Dorador C, Cornejo-D'Ottone M, Celis-Plá PSM, Aguilar P, Molina V. Virus-to-prokaryote ratio in the Salar de Huasco and different ecosystems of the Southern hemisphere and its relationship with physicochemical and biological parameters. Front Microbiol 2022; 13:938066. [PMID: 36060762 PMCID: PMC9434117 DOI: 10.3389/fmicb.2022.938066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/31/2022] [Indexed: 11/13/2022] Open
Abstract
The virus-to-prokaryote ratio (VPR) has been used in many ecosystems to study the relationship between viruses and their hosts. While high VPR values indicate a high rate of prokaryotes' cell lysis, low values are interpreted as a decrease in or absence of viral activity. Salar de Huasco is a high-altitude wetland characterized by a rich microbial diversity associated with aquatic sites like springs, ponds, streams and a lagoon with variable physicochemical conditions. Samples from two ponds, Poza Rosada (PR) and Poza Verde (PV), were analyzed by epifluorescence microscopy to determine variability of viral and prokaryotic abundance and to calculate the VPR in a dry season. In addition, to put Salar de Huasco results into perspective, a compilation of research articles on viral and prokaryotic abundance, VPR, and metadata from various Southern hemisphere ecosystems was revised. The ecosystems were grouped into six categories: high-altitude wetlands, Pacific, Atlantic, Indian, and Southern Oceans and Antarctic lakes. Salar de Huasco ponds recorded similar VPR values (an average of 7.4 and 1.7 at PR and PV, respectively), ranging from 3.22 to 15.99 in PR. The VPR variability was associated with VA and chlorophyll a, when considering all data available for this ecosystem. In general, high-altitude wetlands recorded the highest VPR average (53.22 ± 95.09), followed by the Oceans, Southern (21.91 ± 25.72), Atlantic (19.57 ± 15.77) and Indian (13.43 ± 16.12), then Antarctic lakes (11.37 ± 15.82) and the Pacific Ocean (6.34 ± 3.79). Physicochemical variables, i.e., temperature, conductivity, nutrients (nitrate, ammonium, and phosphate) and chlorophyll a as a biological variable, were found to drive the VPR in the ecosystems analyzed. Thus, the viral activity in the Wetland followed similar trends of previous reports based on larger sets of metadata analyses. In total, this study highlights the importance of including viruses as a biological variable to study microbial temporal dynamics in wetlands considering their crucial role in the carbon budgets of these understudied ecosystems in the southern hemisphere.
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Affiliation(s)
- Yoanna Eissler
- Instituto de Química y Bioquímica, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, Chile
- *Correspondence: Yoanna Eissler
| | - Alonso Castillo-Reyes
- Escuela de Biología Marina, Facultad de Ciencias del Mar y de Recursos Naturales, Universidad de Valparaíso, Viña del Mar, Chile
| | - Cristina Dorador
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto de Antofagasta, Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
- Centre for Biotechnology and Bioengineering, Universidad de Chile, Santiago, Chile
| | - Marcela Cornejo-D'Ottone
- Escuela de Ciencias del Mar e Instituto Milenio de Oceanografía, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Paula S. M. Celis-Plá
- Laboratory of Aquatic Environmental Research, Centro de Estudios Avanzados, Universidad de Playa Ancha, Viña del Mar, Chile
- HUB Ambiental UPLA, Universidad de Playa Ancha, Valparaíso, Chile
| | - Polette Aguilar
- HUB Ambiental UPLA, Universidad de Playa Ancha, Valparaíso, Chile
| | - Verónica Molina
- HUB Ambiental UPLA, Universidad de Playa Ancha, Valparaíso, Chile
- Departamento de Ciencias y Geografía, Facultad de Ciencias Naturales y Exactas, Universidad de Playa Ancha, Valparaíso, Chile
- Centro de Investigación Oceanográfica COPAS COASTAL, Universidad de Concepción, Concepción, Chile
- Verónica Molina
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Homma M, Nishikino T, Kojima S. Achievements in bacterial flagellar research with focus on Vibrio species. Microbiol Immunol 2021; 66:75-95. [PMID: 34842307 DOI: 10.1111/1348-0421.12954] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 11/24/2021] [Accepted: 11/25/2021] [Indexed: 12/01/2022]
Abstract
In 1980's, the most genes involved in the bacterial flagellar function and formation had been isolated though many of their functions or roles were not clarified. Bacterial flagella are the primary locomotive organ and are not necessary for growing in vitro but are probably essential for living in natural condition and are involved in the pathogenicity. In vitro, the flagella-deficient strains can grow at rates similar to wild-type strains. More than 50 genes are responsible for flagellar function, and the flagellum is constructed by more than 20 structural proteins. The maintenance cost of flagellum is high as several genes are required for its development. The fact that it evolved as a motor organ even with such the high cost shows that the motility is indispensable to survive under the harsh environment of Earth. In this review, we focus on flagella-related research conducted by the authors for about 40 years and flagellar research focused on Vibrio spp. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Michio Homma
- Division of Biological Science, Graduate School of Science, Nagoya University
| | | | - Seiji Kojima
- Division of Biological Science, Graduate School of Science, Nagoya University
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11
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Kudo H, Matsuo M, Satoh S, Hata T, Hachisu R, Nakamura M, Yamamoto YY, Kimura H, Matsui M, Obokata J. Cryptic promoter activation occurs by at least two different mechanisms in the Arabidopsis genome. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:29-39. [PMID: 34252235 DOI: 10.1111/tpj.15420] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 07/08/2021] [Indexed: 06/13/2023]
Abstract
In gene-trap screening of plant genomes, promoterless reporter constructs are often expressed without trapping of annotated gene promoters. The molecular basis of this phenomenon, which has been interpreted as the trapping of cryptic promoters, is poorly understood. Here, we found that cryptic promoter activation occurs by at least two different mechanisms using Arabidopsis gene-trap lines in which a firefly luciferase (LUC) open reading frame (ORF) without an apparent promoter sequence was expressed from intergenic regions: one mechanism is 'cryptic promoter capturing', in which the LUC ORF captured pre-existing promoter-like chromatin marked by H3K4me3 and H2A.Z, and the other is 'promoter de novo origination', in which the promoter chromatin was newly formed near the 5' end of the inserted LUC ORF. The latter finding raises a question as to how the inserted LUC ORF sequence is involved in this phenomenon. To examine this, we performed a model experiment with chimeric LUC genes in transgenic plants. Using Arabidopsis psaH1 promoter-LUC constructs, we found that the functional core promoter region, where transcription start sites (TSSs) occur, cannot simply be determined by the upstream nor core promoter sequences; rather, its positioning proximal to the inserted LUC ORF sequence was more critical. This result suggests that the insertion of the coding sequence alters the local distribution of TSSs in the plant genome. The possible impact of the two types of cryptic promoter activation mechanisms on plant genome evolution and endosymbiotic gene transfer is discussed.
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Affiliation(s)
- Hisayuki Kudo
- Center for G Research, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan
| | - Mitsuhiro Matsuo
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Sakyo-ku, Kyoto, 606-8522, Japan
| | - Soichirou Satoh
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Sakyo-ku, Kyoto, 606-8522, Japan
| | - Takayuki Hata
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Sakyo-ku, Kyoto, 606-8522, Japan
| | - Rei Hachisu
- Center for G Research, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan
| | - Masayuki Nakamura
- Center for G Research, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan
| | - Yoshiharu Y Yamamoto
- Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagito, Gihu-shi, Gifu, 501-1193, Japan
| | - Hiroshi Kimura
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama City, Kanagawa, 226-8501, Japan
| | - Minami Matsui
- RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Junichi Obokata
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Sakyo-ku, Kyoto, 606-8522, Japan
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12
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Chen Z, Shen M, Mao C, Wang C, Yuan P, Wang T, Sun D. A Type I Restriction Modification System Influences Genomic Evolution Driven by Horizontal Gene Transfer in Paenibacillus polymyxa. Front Microbiol 2021; 12:709571. [PMID: 34413842 PMCID: PMC8370563 DOI: 10.3389/fmicb.2021.709571] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 06/29/2021] [Indexed: 11/13/2022] Open
Abstract
Considered a “Generally Recognized As Safe” (GRAS) bacterium, the plant growth–promoting rhizobacterium Paenibacillus polymyxa has been widely applied in agriculture and animal husbandry. It also produces valuable compounds that are used in medicine and industry. Our previous work showed the presence of restriction modification (RM) system in P. polymyxa ATCC 842. Here, we further analyzed its genome and methylome by using SMRT sequencing, which revealed the presence of a larger number of genes, as well as a plasmid documented as a genomic region in a previous report. A number of mobile genetic elements (MGEs), including 78 insertion sequences, six genomic islands, and six prophages, were identified in the genome. A putative lysozyme-encoding gene from prophage P6 was shown to express lysin which caused cell lysis. Analysis of the methylome and genome uncovered a pair of reverse-complementary DNA methylation motifs which were widespread in the genome, as well as genes potentially encoding their cognate type I restriction-modification system PpoAI. Further genetic analysis confirmed the function of PpoAI as a RM system in modifying and restricting DNA. The average frequency of the DNA methylation motifs in MGEs was lower than that in the genome, implicating a role of PpoAI in restricting MGEs during genomic evolution of P. polymyxa. Finally, comparative analysis of R, M, and S subunits of PpoAI showed that homologs of the PpoAI system were widely distributed in species belonging to other classes of Firmicute, implicating a role of the ancestor of PpoAI in the genomic evolution of species beyond Paenibacillus.
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Affiliation(s)
- Ziyan Chen
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Minjia Shen
- UMR 9198 Institut de Biologie Intégrative de la Cellule (I2BC), Gif-sur-Yvette, France
| | - Chengyao Mao
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Chenyu Wang
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Panhong Yuan
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Tingzhang Wang
- Key Laboratory of Microbial Technology and Bioinformatics, Hangzhou, China
| | - Dongchang Sun
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
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13
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Huang Y, Huang W, Meng Z, Braz GT, Li Y, Wang K, Wang H, Lai J, Jiang J, Dong Z, Jin W. Megabase-scale presence-absence variation with Tripsacum origin was under selection during maize domestication and adaptation. Genome Biol 2021; 22:237. [PMID: 34416918 PMCID: PMC8377971 DOI: 10.1186/s13059-021-02448-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 08/02/2021] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Structural variants (SVs) significantly drive genome diversity and environmental adaptation for diverse species. Unlike the prevalent small SVs (< kilobase-scale) in higher eukaryotes, large-size SVs rarely exist in the genome, but they function as one of the key evolutionary forces for speciation and adaptation. RESULTS In this study, we discover and characterize several megabase-scale presence-absence variations (PAVs) in the maize genome. Surprisingly, we identify a 3.2 Mb PAV fragment that shows high integrity and is present as complete presence or absence in the natural diversity panel. This PAV is embedded within the nucleolus organizer region (NOR), where the suppressed recombination is found to maintain the PAV against the evolutionary variation. Interestingly, by analyzing the sequence of this PAV, we not only reveal the domestication trace from teosinte to modern maize, but also the footprints of its origin from Tripsacum, shedding light on a previously unknown contribution from Tripsacum to the speciation of Zea species. The functional consequence of the Tripsacum segment migration is also investigated, and environmental fitness conferred by the PAV may explain the whole segment as a selection target during maize domestication and improvement. CONCLUSIONS These findings provide a novel perspective that Tripsacum contributes to Zea speciation, and also instantiate a strategy for evolutionary and functional analysis of the "fossil" structure variations during genome evolution and speciation.
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Affiliation(s)
- Yumin Huang
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization (MOE), Joint International Research Laboratory of Crop Molecular Breeding (MOE), China Agricultural University, Beijing, 100193, China
| | - Wei Huang
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization (MOE), Joint International Research Laboratory of Crop Molecular Breeding (MOE), China Agricultural University, Beijing, 100193, China
| | - Zhuang Meng
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps (MOE), Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Guilherme Tomaz Braz
- Department of Plant Biology, Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| | - Yunfei Li
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization (MOE), Joint International Research Laboratory of Crop Molecular Breeding (MOE), China Agricultural University, Beijing, 100193, China
| | - Kai Wang
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps (MOE), Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Hai Wang
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization (MOE), Joint International Research Laboratory of Crop Molecular Breeding (MOE), China Agricultural University, Beijing, 100193, China
| | - Jinsheng Lai
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization (MOE), Joint International Research Laboratory of Crop Molecular Breeding (MOE), China Agricultural University, Beijing, 100193, China
| | - Jiming Jiang
- Department of Plant Biology, Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| | - Zhaobin Dong
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization (MOE), Joint International Research Laboratory of Crop Molecular Breeding (MOE), China Agricultural University, Beijing, 100193, China.
| | - Weiwei Jin
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization (MOE), Joint International Research Laboratory of Crop Molecular Breeding (MOE), China Agricultural University, Beijing, 100193, China.
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14
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Hara Y, Shibahara R, Kondo K, Abe W, Kunieda T. Parallel evolution of trehalose production machinery in anhydrobiotic animals via recurrent gene loss and horizontal transfer. Open Biol 2021; 11:200413. [PMID: 34255978 PMCID: PMC8277472 DOI: 10.1098/rsob.200413] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Trehalose is a versatile non-reducing sugar. In some animal groups possessing its intrinsic production machinery, it is used as a potent protectant against environmental stresses, as well as blood sugar. However, the trehalose biosynthesis genes remain unidentified in the large majority of metazoan phyla, including vertebrates. To uncover the evolutionary history of trehalose production machinery in metazoans, we scrutinized the available genome resources and identified bifunctional trehalose-6-phosphate synthase-trehalose-6-phosphate phosphatase (TPS–TPP) genes in various taxa. The scan included our newly sequenced genome assembly of a desiccation-tolerant tardigrade Paramacrobiotus sp. TYO, revealing that this species retains TPS–TPP genes activated upon desiccation. Phylogenetic analyses identified a monophyletic group of the many of the metazoan TPS–TPP genes, namely ‘pan-metazoan’ genes, that were acquired in the early ancestors of metazoans. Furthermore, coordination of our results with the previous horizontal gene transfer studies illuminated that the two tardigrade lineages, nematodes and bdelloid rotifers, all of which include desiccation-tolerant species, independently acquired the TPS–TPP homologues via horizontal transfer accompanied with loss of the ‘pan-metazoan’ genes. Our results indicate that the parallel evolution of trehalose synthesis via recurrent loss and horizontal transfer of the biosynthesis genes resulted in the acquisition and/or augmentation of anhydrobiotic lives in animals.
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Affiliation(s)
- Yuichiro Hara
- Research Center for Genome and Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Reira Shibahara
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Koyuki Kondo
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Wataru Abe
- Department of Biology, Dokkyo Medical University, Tochigi, Japan
| | - Takekazu Kunieda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
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15
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Serrano E, Torres R, Alonso JC. Nucleoid-associated Rok differentially affects chromosomal transformation on Bacillus subtilis recombination-deficient cells. Environ Microbiol 2021; 23:3318-3331. [PMID: 33973337 DOI: 10.1111/1462-2920.15562] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 05/05/2021] [Indexed: 11/29/2022]
Abstract
Rok, a Bacillus subtilis nucleoid-associated protein (NAP), negatively regulates competence development and silences xenogeneic genes. We show that rok inactivation increases rpoB482 natural intraspecies chromosomal transformation (CT) and plasmid transformation to a different extent. In ΔaddAB, ΔrecO, recF15, ΔrecU, ΔruvAB or rec+ cells intraspecies CT significantly increases, but the ΔrecD2 mutation reduces, and the ΔrecX, ΔradA or ΔdprA mutation further decreases CT in the Δrok context when compared to rok+ cells. These observations support the idea that rok inactivation, by altering the topology of the recipient DNA, differentially affects the integration of homologous DNA in rec-deficient strains, and in minor extent the competent subpopulation size. The impairment of other NAP (Hbsu or LrpC) also increased intra- and interspecies CT (nonself-DNA, ~8% nucleotide sequence divergence) in rec+ cells, but differentially reduced both types of CTs in certain rec-deficient strains. We describe that rok inactivation significantly stimulates intra and interspecies CT but differentially reduces them in transformation-deficient cells, perhaps by altering the nucleoid architecture. We extend the observation to other NAPs (Hbsu, LrpC).
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Affiliation(s)
- Ester Serrano
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, Madrid, 28049, Spain
| | - Rubén Torres
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, Madrid, 28049, Spain
| | - Juan C Alonso
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, Madrid, 28049, Spain
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16
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Hao Y, Lee HJ, Baraboo M, Burch K, Maurer T, Somarelli JA, Conant GC. Baby Genomics: Tracing the Evolutionary Changes That Gave Rise to Placentation. Genome Biol Evol 2021; 12:35-47. [PMID: 32053193 PMCID: PMC7144826 DOI: 10.1093/gbe/evaa026] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/02/2020] [Indexed: 12/12/2022] Open
Abstract
It has long been challenging to uncover the molecular mechanisms behind striking morphological innovations such as mammalian pregnancy. We studied the power of a robust comparative orthology pipeline based on gene synteny to address such problems. We inferred orthology relations between human genes and genes from each of 43 other vertebrate genomes, resulting in ∼18,000 orthologous pairs for each genome comparison. By identifying genes that first appear coincident with origin of the placental mammals, we hypothesized that we would define a subset of the genome enriched for genes that played a role in placental evolution. We thus pinpointed orthologs that appeared before and after the divergence of eutherian mammals from marsupials. Reinforcing previous work, we found instead that much of the genetic toolkit of mammalian pregnancy evolved through the repurposing of preexisting genes to new roles. These genes acquired regulatory controls for their novel roles from a group of regulatory genes, many of which did in fact originate at the appearance of the eutherians. Thus, orthologs appearing at the origin of the eutherians are enriched in functions such as transcriptional regulation by Krüppel-associated box-zinc-finger proteins, innate immune responses, keratinization, and the melanoma-associated antigen protein class. Because the cellular mechanisms of invasive placentae are similar to those of metastatic cancers, we then used our orthology inferences to explore the association between placenta invasion and cancer metastasis. Again echoing previous work, we find that genes that are phylogenetically older are more likely to be implicated in cancer development.
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Affiliation(s)
- Yue Hao
- Bioinformatics Research Center, North Carolina State University
| | - Hyuk Jin Lee
- Division of Biological Sciences, University of Missouri-Columbia
| | | | | | | | - Jason A Somarelli
- Duke Cancer Institute, Duke University Medical Center.,Department of Medicine, Duke University School of Medicine
| | - Gavin C Conant
- Bioinformatics Research Center, North Carolina State University.,Division of Animal Sciences, University of Missouri-Columbia.,Program in Genetics, North Carolina State University.,Department of Biological Sciences, North Carolina State University
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17
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Nishikino T, Kojima S, Homma M. [Flagellar related genes and functions in Vibrio]. Nihon Saikingaku Zasshi 2021; 75:195-214. [PMID: 33390367 DOI: 10.3412/jsb.75.195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Bacteria can move or swim by flagella. On the other hand, the motile ability is not necessary to live at all. In laboratory, the flagella-deficient strains can grow just like the wild-type strains. The flagellum is assembled from more than 20 structural proteins and there are more than 50 genes including the structural genes to regulate or support the flagellar formation. The cost to construct the flagellum is so expensive. The fact that it evolved as a motor organ means even at such the large cost shows that the flagellum is essential for survival in natural condition. In this review, we would like to focus on the flagella-related researches conducted by the authors and the flagellar research on Vibrio spp.
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Affiliation(s)
| | - Seiji Kojima
- Division of Biological Science, Graduate School of Science, Nagoya University
| | - Michio Homma
- Division of Biological Science, Graduate School of Science, Nagoya University
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18
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Abe T, Akazawa Y, Toyoda A, Niki H, Baba T. Batch-Learning Self-Organizing Map Identifies Horizontal Gene Transfer Candidates and Their Origins in Entire Genomes. Front Microbiol 2020; 11:1486. [PMID: 32719664 PMCID: PMC7350273 DOI: 10.3389/fmicb.2020.01486] [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: 02/05/2020] [Accepted: 06/08/2020] [Indexed: 02/05/2023] Open
Abstract
Horizontal gene transfer (HGT) has been widely suggested to play a critical role in the environmental adaptation of microbes; however, the number and origin of the genes in microbial genomes obtained through HGT remain unknown as the frequency of detected HGT events is generally underestimated, particularly in the absence of information on donor sequences. As an alternative to phylogeny-based methods that rely on sequence alignments, we have developed an alignment-free clustering method on the basis of an unsupervised neural network “Batch-Learning Self-Organizing Map (BLSOM)” in which sequence fragments are clustered based solely on oligonucleotide similarity without taxonomical information, to detect HGT candidates and their origin in entire genomes. By mapping the microbial genomic sequences on large-scale BLSOMs constructed with nearly all prokaryotic genomes, HGT candidates can be identified, and their origin assigned comprehensively, even for microbial genomes that exhibit high novelty. By focusing on two types of Alphaproteobacteria, specifically psychrotolerant Sphingomonas strains from an Antarctic lake, we detected HGT candidates using BLSOM and found higher proportions of HGT candidates from organisms belonging to Betaproteobacteria in the genomes of these two Antarctic strains compared with those of continental strains. Further, an origin difference was noted in the HGT candidates found in the two Antarctic strains. Although their origins were highly diversified, gene functions related to the cell wall or membrane biogenesis were shared among the HGT candidates. Moreover, analyses of amino acid frequency suggested that housekeeping genes and some HGT candidates of the Antarctic strains exhibited different characteristics to other continental strains. Lys, Ser, Thr, and Val were the amino acids found to be increased in the Antarctic strains, whereas Ala, Arg, Glu, and Leu were decreased. Our findings strongly suggest a low-temperature adaptation process for microbes that may have arisen convergently as an independent evolutionary strategy in each Antarctic strain. Hence, BLSOM analysis could serve as a powerful tool in not only detecting HGT candidates and their origins in entire genomes, but also in providing novel perspectives into the environmental adaptations of microbes.
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Affiliation(s)
- Takashi Abe
- Department of Information Engineering, Faculty of Engineering, Niigata University, Niigata, Japan
| | - Yu Akazawa
- Department of Information Engineering, Faculty of Engineering, Niigata University, Niigata, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Japan.,Advanced Genomics Center, National Institute of Genetics, Mishima, Japan
| | - Hironori Niki
- Microbial Physiology Laboratory, National Institute of Genetics, Mishima, Japan
| | - Tomoya Baba
- Advanced Genomics Center, National Institute of Genetics, Mishima, Japan.,Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Tokyo, Japan
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19
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Daugavet MA, Shabelnikov SV, Podgornaya OI. Amino acid sequence associated with bacteriophage recombination site helps to reveal genes potentially acquired through horizontal gene transfer. BMC Bioinformatics 2020; 21:305. [PMID: 32703190 PMCID: PMC7379824 DOI: 10.1186/s12859-020-03599-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 06/10/2020] [Indexed: 12/04/2022] Open
Abstract
Background Horizontal gene transfer, i.e. the acquisition of genetic material from nonparent organism, is considered an important force driving species evolution. Many cases of horizontal gene transfer from prokaryotes to eukaryotes have been registered, but no transfer mechanism has been deciphered so far, although viruses were proposed as possible vectors in several studies. In agreement with this idea, in our previous study we discovered that in two eukaryotic proteins bacteriophage recombination site (AttP) was adjacent to the regions originating via horizontal gene transfer. In one of those cases AttP site was present inside the introns of cysteine-rich repeats. In the present study we aimed to apply computational tools for finding multiple horizontal gene transfer events in large genome databases. For that purpose we used a sequence of cysteine-rich repeats to identify genes potentially acquired through horizontal transfer. Results HMMER remote similarity search significantly detected 382 proteins containing cysteine-rich repeats. All of them, except 8 sequences, belong to eukaryotes. In 124 proteins the presence of conserved structural domains was predicted. In spite of the fact that cysteine-rich repeats are found almost exclusively in eukaryotic proteins, many predicted domains are most common for prokaryotes or bacteriophages. Ninety-eight proteins out of 124 contain typical prokaryotic domains. In those cases proteins were considered as potentially originating via horizontal transfer. In addition, HHblits search revealed that two domains of the same fungal protein, Glycoside hydrolase and Peptidase M15, have high similarity with proteins of two different prokaryotic species, hinting at independent horizontal gene transfer events. Conclusions Cysteine-rich repeats in eukaryotic proteins are usually accompanied by conserved domains typical for prokaryotes or bacteriophages. These proteins, containing both cysteine-rich repeats, and characteristic prokaryotic domains, might represent multiple independent horizontal gene transfer events from prokaryotes to eukaryotes. We believe that the presence of bacteriophage recombination site inside cysteine-rich repeat coding sequence may facilitate horizontal genes transfer. Thus computational approach, described in the present study, can help finding multiple sequences originated from horizontal transfer in eukaryotic genomes.
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Affiliation(s)
| | | | - Olga I Podgornaya
- Institute of Cytology, St. Petersburg, Russia, 194064.,School of Biomedicine, Far Eastern Federal University, Vladivostok, Russia, 690090.,Department of Cytology and Histology, St. Pb State University, St. Petersburg, Russia, 199034
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20
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Shuffling type of biological evolution based on horizontal gene transfer and the biosphere gene pool hypothesis. Biosystems 2020; 193-194:104131. [DOI: 10.1016/j.biosystems.2020.104131] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 03/12/2020] [Accepted: 03/12/2020] [Indexed: 02/08/2023]
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21
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FORERO DIMITRI, CAMPOS LUIZALEXANDRE, CASTRO-HUERTAS VALENTINA, BIANCHI FILIPEM. Evolutionary mechanisms for camouflage in Cladomorphus phyllinus (Phasmatodea): A reflection on the role of evidence for hypotheses proposition. AN ACAD BRAS CIENC 2020; 92:e20200197. [DOI: 10.1590/0001-3765202020200197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 03/20/2020] [Indexed: 11/21/2022] Open
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22
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Horizontal Gene Transfer as an Indispensable Driver for Evolution of Neocallimastigomycota into a Distinct Gut-Dwelling Fungal Lineage. Appl Environ Microbiol 2019; 85:AEM.00988-19. [PMID: 31126947 DOI: 10.1128/aem.00988-19] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 05/19/2019] [Indexed: 01/01/2023] Open
Abstract
Survival and growth of the anaerobic gut fungi (AGF; Neocallimastigomycota) in the herbivorous gut necessitate the possession of multiple abilities absent in other fungal lineages. We hypothesized that horizontal gene transfer (HGT) was instrumental in forging the evolution of AGF into a phylogenetically distinct gut-dwelling fungal lineage. The patterns of HGT were evaluated in the transcriptomes of 27 AGF strains, 22 of which were isolated and sequenced in this study, and 4 AGF genomes broadly covering the breadth of AGF diversity. We identified 277 distinct incidents of HGT in AGF transcriptomes, with subsequent gene duplication resulting in an HGT frequency of 2 to 3.5% in AGF genomes. The majority of HGT events were AGF specific (91.7%) and wide (70.8%), indicating their occurrence at early stages of AGF evolution. The acquired genes allowed AGF to expand their substrate utilization range, provided new venues for electron disposal, augmented their biosynthetic capabilities, and facilitated their adaptation to anaerobiosis. The majority of donors were anaerobic fermentative bacteria prevalent in the herbivorous gut. This study strongly indicates that HGT indispensably forged the evolution of AGF as a distinct fungal phylum and provides a unique example of the role of HGT in shaping the evolution of a high-rank taxonomic eukaryotic lineage.IMPORTANCE The anaerobic gut fungi (AGF) represent a distinct basal phylum lineage (Neocallimastigomycota) commonly encountered in the rumen and alimentary tracts of herbivores. Survival and growth of anaerobic gut fungi in these anaerobic, eutrophic, and prokaryote-dominated habitats necessitates the acquisition of several traits absent in other fungal lineages. We assess here the role of horizontal gene transfer as a relatively fast mechanism for trait acquisition by the Neocallimastigomycota postsequestration in the herbivorous gut. Analysis of 27 transcriptomes that represent the broad diversity of Neocallimastigomycota identified 277 distinct HGT events, with subsequent gene duplication resulting in an HGT frequency of 2 to 3.5% in AGF genomes. These HGT events have allowed AGF to survive in the herbivorous gut by expanding their substrate utilization range, augmenting their biosynthetic pathway, providing new routes for electron disposal by expanding fermentative capacities, and facilitating their adaptation to anaerobiosis. HGT in the AGF is also shown to be mainly a cross-kingdom affair, with the majority of donors belonging to the bacteria. This study represents a unique example of the role of HGT in shaping the evolution of a high-rank taxonomic eukaryotic lineage.
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23
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Ayala‐Ruano S, Santander‐Gordón D, Tejera E, Perez‐Castillo Y, Armijos-Jaramillo V. A putative antimicrobial peptide from Hymenoptera in the megaplasmid pSCL4 of Streptomyces clavuligerus ATCC 27064 reveals a singular case of horizontal gene transfer with potential applications. Ecol Evol 2019; 9:2602-2614. [PMID: 30891203 PMCID: PMC6406012 DOI: 10.1002/ece3.4924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 12/31/2018] [Accepted: 01/02/2019] [Indexed: 11/06/2022] Open
Abstract
Streptomyces clavuligerus is a Gram-positive bacterium that is a high producer of secondary metabolites with industrial applications. The production of antibiotics such as clavulanic acid or cephamycin has been extensively studied in this species; nevertheless, other aspects, such as evolution or ecology, have received less attention. Furthermore, genes that arise from ancient events of lateral transfer have been demonstrated to be implicated in important functions of host species. This approximation discovered relevant genes that genomic analyses overlooked. Thus, we studied the impact of horizontal gene transfer in the S. clavuligerus genome. To perform this task, we applied whole-genome analysis to identify a laterally transferred sequence from different domains. The most relevant result was a putative antimicrobial peptide (AMP) with a clear origin in the Hymenoptera order of insects. Next, we determined that two copies of these genes were present in the megaplasmid pSCL4 but absent in the S. clavuligerus ATCC 27064 chromosome. Additionally, we found that these sequences were exclusive to the ATCC 27064 strain (and so were not present in any other bacteria) and we also verified the expression of the genes using RNAseq data. Next, we used several AMP predictors to validate the original annotation extracted from Hymenoptera sequences and explored the possibility that these proteins had post-translational modifications using peptidase cleavage prediction. We suggest that Hymenoptera AMP-like proteins of S. clavuligerus ATCC 27064 may be useful for both species adaptation and as an antimicrobial molecule with industrial applications.
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Affiliation(s)
- Sebastián Ayala‐Ruano
- Universidad San Francisco de Quito, Colegio de Ciencias Biológicas y Ambientales (COCIBA‐USFQ)QuitoEcuador
| | - Daniela Santander‐Gordón
- Carrera de Ingeniería en Biotecnología, Facultad de Ingeniería y Ciencias AplicadasUniversidad de Las AméricasQuitoEcuador
| | - Eduardo Tejera
- Carrera de Ingeniería en Biotecnología, Facultad de Ingeniería y Ciencias AplicadasUniversidad de Las AméricasQuitoEcuador
- Grupo de Bio‐QuimioinformáticaUniversidad de Las AméricasQuitoEcuador
| | - Yunierkis Perez‐Castillo
- Grupo de Bio‐QuimioinformáticaUniversidad de Las AméricasQuitoEcuador
- Ciencias Físicas y Matemáticas‐Facultad de Formación GeneralUniversidad de Las AméricasQuitoEcuador
| | - Vinicio Armijos-Jaramillo
- Carrera de Ingeniería en Biotecnología, Facultad de Ingeniería y Ciencias AplicadasUniversidad de Las AméricasQuitoEcuador
- Grupo de Bio‐QuimioinformáticaUniversidad de Las AméricasQuitoEcuador
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24
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Liao C, Seebeck FP. In Vitro Reconstitution of Bacterial DMSP Biosynthesis. Angew Chem Int Ed Engl 2019; 58:3553-3556. [DOI: 10.1002/anie.201814662] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Indexed: 11/09/2022]
Affiliation(s)
- Cangsong Liao
- Department for Chemistry; University of Basel; Mattenstrasse 24a 4002 Basel Switzerland
| | - Florian P. Seebeck
- Department for Chemistry; University of Basel; Mattenstrasse 24a 4002 Basel Switzerland
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Affiliation(s)
- Cangsong Liao
- Department for Chemistry; University of Basel; Mattenstrasse 24a 4002 Basel Switzerland
| | - Florian P. Seebeck
- Department for Chemistry; University of Basel; Mattenstrasse 24a 4002 Basel Switzerland
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Features of a novel protein, rusticalin, from the ascidian Styela rustica reveal ancestral horizontal gene transfer event. Mob DNA 2019; 10:4. [PMID: 30675192 PMCID: PMC6339383 DOI: 10.1186/s13100-019-0146-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 01/02/2019] [Indexed: 12/18/2022] Open
Abstract
Background The transfer of genetic material from non-parent organisms is called horizontal gene transfer (HGT). One of the most conclusive cases of HGT in metazoans was previously described for the cellulose synthase gene in ascidians. Results In this study we identified a new protein, rusticalin, from the ascidian Styela rustica and presented evidence for its likely origin by HGT. Discernible homologues of rusticalin were found in placozoans, coral, and basal Chordates. Rusticalin was predicted to consist of two distinct regions, an N-terminal domain and a C-terminal domain. The N-terminal domain comprises two cysteine-rich repeats and shows remote similarity to the tick carboxypeptidase inhibitor. The C-terminal domain shares significant sequence similarity with bacterial MD peptidases and bacteriophage A500 L-alanyl-D-glutamate peptidase. A possible transfer of the C-terminal domain by bacteriophage was confirmed by an analysis of noncoding sequences of C. intestinalis rusticalin-like gene, which was found to contain a sequence similar to the bacteriophage A500 recombination site. Moreover, a sequence similar to the bacteriophage recombination site was found to be adjacent to the cellulose synthase catalytic subunit gene in the genome of Streptomices sp., the donor of ascidian cellulose synthase. Conclusions The C-terminal domain of rusticalin and rusticalin-like proteins is likely to be horizontally transferred by the bacteriophage A500. A common mechanism involving bacteriophage mediated gene transfer can be proposed for at least two HGT events in ascidians.
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Petersen M, Armisén D, Gibbs RA, Hering L, Khila A, Mayer G, Richards S, Niehuis O, Misof B. Diversity and evolution of the transposable element repertoire in arthropods with particular reference to insects. BMC Evol Biol 2019; 19:11. [PMID: 30626321 PMCID: PMC6327564 DOI: 10.1186/s12862-018-1324-9] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 12/11/2018] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Transposable elements (TEs) are a major component of metazoan genomes and are associated with a variety of mechanisms that shape genome architecture and evolution. Despite the ever-growing number of insect genomes sequenced to date, our understanding of the diversity and evolution of insect TEs remains poor. RESULTS Here, we present a standardized characterization and an order-level comparison of arthropod TE repertoires, encompassing 62 insect and 11 outgroup species. The insect TE repertoire contains TEs of almost every class previously described, and in some cases even TEs previously reported only from vertebrates and plants. Additionally, we identified a large fraction of unclassifiable TEs. We found high variation in TE content, ranging from less than 6% in the antarctic midge (Diptera), the honey bee and the turnip sawfly (Hymenoptera) to more than 58% in the malaria mosquito (Diptera) and the migratory locust (Orthoptera), and a possible relationship between the content and diversity of TEs and the genome size. CONCLUSION While most insect orders exhibit a characteristic TE composition, we also observed intraordinal differences, e.g., in Diptera, Hymenoptera, and Hemiptera. Our findings shed light on common patterns and reveal lineage-specific differences in content and evolution of TEs in insects. We anticipate our study to provide the basis for future comparative research on the insect TE repertoire.
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Affiliation(s)
- Malte Petersen
- University of Bonn, Bonn, Germany
- Zoological Research Museum Alexander Koenig, Center for Molecular Biodiversity Research, Adenauerallee 160, Bonn, 53113 Germany
- Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, Frankfurt, 60325 Germany
| | - David Armisén
- Université de Lyon, Institut de Génomique Fonctionnelle de Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, 46 allée d’Italie, Lyon, 69364 France
| | - Richard A. Gibbs
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, 77030 TX USA
| | - Lars Hering
- Department of Zoology, Institute of Biology, University of Kassel, Heinrich-Plett-Str. 40, Kassel, 34132 Germany
| | - Abderrahman Khila
- Université de Lyon, Institut de Génomique Fonctionnelle de Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, 46 allée d’Italie, Lyon, 69364 France
| | - Georg Mayer
- Department of Zoology, Institute of Biology, University of Kassel, Heinrich-Plett-Str. 40, Kassel, 34132 Germany
| | - Stephen Richards
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, 77030 TX USA
| | - Oliver Niehuis
- Department of Evolutionary Biology and Ecology, Institute for Biology I (Zoology), University of Freiburg, Freiburg (Brsg.), 79104 Germany
| | - Bernhard Misof
- Zoological Research Museum Alexander Koenig, Center for Molecular Biodiversity Research, Adenauerallee 160, Bonn, 53113 Germany
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Lazebnik Y. Gestational tumors as a model to probe reticulate evolution in human neoplasia. Oncotarget 2019; 10:259-262. [PMID: 30719223 PMCID: PMC6349447 DOI: 10.18632/oncotarget.26510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 12/12/2018] [Indexed: 11/25/2022] Open
Abstract
Reticulate evolution, which involves the transfer of genes and other inheritable information between organisms, is of interest to a cancer researcher if only because "pirating" a trait can help a cell and its progeny adapt, survive, or take over much faster than by accumulating random mutations. However, despite being observed repeatedly in experimental models of neoplasia, reticulate evolution is assumed to be negligible in human cancer primarily because detecting gene transfer between the cells of the same genetic background can be difficult or impossible. This commentary suggests that gestational tumors, which are genetically distinct from the women who carry them, provide an opportunity to test whether reticulate evolution affects the development of human neoplasia.
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Zhang QY, Gui JF. Diversity, evolutionary contribution and ecological roles of aquatic viruses. SCIENCE CHINA-LIFE SCIENCES 2018; 61:1486-1502. [DOI: 10.1007/s11427-018-9414-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 09/26/2018] [Indexed: 01/21/2023]
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Bobay LM, Ochman H. Factors driving effective population size and pan-genome evolution in bacteria. BMC Evol Biol 2018; 18:153. [PMID: 30314447 PMCID: PMC6186134 DOI: 10.1186/s12862-018-1272-4] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 10/04/2018] [Indexed: 02/07/2023] Open
Abstract
Background Knowledge of population-level processes is essential to understanding the efficacy of selection operating within a species. However, attempts at estimating effective population sizes (Ne) are particularly challenging in bacteria due to their extremely large census populations sizes, varying rates of recombination and arbitrary species boundaries. Results In this study, we estimated Ne for 153 species (152 bacteria and one archaeon) defined under a common framework and found that ecological lifestyle and growth rate were major predictors of Ne; and that contrary to theoretical expectations, Ne was unaffected by recombination rate. Additionally, we found that Ne shapes the evolution and diversity of total gene repertoires of prokaryotic species. Conclusion Together, these results point to a new model of genome architecture evolution in prokaryotes, in which pan-genome sizes, not individual genome sizes, are governed by drift-barrier evolution. Electronic supplementary material The online version of this article (10.1186/s12862-018-1272-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Louis-Marie Bobay
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA. .,Department of Biology, University of North Carolina at Greensboro, 321 McIver Street, PO Box 26170, Greensboro, NC, 27402, USA.
| | - Howard Ochman
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA
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Dotto BR, Carvalho EL, da Silva AF, Dezordi FZ, Pinto PM, Campos TDL, Rezende AM, Wallau GDL. HTT-DB: new features and updates. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2018; 2018:4791205. [PMID: 29315358 PMCID: PMC7206651 DOI: 10.1093/database/bax102] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 12/12/2017] [Indexed: 11/25/2022]
Abstract
Horizontal Transfer (HT) of genetic material between species is a common phenomenon among Bacteria and Archaea species and several databases are available for information retrieval and data mining. However, little attention has been given to this phenomenon among eukaryotic species mainly due to the lower proportion of these events. In the last years, a vertiginous amount of new HT events involving eukaryotic species was reported in the literature, highlighting the need of a common repository to keep the scientific community up to date and describe overall trends. Recently, we published the first HT database focused on HT of transposable elements among eukaryotes: the Horizontal Transposon Transfer DataBase: Database URL: (http://lpa.saogabriel.unipampa.edu.br: 8080/httdatabase/). Here, we present new features and updates of this unique database: (i) its expansion to include virus-host exchange of genetic material, which we called Horizontal Virus Transfer (HVT) and (ii) the availability of a web server for HT detection, where we implemented the online version of vertical and horizontal inheritance consistence analysis (VHICA), an R package developed for HT detection. These improvements will help researchers to navigate through known HVT cases, take data-informed decision and export figures based on keywords searches. Moreover, the availability of the VHICA as an online tool will make this software easily reachable even for researchers with no or little computation knowledge as well as foster our capability to detect new HT events in a wide variety of taxa. Database URL: http://lpa.saogabriel.unipampa.edu.br:8080/httdatabase/
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Affiliation(s)
- Bruno Reis Dotto
- Campus São Gabriel, Universidade Federal do Pampa, Avenida Antonio Trilha, 1847, São Gabriel, Rio Grande do Sul
| | - Evelise Leis Carvalho
- Pos Graduation in Biological Sciences, Universidade Federal do Pampa, Avenida Antonio Trilha, 1847, São Gabriel, Rio Grande do Sul
| | - Alexandre Freitas da Silva
- Pos Graduation in Biosciences and Health Biotechnology, Aggeu Magalhães Institute (IAM), Avenida Professor Moraes Rego, s/n, Recife, Pernambuco
| | - Filipe Zimmer Dezordi
- Campus São Gabriel, Universidade Federal do Pampa, Avenida Antonio Trilha, 1847, São Gabriel, Rio Grande do Sul.,Pos Graduation in Biosciences and Health Biotechnology, Aggeu Magalhães Institute (IAM), Avenida Professor Moraes Rego, s/n, Recife, Pernambuco
| | - Paulo Marcos Pinto
- Campus São Gabriel, Universidade Federal do Pampa, Avenida Antonio Trilha, 1847, São Gabriel, Rio Grande do Sul.,Pos Graduation in Biological Sciences, Universidade Federal do Pampa, Avenida Antonio Trilha, 1847, São Gabriel, Rio Grande do Sul
| | - Tulio de Lima Campos
- Bioinformatic Core, Aggeu Magalhães Institute (IAM), Avenida Professor Moraes Rego, s/n, Recife, Pernambuco
| | - Antonio Mauro Rezende
- Department of Microbiology, Aggeu Magalhães Institute (IAM), Avenida Professor Moraes Rego, s/n, Recife, Pernambuco
| | - Gabriel da Luz Wallau
- Department of Entomology, Aggeu Magalhães Institute (IAM), Avenida Professor Moraes Rego, s/n, Recife, Pernambuco
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Pluta R, Espinosa M. Antisense and yet sensitive: Copy number control of rolling circle-replicating plasmids by small RNAs. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 9:e1500. [PMID: 30074293 DOI: 10.1002/wrna.1500] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 06/27/2018] [Accepted: 07/01/2018] [Indexed: 12/27/2022]
Abstract
Bacterial plasmids constitute a wealth of shared DNA amounting to about 20% of the total prokaryotic pangenome. Plasmids replicate autonomously and control their replication by maintaining a fairly constant number of copies within a given host. Plasmids should acquire a good fitness to their hosts so that they do not constitute a genetic load. Here we review some basic concepts in plasmid biology, pertaining to the control of replication and distribution of plasmid copies among daughter cells. A particular class of plasmids is constituted by those that replicate by the rolling circle mode (rolling circle-replicating [RCR]-plasmids). They are small double-stranded DNA molecules, with a rather high number of copies in the original host. RCR-plasmids control their replication by means of a small short-lived antisense RNA, alone or in combination with a plasmid-encoded transcriptional repressor protein. Two plasmid prototypes have been studied in depth, namely the staphylococcal plasmid pT181 and the streptococcal plasmid pMV158, each corresponding to the two types of replication control circuits, respectively. We further discuss possible applications of the plasmid-encoded antisense RNAs and address some future directions that, in our opinion, should be pursued in the study of these small molecules. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems.
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Affiliation(s)
- Radoslaw Pluta
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Manuel Espinosa
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu, Madrid, Spain
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A Reverse Ecology Framework for Bacteria and Archaea. POPULATION GENOMICS: MICROORGANISMS 2018. [DOI: 10.1007/13836_2018_46] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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35
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Beyond Agrobacterium-Mediated Transformation: Horizontal Gene Transfer from Bacteria to Eukaryotes. Curr Top Microbiol Immunol 2018; 418:443-462. [DOI: 10.1007/82_2018_82] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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36
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Shapiro JA. Living Organisms Author Their Read-Write Genomes in Evolution. BIOLOGY 2017; 6:E42. [PMID: 29211049 PMCID: PMC5745447 DOI: 10.3390/biology6040042] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 11/17/2017] [Accepted: 11/28/2017] [Indexed: 12/18/2022]
Abstract
Evolutionary variations generating phenotypic adaptations and novel taxa resulted from complex cellular activities altering genome content and expression: (i) Symbiogenetic cell mergers producing the mitochondrion-bearing ancestor of eukaryotes and chloroplast-bearing ancestors of photosynthetic eukaryotes; (ii) interspecific hybridizations and genome doublings generating new species and adaptive radiations of higher plants and animals; and, (iii) interspecific horizontal DNA transfer encoding virtually all of the cellular functions between organisms and their viruses in all domains of life. Consequently, assuming that evolutionary processes occur in isolated genomes of individual species has become an unrealistic abstraction. Adaptive variations also involved natural genetic engineering of mobile DNA elements to rewire regulatory networks. In the most highly evolved organisms, biological complexity scales with "non-coding" DNA content more closely than with protein-coding capacity. Coincidentally, we have learned how so-called "non-coding" RNAs that are rich in repetitive mobile DNA sequences are key regulators of complex phenotypes. Both biotic and abiotic ecological challenges serve as triggers for episodes of elevated genome change. The intersections of cell activities, biosphere interactions, horizontal DNA transfers, and non-random Read-Write genome modifications by natural genetic engineering provide a rich molecular and biological foundation for understanding how ecological disruptions can stimulate productive, often abrupt, evolutionary transformations.
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Affiliation(s)
- James A Shapiro
- Department of Biochemistry and Molecular Biology, University of Chicago GCIS W123B, 979 E. 57th Street, Chicago, IL 60637, USA.
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Wang Y, Kim KS, Guo W, Li Q, Zhang Y, Wang Z, Coates BS. Introgression between divergent corn borer species in a region of sympatry: Implications on the evolution and adaptation of pest arthropods. Mol Ecol 2017; 26:6892-6907. [PMID: 29105878 DOI: 10.1111/mec.14387] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 09/09/2017] [Accepted: 09/26/2017] [Indexed: 11/29/2022]
Abstract
The Asian corn borer, Ostrinia furnacalis, and European corn borer, O. nubilalis (Lepidoptera: Crambidae), cause damage to cultivated maize in spatially distinct geographies and have evolved divergent hydrocarbons as the basis of sexual communication. The Yili area of Xinjiang Uyghur Autonomous Region in China represents the only known region where O. furnacalis has invaded a native O. nubilalis range, and these two corn borer species have made secondary contact. Genetic differentiation was estimated between Ostrinia larvae collected from maize plants at 11 locations in Xinjiang and genotyped using high-throughput SNP and microsatellite markers. Maternal lineages were assessed by direct sequencing of mitochondrial cytochrome c oxidase subunit I and II haplotypes, and a high degree of genotypic diversity was demonstrated between lineages based on SNP genotypes. Furthermore, historical introgression was predicted among SNP genotypes only at sympatric locations in the Yili area, whereas in Xinjiang populations only O. furnacalis haplotypes were detected and no analogous introgressed genotypes were predicted. Our detection of putative hybrids and historical evidence of introgression defines Yili area as a hybrid zone between the species in normal ecological interactions and furthermore, might indicate that adaptive traits could spread even between seemingly divergent species through horizontal transmission. Results of this study indicate there may be a continuum in the degree of reproductive isolation between Ostrinia species and that the elegance of distinct and complete speciation based on modifications to the pheromone communication might need to be reconsidered.
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Affiliation(s)
- Yangzhou Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China.,Jilin Academy of Agricultural Sciences, Changchun, China
| | - Kyung Seok Kim
- Iowa State University, Department of Natural Resource Ecology and Management, Ames, IA, USA
| | - Wenchao Guo
- Research Institute of Plant Protection, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Qiyun Li
- Jilin Academy of Agricultural Sciences, Changchun, China
| | - Yunyue Zhang
- Jilin Academy of Agricultural Sciences, Changchun, China
| | - Zhenying Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Brad S Coates
- United States Department of Agriculture, Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Iowa State University, Ames, IA, USA
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Conjugation-Mediated Horizontal Gene Transfer of Clostridium perfringens Plasmids in the Chicken Gastrointestinal Tract Results in the Formation of New Virulent Strains. Appl Environ Microbiol 2017; 83:AEM.01814-17. [PMID: 29030439 DOI: 10.1128/aem.01814-17] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 10/02/2017] [Indexed: 12/12/2022] Open
Abstract
Clostridium perfringens is a gastrointestinal pathogen capable of causing disease in a variety of hosts. Necrotic enteritis in chickens is caused by C. perfringens strains that produce the pore-forming toxin NetB, the major virulence factor for this disease. Like many other C. perfringens toxins and antibiotic resistance genes, NetB is encoded on a conjugative plasmid. Conjugative transfer of the netB-containing plasmid pJIR3535 has been demonstrated in vitro with a netB-null mutant. This study has investigated the effect of plasmid transfer on disease pathogenesis, with two genetically distinct transconjugants constructed under in vitro conditions, within the intestinal tract of chickens. This study also demonstrates that plasmid transfer can occur naturally in the host gut environment without the need for antibiotic selective pressure to be applied. The demonstration of plasmid transfer within the chicken host may have implications for the progression and pathogenesis of C. perfringens-mediated disease. Such horizontal gene transfer events are likely to be common in the clostridia and may be a key factor in strain evolution, both within animals and in the wider environment.IMPORTANCE Clostridium perfringens is a major gastrointestinal pathogen of poultry. C. perfringens strains that express the NetB pore-forming toxin, which is encoded on a conjugative plasmid, cause necrotic enteritis. This study demonstrated that the conjugative transfer of the netB-containing plasmid to two different nonpathogenic strains converted them into disease-causing strains with disease-causing capability similar to that of the donor strain. Plasmid transfer of netB and antibiotic resistance was also demonstrated to occur within the gastrointestinal tract of chickens, with approximately 14% of the isolates recovered comprising three distinct, in vivo-derived, transconjugant types. The demonstration of in vivo plasmid transfer indicates the potential importance of strain plasticity and the contribution of plasmids to strain virulence.
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Drezen JM, Josse T, Bézier A, Gauthier J, Huguet E, Herniou EA. Impact of Lateral Transfers on the Genomes of Lepidoptera. Genes (Basel) 2017; 8:E315. [PMID: 29120392 PMCID: PMC5704228 DOI: 10.3390/genes8110315] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Revised: 10/31/2017] [Accepted: 11/01/2017] [Indexed: 11/25/2022] Open
Abstract
Transfer of DNA sequences between species regardless of their evolutionary distance is very common in bacteria, but evidence that horizontal gene transfer (HGT) also occurs in multicellular organisms has been accumulating in the past few years. The actual extent of this phenomenon is underestimated due to frequent sequence filtering of "alien" DNA before genome assembly. However, recent studies based on genome sequencing have revealed, and experimentally verified, the presence of foreign DNA sequences in the genetic material of several species of Lepidoptera. Large DNA viruses, such as baculoviruses and the symbiotic viruses of parasitic wasps (bracoviruses), have the potential to mediate these transfers in Lepidoptera. In particular, using ultra-deep sequencing, newly integrated transposons have been identified within baculovirus genomes. Bacterial genes have also been acquired by genomes of Lepidoptera, as in other insects and nematodes. In addition, insertions of bracovirus sequences were present in the genomes of certain moth and butterfly lineages, that were likely corresponding to rearrangements of ancient integrations. The viral genes present in these sequences, sometimes of hymenopteran origin, have been co-opted by lepidopteran species to confer some protection against pathogens.
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Affiliation(s)
- Jean-Michel Drezen
- Institut de Recherche sur la Biologie de l'Insecte, UMR CNRS 7261, UFR des Sciences et Techniques, Université de Tours-François Rabelais, 37200 Tours, France.
| | - Thibaut Josse
- Institut de Recherche sur la Biologie de l'Insecte, UMR CNRS 7261, UFR des Sciences et Techniques, Université de Tours-François Rabelais, 37200 Tours, France.
| | - Annie Bézier
- Institut de Recherche sur la Biologie de l'Insecte, UMR CNRS 7261, UFR des Sciences et Techniques, Université de Tours-François Rabelais, 37200 Tours, France.
| | - Jérémy Gauthier
- Institut de Recherche sur la Biologie de l'Insecte, UMR CNRS 7261, UFR des Sciences et Techniques, Université de Tours-François Rabelais, 37200 Tours, France.
| | - Elisabeth Huguet
- Institut de Recherche sur la Biologie de l'Insecte, UMR CNRS 7261, UFR des Sciences et Techniques, Université de Tours-François Rabelais, 37200 Tours, France.
| | - Elisabeth Anne Herniou
- Institut de Recherche sur la Biologie de l'Insecte, UMR CNRS 7261, UFR des Sciences et Techniques, Université de Tours-François Rabelais, 37200 Tours, France.
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Alamos P, Tello M, Bustamante P, Gutiérrez F, Shmaryahu A, Maldonado J, Levicán G, Orellana O. Functionality of tRNAs encoded in a mobile genetic element from an acidophilic bacterium. RNA Biol 2017; 15:518-527. [PMID: 28708455 DOI: 10.1080/15476286.2017.1349049] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
The genome of the acidophilic, bioleaching bacterium Acidithiobacillus ferrooxidans, strain ATCC 23270, contains 95 predicted tRNA genes. Thirty-six of these genes (all 20 species) are clustered within an actively excising integrative-conjugative element (ICEAfe1). We speculated that these tRNA genes might have a role in adapting the bacterial tRNA pool to the codon usage of ICEAfe1 genes. To answer this question, we performed theoretical calculations of the global tRNA adaptation index to the entire A. ferrooxidans genome with and without the ICEAfe1 encoded tRNA genes. Based on these calculations, we observed that tRNAs encoded in ICEAfe1 negatively contribute to adapt the tRNA pool to the codon use in A. ferrooxidans. Although some of the tRNAs encoded in ICEAfe1 are functional in aminoacylation or protein synthesis, we found that they are expressed at low levels. These findings, along with the identification of a tRNA-like RNA encoded in the same cluster, led us to speculate that tRNA genes encoded in the mobile genetic element ICEAfe1 might have acquired mutations that would result in either inactivation or the acquisition of new functions.
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Affiliation(s)
- Pamela Alamos
- a Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Independencia 1027 , Santiago , Chile
| | - Mario Tello
- b Centro de Biotecnología Acuícola, Departamento de Biología , Facultad de Química y Biología, Universidad de Santiago de Chile
| | - Paula Bustamante
- a Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Independencia 1027 , Santiago , Chile
| | - Fernanda Gutiérrez
- a Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Independencia 1027 , Santiago , Chile
| | - Amir Shmaryahu
- c Fundación Ciencia y Vida , Zañartu 1482, Santiago , Chile
| | - Juan Maldonado
- a Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Independencia 1027 , Santiago , Chile
| | - Gloria Levicán
- d Departamento de Biología , Facultad de Química y Biología, Universidad de Santiago de Chile , Santiago , Chile
| | - Omar Orellana
- a Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Independencia 1027 , Santiago , Chile
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Gong X, Hung KH, Ting YW, Hsu TW, Malikova L, Tran HT, Huang CL, Liu SH, Chiang TY. Frequent gene flow blurred taxonomic boundaries of sections in Lilium L. (Liliaceae). PLoS One 2017; 12:e0183209. [PMID: 28841664 PMCID: PMC5571923 DOI: 10.1371/journal.pone.0183209] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 08/01/2017] [Indexed: 12/13/2022] Open
Abstract
Gene flow between species may last a long time in plants. Reticulation inevitably causes difficulties in phylogenetic reconstruction. In this study, we looked into the genetic divergence and phylogeny of 20 Lilium species based on multilocus analyses of 8 genes of chloroplast DNA (cpDNA), the internally transcribed nuclear ribosomal DNA (nrITS) spacer and 20 loci extracted from the expressed sequence tag (EST) libraries of L. longiflorum Thunb. and L. formosanum Wallace. The phylogeny based on the combined data of the maternally inherited cpDNA and nrITS was largely consistent with the taxonomy of Lilium sections. This phylogeny was deemed the hypothetical species tree and uncovered three groups, i.e., Cluster A consisting of 4 taxa from the sections Pseudolirium and Liriotypus, Cluster B consisting of the 4 taxa from the sections Leucolirion, Archelirion and Daurolirion, and Cluster C comprising 10 taxa mostly from the sections Martagon and Sinomartagon. In contrast, systematic inconsistency occurred across the EST loci, with up to 19 genes (95%) displaying tree topologies deviating from the hypothetical species tree. The phylogenetic incongruence was likely attributable to the frequent genetic exchanges between species/sections, as indicated by the high levels of genetic recombination and the IMa analyses with the EST loci. Nevertheless, multilocus analysis could provide complementary information among the loci on the species split and the extent of gene flow between the species. In conclusion, this study not only detected frequent gene flow among Lilium sections that resulted in phylogenetic incongruence but also reconstructed a hypothetical species tree that gave insights into the nature of the complex relationships among Lilium species.
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Affiliation(s)
- Xun Gong
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Kuo-Hsiang Hung
- Graduate Institute of Bioresources, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Yu-Wei Ting
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Tsai-Wen Hsu
- Endemic Species Research Institute, Nantou, Taiwan
| | - Lenka Malikova
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
- Institute of Botany CAS, Třeboň, Czech Republic
| | - Huyen Trang Tran
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
- Institute of Natural Science Education, Vinh University, Vinh, Nghe An, Vietnam
| | - Chao-Li Huang
- Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan, Taiwan
- * E-mail: (TYC); (SHL); (CLH)
| | - Shih-Hui Liu
- Department of Biology, Saint Louis University, Saint Louis, Missouri, United States of America
- Missouri Botanical Garden, Saint Louis, Missouri, United States of America
- * E-mail: (TYC); (SHL); (CLH)
| | - Tzen-Yuh Chiang
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
- University Center for Bioscience and Biotechnology, National Cheng Kung University, Tainan, Taiwan
- * E-mail: (TYC); (SHL); (CLH)
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43
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Ancestor of land plants acquired the DNA-3-methyladenine glycosylase (MAG) gene from bacteria through horizontal gene transfer. Sci Rep 2017; 7:9324. [PMID: 28839126 PMCID: PMC5570899 DOI: 10.1038/s41598-017-05066-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 05/23/2017] [Indexed: 02/07/2023] Open
Abstract
The origin and evolution of land plants was an important event in the history of life and initiated the establishment of modern terrestrial ecosystems. From water to terrestrial environments, plants needed to overcome the enhanced ultraviolet (UV) radiation and many other DNA-damaging agents. Evolving new genes with the function of DNA repair is critical for the origin and radiation of land plants. In bacteria, the DNA-3-methyladenine glycosylase (MAG) recognizes of a variety of base lesions and initiates the process of the base excision repair for damaged DNA. The homologs of MAG gene are present in all major lineages of streptophytes, and both the phylogenic and sequence similarity analyses revealed that green plant MAG gene originated through an ancient horizontal gene transfer (HGT) event from bacteria. Experimental evidence demonstrated that the expression of the maize ZmMAG gene was induced by UV and zeocin, both of which are known as DNA-damaging agents. Further investigation revealed that Streptophyta MAG genes had undergone positive selection during the initial evolutionary period in the ancestor of land plants. Our findings demonstrated that the ancient HGT of MAG to the ancestor of land plants probably played an important role in preadaptation to DNA-damaging agents in terrestrial environments.
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Abstract
Many of the most important evolutionary variations that generated phenotypic adaptations and originated novel taxa resulted from complex cellular activities affecting genome content and expression. These activities included (i) the symbiogenetic cell merger that produced the mitochondrion-bearing ancestor of all extant eukaryotes, (ii) symbiogenetic cell mergers that produced chloroplast-bearing ancestors of photosynthetic eukaryotes, and (iii) interspecific hybridizations and genome doublings that generated new species and adaptive radiations of higher plants and animals. Adaptive variations also involved horizontal DNA transfers and natural genetic engineering by mobile DNA elements to rewire regulatory networks, such as those essential to viviparous reproduction in mammals. In the most highly evolved multicellular organisms, biological complexity scales with 'non-coding' DNA content rather than with protein-coding capacity in the genome. Coincidentally, 'non-coding' RNAs rich in repetitive mobile DNA sequences function as key regulators of complex adaptive phenotypes, such as stem cell pluripotency. The intersections of cell fusion activities, horizontal DNA transfers and natural genetic engineering of Read-Write genomes provide a rich molecular and biological foundation for understanding how ecological disruptions can stimulate productive, often abrupt, evolutionary transformations.
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Affiliation(s)
- James A Shapiro
- Department of Biochemistry and Molecular Biology, University of Chicago, GCISW123B, 979 E. 57th Street, Chicago, IL 60637, USA
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45
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Raghuram GV, Gupta D, Subramaniam S, Gaikwad A, Khare NK, Nobre M, Nair NK, Mittra I. Physical shearing imparts biological activity to DNA and ability to transmit itself horizontally across species and kingdom boundaries. BMC Mol Biol 2017; 18:21. [PMID: 28793862 PMCID: PMC5550992 DOI: 10.1186/s12867-017-0098-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 07/31/2017] [Indexed: 11/24/2022] Open
Abstract
Background We have recently reported that cell-free DNA (cfDNA) fragments derived from dying cells that circulate in blood are biologically active molecules and can readily enter into healthy cells to activate DNA damage and apoptotic responses in the recipients. However, DNA is not conventionally known to spontaneously enter into cells or to have any intrinsic biological activity. We hypothesized that cellular entry and acquisition of biological properties are functions of the size of DNA. Results To test this hypothesis, we generated small DNA fragments by sonicating high molecular weight DNA (HMW DNA) to mimic circulating cfDNA. Sonication of HMW DNA isolated from cancerous and non-cancerous human cells, bacteria and plant generated fragments 300–3000 bp in size which are similar to that reported for circulating cfDNA. We show here that while HMW DNAs were incapable of entering into cells, sonicated DNA (sDNA) from different sources could do so indiscriminately without heed to species or kingdom boundaries. Thus, sDNA from human cells and those from bacteria and plant could enter into nuclei of mouse cells and sDNA from human, bacterial and plant sources could spontaneously enter into bacteria. The intracellular sDNA associated themselves with host cell chromosomes and integrated into their genomes. Furthermore, sDNA, but not HMW DNA, from all four sources could phosphorylate H2AX and activate the pro-inflammatory transcription factor NFκB in mouse cells, indicating that sDNAs had acquired biological activities. Conclusions Our results show that small fragments of DNA from different sources can indiscriminately enter into other cells across species and kingdom boundaries to integrate into their genomes and activate biological processes. This raises the possibility that fragmented DNA that are generated following organismal cell-death may have evolutionary implications by acting as mobile genetic elements that are involved in horizontal gene transfer. Electronic supplementary material The online version of this article (doi:10.1186/s12867-017-0098-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gorantla Venkata Raghuram
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi-Mumbai, 410210, India
| | - Deepika Gupta
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi-Mumbai, 410210, India
| | - Siddharth Subramaniam
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi-Mumbai, 410210, India
| | - Ashwini Gaikwad
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi-Mumbai, 410210, India
| | - Naveen Kumar Khare
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi-Mumbai, 410210, India
| | - Malcolm Nobre
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi-Mumbai, 410210, India
| | - Naveen Kumar Nair
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi-Mumbai, 410210, India
| | - Indraneel Mittra
- Translational Research Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi-Mumbai, 410210, India.
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46
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Lorenzo-Díaz F, Fernández-López C, Lurz R, Bravo A, Espinosa M. Crosstalk between vertical and horizontal gene transfer: plasmid replication control by a conjugative relaxase. Nucleic Acids Res 2017; 45:7774-7785. [PMID: 28525572 PMCID: PMC5737340 DOI: 10.1093/nar/gkx450] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 04/25/2017] [Accepted: 05/09/2017] [Indexed: 01/09/2023] Open
Abstract
Horizontal gene transfer is a key process in the evolution of bacteria and also represents a source of genetic variation in eukaryotes. Among elements participating in gene transfer, thousands of small (<10 kb) mobile bacterial plasmids that replicate by the rolling circle mechanism represent a driving force in the spread of antibiotic resistances. In general, these plasmids are built as genetic modules that encode a replicase, an antibiotic-resistance determinant, and a relaxase that participates in their conjugative mobilization. Further, they control their relatively high copy number (∼30 copies per genome equivalent) by antisense RNAs alone or combined with a repressor protein. We report here that the MobM conjugative relaxase encoded by the promiscuous plasmid pMV158 participates in regulation of the plasmid copy number by transcriptional repression of the antisense RNA, thus increasing the number of plasmid molecules ready to be horizontally transferred (mobilization) and/or vertically inherited (replication). This type of crosstalk between genetic modules involved in vertical and horizontal gene flow has not been reported before.
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MESH Headings
- Bacterial Proteins/genetics
- Bacterial Proteins/metabolism
- Binding Sites
- Conjugation, Genetic
- DNA Copy Number Variations
- DNA Replication
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Bacterial/metabolism
- DNA, Superhelical/chemistry
- DNA, Superhelical/genetics
- DNA, Superhelical/metabolism
- Drug Resistance, Bacterial/genetics
- Endodeoxyribonucleases/genetics
- Endodeoxyribonucleases/metabolism
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Evolution, Molecular
- Gene Flow
- Gene Transfer, Horizontal
- Microscopy, Electron
- Models, Biological
- Plasmids/genetics
- Promoter Regions, Genetic
- Replicon
- Streptococcus pneumoniae/genetics
- Streptococcus pneumoniae/metabolism
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Affiliation(s)
- Fabián Lorenzo-Díaz
- Departamento de Bioquímica, Microbiología, Biología Celular y Genética, Universidad de La Laguna. Av. Astrofísico Francisco Sánchez s/n, 38071 Santa Cruz de Tenerife, Spain
- Unidad de Investigación, Hospital Universitario Nuestra Señora de Candelaria, 38010 Santa Cruz de Tenerife, Spain
| | - Cris Fernández-López
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu, 9, 28040 Madrid, Spain
| | - Rudi Lurz
- Max-Plank Institut für molekulare Genetik, Ihnestrasse 63-73, D-14195 Berlin, Germany
| | - Alicia Bravo
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu, 9, 28040 Madrid, Spain
| | - Manuel Espinosa
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu, 9, 28040 Madrid, Spain
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47
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Dorman CJ, Dorman MJ. Control of virulence gene transcription by indirect readout in Vibrio cholerae and Salmonella enterica serovar Typhimurium. Environ Microbiol 2017. [PMID: 28631437 PMCID: PMC5655915 DOI: 10.1111/1462-2920.13838] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Indirect readout mechanisms of transcription control rely on the recognition of DNA shape by transcription factors (TFs). TFs may also employ a direct readout mechanism that involves the reading of the base sequence in the DNA major groove at the binding site. TFs with winged helix-turn-helix (wHTH) motifs use an alpha helix to read the base sequence in the major groove while inserting a beta sheet 'wing' into the adjacent minor groove. Such wHTH proteins are important regulators of virulence gene transcription in many pathogens; they also control housekeeping genes. This article considers the cases of the non-invasive Gram-negative pathogen Vibrio cholerae and the invasive pathogen Salmonella enterica serovar Typhimurium. Both possess clusters of A + T-rich horizontally acquired virulence genes that are silenced by the nucleoid-associated protein H-NS and regulated positively or negatively by wHTH TFs: for example, ToxR and LeuO in V. cholerae; HilA, LeuO, SlyA and OmpR in S. Typhimurium. Because of their relatively relaxed base sequence requirements for target recognition, indirect readout mechanisms have the potential to engage regulatory proteins with many more targets than might be the case using direct readout, making indirect readout an important, yet often ignored, contributor to the expression of pathogenic phenotypes.
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Affiliation(s)
- Charles J Dorman
- Department of Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin, Ireland
| | - Matthew J Dorman
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
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48
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Drezen JM, Gauthier J, Josse T, Bézier A, Herniou E, Huguet E. Foreign DNA acquisition by invertebrate genomes. J Invertebr Pathol 2017; 147:157-168. [DOI: 10.1016/j.jip.2016.09.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 09/09/2016] [Accepted: 09/14/2016] [Indexed: 12/14/2022]
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49
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Klahn P, Brönstrup M. Bifunctional antimicrobial conjugates and hybrid antimicrobials. Nat Prod Rep 2017; 34:832-885. [PMID: 28530279 DOI: 10.1039/c7np00006e] [Citation(s) in RCA: 119] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Covering: up to the end of 2016Novel antimicrobial drugs are continuously needed to counteract bacterial resistance development. An innovative molecular design strategy for novel antibiotic drugs is based on the hybridization of an antibiotic with a second functional entity. Such conjugates can be grouped into two major categories. In the first category (antimicrobial hybrids), both functional elements of the hybrid exert antimicrobial activity. Due to the dual targeting, resistance development can be significantly impaired, the pharmacokinetic properties can be superior compared to combination therapies with the single antibiotics, and the antibacterial potency is often enhanced in a synergistic manner. In the second category (antimicrobial conjugates), one functional moiety controls the accumulation of the other part of the conjugate, e.g. by mediating an active transport into the bacterial cell or blocking the efflux. This approach is mostly applied to translocate compounds across the cell envelope of Gram-negative bacteria through membrane-embedded transporters (e.g. siderophore transporters) that provide nutrition and signalling compounds to the cell. Such 'Trojan Horse' approaches can expand the antibacterial activity of compounds against Gram-negative pathogens, or offer new options for natural products that could not be developed as standalone antibiotics, e.g. due to their toxicity.
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Affiliation(s)
- P Klahn
- Department for Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany. and Institute for Organic Chemistry, Technische Universität Braunschweig, Hagenring 30, 38106 Braunschweig, Germany.
| | - M Brönstrup
- Department for Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany.
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50
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Liu L, Cheng J, Fu Y, Liu H, Jiang D, Xie J. New insights into reovirus evolution: implications from a newly characterized mycoreovirus. J Gen Virol 2017; 98:1132-1141. [DOI: 10.1099/jgv.0.000752] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Lijiang Liu
- State Key Laboratory of Agricultural Microbiology, Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of PR China, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, PR China
| | - Jiasen Cheng
- State Key Laboratory of Agricultural Microbiology, Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Yanping Fu
- State Key Laboratory of Agricultural Microbiology, Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Huiquan Liu
- NWAFU-PU Joint Research Center, State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling 712100, Shanxi Province, PR China
| | - Daohong Jiang
- State Key Laboratory of Agricultural Microbiology, Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Jiatao Xie
- State Key Laboratory of Agricultural Microbiology, Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
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