1
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Wang G, Wang Q, Qi Q, Wang Q. Dynamic plasmid copy number control for synthetic biology. Trends Biotechnol 2024; 42:147-150. [PMID: 37689527 DOI: 10.1016/j.tibtech.2023.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/18/2023] [Accepted: 08/22/2023] [Indexed: 09/11/2023]
Abstract
Plasmids that replicate independently from chromosomes are valuable genetic tools for biological research. Dynamic control of plasmid copy number facilitates flexible regulation of the gene of interest or the genetic circuit installed in the plasmid. This useful strategy is being integrated into synthetic biology for metabolic reprogramming and biosensing applications.
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Affiliation(s)
- Gege Wang
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, PR China
| | - Qi Wang
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, PR China
| | - Qingsheng Qi
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, PR China
| | - Qian Wang
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, PR China.
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2
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Niault T, Czarnecki J, Lambérioux M, Mazel D, Val ME. Cell cycle-coordinated maintenance of the Vibrio bipartite genome. EcoSal Plus 2023; 11:eesp00082022. [PMID: 38277776 PMCID: PMC10729929 DOI: 10.1128/ecosalplus.esp-0008-2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2024]
Abstract
To preserve the integrity of their genome, bacteria rely on several genome maintenance mechanisms that are co-ordinated with the cell cycle. All members of the Vibrio family have a bipartite genome consisting of a primary chromosome (Chr1) homologous to the single chromosome of other bacteria such as Escherichia coli and a secondary chromosome (Chr2) acquired by a common ancestor as a plasmid. In this review, we present our current understanding of genome maintenance in Vibrio cholerae, which is the best-studied model for bacteria with multi-partite genomes. After a brief overview on the diversity of Vibrio genomic architecture, we describe the specific, common, and co-ordinated mechanisms that control the replication and segregation of the two chromosomes of V. cholerae. Particular attention is given to the unique checkpoint mechanism that synchronizes Chr1 and Chr2 replication.
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Affiliation(s)
- Théophile Niault
- Bacterial Genome Plasticity Unit, CNRS UMR3525, Institut Pasteur, Université Paris Cité, Paris, France
- Collège Doctoral, Sorbonne Université, Paris, France
| | - Jakub Czarnecki
- Bacterial Genome Plasticity Unit, CNRS UMR3525, Institut Pasteur, Université Paris Cité, Paris, France
| | - Morgan Lambérioux
- Bacterial Genome Plasticity Unit, CNRS UMR3525, Institut Pasteur, Université Paris Cité, Paris, France
- Collège Doctoral, Sorbonne Université, Paris, France
| | - Didier Mazel
- Bacterial Genome Plasticity Unit, CNRS UMR3525, Institut Pasteur, Université Paris Cité, Paris, France
| | - Marie-Eve Val
- Bacterial Genome Plasticity Unit, CNRS UMR3525, Institut Pasteur, Université Paris Cité, Paris, France
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3
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Anda M, Yamanouchi S, Cosentino S, Sakamoto M, Ohkuma M, Takashima M, Toyoda A, Iwasaki W. Bacteria can maintain rRNA operons solely on plasmids for hundreds of millions of years. Nat Commun 2023; 14:7232. [PMID: 37963895 PMCID: PMC10645730 DOI: 10.1038/s41467-023-42681-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 10/17/2023] [Indexed: 11/16/2023] Open
Abstract
It is generally assumed that all bacteria must have at least one rRNA operon (rrn operon) on the chromosome, but some strains of the genera Aureimonas and Oecophyllibacter carry their sole rrn operon on a plasmid. However, other related strains and species have chromosomal rrn loci, suggesting that the exclusive presence of rrn operons on a plasmid is rare and unlikely to be stably maintained over long evolutionary periods. Here, we report the results of a systematic search for additional bacteria without chromosomal rrn operons. We find that at least four bacterial clades in the phyla Bacteroidota, Spirochaetota, and Pseudomonadota (Proteobacteria) lost chromosomal rrn operons independently. Remarkably, Persicobacteraceae have apparently maintained this peculiar genome organization for hundreds of millions of years. In our study, all the rrn-carrying plasmids in bacteria lacking chromosomal rrn loci possess replication initiator genes of the Rep_3 family. Furthermore, the lack of chromosomal rrn operons is associated with differences in copy numbers of rrn operons, plasmids, and chromosomal tRNA genes. Thus, our findings indicate that the absence of rrn loci in bacterial chromosomes can be stably maintained over long evolutionary periods.
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Affiliation(s)
- Mizue Anda
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, the University of Tokyo, Kashiwa, Chiba, 277-0882, Japan.
- Department of Biological Sciences, Graduate School of Science, the University of Tokyo, Bunkyo-ku, Tokyo, 113-0032, Japan.
| | - Shun Yamanouchi
- Department of Biological Sciences, Graduate School of Science, the University of Tokyo, Bunkyo-ku, Tokyo, 113-0032, Japan
| | - Salvatore Cosentino
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, the University of Tokyo, Kashiwa, Chiba, 277-0882, Japan
- Department of Biological Sciences, Graduate School of Science, the University of Tokyo, Bunkyo-ku, Tokyo, 113-0032, Japan
| | - Mitsuo Sakamoto
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Masako Takashima
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Atsushi Toyoda
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Wataru Iwasaki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, the University of Tokyo, Kashiwa, Chiba, 277-0882, Japan.
- Department of Biological Sciences, Graduate School of Science, the University of Tokyo, Bunkyo-ku, Tokyo, 113-0032, Japan.
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, the University of Tokyo, Kashiwa, Chiba, 277-0882, Japan.
- Atmosphere and Ocean Research Institute, the University of Tokyo, Kashiwa, Chiba, 277-0882, Japan.
- Institute for Quantitative Biosciences, the University of Tokyo, Bunkyo-ku, Tokyo, 113-0032, Japan.
- Collaborative Research Institute for Innovative Microbiology, the University of Tokyo, Bunkyo-ku, Tokyo, 113-0032, Japan.
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4
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Decewicz P, Romaniuk K, Gorecki A, Radlinska M, Dabrowska M, Wyszynska A, Dziewit L. Structure and functions of a multireplicon genome of Antarctic Psychrobacter sp. ANT_H3: characterization of the genetic modules suitable for the construction of the plasmid-vectors for cold-active bacteria. J Appl Genet 2023; 64:545-557. [PMID: 37145222 PMCID: PMC10457243 DOI: 10.1007/s13353-023-00759-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 04/01/2023] [Accepted: 04/22/2023] [Indexed: 05/06/2023]
Abstract
Among Psychrobacter spp., there are several multireplicon strains, carrying more than two plasmids. Psychrobacter sp. ANT_H3 carries as many as 11 extrachromosomal replicons, which is the highest number in Psychrobacter spp. Plasmids of this strain were subjected to detailed genomic analysis, which enables an insight into the structure and functioning of this multireplicon genome. The replication and conjugal transfer modules of ANT_H3 plasmids were analyzed functionally to discover their potential for being used as building blocks for the construction of novel plasmid-vectors for cold-active bacteria. It was shown that two plasmids have a narrow host range as they were not able to replicate in species other than Psychrobacter, while remaining plasmids had a wider host range and were functional in various Alpha- and Gammaproteobacteria. Moreover, it was confirmed that mobilization modules of seven plasmids were functional, i.e., could be mobilized for conjugal transfer by the RK2 conjugation system. Auxiliary genes were also distinguished in ANT_H3 plasmids, including these encoding putative DNA-protecting protein DprA, multidrug efflux SMR transporter of EmrE family, glycine cleavage system T protein, MscS small-conductance mechanosensitive channel protein, and two type II restriction-modification systems. Finally, all genome-retrieved plasmids of Psychrobacter spp. were subjected to complex genome- and proteome-based comparative analyses showing that Antarctic replicons are significantly different from plasmids from other locations.
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Affiliation(s)
- Przemyslaw Decewicz
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, Australia
| | - Krzysztof Romaniuk
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Adrian Gorecki
- Department of Biochemistry and Microbiology, Institute of Biology, Warsaw University of Life Sciences (SGGW), Warsaw, Poland
| | - Monika Radlinska
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Maria Dabrowska
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Agnieszka Wyszynska
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Lukasz Dziewit
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland.
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5
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Köhler R, Sadhir I, Murray SM. ★Track: Inferred counting and tracking of replicating DNA loci. Biophys J 2023; 122:1577-1585. [PMID: 36966362 PMCID: PMC10183378 DOI: 10.1016/j.bpj.2023.03.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 03/10/2023] [Accepted: 03/22/2023] [Indexed: 03/27/2023] Open
Abstract
Fluorescent microscopy is the primary method to study DNA organization within cells. However, the variability and low signal/noise commonly associated with live-cell time-lapse imaging challenges quantitative measurements. In particular, obtaining quantitative or mechanistic insight often depends on the accurate tracking of fluorescent particles. Here, we present ★Track, an inference method that determines the most likely temporal tracking of replicating intracellular particles such DNA loci while accounting for missing, merged, and spurious detections. It allows the accurate prediction of particle copy numbers as well as the timing of replication events. We demonstrate ★Track's abilities and gain new insight into plasmid copy number control and the volume dependence of bacterial chromosome replication initiation. By enabling the accurate tracking of DNA loci, ★Track can help to uncover the mechanistic principles of chromosome organization and dynamics across a range of systems.
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Affiliation(s)
- Robin Köhler
- Max Planck Institute for Terrestrial Microbiology and LOEWE Centre for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Ismath Sadhir
- Max Planck Institute for Terrestrial Microbiology and LOEWE Centre for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Seán M Murray
- Max Planck Institute for Terrestrial Microbiology and LOEWE Centre for Synthetic Microbiology (SYNMIKRO), Marburg, Germany.
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6
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Maurya AP, Lazdins A, Wilson H, Lloyd GS, Stephens ER, Haines AS, Thomas CM. Iteron control of oriV function in IncP-1 plasmid RK2. Plasmid 2023; 126:102681. [PMID: 36990191 DOI: 10.1016/j.plasmid.2023.102681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 03/07/2023] [Accepted: 03/22/2023] [Indexed: 03/30/2023]
Abstract
Replication control of many plasmids is mediated by the balance between the positive and negative effects of Rep protein binding repeated sequences (iterons) associated with the replication origin, oriV. Negative control is thought to be mediated by dimeric Rep protein linking iterons in a process termed "handcuffing". The well-studied oriV region of RK2 contains 9 iterons arranged as a singleton (iteron 1), a group of 3 (iterons 2-4) and a group of 5 (iterons 5-9), but only iterons 5 to 9 are essential for replication. An additional iteron (iteron 10), oriented in the opposite direction, is also involved and reduces copy-number nearly two-fold. Since iterons 1 and 10 share an identical upstream hexamer (5' TTTCAT 3') it has been hypothesised that they form a TrfA-mediated loop facilitated by their inverted orientation. Here we report that contrary to the hypothesis, flipping one or other so they are in direct orientation results in marginally lower rather than higher copy-number. In addition, following mutagenesis of the hexamer upstream of iteron 10, we report that the Logo for the hexamer "upstream" of the regulatory iterons (1 to 4 and 10) differs from that of the essential iterons, suggesting functional differences in their interaction with TrfA.
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Affiliation(s)
- Anand P Maurya
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Alessandro Lazdins
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Helen Wilson
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Georgina S Lloyd
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Elton R Stephens
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Anthony S Haines
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Christopher M Thomas
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
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7
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Wang YC, Lu MC, Li YT, Tang HL, Hsiao PY, Chen BH, Teng RH, Chiou CS, Lai YC. Microevolution of CG23-I Hypervirulent Klebsiella pneumoniae during Recurrent Infections in a Single Patient. Microbiol Spectr 2022; 10:e0207722. [PMID: 36129301 PMCID: PMC9602619 DOI: 10.1128/spectrum.02077-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 09/05/2022] [Indexed: 12/31/2022] Open
Abstract
CG23-I lineage constitutes the majority of hypervirulent Klebsiella pneumoniae. A diabetic patient suffered six episodes of infections caused by CG23-I K. pneumoniae. A total of nine isolates were collected in 2020. We performed whole-genome sequencing to elucidate the within-patient evolution of CG23-I K. pneumoniae. The maximum pairwise difference among the nine longitudinally collected isolates was five single nucleotide polymorphisms. One of the mutations was at the Asp87 position of GyrA. Four indels were identified, including an initiator tRNAfMet duplication, a tRNAArg deletion, a 7-bp insertion, and a 22-bp deletion. All 9 isolates had the genomic features of CG23-I K. pneumoniae, a chromosome-borne ICEKp10, and a large virulence plasmid. The carriage of a complete set of genes for the biosynthesis of colibactin by ICEKp10 gave the nine isolates an ability to cause DNA damage to RAW264.7 cells. Compared with the initial isolate, the last isolate with an additional copy of initiator tRNAfMet grew faster in a nutrient-limiting condition and exhibited enhanced virulence in BALB/c mice. Collectively, we characterized the within-patient microevolution of CG23-I K. pneumoniae through an in-depth comparison of genome sequences. Using the in vitro experiments and mouse models, we also demonstrated that these genomic alterations endowed the isolates with advantages to pass through in vivo selection. IMPORTANCE CG23-I is a significant lineage of hypervirulent Klebsiella pneumoniae. This study characterizes the within-patient microevolution of CG23-I K. pneumoniae. Selective pressures from continuous use of antibiotics favored point mutations contributing to bacterial resistance to antibiotics. The duplication of an initiator tRNAfMet gene helped CG23-I K. pneumoniae proliferate to reach a maximal population size during infections. For longer persistence inside a human host, the large virulence plasmid evolved with more flexible control of replication through duplication of the iteron-1 region. With the genomic alterations, the last isolate had a growth advantage over the initial isolate and exhibited enhanced virulence in BALB/c mice. This study gives us a deeper understanding of the genome evolution during the within-patient pathoadaptation of CG23-I K. pneumoniae.
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Affiliation(s)
- Yao-Chen Wang
- Department of Internal Medicine, Chung Shan Medical University Hospital, Taichung, Taiwan
- School of Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - Min-Chi Lu
- Department of Microbiology and Immunology, School of Medicine, China Medical University, Taichung, Taiwan
- Division of Infectious Diseases, Department of Internal Medicine, China Medical University Hospital, Taichung, Taiwan
| | - Yia-Ting Li
- Division of Respiratory Therapy, Department of Internal Medicine, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Hui-Ling Tang
- Department of Microbiology and Immunology, School of Medicine, China Medical University, Taichung, Taiwan
| | - Pei-Yi Hsiao
- Department of Microbiology and Immunology, School of Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - Bo-Han Chen
- Central Region Laboratory, Center for Diagnostics and Vaccine Development, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
| | - Ru-Hsiou Teng
- Central Region Laboratory, Center for Diagnostics and Vaccine Development, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
| | - Chien-Shun Chiou
- Central Region Laboratory, Center for Diagnostics and Vaccine Development, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
| | - Yi-Chyi Lai
- Department of Internal Medicine, Chung Shan Medical University Hospital, Taichung, Taiwan
- Department of Microbiology and Immunology, School of Medicine, Chung Shan Medical University, Taichung, Taiwan
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8
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Chen L, Ai W, Zhou Y, Wu C, Guo Y, Wu X, Wang B, Rao L, Xu Y, Zhang J, Chen L, Yu F. Outbreak of IncX8 Plasmid-Mediated KPC-3-Producing Enterobacterales Infection, China. Emerg Infect Dis 2022; 28:1421-1430. [PMID: 35731165 PMCID: PMC9239885 DOI: 10.3201/eid2807.212181] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Carbapenem-resistant Enterobacterales (CRE) infection is highly endemic in China; Klebsiella pneumoniae carbapenemase (KPC) 2-producing CRE is the most common, whereas KPC-3-producing CRE is rare. We report an outbreak of KPC-3-producing Enterobacterales infection in China. During August 2020-June 2021, 25 blaKPC-3-positive Enterobacteriale isolates were detected from 24 patients in China. Whole-genome sequencing analysis revealed that the blaKPC-3 genes were harbored by IncX8 plasmids. The outbreak involved clonal expansion of KPC-3-producing Serratia marcescens and transmission of blaKPC-3 plasmids across different species. The blaKPC-3 plasmids demonstrated high conjugation frequencies (10-3 to 10-4). A Galleria mellonella infection model showed that 2 sequence type 65 K2 K. pneumoniae strains containing blaKPC-3 plasmids were highly virulent. A ceftazidime/avibactam in vitro selection assay indicated that the KPC-3-producing strains can readily develop resistance. The spread of blaKPC-3-harboring IncX8 plasmids and these KPC-3 strains should be closely monitored in China and globally.
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9
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Convergent evolution in two bacterial replicative helicase loaders. Trends Biochem Sci 2022; 47:620-630. [DOI: 10.1016/j.tibs.2022.02.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 02/06/2022] [Accepted: 02/08/2022] [Indexed: 12/23/2022]
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10
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Castro-Jaimes S, Guerrero G, Bello-López E, Cevallos MA. Replication initiator proteins of Acinetobacter baumannii plasmids: An update note. Plasmid 2021; 119-120:102616. [PMID: 34953823 DOI: 10.1016/j.plasmid.2021.102616] [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: 06/08/2021] [Revised: 12/15/2021] [Accepted: 12/16/2021] [Indexed: 11/26/2022]
Abstract
The bioinformatic analysis that we made of 492 Acinetobacter baumannii plasmid sequences identified 418 genes encoding Replication Initiator (Rep) proteins that fell into at least fourteen groups according to the protein domains that they contained. The most abundant group of Rep proteins contained a Rep_3 superfamily domain, followed by Rep proteins containing Replicase/PriCT_1 superfamily domains, and then by Reps possessing only an HTH_MerR-SF superfamily domain. The remaining eleven groups contain only a few members. To evaluate the diversity of these Rep proteins, we classify them using the current scheme of GR homology groups, which contains 34 groups. However, we needed to create 22 additional GR homology groups to capture all the Rep protein diversity of the plasmid collection. Finally, our bioinformatic analysis suggests that a large fraction of the plasmids seem to have a restricted host range limited to Acinetobacter species, except for those belonging to GR38 that have a very wide host range. To facilitate the future analysis of the Rep proteins, we included a list of the DNA and protein sequences, in fasta format, of the representatives of each one of the GR homology groups.
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Affiliation(s)
- Semiramis Castro-Jaimes
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca CP62210, Morelos, Mexico
| | - Gabriela Guerrero
- Unidad de Análisis Bioinformático, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca CP62210, Morelos, Mexico
| | - Elena Bello-López
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca CP62210, Morelos, Mexico
| | - Miguel A Cevallos
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca CP62210, Morelos, Mexico.
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11
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Fournes F, Niault T, Czarnecki J, Tissier-Visconti A, Mazel D, Val ME. The coordinated replication of Vibrio cholerae's two chromosomes required the acquisition of a unique domain by the RctB initiator. Nucleic Acids Res 2021; 49:11119-11133. [PMID: 34643717 PMCID: PMC8565311 DOI: 10.1093/nar/gkab903] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 08/30/2021] [Accepted: 09/22/2021] [Indexed: 12/21/2022] Open
Abstract
Vibrio cholerae, the pathogenic bacterium that causes cholera, has two chromosomes (Chr1, Chr2) that replicate in a well-orchestrated sequence. Chr2 initiation is triggered only after the replication of the crtS site on Chr1. The initiator of Chr2 replication, RctB, displays activities corresponding with its different binding sites: initiator at the iteron sites, repressor at the 39m sites, and trigger at the crtS site. The mechanism by which RctB relays the signal to initiate Chr2 replication from crtS is not well-understood. In this study, we provide new insights into how Chr2 replication initiation is regulated by crtS via RctB. We show that crtS (on Chr1) acts as an anti-inhibitory site by preventing 39m sites (on Chr2) from repressing initiation. The competition between these two sites for RctB binding is explained by the fact that RctB interacts with crtS and 39m via the same DNA-binding surface. We further show that the extreme C-terminal tail of RctB, essential for RctB self-interaction, is crucial for the control exerted by crtS. This subregion of RctB is conserved in all Vibrio, but absent in other Rep-like initiators. Hence, the coordinated replication of both chromosomes likely results from the acquisition of this unique domain by RctB.
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MESH Headings
- Amino Acid Sequence
- Bacterial Proteins/chemistry
- Bacterial Proteins/genetics
- Bacterial Proteins/metabolism
- Base Sequence
- Binding Sites
- Binding, Competitive
- Chromosomes, Bacterial/chemistry
- Chromosomes, Bacterial/metabolism
- Cloning, Molecular
- DNA Replication
- DNA, Bacterial/genetics
- DNA, Bacterial/metabolism
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Gene Expression Regulation, Bacterial
- Genetic Vectors/chemistry
- Genetic Vectors/metabolism
- Models, Molecular
- Protein Binding
- Protein Conformation, alpha-Helical
- Protein Conformation, beta-Strand
- Protein Interaction Domains and Motifs
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- Replication Origin
- Sequence Alignment
- Sequence Homology, Amino Acid
- Signal Transduction
- Vibrio cholerae/genetics
- Vibrio cholerae/metabolism
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Affiliation(s)
- Florian Fournes
- Institut Pasteur, Université de Paris, Unité Plasticité du Génome Bactérien, Département Génomes et Génétique, Paris 75015, France
- Centre National de la Recherche Scientifique, UMR3525, Paris 75015, France
| | - Theophile Niault
- Institut Pasteur, Université de Paris, Unité Plasticité du Génome Bactérien, Département Génomes et Génétique, Paris 75015, France
- Centre National de la Recherche Scientifique, UMR3525, Paris 75015, France
- Sorbonne Université, Collège Doctoral, Paris 75005, France
| | - Jakub Czarnecki
- Institut Pasteur, Université de Paris, Unité Plasticité du Génome Bactérien, Département Génomes et Génétique, Paris 75015, France
- Centre National de la Recherche Scientifique, UMR3525, Paris 75015, France
- University of Warsaw, Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, Warsaw 02-096, Poland
| | - Alvise Tissier-Visconti
- Institut Pasteur, Université de Paris, Unité Plasticité du Génome Bactérien, Département Génomes et Génétique, Paris 75015, France
- Centre National de la Recherche Scientifique, UMR3525, Paris 75015, France
| | - Didier Mazel
- Institut Pasteur, Université de Paris, Unité Plasticité du Génome Bactérien, Département Génomes et Génétique, Paris 75015, France
- Centre National de la Recherche Scientifique, UMR3525, Paris 75015, France
| | - Marie-Eve Val
- Institut Pasteur, Université de Paris, Unité Plasticité du Génome Bactérien, Département Génomes et Génétique, Paris 75015, France
- Centre National de la Recherche Scientifique, UMR3525, Paris 75015, France
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12
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Mindlin S, Maslova O, Beletsky A, Nurmukanova V, Zong Z, Mardanov A, Petrova M. Ubiquitous Conjugative Mega-Plasmids of Acinetobacter Species and Their Role in Horizontal Transfer of Multi-Drug Resistance. Front Microbiol 2021; 12:728644. [PMID: 34621254 PMCID: PMC8490738 DOI: 10.3389/fmicb.2021.728644] [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] [Received: 06/21/2021] [Accepted: 08/25/2021] [Indexed: 02/05/2023] Open
Abstract
Conjugative mega-plasmids play a special role in adaptation since they carry a huge number of accessory genes, often allowing the host to develop in new niches. In addition, due to conjugation they are able to effectively spread themselves and participate in the transfer of small mobilizable plasmids. In this work, we present a detailed characterization of a recently discovered family of multiple-drug resistance mega-plasmids of Acinetobacter species, termed group III-4a. We describe the structure of the plasmid backbone region, identify the rep gene and the origin of plasmid replication, and show that plasmids from this group are able not only to move between different Acinetobacter species but also to efficiently mobilize small plasmids containing different mob genes. Furthermore, we show that the population of natural Acinetobacter strains contains a significant number of mega-plasmids and reveal a clear correlation between the living conditions of Acinetobacter strains and the structure of their mega-plasmids. In particular, comparison of the plasmids from environmental and clinical strains shows that the genes for resistance to heavy metals were eliminated in the latter, with the simultaneous accumulation of antibiotic resistance genes by incorporation of transposons and integrons carrying these genes. The results demonstrate that this group of mega-plasmids plays a key role in the dissemination of multi-drug resistance among Acinetobacter species.
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Affiliation(s)
- Sofia Mindlin
- Institute of Molecular Genetics of National Research Center "Kurchatov Institute", Moscow, Russia
| | - Olga Maslova
- Institute of Molecular Genetics of National Research Center "Kurchatov Institute", Moscow, Russia
| | - Alexey Beletsky
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Varvara Nurmukanova
- Institute of Molecular Genetics of National Research Center "Kurchatov Institute", Moscow, Russia
| | - Zhiyong Zong
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
| | - Andrey Mardanov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Mayya Petrova
- Institute of Molecular Genetics of National Research Center "Kurchatov Institute", Moscow, Russia
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Szabó M, Murányi G, Kiss J. IncC helper dependent plasmid-like replication of Salmonella Genomic Island 1. Nucleic Acids Res 2021; 49:832-846. [PMID: 33406256 PMCID: PMC7826253 DOI: 10.1093/nar/gkaa1257] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 11/24/2020] [Accepted: 12/17/2020] [Indexed: 12/16/2022] Open
Abstract
The Salmonella genomic island 1 (SGI1) and its variants are mobilized by IncA and IncC conjugative plasmids. SGI1-family elements and their helper plasmids are effective transporters of multidrug resistance determinants. SGI1 exploits the transfer apparatus of the helper plasmid and hijacks its activator complex, AcaCD, to trigger the expression of several SGI1 genes. In this way, SGI1 times its excision from the chromosome to the helper entry and expresses mating pore components that enhance SGI1 transfer. The SGI1-encoded T4SS components and the FlhDC-family activator proved to be interchangeable with their IncC-encoded homologs, indicating multiple interactions between SGI1 and its helpers. As a new aspect of this crosstalk, we report here the helper-induced replication of SGI1, which requires both activators, AcaCD and FlhDCSGI1, and significantly increases the stability of SGI1 when coexists with the helper plasmid. We have identified the oriVSGI1 and shown that S004-repA operon encodes for a translationally coupled leader protein and an IncN2/N3-related RepA that are expressed under the control of the AcaCD-responsive promoter PS004. This replicon transiently maintains SGI1 as a 4–8-copy plasmid, not only stabilizing the island but also contributing to the fast displacement of the helper plasmid.
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Affiliation(s)
- Mónika Szabó
- Agricultural Biotechnology Institute, National Agricultural Research and Innovation Centre, Gödöllő H2100, Hungary
| | - Gábor Murányi
- Agricultural Biotechnology Institute, National Agricultural Research and Innovation Centre, Gödöllő H2100, Hungary
| | - János Kiss
- Agricultural Biotechnology Institute, National Agricultural Research and Innovation Centre, Gödöllő H2100, Hungary
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Kim JW, Bugata V, Cortés-Cortés G, Quevedo-Martínez G, Camps M. Mechanisms of Theta Plasmid Replication in Enterobacteria and Implications for Adaptation to Its Host. EcoSal Plus 2020; 9:10.1128/ecosalplus.ESP-0026-2019. [PMID: 33210586 PMCID: PMC7724965 DOI: 10.1128/ecosalplus.esp-0026-2019] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Indexed: 11/20/2022]
Abstract
Plasmids are autonomously replicating sequences that help cells adapt to diverse stresses. Theta plasmids are the most frequent plasmid class in enterobacteria. They co-opt two host replication mechanisms: replication at oriC, a DnaA-dependent pathway leading to replisome assembly (theta class A), and replication fork restart, a PriA-dependent pathway leading to primosome assembly through primer extension and D-loop formation (theta classes B, C, and D). To ensure autonomy from the host's replication and to facilitate copy number regulation, theta plasmids have unique mechanisms of replication initiation at the plasmid origin of replication (ori). Tight plasmid copy number regulation is essential because of the major and direct impact plasmid gene dosage has on gene expression. The timing of plasmid replication and segregation are also critical for optimizing plasmid gene expression. Therefore, we propose that plasmid replication needs to be understood in its biological context, where complex origins of replication (redundant origins, mosaic and cointegrated replicons), plasmid segregation, and toxin-antitoxin systems are often present. Highlighting their tight functional integration with ori function, we show that both partition and toxin-antitoxin systems tend to be encoded in close physical proximity to the ori in a large collection of Escherichia coli plasmids. We also propose that adaptation of plasmids to their host optimizes their contribution to the host's fitness while restricting access to broad genetic diversity, and we argue that this trade-off between adaptation to host and access to genetic diversity is likely a determinant factor shaping the distribution of replicons in populations of enterobacteria.
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Affiliation(s)
- Jay W Kim
- Department of Microbiology and Environmental Toxicology, University of California at Santa Cruz, Santa Cruz, CA, 95064
| | - Vega Bugata
- Department of Microbiology and Environmental Toxicology, University of California at Santa Cruz, Santa Cruz, CA, 95064
| | - Gerardo Cortés-Cortés
- Department of Microbiology and Environmental Toxicology, University of California at Santa Cruz, Santa Cruz, CA, 95064
| | - Giselle Quevedo-Martínez
- Department of Microbiology and Environmental Toxicology, University of California at Santa Cruz, Santa Cruz, CA, 95064
| | - Manel Camps
- Department of Microbiology and Environmental Toxicology, University of California at Santa Cruz, Santa Cruz, CA, 95064
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Huguet KT, Rivard N, Garneau D, Palanee J, Burrus V. Replication of the Salmonella Genomic Island 1 (SGI1) triggered by helper IncC conjugative plasmids promotes incompatibility and plasmid loss. PLoS Genet 2020; 16:e1008965. [PMID: 32760058 PMCID: PMC7433901 DOI: 10.1371/journal.pgen.1008965] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 08/18/2020] [Accepted: 06/30/2020] [Indexed: 12/27/2022] Open
Abstract
The mobilizable resistance island Salmonella genomic island 1 (SGI1) is specifically mobilized by IncA and IncC conjugative plasmids. SGI1, its variants and IncC plasmids propagate multidrug resistance in pathogenic enterobacteria such as Salmonella enterica serovars and Proteus mirabilis. SGI1 modifies and uses the conjugation apparatus encoded by the helper IncC plasmid, thus enhancing its own propagation. Remarkably, although SGI1 needs a coresident IncC plasmid to excise from the chromosome and transfer to a new host, these elements have been reported to be incompatible. Here, the stability of SGI1 and its helper IncC plasmid, each expressing a different fluorescent reporter protein, was monitored using fluorescence-activated cell sorting (FACS). Without selective pressure, 95% of the cells segregated into two subpopulations containing either SGI1 or the helper plasmid. Furthermore, FACS analysis revealed a high level of SGI1-specific fluorescence in IncC+ cells, suggesting that SGI1 undergoes active replication in the presence of the helper plasmid. SGI1 replication was confirmed by quantitative PCR assays, and extraction and restriction of its plasmid form. Deletion of genes involved in SGI1 excision from the chromosome allowed a stable coexistence of SGI1 with its helper plasmid without selective pressure. In addition, deletion of S003 (rep) or of a downstream putative iteron-based origin of replication, while allowing SGI1 excision, abolished its replication, alleviated the incompatibility with the helper plasmid and enabled its cotransfer to a new host. Like SGI1 excision functions, rep expression was found to be controlled by AcaCD, the master activator of IncC plasmid transfer. Transient SGI1 replication seems to be a key feature of the life cycle of this family of genomic islands. Sequence database analysis revealed that SGI1 variants encode either a replication initiator protein with a RepA_C domain, or an alternative replication protein with N-terminal replicase and primase C terminal 1 domains. The Salmonella genomic island 1 (SGI1) and its variants propagate multidrug resistance in several species of human and animal pathogens with the help of IncA and IncC conjugative plasmids that are absolutely required for SGI1 dissemination. These helper plasmids are known to trigger the excision of SGI1 from the chromosome. Here, we found that IncC plasmids also trigger the replication of the excised, circular form of SGI1 by enabling the expression of an SGI1-borne replication initiator gene. In return, high-copy replication of SGI1 interferes with the persistence of the IncC plasmid and prevents its cotransfer into a recipient cell, thereby allowing integration and stabilization of SGI1 into the chromosome of the new host. This finding is important to better understand the complex interactions between SGI1-like elements and their helper plasmids that lead to widespread and highly efficient propagation of multidrug resistance genes to a broad range of human and animal pathogens.
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Affiliation(s)
- Kévin T. Huguet
- Département de biologie, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Nicolas Rivard
- Département de biologie, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Daniel Garneau
- Département de biologie, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Jason Palanee
- Département de biologie, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Vincent Burrus
- Département de biologie, Université de Sherbrooke, Sherbrooke, Québec, Canada
- * E-mail:
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16
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Zheng Z, Ye L, Chan EWC, Chen S. Identification and characterization of a conjugative blaVIM-1-bearing plasmid in Vibrio alginolyticus of food origin. J Antimicrob Chemother 2020; 74:1842-1847. [PMID: 30993329 DOI: 10.1093/jac/dkz140] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 02/21/2019] [Accepted: 03/10/2019] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES To investigate the genetic features of the blaVIM-1 gene first detected in a cephalosporin-resistant Vibrio alginolyticus isolate, Vb1978. METHODS The MICs of V. alginolyticus strain Vb1978 were determined, and the β-lactamases produced were screened and analysed using conjugation, S1-PFGE and Southern blotting. The complete sequence of the blaVIM-1-encoding plasmid was also obtained using the Illumina and MinION sequencing platforms. RESULTS V. alginolyticus strain Vb1978, isolated from a retail shrimp sample, was resistant to cephalosporins and exhibited reduced susceptibility to carbapenems. A novel blaVIM-1-carrying conjugative plasmid, designated pVb1978, was identified in this strain. Plasmid pVb1978 had 50 001 bp and comprised 59 predicted coding sequences (CDSs). The plasmid backbone of pVb1978 was homologous to those of IncP-type plasmids, while its replication region was structurally similar to non-IncP plasmids. The blaVIM-1 gene was found to be carried by the class 1 integron In70 and associated with a defective Tn402-like transposon. CONCLUSIONS A novel blaVIM-1-carrying conjugative plasmid, pVb1978, was reported for the first time in V. alginolyticus, which warrants further investigation in view of its potential pathogenicity towards humans and widespread occurrence in the environment.
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Affiliation(s)
- Zhiwei Zheng
- Shenzhen Key Laboratory for Food Biological Safety Control, Food Safety and Technology Research Centre, The Hong Kong PolyU Shenzhen Research Institute, Shenzhen, P. R. China.,State Key Laboratory of Chirosciences, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - Lianwei Ye
- Shenzhen Key Laboratory for Food Biological Safety Control, Food Safety and Technology Research Centre, The Hong Kong PolyU Shenzhen Research Institute, Shenzhen, P. R. China.,State Key Laboratory of Chirosciences, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - Edward Wai-Chi Chan
- Shenzhen Key Laboratory for Food Biological Safety Control, Food Safety and Technology Research Centre, The Hong Kong PolyU Shenzhen Research Institute, Shenzhen, P. R. China.,State Key Laboratory of Chirosciences, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - Sheng Chen
- Shenzhen Key Laboratory for Food Biological Safety Control, Food Safety and Technology Research Centre, The Hong Kong PolyU Shenzhen Research Institute, Shenzhen, P. R. China.,State Key Laboratory of Chirosciences, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
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Brovedan MA, Cameranesi MM, Limansky AS, Morán-Barrio J, Marchiaro P, Repizo GD. What do we know about plasmids carried by members of the Acinetobacter genus? World J Microbiol Biotechnol 2020; 36:109. [PMID: 32656745 DOI: 10.1007/s11274-020-02890-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 07/04/2020] [Indexed: 02/07/2023]
Abstract
Several Acinetobacter spp. act as opportunistic pathogens causing healthcare-associated infections worldwide, and in this respect their ability to resist antimicrobial compounds has certainly boosted up their global propagation. Acinetobacter clinical strains have demonstrated a remarkable ability to evolve and become resistant to almost all available drugs in the antimicrobial arsenal, including the last-resort carbapenem β-lactams. The dissemination of antimicrobial resistant genes (ARG), heavy metals-detoxification systems and other traits such as virulence factors is facilitated by mobile genetic elements (MGE) through horizontal gene transfer. Among them, plasmids have been shown to play a critical role in this genus. Despite the continuous increase of Acinetobacter plasmid sequences present in databases, there are no reports describing the basic traits carried by these MGE. To fill this gap, a broad analysis of the Acinetobacter plasmidome was performed. A search for Acinetobacter complete plasmids indicated that 905 sequences have been deposited in the NCBI-GenBank public database, of which 492 are harbored by Acinetobacter baumannii strains. Plasmid-classification schemes based on Rep proteins homology have so far described 23 different groups for A. baumannii (GR1-23), and 16 Acinetobacter Rep3 Groups (AR3G1-16) for the complete genus. Acinetobacter plasmids size ranges from 1.3 to 400 kb. Interestingly, widespread plasmids which are < 20 kb make up 56% of the total present in members of this genus. This led to the proposal of Acinetobacter plasmid assignation to two groups according to their size (< 20 kb and > 20 kb). Usually, smaller plasmids are not self-transmissible, and thereby employ alternative mechanisms of dissemination. For instance, a subgroup of < 20 kb-plasmids belonging to the pRAY-family, lack a rep gene, but encode a relaxase enabling their mobilization by conjugative plasmids. Other subgroup, including small GR2 Acinetobacter plasmids, does not encode a relaxase gene. However, they could still be mobilized by conjugative plasmids which recognize an oriT region carried by these small plasmids. Also, these < 20 kb-plasmids usually carry accessory genes bordered by XerC/D-recombinases recognition sites which have been hypothesized to mediate plasmid plasticity. Conversely, many cases of larger plasmids are self-transmissible and might encode virulence factors and their regulators, thus controlling strain pathogenicity. The ARGs carried by the > 20 kb-plasmids are usually encoded within other MGEs such as transposons, or as part of integrons. It has been recently noted that some of the > 20 kb-plasmids are derived from excised phages, and thus dubbed as phage-like plasmids. All in all, the plethora of plasmids found in strains of this genus and the multiple strategies promoting their evolution and dissemination have certainly contributed to survival of the Acinetobacter members in different habitats, including the clinical environment.
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Affiliation(s)
- Marco A Brovedan
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET), Laboratorio de Resistencia a Antimicrobianos, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - María M Cameranesi
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET), Laboratorio de Resistencia a Antimicrobianos, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Adriana S Limansky
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET), Laboratorio de Resistencia a Antimicrobianos, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Jorgelina Morán-Barrio
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET), Laboratorio de Resistencia a Antimicrobianos, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Patricia Marchiaro
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET), Laboratorio de Resistencia a Antimicrobianos, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Guillermo D Repizo
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET), Laboratorio de Resistencia a Antimicrobianos, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina.
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18
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Szabo KV, O’Neill CE, Clarke IN. Diversity in Chlamydial plasmids. PLoS One 2020; 15:e0233298. [PMID: 32469898 PMCID: PMC7259575 DOI: 10.1371/journal.pone.0233298] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 05/01/2020] [Indexed: 11/30/2022] Open
Abstract
Background Evolutionary studies have been conducted that have investigated the chromosomal variance in the genus of Chlamydia. However, no all-encompassing genus-wide comparison has been performed on the plasmid. Therefore, there is a gap in the current knowledge on Chlamydia plasmid diversity. Aims This project is aimed to investigate and establish the nature and extent of diversity across the entire genus of Chlamydia, by comparing the sequences of all currently available plasmid carrying strains. Methods The PUBMED database was used to identify plasmid sequences from all available strains that met the set quality criteria for their inclusion in the study. Alignments were performed on the 51 strains that fulfilled the criteria using MEGA X software. Following that Maximum Likelihood estimation was used to construct 11 phylogenetic trees of the whole plasmid sequence, the individual 8 coding sequences, the iteron and a chromosomal gene ompA as a comparator. Results The genus-wide plasmid phylogeny produced three distinct lineages labelled as alpha, beta and gamma. Nineteen genotypes were found in the initial whole plasmid analysis. Their distribution was allocated as six C. pecorum, two C. pneumoniae, one C. gallinacea, one C. avium, one C. caviae, one C. felis, two C. psittaci, one C. trachomatis, one C. muridarum, and two C. suis. The chromosomal comparative gene ompA supported this distribution, with the same number of primary clades with the same species distribution. However, ompA sequence comparison resulted in fewer genotypes due to a reduced amount of available sequences (33 out of 51). All results were statistically significant. Conclusion The results of this study indicate that the common bacterial ancestor of all the species had a plasmid, which has diverged over time. Moreover, it suggests that there is a strong evolutionary selection towards these species retaining their plasmids due to its high level of conservation across the genus, with the notable exception of C. pneumoniae. Furthermore, the evolutionary analysis showed that the plasmid and the chromosome have co-evolved.
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Affiliation(s)
- Kolos V. Szabo
- Faculty of Medicine, University of Southampton, Southampton, Hampshire, United Kingdom
- * E-mail:
| | - Colette E. O’Neill
- Molecular Microbiology Group, Clinical and Experimental Sciences, University Hospital Southampton, Southampton, Hampshire, United Kingdom
| | - Ian N. Clarke
- Molecular Microbiology Group, Clinical and Experimental Sciences, University Hospital Southampton, Southampton, Hampshire, United Kingdom
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19
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Luo H, Gao F. DoriC 10.0: an updated database of replication origins in prokaryotic genomes including chromosomes and plasmids. Nucleic Acids Res 2020; 47:D74-D77. [PMID: 30364951 PMCID: PMC6323995 DOI: 10.1093/nar/gky1014] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 10/11/2018] [Indexed: 12/11/2022] Open
Abstract
DoriC, a database of replication origins, was initially created to present the bacterial oriCs predicted by Ori-Finder or determined by experiments in 2007. DoriC 5.0, an updated database of oriC regions in both bacterial and archaeal genomes, was published in the 2013 Nucleic Acids Research database issue. Now, the latest release DoriC 10, a large-scale update of replication origins in prokaryotic genomes including chromosomes and plasmids, has been presented with a completely redesigned user interface, which is freely available at http://tubic.org/doric/ and http://tubic.tju.edu.cn/doric/. In the current release, the database of DoriC has made significant improvements compared with version 5.0 as follows: (i) inclusion of oriCs on more bacterial chromosomes increased from 1633 to 7580; (ii) inclusion of oriCs on more archaeal chromosomes increased from 86 to 226; (iii) inclusion of 1209 plasmid replication origins retrieved from NCBI annotations or predicted by in silico analysis; (iv) inclusion of more replication origin elements on bacterial chromosomes including DnaA-trio motifs. Now, DoriC becomes the most complete and scalable database of replication origins in prokaryotic genomes, and facilitates the studies in large-scale oriC data mining, strand-biased analyses and replication origin predictions.
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Affiliation(s)
- Hao Luo
- Department of Physics, School of Science, Tianjin University, Tianjin 300072, China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, China
| | - Feng Gao
- Department of Physics, School of Science, Tianjin University, Tianjin 300072, China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, China
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20
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Jones CA, Hadfield J, Thomson NR, Cleary DW, Marsh P, Clarke IN, O’Neill CE. The Nature and Extent of Plasmid Variation in Chlamydia trachomatis. Microorganisms 2020; 8:microorganisms8030373. [PMID: 32155798 PMCID: PMC7143637 DOI: 10.3390/microorganisms8030373] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 03/02/2020] [Accepted: 03/03/2020] [Indexed: 01/03/2023] Open
Abstract
Chlamydia trachomatis is an obligate intracellular pathogen of humans, causing both the sexually transmitted infection, chlamydia, and the most common cause of infectious blindness, trachoma. The majority of sequenced C. trachomatis clinical isolates carry a 7.5-Kb plasmid, and it is becoming increasingly evident that this is a key determinant of pathogenicity. The discovery of the Swedish New Variant and the more recent Finnish variant highlight the importance of understanding the natural extent of variation in the plasmid. In this study we analysed 524 plasmid sequences from publicly available whole-genome sequence data. Single nucleotide polymorphisms (SNP) in each of the eight coding sequences (CDS) were identified and analysed. There were 224 base positions out of a total 7550 bp that carried a SNP, which equates to a SNP rate of 2.97%, nearly three times what was previously calculated. After normalising for CDS size, CDS8 had the highest SNP rate at 3.97% (i.e., number of SNPs per total number of nucleotides), whilst CDS6 had the lowest at 1.94%. CDS5 had the highest total number of SNPs across the 524 sequences analysed (2267 SNPs), whereas CDS6 had the least SNPs with only 85 SNPs. Calculation of the genetic distances identified CDS6 as the least variable gene at the nucleotide level (d = 0.001), and CDS5 as the most variable (d = 0.007); however, at the amino acid level CDS2 was the least variable (d = 0.001), whilst CDS5 remained the most variable (d = 0.013). This study describes the largest in-depth analysis of the C. trachomatis plasmid to date, through the analysis of plasmid sequence data mined from whole genome sequences spanning 50 years and from a worldwide distribution, providing insights into the nature and extent of existing variation within the plasmid as well as guidance for the design of future diagnostic assays. This is crucial at a time when single-target diagnostic assays are failing to detect natural mutants, putting those infected at risk of a serious long-term and life-changing illness.
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Affiliation(s)
- Charlotte A. Jones
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton SO166YD, UK; (C.A.J.); (D.W.C.); (I.N.C.)
| | - James Hadfield
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA;
| | - Nicholas R. Thomson
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK;
| | - David W. Cleary
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton SO166YD, UK; (C.A.J.); (D.W.C.); (I.N.C.)
| | - Peter Marsh
- Public Health England, Porton Down, Wiltshire SP40JG, UK;
| | - Ian N. Clarke
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton SO166YD, UK; (C.A.J.); (D.W.C.); (I.N.C.)
| | - Colette E. O’Neill
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton SO166YD, UK; (C.A.J.); (D.W.C.); (I.N.C.)
- Correspondence:
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21
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Brovedan M, Repizo GD, Marchiaro P, Viale AM, Limansky A. Characterization of the diverse plasmid pool harbored by the blaNDM-1-containing Acinetobacter bereziniae HPC229 clinical strain. PLoS One 2019; 14:e0220584. [PMID: 31743332 PMCID: PMC6863613 DOI: 10.1371/journal.pone.0220584] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 10/24/2019] [Indexed: 11/18/2022] Open
Abstract
Acinetobacter bereziniae is an environmental microorganism with increasing clinical incidence, and may thus provide a model for a bacterial species bridging the gap between the environment and the clinical setting. A. bereziniae plasmids have been poorly studied, and their characterization could offer clues on the causes underlying the leap between these two different habitats. Here we characterized the whole plasmid content of A. bereziniae HPC229, a clinical strain previously reported to harbor a 44-kbp plasmid, pNDM229, conferring carbapenem and aminoglycoside resistance. We identified five extra plasmids in HPC229 ranging from 114 to 1.3 kbp, including pAbe229-114 (114 kbp) encoding a MOBP111 relaxase and carrying heavy metal resistance, a bacteriophage defense BREX system and four different toxin-antitoxin (TA) systems. Two other replicons, pAbe229-15 (15.4 kbp) and pAbe229-9 (9.1 kbp), both encoding MOBQ1 relaxases and also carrying TA systems, were found. The three latter plasmids contained Acinetobacter Rep_3 superfamily replication initiator protein genes, and functional analysis of their transfer regions revealed the mobilizable nature of them. HPC229 also harbors two smaller plasmids, pAbe229-4 (4.4 kbp) and pAbe229-1 (1.3 kbp), the former bearing a ColE1-type replicon and a TA system, and the latter lacking known replication functions. Comparative sequence analyses against deposited Acinetobacter genomes indicated that the above five HPC229 plasmids were unique, although some regions were also present in other of these genomes. The transfer, replication, and adaptive modules in pAbe229-15, and the stability module in pAbe229-9, were bordered by sites potentially recognized by XerC/XerD site-specific tyrosine recombinases, thus suggesting a potential mechanism for their acquisition. The presence of Rep_3 and ColE1-based replication modules, different mob genes, distinct adaptive functions including resistance to heavy metal and other environmental stressors, as well as antimicrobial resistance genes, and a high content of XerC/XerD sites among HPC229 plasmids provide evidence of substantial links with bacterial species derived from both environmental and clinical habitats.
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Affiliation(s)
- Marco Brovedan
- Instituto de Biología Molecular y Celular de Rosario (IBR), Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, CONICET, Universidad Nacional de Rosario (UNR), Rosario, Argentina
| | - Guillermo D. Repizo
- Instituto de Biología Molecular y Celular de Rosario (IBR), Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, CONICET, Universidad Nacional de Rosario (UNR), Rosario, Argentina
| | - Patricia Marchiaro
- Instituto de Biología Molecular y Celular de Rosario (IBR), Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, CONICET, Universidad Nacional de Rosario (UNR), Rosario, Argentina
| | - Alejandro M. Viale
- Instituto de Biología Molecular y Celular de Rosario (IBR), Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, CONICET, Universidad Nacional de Rosario (UNR), Rosario, Argentina
- * E-mail: (AMV); (AL)
| | - Adriana Limansky
- Instituto de Biología Molecular y Celular de Rosario (IBR), Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, CONICET, Universidad Nacional de Rosario (UNR), Rosario, Argentina
- * E-mail: (AMV); (AL)
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22
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Diversity and Horizontal Transfer of Antarctic Pseudomonas spp. Plasmids. Genes (Basel) 2019; 10:genes10110850. [PMID: 31661808 PMCID: PMC6896180 DOI: 10.3390/genes10110850] [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: 09/12/2019] [Revised: 10/22/2019] [Accepted: 10/26/2019] [Indexed: 12/23/2022] Open
Abstract
Pseudomonas spp. are widely distributed in various environments around the world. They are also common in the Antarctic regions. To date, almost 200 plasmids of Pseudomonas spp. have been sequenced, but only 12 of them were isolated from psychrotolerant strains. In this study, 15 novel plasmids of cold-active Pseudomonas spp. originating from the King George Island (Antarctica) were characterized using a combined, structural and functional approach, including thorough genomic analyses, functional analyses of selected genetic modules, and identification of active transposable elements localized within the plasmids and comparative genomics. The analyses performed in this study increased the understanding of the horizontal transfer of plasmids found within Pseudomonas populations inhabiting Antarctic soils. It was shown that the majority of the studied plasmids are narrow-host-range replicons, whose transfer across taxonomic boundaries may be limited. Moreover, structural and functional analyses enabled identification and characterization of various accessory genetic modules, including genes encoding major pilin protein (PilA), that enhance biofilm formation, as well as active transposable elements. Furthermore, comparative genomic analyses revealed that the studied plasmids of Antarctic Pseudomonas spp. are unique, as they are highly dissimilar to the other known plasmids of Pseudomonas spp.
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23
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Benefits and Drawbacks of Harboring Plasmid pP32BP2, Identified in Arctic Psychrophilic Bacterium Psychrobacter sp. DAB_AL32B. Int J Mol Sci 2019; 20:ijms20082015. [PMID: 31022896 PMCID: PMC6514802 DOI: 10.3390/ijms20082015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 04/11/2019] [Accepted: 04/22/2019] [Indexed: 12/18/2022] Open
Abstract
Psychrobacter sp. DAB_AL32B, originating from Spitsbergen island (Arctic), carries the large plasmid pP32BP2 (54,438 bp). Analysis of the pP32BP2 nucleotide sequence revealed the presence of three predicted phenotypic modules that comprise nearly 30% of the plasmid genome. These modules appear to be involved in fimbriae synthesis via the chaperone-usher pathway (FIM module) and the aerobic and anaerobic metabolism of carnitine (CAR and CAI modules, respectively). The FIM module was found to be functional in diverse hosts since it facilitated the attachment of bacterial cells to abiotic surfaces, enhancing biofilm formation. The CAI module did not show measurable activity in any of the tested strains. Interestingly, the CAR module enabled the enzymatic breakdown of carnitine, but this led to the formation of the toxic by-product trimethylamine, which inhibited bacterial growth. Thus, on the one hand, pP32BP2 can enhance biofilm formation, a highly advantageous feature in cold environments, while on the other, it may prevent bacterial growth under certain environmental conditions. The detrimental effect of harboring pP32BP2 (and its CAR module) seems to be conditional, since this replicon may also confer the ability to use carnitine as an alternative carbon source, although a pathway to utilize trimethylamine is most probably necessary to make this beneficial. Therefore, the phenotype determined by this CAR-containing plasmid depends on the metabolic background of the host strain.
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24
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Krupovic M, Makarova KS, Wolf YI, Medvedeva S, Prangishvili D, Forterre P, Koonin EV. Integrated mobile genetic elements in Thaumarchaeota. Environ Microbiol 2019; 21:2056-2078. [PMID: 30773816 PMCID: PMC6563490 DOI: 10.1111/1462-2920.14564] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 02/10/2019] [Accepted: 02/13/2019] [Indexed: 12/20/2022]
Abstract
To explore the diversity of mobile genetic elements (MGE) associated with archaea of the phylum Thaumarchaeota, we exploited the property of most MGE to integrate into the genomes of their hosts. Integrated MGE (iMGE) were identified in 20 thaumarchaeal genomes amounting to 2 Mbp of mobile thaumarchaeal DNA. These iMGE group into five major classes: (i) proviruses, (ii) casposons, (iii) insertion sequence-like transposons, (iv) integrative-conjugative elements and (v) cryptic integrated elements. The majority of the iMGE belong to the latter category and might represent novel families of viruses or plasmids. The identified proviruses are related to tailed viruses of the order Caudovirales and to tailless icosahedral viruses with the double jelly-roll capsid proteins. The thaumarchaeal iMGE are all connected within a gene sharing network, highlighting pervasive gene exchange between MGE occupying the same ecological niche. The thaumarchaeal mobilome carries multiple auxiliary metabolic genes, including multicopper oxidases and ammonia monooxygenase subunit C (AmoC), and stress response genes, such as those for universal stress response proteins (UspA). Thus, iMGE might make important contributions to the fitness and adaptation of their hosts. We identified several iMGE carrying type I-B CRISPR-Cas systems and spacers matching other thaumarchaeal iMGE, suggesting antagonistic interactions between coexisting MGE and symbiotic relationships with the ir archaeal hosts.
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Affiliation(s)
- Mart Krupovic
- Institut Pasteur, Unité Biologie Moléculaire du Gène chez les Extrêmophiles, 75015, Paris, France
| | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
| | - Sofia Medvedeva
- Institut Pasteur, Unité Biologie Moléculaire du Gène chez les Extrêmophiles, 75015, Paris, France.,Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, Russia.,Sorbonne Université, Collège doctoral, 75005, Paris, France
| | - David Prangishvili
- Institut Pasteur, Unité Biologie Moléculaire du Gène chez les Extrêmophiles, 75015, Paris, France
| | - Patrick Forterre
- Institut Pasteur, Unité Biologie Moléculaire du Gène chez les Extrêmophiles, 75015, Paris, France.,Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris- Sud, Université Paris-Saclay, Gif-sur-Yvette cedex, Paris, France
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
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25
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Reveillaud J, Bordenstein SR, Cruaud C, Shaiber A, Esen ÖC, Weill M, Makoundou P, Lolans K, Watson AR, Rakotoarivony I, Bordenstein SR, Eren AM. The Wolbachia mobilome in Culex pipiens includes a putative plasmid. Nat Commun 2019; 10:1051. [PMID: 30837458 PMCID: PMC6401122 DOI: 10.1038/s41467-019-08973-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 02/06/2019] [Indexed: 12/21/2022] Open
Abstract
Wolbachia is a genus of obligate intracellular bacteria found in nematodes and arthropods worldwide, including insect vectors that transmit dengue, West Nile, and Zika viruses. Wolbachia's unique ability to alter host reproductive behavior through its temperate bacteriophage WO has enabled the development of new vector control strategies. However, our understanding of Wolbachia's mobilome beyond its bacteriophages is incomplete. Here, we reconstruct near-complete Wolbachia genomes from individual ovary metagenomes of four wild Culex pipiens mosquitoes captured in France. In addition to viral genes missing from the Wolbachia reference genome, we identify a putative plasmid (pWCP), consisting of a 9.23-kbp circular element with 14 genes. We validate its presence in additional Culex pipiens mosquitoes using PCR, long-read sequencing, and screening of existing metagenomes. The discovery of this previously unrecognized extrachromosomal element opens additional possibilities for genetic manipulation of Wolbachia.
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Affiliation(s)
- Julie Reveillaud
- ASTRE, INRA, CIRAD, University of Montpellier, Montpellier, 34398, France.
| | - Sarah R Bordenstein
- Department of Biological Sciences, Vanderbilt University, Nashville, 37235, TN, USA
| | - Corinne Cruaud
- Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Institut de Biologie François Jacob, Genoscope, Evry, 91057, France
| | - Alon Shaiber
- Graduate Program in the Biophysical Sciences, University of Chicago, Chicago, IL, 60637, USA
- Department of Medicine, University of Chicago, Chicago, 60637, IL, USA
| | - Özcan C Esen
- Department of Medicine, University of Chicago, Chicago, 60637, IL, USA
| | - Mylène Weill
- Institut des Sciences de l'Evolution de Montpellier (ISEM), UMR CNRS-IRD-EPHE-Université de Montpellier, Montpellier, 34095, France
| | - Patrick Makoundou
- Institut des Sciences de l'Evolution de Montpellier (ISEM), UMR CNRS-IRD-EPHE-Université de Montpellier, Montpellier, 34095, France
| | - Karen Lolans
- Department of Medicine, University of Chicago, Chicago, 60637, IL, USA
| | - Andrea R Watson
- Department of Medicine, University of Chicago, Chicago, 60637, IL, USA
| | | | - Seth R Bordenstein
- Department of Biological Sciences, Vanderbilt University, Nashville, 37235, TN, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, 37235, TN, USA
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University, Nashville, 37235, TN, USA
| | - A Murat Eren
- Graduate Program in the Biophysical Sciences, University of Chicago, Chicago, IL, 60637, USA.
- Department of Medicine, University of Chicago, Chicago, 60637, IL, USA.
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, 02543, MA, USA.
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26
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Abstract
Strains of Staphylococcus aureus, and to a lesser extent other staphylococcal species, are a significant cause of morbidity and mortality. An important factor in the notoriety of these organisms stems from their frequent resistance to many antimicrobial agents used for chemotherapy. This review catalogues the variety of mobile genetic elements that have been identified in staphylococci, with a primary focus on those associated with the recruitment and spread of antimicrobial resistance genes. These include plasmids, transposable elements such as insertion sequences and transposons, and integrative elements including ICE and SCC elements. In concert, these diverse entities facilitate the intra- and inter-cellular gene mobility that enables horizontal genetic exchange, and have also been found to play additional roles in modulating gene expression and genome rearrangement.
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27
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Chase J, Catalano A, Noble AJ, Eng ET, Olinares PD, Molloy K, Pakotiprapha D, Samuels M, Chait B, des Georges A, Jeruzalmi D. Mechanisms of opening and closing of the bacterial replicative helicase. eLife 2018; 7:41140. [PMID: 30582519 PMCID: PMC6391071 DOI: 10.7554/elife.41140] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 12/21/2018] [Indexed: 12/31/2022] Open
Abstract
Assembly of bacterial ring-shaped hexameric replicative helicases on single-stranded (ss) DNA requires specialized loading factors. However, mechanisms implemented by these factors during opening and closing of the helicase, which enable and restrict access to an internal chamber, are not known. Here, we investigate these mechanisms in the Escherichia coli DnaB helicase•bacteriophage λ helicase loader (λP) complex. We show that five copies of λP bind at DnaB subunit interfaces and reconfigure the helicase into an open spiral conformation that is intermediate to previously observed closed ring and closed spiral forms; reconfiguration also produces openings large enough to admit ssDNA into the inner chamber. The helicase is also observed in a restrained inactive configuration that poises it to close on activating signal, and transition to the translocation state. Our findings provide insights into helicase opening, delivery to the origin and ssDNA entry, and closing in preparation for translocation.
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Affiliation(s)
- Jillian Chase
- Department of Chemistry and Biochemistry, City College of New York, New York, United States.,PhD Program in Biochemistry, The Graduate Center of the City University of New York, New York, United States
| | - Andrew Catalano
- Department of Chemistry and Biochemistry, City College of New York, New York, United States
| | - Alex J Noble
- Simons Electron Microscopy Center, The New York Structural Biology Center, New York, United States
| | - Edward T Eng
- Simons Electron Microscopy Center, The New York Structural Biology Center, New York, United States
| | - Paul Db Olinares
- Laboratory for Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, United States
| | - Kelly Molloy
- Laboratory for Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, United States
| | - Danaya Pakotiprapha
- Department of Biochemistry, Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Martin Samuels
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Brian Chait
- Laboratory for Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, United States
| | - Amedee des Georges
- Department of Chemistry and Biochemistry, City College of New York, New York, United States.,PhD Program in Biochemistry, The Graduate Center of the City University of New York, New York, United States.,Structural Biology Initiative, CUNY Advanced Science Research Center, New York, United States.,PhD Program in Chemistry, The Graduate Center of the City University of New York, New York, United States
| | - David Jeruzalmi
- Department of Chemistry and Biochemistry, City College of New York, New York, United States.,PhD Program in Biochemistry, The Graduate Center of the City University of New York, New York, United States.,PhD Program in Chemistry, The Graduate Center of the City University of New York, New York, United States.,PhD Program in Biology, The Graduate Center of the City University of New York, New York, United States
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28
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de Lemos Martins F, Fournes F, Mazzuoli MV, Mazel D, Val ME. Vibrio cholerae chromosome 2 copy number is controlled by the methylation-independent binding of its monomeric initiator to the chromosome 1 crtS site. Nucleic Acids Res 2018; 46:10145-10156. [PMID: 30184118 PMCID: PMC6212839 DOI: 10.1093/nar/gky790] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 08/20/2018] [Accepted: 08/22/2018] [Indexed: 12/13/2022] Open
Abstract
Bacteria contain a primary chromosome and, frequently, either essential secondary chromosomes or dispensable megaplasmids of plasmid origin. Incoming plasmids are often poorly adapted to their hosts and their stabilization requires integration with the host's cellular mechanisms in a process termed domestication. All Vibrio, including pathogenic species, carry a domesticated secondary chromosome (Chr2) where replication is coordinated with that of the primary chromosome (Chr1). Chr2 replication is triggered by the replication of an intergenic sequence (crtS) located on Chr1. Yet, the molecular mechanisms by which crtS replication controls the initiation of Chr2 replication are still largely unknown. In this study, we show that crtS not only regulates the timing of Chr2 initiation but also controls Chr2 copy number. We observed and characterized the direct binding of the Chr2 initiator (RctB) on crtS. RctB binding to crtS is independent of its methylation state. RctB molecules, which naturally form dimers, preferentially bind to crtS as monomers, with DnaK/J protein chaperones shown to stimulate binding of additional RctB monomers on crtS. In this study, we addressed various hypothesis of how replication of crtS could trigger Chr2 replication and provide new insights into its mode of action.
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Affiliation(s)
- Francisco de Lemos Martins
- Bacterial Genome Plasticity, Genomes & Genetics Department, Institut Pasteur, Paris 75015, France
- UMR3525, Centre National de la Recherche Scientifique, Paris 75015, France
| | - Florian Fournes
- Bacterial Genome Plasticity, Genomes & Genetics Department, Institut Pasteur, Paris 75015, France
- UMR3525, Centre National de la Recherche Scientifique, Paris 75015, France
| | - Maria-Vittoria Mazzuoli
- Bacterial Genome Plasticity, Genomes & Genetics Department, Institut Pasteur, Paris 75015, France
- UMR3525, Centre National de la Recherche Scientifique, Paris 75015, France
| | - Didier Mazel
- Bacterial Genome Plasticity, Genomes & Genetics Department, Institut Pasteur, Paris 75015, France
- UMR3525, Centre National de la Recherche Scientifique, Paris 75015, France
| | - Marie-Eve Val
- Bacterial Genome Plasticity, Genomes & Genetics Department, Institut Pasteur, Paris 75015, France
- UMR3525, Centre National de la Recherche Scientifique, Paris 75015, France
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29
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Partridge SR, Kwong SM, Firth N, Jensen SO. Mobile Genetic Elements Associated with Antimicrobial Resistance. Clin Microbiol Rev 2018; 31:e00088-17. [PMID: 30068738 PMCID: PMC6148190 DOI: 10.1128/cmr.00088-17] [Citation(s) in RCA: 1141] [Impact Index Per Article: 190.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Strains of bacteria resistant to antibiotics, particularly those that are multiresistant, are an increasing major health care problem around the world. It is now abundantly clear that both Gram-negative and Gram-positive bacteria are able to meet the evolutionary challenge of combating antimicrobial chemotherapy, often by acquiring preexisting resistance determinants from the bacterial gene pool. This is achieved through the concerted activities of mobile genetic elements able to move within or between DNA molecules, which include insertion sequences, transposons, and gene cassettes/integrons, and those that are able to transfer between bacterial cells, such as plasmids and integrative conjugative elements. Together these elements play a central role in facilitating horizontal genetic exchange and therefore promote the acquisition and spread of resistance genes. This review aims to outline the characteristics of the major types of mobile genetic elements involved in acquisition and spread of antibiotic resistance in both Gram-negative and Gram-positive bacteria, focusing on the so-called ESKAPEE group of organisms (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp., and Escherichia coli), which have become the most problematic hospital pathogens.
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Affiliation(s)
- Sally R Partridge
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, The University of Sydney and Westmead Hospital, Westmead, New South Wales, Australia
| | - Stephen M Kwong
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Neville Firth
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Slade O Jensen
- Microbiology and Infectious Diseases, School of Medicine, Western Sydney University, Sydney, New South Wales, Australia
- Antibiotic Resistance & Mobile Elements Group, Ingham Institute for Applied Medical Research, Sydney, New South Wales, Australia
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30
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A novel plasmid, pSAA0430-08, from Streptococcus anginosus subsp. anginosus strain 0430-08. Plasmid 2018; 95:16-27. [DOI: 10.1016/j.plasmid.2018.01.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 01/02/2018] [Accepted: 01/11/2018] [Indexed: 11/21/2022]
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31
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Kwong SM, Ramsay JP, Jensen SO, Firth N. Replication of Staphylococcal Resistance Plasmids. Front Microbiol 2017; 8:2279. [PMID: 29218034 PMCID: PMC5703833 DOI: 10.3389/fmicb.2017.02279] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Accepted: 11/06/2017] [Indexed: 11/16/2022] Open
Abstract
The currently widespread and increasing prevalence of resistant bacterial pathogens is a significant medical problem. In clinical strains of staphylococci, the genetic determinants that confer resistance to antimicrobial agents are often located on mobile elements, such as plasmids. Many of these resistance plasmids are capable of horizontal transmission to other bacteria in their surroundings, allowing extraordinarily rapid adaptation of bacterial populations. Once the resistance plasmids have been spread, they are often perpetually maintained in the new host, even in the absence of selective pressure. Plasmid persistence is accomplished by plasmid-encoded genetic systems that ensure efficient replication and segregational stability during cell division. Staphylococcal plasmids utilize proteins of evolutionarily diverse families to initiate replication from the plasmid origin of replication. Several distinctive plasmid copy number control mechanisms have been studied in detail and these appear conserved within plasmid classes. The initiators utilize various strategies and serve a multifunctional role in (i) recognition and processing of the cognate replication origin to an initiation active form and (ii) recruitment of host-encoded replication proteins that facilitate replisome assembly. Understanding the detailed molecular mechanisms that underpin plasmid replication may lead to novel approaches that could be used to reverse or slow the development of resistance.
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Affiliation(s)
- Stephen M Kwong
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Joshua P Ramsay
- School of Biomedical Sciences, Curtin University, Perth, WA, Australia
| | - Slade O Jensen
- Antimicrobial Resistance and Mobile Elements Group, Ingham Institute for Applied Medical Research, Sydney, NSW, Australia
| | - Neville Firth
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
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32
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Lean SS, Yeo CC. Small, Enigmatic Plasmids of the Nosocomial Pathogen, Acinetobacter baumannii: Good, Bad, Who Knows? Front Microbiol 2017; 8:1547. [PMID: 28861061 PMCID: PMC5559437 DOI: 10.3389/fmicb.2017.01547] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 07/31/2017] [Indexed: 12/16/2022] Open
Abstract
Acinetobacter baumannii is a Gram-negative nosocomial pathogen that has become a serious healthcare concern within a span of two decades due to its ability to rapidly acquire resistance to all classes of antimicrobial compounds. One of the key features of the A. baumannii genome is an open pan genome with a plethora of plasmids, transposons, integrons, and genomic islands, all of which play important roles in the evolution and success of this clinical pathogen, particularly in the acquisition of multidrug resistance determinants. An interesting genetic feature seen in majority of A. baumannii genomes analyzed is the presence of small plasmids that usually ranged from 2 to 10 kb in size, some of which harbor antibiotic resistance genes and homologs of plasmid mobilization genes. These plasmids are often overlooked when compared to their larger, conjugative counterparts that harbor multiple antibiotic resistance genes and transposable elements. In this mini-review, we will examine our current knowledge of these small A. baumannii plasmids and look into their genetic diversity and phylogenetic relationships. Some of these plasmids, such as the Rep-3 superfamily group and the pRAY-type, which has no recognizable replicase genes, are quite widespread among diverse A. baumannii clinical isolates worldwide, hinting at their usefulness to the lifestyle of this pathogen. Other small plasmids especially those from the Rep-1 superfamily are truly enigmatic, encoding only hypothetical proteins of unknown function, leading to the question of whether these small plasmids are “good” or “bad” to their host A. baumannii.
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Affiliation(s)
- Soo Sum Lean
- Saw Swee Hock School of Public Health, National University of SingaporeSingapore, Singapore
| | - Chew Chieng Yeo
- Faculty of Medicine, Biomedical Research Centre, Universiti Sultan Zainal AbidinKuala Terengganu, Malaysia
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33
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Molecular characterization of the pA3J1 plasmid from the psychrotolerant Antarctic bacterium Pseudomonas sp. ANT_J3. Plasmid 2017; 92:49-56. [DOI: 10.1016/j.plasmid.2017.08.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2017] [Revised: 08/05/2017] [Accepted: 08/07/2017] [Indexed: 01/08/2023]
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34
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Parker MS, Sallee FR, Park EA, Parker SL. Homoiterons and expansion in ribosomal RNAs. FEBS Open Bio 2015; 5:864-76. [PMID: 26636029 PMCID: PMC4637361 DOI: 10.1016/j.fob.2015.10.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 09/30/2015] [Accepted: 10/14/2015] [Indexed: 11/27/2022] Open
Abstract
Homoiterons like GGGGGGG stabilize ribosomal RNAs of thermophile prokaryotes. In eukaryotes, homoiterons are much more abundant in RNA of the larger subunit (LSU). The LSU repeats increase with phylogenetic rank to 28% entire RNA sequence in hominids. In mammal LSU RNAs, these repeats constitute 45% of the massive expansion segments. These repeats may help in anchoring of ribosomes and export of secretory proteins.
Ribosomal RNAs in both prokaryotes and eukaryotes feature numerous repeats of three or more nucleotides with the same nucleobase (homoiterons). In prokaryotes these repeats are much more frequent in thermophile compared to mesophile or psychrophile species, and have similar frequency in both large RNAs. These features point to use of prokaryotic homoiterons in stabilization of both ribosomal subunits. The two large RNAs of eukaryotic cytoplasmic ribosomes have expanded to a different degree across the evolutionary ladder. The big RNA of the larger subunit (60S LSU) evolved expansion segments of up to 2400 nucleotides, and the smaller subunit (40S SSU) RNA acquired expansion segments of not more than 700 nucleotides. In the examined eukaryotes abundance of rRNA homoiterons generally follows size and nucleotide bias of the expansion segments, and increases with GC content and especially with phylogenetic rank. Both the nucleotide bias and frequency of homoiterons are much larger in metazoan and angiosperm LSU compared to the respective SSU RNAs. This is especially pronounced in the tetrapod vertebrates and seems to culminate in the hominid mammals. The stability of secondary structure in polyribonucleotides would significantly connect to GC content, and should also relate to G and C homoiteron content. RNA modeling points to considerable presence of homoiteron-rich double-stranded segments especially in vertebrate LSU RNAs, and homoiterons with four or more nucleotides in the vertebrate and angiosperm LSU RNAs are largely confined to the expansion segments. These features could mainly relate to protein export function and attachment of LSU to endoplasmic reticulum and other subcellular networks.
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Key Words
- ES, an expansion segment
- LSU, large cytoplasmic ribosome subunit (50S in prokaryotes and archaea, 60S in eukaryotes)
- PCN, homoionic motifs with ⩾3% and ⩾50% ionic residues, found especially in Polynucleotide-binding proteins, Carrier proteins and Nuclear localization signals
- RNA expansion segment
- RNA nucleotide bias
- RNA nucleotide repeat
- SSU, small cytoplasmic ribosome subunit (30S in prokaryotes and archaea, 40S in eukaryotes)
- XN or NX, [X = a number] a nucleotide unit with same nucleobases (homoiteron), such as 4U or U4 for UUUU
- aa, amino acid residues
- mRNP, messenger ribonucleoprotein
- ncRNA, non-coding RNA
- nt, nucleotides
- u, nucleotide unit
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Affiliation(s)
- Michael S Parker
- Department of Microbiology and Molecular Cell Sciences, University of Memphis, Memphis, TN 38152, USA
| | - Floyd R Sallee
- Department of Psychiatry, University of Cincinnati School of Medicine, Cincinnati, OH 45276, USA
| | - Edwards A Park
- Department of Pharmacology, University of Tennessee Health Sciences Center, Memphis, TN 38163, USA
| | - Steven L Parker
- Department of Pharmacology, University of Tennessee Health Sciences Center, Memphis, TN 38163, USA
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