1
|
Durrant MG, Perry NT, Pai JJ, Jangid AR, Athukoralage JS, Hiraizumi M, McSpedon JP, Pawluk A, Nishimasu H, Konermann S, Hsu PD. Bridge RNAs direct programmable recombination of target and donor DNA. Nature 2024; 630:984-993. [PMID: 38926615 PMCID: PMC11208160 DOI: 10.1038/s41586-024-07552-4] [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: 09/07/2023] [Accepted: 05/09/2024] [Indexed: 06/28/2024]
Abstract
Genomic rearrangements, encompassing mutational changes in the genome such as insertions, deletions or inversions, are essential for genetic diversity. These rearrangements are typically orchestrated by enzymes that are involved in fundamental DNA repair processes, such as homologous recombination, or in the transposition of foreign genetic material by viruses and mobile genetic elements1,2. Here we report that IS110 insertion sequences, a family of minimal and autonomous mobile genetic elements, express a structured non-coding RNA that binds specifically to their encoded recombinase. This bridge RNA contains two internal loops encoding nucleotide stretches that base-pair with the target DNA and the donor DNA, which is the IS110 element itself. We demonstrate that the target-binding and donor-binding loops can be independently reprogrammed to direct sequence-specific recombination between two DNA molecules. This modularity enables the insertion of DNA into genomic target sites, as well as programmable DNA excision and inversion. The IS110 bridge recombination system expands the diversity of nucleic-acid-guided systems beyond CRISPR and RNA interference, offering a unified mechanism for the three fundamental DNA rearrangements-insertion, excision and inversion-that are required for genome design.
Collapse
Affiliation(s)
- Matthew G Durrant
- Arc Institute, Palo Alto, CA, USA
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Nicholas T Perry
- Arc Institute, Palo Alto, CA, USA
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- University of California, Berkeley-University of California, San Francisco Graduate Program in Bioengineering, Berkeley, CA, USA
| | | | - Aditya R Jangid
- Arc Institute, Palo Alto, CA, USA
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | | | - Masahiro Hiraizumi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo, Japan
| | | | | | - Hiroshi Nishimasu
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo, Japan
- Structural Biology Division, Research Center for Advanced Science and Technology, University of Tokyo, Tokyo, Japan
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan
- Inamori Research Institute for Science, Kyoto, Japan
- Japan Science and Technology Agency, Core Research for Evolutional Science and Technology, Saitama, Japan
| | - Silvana Konermann
- Arc Institute, Palo Alto, CA, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Patrick D Hsu
- Arc Institute, Palo Alto, CA, USA.
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA.
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA.
| |
Collapse
|
2
|
Comba-González NB, Chaves-Moreno D, Santamaría-Vanegas J, Montoya-Castaño D. A pan-genomic assessment: Delving into the genome of the marine epiphyte Bacillus altitudinis strain 19_A and other very close Bacillus strains from multiple environments. Heliyon 2024; 10:e27820. [PMID: 38560215 PMCID: PMC10981035 DOI: 10.1016/j.heliyon.2024.e27820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 02/14/2024] [Accepted: 03/07/2024] [Indexed: 04/04/2024] Open
Abstract
Marine macroalgae are the habitat of epiphytic bacteria and provide several conditions for a beneficial biological interaction to thrive. Although Bacillus is one of the most abundant epiphytic genera, genomic information on marine macroalgae-associated Bacillus species remains scarce. In this study, we further investigated our previously published genome of the epiphytic strain Bacillus altitudinis 19_A to find features that could be translated to potential metabolites produced by this microorganism, as well as genes that play a role in its interaction with its macroalgal host. To achieve this goal, we performed a pan-genome analysis of Bacillus sp. and a codon bias assessment, including the genome of the strain Bacillus altitudinis 19_A and 29 complete genome sequences of closely related Bacillus strains isolated from soil, marine environments, plants, extreme environments, air, and food. This genomic analysis revealed that Bacillus altitudinis 19_A possessed unique genes encoding proteins involved in horizontal gene transfer, DNA repair, transcriptional regulation, and bacteriocin biosynthesis. In this comparative analysis, codon bias was not associated with the habitat of the strains studied. Some accessory genes were identified in the Bacillus altitudinis 19_A genome that could be related to its epiphytic lifestyle, as well as gene clusters for the biosynthesis of a sporulation-killing factor and a bacteriocin, showing their potential as a source of antimicrobial peptides. Our results provide a comprehensive view of the Bacillus altitudinis 19_A genome to understand its adaptation to the marine environment and its potential as a producer of bioactive compounds.
Collapse
Affiliation(s)
| | - Diego Chaves-Moreno
- Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | | | - Dolly Montoya-Castaño
- Bioprocesses and Bioprospecting Group, Biotechnology Institute, Universidad Nacional de Colombia, Colombia
| |
Collapse
|
3
|
Li Z, Liu X, Ning N, Li T, Wang H. Diversity, Distribution, and Chromosomal Rearrangements of TRIP1 Repeat Sequences in Escherichia coli. Genes (Basel) 2024; 15:236. [PMID: 38397225 PMCID: PMC10888264 DOI: 10.3390/genes15020236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/07/2024] [Accepted: 02/10/2024] [Indexed: 02/25/2024] Open
Abstract
The bacterial genome contains numerous repeated sequences that greatly affect its genomic plasticity. The Escherichia coli K-12 genome contains three copies of the TRIP1 repeat sequence (TRIP1a, TRIP1b, and TRIP1c). However, the diversity, distribution, and role of the TRIP1 repeat sequence in the E. coli genome are still unclear. In this study, after screening 6725 E. coli genomes, the TRIP1 repeat was found in the majority of E. coli strains (96%: 6454/6725). The copy number and direction of the TRIP1 repeat sequence varied in each genome. Overall, 2449 genomes (36%: 2449/6725) had three copies of TRIP1 (TRIP1a, TRIP1b, and TRIP1c), which is the same as E. coli K-12. Five types of TRIP1 repeats, including two new types (TRIP1d and TRIP1e), are identified in E. coli genomes, located in 4703, 3529, 5741, 1565, and 232 genomes, respectively. Each type of TRIP1 repeat is localized to a specific locus on the chromosome. TRIP1 repeats can cause intra-chromosomal rearrangements. A total of 156 rearrangement events were identified, of which 88% (137/156) were between TRIP1a and TRIP1c. These findings have important implications for future research on TRIP1 repeats.
Collapse
Affiliation(s)
- Zhan Li
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No. 20 Dongda Street, Fengtai District, Beijing 100071, China; (Z.L.); (N.N.); (T.L.)
| | - Xiong Liu
- Chinese PLA Center for Disease Control and Prevention, Dongda Street 20#, Fengtai District, Beijing 100071, China;
| | - Nianzhi Ning
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No. 20 Dongda Street, Fengtai District, Beijing 100071, China; (Z.L.); (N.N.); (T.L.)
| | - Tao Li
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No. 20 Dongda Street, Fengtai District, Beijing 100071, China; (Z.L.); (N.N.); (T.L.)
| | - Hui Wang
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No. 20 Dongda Street, Fengtai District, Beijing 100071, China; (Z.L.); (N.N.); (T.L.)
| |
Collapse
|
4
|
Durrant MG, Perry NT, Pai JJ, Jangid AR, Athukoralage JS, Hiraizumi M, McSpedon JP, Pawluk A, Nishimasu H, Konermann S, Hsu PD. Bridge RNAs direct modular and programmable recombination of target and donor DNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.24.577089. [PMID: 38328150 PMCID: PMC10849738 DOI: 10.1101/2024.01.24.577089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Genomic rearrangements, encompassing mutational changes in the genome such as insertions, deletions, or inversions, are essential for genetic diversity. These rearrangements are typically orchestrated by enzymes involved in fundamental DNA repair processes such as homologous recombination or in the transposition of foreign genetic material by viruses and mobile genetic elements (MGEs). We report that IS110 insertion sequences, a family of minimal and autonomous MGEs, express a structured non-coding RNA that binds specifically to their encoded recombinase. This bridge RNA contains two internal loops encoding nucleotide stretches that base-pair with the target DNA and donor DNA, which is the IS110 element itself. We demonstrate that the target-binding and donor-binding loops can be independently reprogrammed to direct sequence-specific recombination between two DNA molecules. This modularity enables DNA insertion into genomic target sites as well as programmable DNA excision and inversion. The IS110 bridge system expands the diversity of nucleic acid-guided systems beyond CRISPR and RNA interference, offering a unified mechanism for the three fundamental DNA rearrangements required for genome design.
Collapse
Affiliation(s)
- Matthew G. Durrant
- Arc Institute, 3181 Porter Drive, Palo Alto, CA 94304, USA
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Nicholas T. Perry
- Arc Institute, 3181 Porter Drive, Palo Alto, CA 94304, USA
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- University of California, Berkeley - University of California, San Francisco Graduate Program in Bioengineering, Berkeley, CA, USA
| | - James J. Pai
- Arc Institute, 3181 Porter Drive, Palo Alto, CA 94304, USA
| | - Aditya R. Jangid
- Arc Institute, 3181 Porter Drive, Palo Alto, CA 94304, USA
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | | | - Masahiro Hiraizumi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | | | - April Pawluk
- Arc Institute, 3181 Porter Drive, Palo Alto, CA 94304, USA
| | - Hiroshi Nishimasu
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- Structural Biology Division, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Inamori Research Institute for Science, 620 Suiginya-cho, Shimogyo-ku, Kyoto 600-8411, Japan
- Japan Science and Technology Agency, Core Research for Evolutional Science and Technology, 4-1-8, Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
| | - Silvana Konermann
- Arc Institute, 3181 Porter Drive, Palo Alto, CA 94304, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Patrick D. Hsu
- Arc Institute, 3181 Porter Drive, Palo Alto, CA 94304, USA
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
| |
Collapse
|
5
|
Abante J, Wang PL, Salzman J. DIVE: a reference-free statistical approach to diversity-generating and mobile genetic element discovery. Genome Biol 2023; 24:240. [PMID: 37864197 PMCID: PMC10589994 DOI: 10.1186/s13059-023-03038-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Accepted: 08/14/2023] [Indexed: 10/22/2023] Open
Abstract
Diversity-generating and mobile genetic elements are key to microbial and viral evolution and can result in evolutionary leaps. State-of-the-art algorithms to detect these elements have limitations. Here, we introduce DIVE, a new reference-free approach to overcome these limitations using information contained in sequencing reads alone. We show that DIVE has improved detection power compared to existing reference-based methods using simulations and real data. We use DIVE to rediscover and characterize the activity of known and novel elements and generate new biological hypotheses about the mobilome. Building on DIVE, we develop a reference-free framework capable of de novo discovery of mobile genetic elements.
Collapse
Affiliation(s)
- Jordi Abante
- Biomedical Data Science, Stanford University, 1265 Welch Rd, Palo Alto, 94305, CA, USA
- Center for Computational, Evolutionary and Human Genomics, Stanford University, 327 Campus Drive, Stanford, 94305, CA, USA
- Current address: Department of Biomedical Sciences, Universitat de Barcelona, Casanova 143, Barcelona, 08036, Spain
| | - Peter L Wang
- Biomedical Data Science, Stanford University, 1265 Welch Rd, Palo Alto, 94305, CA, USA
- Department of Biochemistry, Stanford University, 279 Campus Drive, Stanford, 94305, CA, USA
| | - Julia Salzman
- Biomedical Data Science, Stanford University, 1265 Welch Rd, Palo Alto, 94305, CA, USA.
- Department of Biochemistry, Stanford University, 279 Campus Drive, Stanford, 94305, CA, USA.
- Department of Statistics, Stanford University, 390 Serra Mall, Stanford, 94305, CA, USA.
| |
Collapse
|
6
|
Bobbadi S, Bobby MN, Chinnam BK, Reddy PN, Kandhan S. Phenotypic and genetic screening of Klebsiella pneumoniae isolates from human UTI patients for beta-lactamases and their genetic diversity analysis by ERIC and REP PCRs. Braz J Microbiol 2023; 54:1723-1736. [PMID: 37198419 PMCID: PMC10484876 DOI: 10.1007/s42770-023-00984-6] [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: 11/01/2022] [Accepted: 04/18/2023] [Indexed: 05/19/2023] Open
Abstract
Klebsiella pneumoniae is one of the major nosocomial pathogens responsible for pneumoniae, septicaemia, liver abscesses, and urinary tract infections. Coordinated efforts by antibiotic stewardship and clinicians are underway to curtail the emergence of antibiotic-resistant strains. The objective of the present study is to characterize K. pneumoniae strains through antibiotic resistance screening for production of beta-lactamases (β-lactamases) such as extended spectrum beta lactamases (ESBLs), AmpC β-lactamases, and carbapenemases by phenotypic and genotypic methods and genetic fingerprinting by enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR) and repetitive element palindromic PCR (REP-PCR). A total of 85 K. pneumoniae strains isolated from 504 human urinary tract infections (UTI) were used in this study. Only 76 isolates showed positive in phenotypic screening test (PST), while combination disc method (CDM) as phenotypic confirmatory test (PCT) confirmed 72 isolates as ESBL producers. One or more β-lactamase genes were detected by PCR in 66 isolates (91.66%, 66/72) with blaTEM gene being the most predominant (75.75%, 50/66). AmpC genes could be detected in 21 isolates (31.8%, 21/66) with FOX gene being the predominant (24.24%, 16/66), whereas NDM-I was detected in a single strain (1.51%, 1/66). Genetic fingerprinting using ERIC-PCR and REP-PCR revealed wide heterogeneity among β-lactamase producing isolates with discriminatory power of 0.9995 and 1, respectively.
Collapse
Affiliation(s)
- Suresh Bobbadi
- Department of Biotechnology, Vignan’s Foundation for Science, Technology and Research (Deemed to be University), Vadlamudi, Guntur district, Andhra Pradesh 522 213 India
| | - Md Nazneen Bobby
- Department of Biotechnology, Vignan’s Foundation for Science, Technology and Research (Deemed to be University), Vadlamudi, Guntur district, Andhra Pradesh 522 213 India
| | - Bindu Kiranmayi Chinnam
- Department of Veterinary Public Health and Epidemiology, NTR College of Veterinary Science, Gannavaram, Andhra Pradesh 521101 India
| | - Prakash Narayana Reddy
- Department of Microbiology, Dr. V.S. Krishna Government Degree and PG College (Autonomous), Maddilapalem, Visakhapatnam, Andhra Pradesh 530 013 India
| | - Srinivas Kandhan
- Division of Veterinary Public Health, ICAR – Indian Veterinary Research Institute, Izatnagar, Uttar Pradesh 243 122 India
| |
Collapse
|
7
|
Greenrod STE, Stoycheva M, Elphinstone J, Friman VP. Influence of insertion sequences on population structure of phytopathogenic bacteria in the Ralstonia solanacearum species complex. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001364. [PMID: 37458734 PMCID: PMC10433421 DOI: 10.1099/mic.0.001364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 07/08/2023] [Indexed: 07/20/2023]
Abstract
Ralstonia solanacearum species complex (RSSC) is a destructive group of plant pathogenic bacteria and the causative agent of bacterial wilt disease. Experimental studies have attributed RSSC virulence to insertion sequences (IS), transposable genetic elements which can both disrupt and activate host genes. Yet, the global diversity and distribution of RSSC IS are unknown. In this study, IS were bioinformatically identified in a diverse collection of 356 RSSC isolates representing five phylogenetic lineages and their diversity investigated based on genetic distance measures and comparisons with the ISFinder database. IS phylogenetic associations were determined based on their distribution across the RSSC phylogeny. Moreover, IS positions within genomes were characterised and their potential gene disruptions determined based on IS proximity to coding sequences. In total, we found 24732 IS belonging to eleven IS families and 26 IS subgroups with over half of the IS found in the megaplasmid. While IS families were generally widespread across the RSSC phylogeny, IS subgroups showed strong lineage-specific distributions and genetically similar bacterial isolates had similar IS contents. Similar associations with bacterial host genetic background were also observed with IS insertion positions which were highly conserved in closely related bacterial isolates. Finally, IS were found to disrupt genes with predicted functions in virulence, stress tolerance, and metabolism suggesting that they might be adaptive. This study highlights that RSSC insertion sequences track the evolution of their bacterial hosts potentially contributing to both intra- and inter-lineage genetic diversity.
Collapse
Affiliation(s)
- Samuel T. E. Greenrod
- Department of Biology, University of York, York, UK
- Present address: Department of Biology, University of Oxford, Oxford, UK
| | | | - John Elphinstone
- Fera Science Ltd, National Agri-Food Innovation Campus, Sand Hutton, York, UK
| | - Ville-Petri Friman
- Department of Biology, University of York, York, UK
- Present address: Department of Microbiology, University of Helsinki, 00014, Helsinki, Finland
| |
Collapse
|
8
|
Lee S, Cheon W, Kwon HT, Lee Y, Kim J, Balaraju K, Jeon Y. Identification and Characterization of Pseudomonas syringae pv. syringae, a Causative Bacterium of Apple Canker in Korea. THE PLANT PATHOLOGY JOURNAL 2023; 39:88-107. [PMID: 36760052 PMCID: PMC9929173 DOI: 10.5423/ppj.oa.08.2022.0121] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 12/16/2022] [Accepted: 12/19/2022] [Indexed: 06/18/2023]
Abstract
In the present investigation, bacterial isolates from infected apple trees causing apple canker during winter were studied in the northern Gyeongbuk Province, Korea. The pathogen was identified as Pseudomonas syringae pv. syringae (Pss) through various physiological and biochemical characterization assays such as BIOLOG, gas chromatography of fatty acid methyl esters, and 16S rRNA. Bioassays for the production of phytotoxins were positive for syringopeptin and syringomycin against Bacillus megaterium and Geotrichum candidum, respectively. The polymerase chain reaction (PCR) method enabled the detection of toxin-producing genes, syrB1, and sypB in Pss. The differentiation of strains was performed using LOPAT and GATTa tests. Pss further exhibited ice nucleation activity (INA) at a temperature of -0.7°C, indicating an INA+ bacterium. The ice-nucleating temperature was -4.7°C for a non-treated control (sterilized distilled water), whereas it was -9.6°C for an INA- bacterium Escherichia coli TOP10. These methods detected pathogenic strains from apple orchards. Pss might exist in an apple tree during ice injury, and it secretes a toxin that makes leaves yellow and cause canker symptoms. Until now, Korea has not developed antibiotics targeting Pss. Therefore, it is necessary to develop effective disease control to combat Pss in apple orchards. Pathogenicity test on apple leaves and stems showed canker symptoms. The pathogenic bacterium was re-isolated from symptomatic plant tissue and confirmed as original isolates by 16S rRNA. Repetitive element sequence-based PCR and enterobacterial repetitive intergenic consensus PCR primers revealed different genetic profiles within P. syringae pathovars. High antibiotic susceptibility results showed the misreading of mRNA caused by streptomycin and oxytetracycline.
Collapse
Affiliation(s)
- Seunghee Lee
- Department of Plant Medicals, Andong National University, Andong 36729,
Korea
| | - Wonsu Cheon
- Department of Plant Medicals, Andong National University, Andong 36729,
Korea
| | - Hyeok Tae Kwon
- Department of Plant Medicals, Andong National University, Andong 36729,
Korea
| | - Younmi Lee
- Department of Plant Medicals, Andong National University, Andong 36729,
Korea
| | - Jungyeon Kim
- Department of Plant Medicals, Andong National University, Andong 36729,
Korea
| | - Kotnala Balaraju
- Agricultural Science & Technology Research Institute, Andong National University, Andong 36729,
Korea
| | - Yongho Jeon
- Department of Plant Medicals, Andong National University, Andong 36729,
Korea
| |
Collapse
|
9
|
Bertels F, Rainey PB. Ancient Darwinian replicators nested within eubacterial genomes. Bioessays 2023; 45:e2200085. [PMID: 36456469 DOI: 10.1002/bies.202200085] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 11/17/2022] [Accepted: 11/17/2022] [Indexed: 12/03/2022]
Abstract
Integrative mobile genetic elements (MGEs), such as transposons and insertion sequences, propagate within bacterial genomes, but persistence times in individual lineages are short. For long-term survival, MGEs must continuously invade new hosts by horizontal transfer. Theoretically, MGEs that persist for millions of years in single lineages, and are thus subject to vertical inheritance, should not exist. Here we draw attention to an exception - a class of MGE termed REPIN. REPINs are non-autonomous MGEs whose duplication depends on non-jumping RAYT transposases. Comparisons of REPINs and typical MGEs show that replication rates of REPINs are orders of magnitude lower, REPIN population size fluctuations correlate with changes in available genome space, REPIN conservation depends on RAYT function, and REPIN diversity accumulates within host lineages. These data lead to the hypothesis that REPINs form enduring, beneficial associations with eubacterial chromosomes. Given replicative nesting, our hypothesis predicts conflicts arising from the diverging effects of selection acting simultaneously on REPINs and host genomes. Evidence in support comes from patterns of REPIN abundance and diversity in two distantly related bacterial species. Together this bolsters the conclusion that REPINs are the genetic counterpart of mutualistic endosymbiotic bacteria.
Collapse
Affiliation(s)
- Frederic Bertels
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Paul B Rainey
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany.,Laboratory of Biophysics and Evolution, CBI, ESPCI Paris, Université PSL, CNRS, Paris, France
| |
Collapse
|
10
|
Entfellner E, Li R, Jiang Y, Ru J, Blom J, Deng L, Kurmayer R. Toxic/Bioactive Peptide Synthesis Genes Rearranged by Insertion Sequence Elements Among the Bloom-Forming Cyanobacteria Planktothrix. Front Microbiol 2022; 13:901762. [PMID: 35966708 PMCID: PMC9366434 DOI: 10.3389/fmicb.2022.901762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 06/23/2022] [Indexed: 11/28/2022] Open
Abstract
It has been generally hypothesized that mobile elements can induce genomic rearrangements and influence the distribution and functionality of toxic/bioactive peptide synthesis pathways in microbes. In this study, we performed in depth genomic analysis by completing the genomes of 13 phylogenetically diverse strains of the bloom-forming freshwater cyanobacteria Planktothrix spp. to investigate the role of insertion sequence (IS) elements in seven pathways. Chromosome size varied from 4.7–4.8 Mbp (phylogenetic Lineage 1 of P. agardhii/P. rubescens thriving in shallow waterbodies) to 5.4–5.6 Mbp (Lineage 2 of P. agardhii/P. rubescens thriving in deeper physically stratified lakes and reservoirs) and 6.3–6.6 Mbp (Lineage 3, P. pseudagardhii/P. tepida including planktic and benthic ecotypes). Although the variation in chromosome size was positively related to the proportion of IS elements (1.1–3.7% on chromosome), quantitatively, IS elements and other paralogs only had a minor share in chromosome size variation. Thus, the major part of genomic variation must have resulted from gene loss processes (ancestor of Lineages 1 and 2) and horizontal gene transfer (HGT). Six of seven peptide synthesis gene clusters were found located on the chromosome and occurred already in the ancestor of P. agardhii/P. rubescens, and became partly lost during evolution of Lineage 1. In general, no increased IS element frequency in the vicinity of peptide synthesis gene clusters was observed. We found a higher proportion of IS elements in ten breaking regions related to chromosomal rearrangements and a tendency for colocalization of toxic/bioactive peptide synthesis gene clusters on the chromosome.
Collapse
Affiliation(s)
| | - Ruibao Li
- Research Department for Limnology, University of Innsbruck, Mondsee, Austria
- Institute of Virology, Helmholtz Zentrum München, Munich, Germany
- Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou, China
| | - Yiming Jiang
- Institute of Virology, Helmholtz Zentrum München, Munich, Germany
| | - Jinlong Ru
- Institute of Virology, Helmholtz Zentrum München, Munich, Germany
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University, Giessen, Germany
| | - Li Deng
- Institute of Virology, Helmholtz Zentrum München, Munich, Germany
| | - Rainer Kurmayer
- Research Department for Limnology, University of Innsbruck, Mondsee, Austria
- *Correspondence: Rainer Kurmayer,
| |
Collapse
|
11
|
Pantoja Angles A, Ali Z, Mahfouz M. CS-Cells: A CRISPR-Cas12 DNA Device to Generate Chromosome-Shredded Cells for Efficient and Safe Molecular Biomanufacturing. ACS Synth Biol 2022; 11:430-440. [PMID: 34978812 DOI: 10.1021/acssynbio.1c00516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Synthetic biology holds great promise for translating ideas into products to address the grand challenges facing humanity. Molecular biomanufacturing is an emerging technology that facilitates the production of key products of value, including therapeutics and select chemical compounds. Current biomanufacturing technologies require improvements to overcome limiting factors, including efficient production, cost, and safe release; therefore, developing optimum chassis for biomolecular manufacturing is of great interest for enabling diverse synthetic biology applications. Here, we harnessed the power of the CRISPR-Cas12 system to design, build, and test a DNA device for genome shredding, which fragments the native genome to enable the conversion of bacterial cells into nonreplicative, biosynthetically active, and programmable molecular biomanufacturing chassis. As a proof of concept, we demonstrated the efficient production of green fluorescent protein and violacein, an antimicrobial and antitumorigenic compound. Our CRISPR-Cas12-based chromosome-shredder DNA device has built-in biocontainment features providing a roadmap for the conversion of any bacterial cell into a chromosome-shredded chassis amenable to high-efficiency molecular biomanufacturing, thereby enabling exciting and diverse biotechnological applications.
Collapse
Affiliation(s)
- Aarón Pantoja Angles
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Zahir Ali
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Magdy Mahfouz
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| |
Collapse
|
12
|
Gómez-García G, Ruiz-Enamorado A, Yuste L, Rojo F, Moreno R. Expression of the ISPpu9 transposase of Pseudomonas putida KT2440 is regulated by two small RNAs and the secondary structure of the mRNA 5'-untranslated region. Nucleic Acids Res 2021; 49:9211-9228. [PMID: 34379788 PMCID: PMC8450116 DOI: 10.1093/nar/gkab672] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 06/23/2021] [Accepted: 07/26/2021] [Indexed: 11/20/2022] Open
Abstract
Insertion sequences (ISs) are mobile genetic elements that only carry the information required for their own transposition. Pseudomonas putida KT2440, a model bacterium, has seven copies of an IS called ISPpu9 inserted into repetitive extragenic palindromic sequences. This work shows that the gene for ISPpu9 transposase, tnp, is regulated by two small RNAs (sRNAs) named Asr9 and Ssr9, which are encoded upstream and downstream of tnp, respectively. The tnp mRNA has a long 5′-untranslated region (5′-UTR) that can fold into a secondary structure that likely includes the ribosome-binding site (RBS). Mutations weakening this structure increased tnp mRNA translation. Asr9, an antisense sRNA complementary to the 5′-UTR, was shown to be very stable. Eliminating Asr9 considerably reduced tnp mRNA translation, suggesting that it helps to unfold this secondary structure, exposing the RBS. Ectopic overproduction of Asr9 increased the transposition frequency of a new ISPpu9 entering the cell by conjugation, suggesting improved tnp expression. Ssr9 has significant complementarity to Asr9 and annealed to it in vitro forming an RNA duplex; this would sequester it and possibly facilitate its degradation. Thus, the antisense Asr9 sRNA likely facilitates tnp expression, improving transposition, while Ssr9 might counteract Asr9, keeping tnp expression low.
Collapse
Affiliation(s)
- Guillermo Gómez-García
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CSIC, Madrid 28049, Spain
| | - Angel Ruiz-Enamorado
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CSIC, Madrid 28049, Spain
| | - Luis Yuste
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CSIC, Madrid 28049, Spain
| | - Fernando Rojo
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CSIC, Madrid 28049, Spain
| | - Renata Moreno
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CSIC, Madrid 28049, Spain
| |
Collapse
|
13
|
Fremin BJ, Bhatt AS. Comparative genomics identifies thousands of candidate structured RNAs in human microbiomes. Genome Biol 2021; 22:100. [PMID: 33845850 PMCID: PMC8040213 DOI: 10.1186/s13059-021-02319-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 03/19/2021] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Structured RNAs play varied bioregulatory roles within microbes. To date, hundreds of candidate structured RNAs have been predicted using informatic approaches that search for motif structures in genomic sequence data. The human microbiome contains thousands of species and strains of microbes. Yet, much of the metagenomic data from the human microbiome remains unmined for structured RNA motifs primarily due to computational limitations. RESULTS We sought to apply a large-scale, comparative genomics approach to these organisms to identify candidate structured RNAs. With a carefully constructed, though computationally intensive automated analysis, we identify 3161 conserved candidate structured RNAs in intergenic regions, as well as 2022 additional candidate structured RNAs that may overlap coding regions. We validate the RNA expression of 177 of these candidate structures by analyzing small fragment RNA-seq data from four human fecal samples. CONCLUSIONS This approach identifies a wide variety of candidate structured RNAs, including tmRNAs, antitoxins, and likely ribosome protein leaders, from a wide variety of taxa. Overall, our pipeline enables conservative predictions of thousands of novel candidate structured RNAs from human microbiomes.
Collapse
Affiliation(s)
- Brayon J Fremin
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Ami S Bhatt
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA.
- Department of Medicine (Hematology), Stanford University, Stanford, CA, 94305, USA.
| |
Collapse
|
14
|
Li C, Chen J, Li SC. Deep learning for HGT insertion sites recognition. BMC Genomics 2020; 21:893. [PMID: 33372605 PMCID: PMC7771070 DOI: 10.1186/s12864-020-07296-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 11/28/2020] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Horizontal Gene Transfer (HGT) refers to the sharing of genetic materials between distant species that are not in a parent-offspring relationship. The HGT insertion sites are important to understand the HGT mechanisms. Recent studies in main agents of HGT, such as transposon and plasmid, demonstrate that insertion sites usually hold specific sequence features. This motivates us to find a method to infer HGT insertion sites according to sequence features.
Results
In this paper, we propose a deep residual network, DeepHGT, to recognize HGT insertion sites. To train DeepHGT, we extracted about 1.55 million sequence segments as training instances from 262 metagenomic samples, where the ratio between positive instances and negative instances is about 1:1. These segments are randomly partitioned into three subsets: 80% of them as the training set, 10% as the validation set, and the remaining 10% as the test set. The training loss of DeepHGT is 0.4163 and the validation loss is 0.423. On the test set, DeepHGT has achieved the area under curve (AUC) value of 0.8782. Furthermore, in order to further evaluate the generalization of DeepHGT, we constructed an independent test set containing 689,312 sequence segments from another 147 gut metagenomic samples. DeepHGT has achieved the AUC value of 0.8428, which approaches the previous test AUC value. As a comparison, the gradient boosting classifier model implemented in PyFeat achieve an AUC value of 0.694 and 0.686 on the above two test sets, respectively. Furthermore, DeepHGT could learn discriminant sequence features; for example, DeepHGT has learned a sequence pattern of palindromic subsequences as a significantly (P-value=0.0182) local feature. Hence, DeepHGT is a reliable model to recognize the HGT insertion site.
Conclusion
DeepHGT is the first deep learning model that can accurately recognize HGT insertion sites on genomes according to the sequence pattern.
Collapse
|
15
|
Molecular strain typing of multidrug-resistant Klebsiella pneumoniae: capsular wzi gene sequencing versus multiple locus variable number tandem repeat analysis. Diagn Microbiol Infect Dis 2020; 98:115139. [PMID: 32861156 DOI: 10.1016/j.diagmicrobio.2020.115139] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 07/03/2020] [Accepted: 07/06/2020] [Indexed: 11/23/2022]
Abstract
This study compared genotyping of Klebsiella pneumoniae isolates by 2 molecular methods. Genotyping of 50 multidrug-resistant (MDR) and 10 non-MDR K. pneumoniae subsp. pneumoniae isolates from 2 hospitals was done using multiple locus variable number tandem repeat analysis (MLVA) and capsular typing by wzi gene sequencing. Genotyping of the isolates by the 2 methods showed 100% typeability. Agreement on clustering of the isolates by the 2 methods was 82.6%. Typing by MLVA, however, was more discriminatory (97%) than by wzi gene sequencing (92%). All the 23 K. pneumoniae subsp. pneumoniae isolates randomly selected for wzi gene sequencing showed sequence identity to previously published wzi sequences, which enabled prediction of the K-types of 16 of them. The 2 methods revealed the relatedness of (8/15) isolates from 1 of the 2 hospitals. MLVA may be considered a cheaper and more discriminatory molecular typing method suitable for genotyping of K. pneumoniae isolates in developing countries.
Collapse
|
16
|
The dynamic evolution of mobile open reading frames in plastomes of Hymenophyllum Sm. and new insight on Hymenophyllum coreanum Nakai. Sci Rep 2020; 10:11059. [PMID: 32632087 PMCID: PMC7338519 DOI: 10.1038/s41598-020-68000-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 06/12/2020] [Indexed: 11/08/2022] Open
Abstract
In this study, four plastomes of Hymenophyllum, distributed in the Korean peninsula, were newly sequenced and phylogenomic analysis was conducted to reveal (1) the evolutionary history of plastomes of early-diverging fern species at the species level, (2) the importance of mobile open reading frames in the genus, and (3) plastome sequence divergence providing support for H. coreanum to be recognized as an independent species distinct from H. polyanthos. In addition, 1C-values of H. polyanthos and H. coreanum were measured to compare the genome size of both species and to confirm the diversification between them. The rrn16-trnV intergenic regions in the genus varied in length caused by Mobile Open Reading Frames in Fern Organelles (MORFFO). We investigated enlarged noncoding regions containing MORFFO throughout the fern plastomes and found that they were strongly associated with tRNA genes or palindromic elements. Sequence identity between plastomes of H. polyanthos and H. coreanum is quite low at 93.35% in the whole sequence and 98.13% even if the variation in trnV-rrn16 intergenic spacer was ignored. In addition, different genome sizes were found for these species based on the 1C-value. Consequently, there is no reason to consider them as a conspecies.
Collapse
|
17
|
Dash HR. Attribution of non-convoluted peaks in human STR markers and its possible microbial connection. Forensic Sci Int Genet 2020; 46:102264. [PMID: 32109741 DOI: 10.1016/j.fsigen.2020.102264] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 02/10/2020] [Accepted: 02/10/2020] [Indexed: 11/26/2022]
Affiliation(s)
- Hirak Ranjan Dash
- DNA Fingerprinting Unit, Forensic Science Laboratory, Sagar, Madhya Pradesh, India.
| |
Collapse
|
18
|
Durrant MG, Li MM, Siranosian BA, Montgomery SB, Bhatt AS. A Bioinformatic Analysis of Integrative Mobile Genetic Elements Highlights Their Role in Bacterial Adaptation. Cell Host Microbe 2020; 27:140-153.e9. [PMID: 31862382 PMCID: PMC6952549 DOI: 10.1016/j.chom.2019.10.022] [Citation(s) in RCA: 98] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Revised: 06/18/2019] [Accepted: 10/29/2019] [Indexed: 11/26/2022]
Abstract
Mobile genetic elements (MGEs) contribute to bacterial adaptation and evolution; however, high-throughput, unbiased MGE detection remains challenging. We describe MGEfinder, a bioinformatic toolbox that identifies integrative MGEs and their insertion sites by using short-read sequencing data. MGEfinder identifies the genomic site of each MGE insertion and infers the identity of the inserted sequence. We apply MGEfinder to 12,374 sequenced isolates of 9 prevalent bacterial pathogens, including Mycobacterium tuberculosis, Staphylococcus aureus, and Escherichia coli, and identify thousands of MGEs, including candidate insertion sequences, conjugative transposons, and prophage elements. The MGE repertoire and insertion rates vary across species, and integration sites often cluster near genes related to antibiotic resistance, virulence, and pathogenicity. MGE insertions likely contribute to antibiotic resistance in laboratory experiments and clinical isolates. Additionally, we identified thousands of mobility genes, a subset of which have unknown function opening avenues for exploration. Future application of MGEfinder to commensal bacteria will further illuminate bacterial adaptation and evolution.
Collapse
Affiliation(s)
- Matthew G Durrant
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Michelle M Li
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | | | - Stephen B Montgomery
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Ami S Bhatt
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Medicine (Hematology, Blood and Marrow Transplantation) Stanford University, Stanford, CA 94305, USA.
| |
Collapse
|
19
|
Genomic and pathogenic properties of Pseudomonas syringae pv. syringae strains isolated from apricot in East Azerbaijan province, Iran. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2019. [DOI: 10.1016/j.bcab.2019.101167] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
20
|
Zeng R, Luo Z, Su L, Zhang L, Tang D, Niessner R, Knopp D. Palindromic Molecular Beacon Based Z-Scheme BiOCl-Au-CdS Photoelectrochemical Biodetection. Anal Chem 2019; 91:2447-2454. [PMID: 30609356 DOI: 10.1021/acs.analchem.8b05265] [Citation(s) in RCA: 222] [Impact Index Per Article: 44.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
This work presented an innovative and rationally engineered palindromic molecular beacon (PMB) based "Z-scheme" photoelectrochemical (PEC) biosensing protocol for the selective screening of kanamycin (Kana) through DNA hybridization-induced conformational conversion. Interestingly, the ingeniously designed PMB integrated the multifunctional elements including recognition region, primer-like palindromic fragment, and polymerization-nicking template. The cosensitized structures consisted of CdS quantum dot functionalized hairpin DNA2 (QD-HP2) and region-selectively deposited gold nanoparticles onto {001} facets of bismuth oxychloride (BiOCl-Au). Compared with BiOCl-Au alone, the attachment of CdS QDs onto BiOCl-Au (i.e., BiOCl-Au-CdS QDs) exhibited evidently enhanced photocurrent intensity thanks to the synergistic effect of Z-scheme BiOCl-Au-CdS QDs. After incubation with target Kana, Kana-aptamer binding could induce the exposure of PMB region for hairpin DNA1 (HP1). The exposed palindromic tails hybridized with each other (like a molecular machine) to consume the substrates (dNTPs) and fuels (enzyme) for the releasing of numerous nick fragments (Nick). The as-generated nick fragments could specifically hybridize with the complementary region of QD-HP2, thus resulting in decreasing photocurrent because of the increasing spatial distance for electron transfer between two-type photosensitizers. Under optimum conditions, the PMB-based sensing system exhibited satisfying photocurrent responses toward target Kana within the working range from 50 to 5000 fM at a low detection limit of 29 fM. Impressively, the concept of a palindromic fragment-mediated primer-free biosensing strategy offers a new avenue for advanced development of efficient and convenient biodetection systems.
Collapse
Affiliation(s)
- Ruijin Zeng
- Key Laboratory of Analytical Science for Food Safety and Biology (MOE & Fujian Province), Department of Chemistry , Fuzhou University , Fuzhou 350116 , People's Republic of China
| | - Zhongbin Luo
- Key Laboratory of Analytical Science for Food Safety and Biology (MOE & Fujian Province), Department of Chemistry , Fuzhou University , Fuzhou 350116 , People's Republic of China
| | - Lingshan Su
- Key Laboratory of Analytical Science for Food Safety and Biology (MOE & Fujian Province), Department of Chemistry , Fuzhou University , Fuzhou 350116 , People's Republic of China
| | - Lijia Zhang
- Key Laboratory of Analytical Science for Food Safety and Biology (MOE & Fujian Province), Department of Chemistry , Fuzhou University , Fuzhou 350116 , People's Republic of China
| | - Dianping Tang
- Key Laboratory of Analytical Science for Food Safety and Biology (MOE & Fujian Province), Department of Chemistry , Fuzhou University , Fuzhou 350116 , People's Republic of China
| | - Reinhard Niessner
- Chair for Analytical Chemistry and Water Chemistry, Institute of Hydrochemistry , Technische Universität München , Marchioninistrasse 17 , D-81377 München , Germany
| | - Dietmar Knopp
- Chair for Analytical Chemistry and Water Chemistry, Institute of Hydrochemistry , Technische Universität München , Marchioninistrasse 17 , D-81377 München , Germany
| |
Collapse
|
21
|
Fiedoruk K, Daniluk T, Mahillon J, Leszczynska K, Swiecicka I. Genetic Environment of cry1 Genes Indicates Their Common Origin. Genome Biol Evol 2018; 9:2265-2275. [PMID: 29617829 PMCID: PMC5604178 DOI: 10.1093/gbe/evx165] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/22/2017] [Indexed: 12/21/2022] Open
Abstract
Although in Bacillus thuringiensis the cry genes coding for the insecticidal crystal proteins are plasmid-borne and are usually associated with mobile genetic elements, several aspects related to their genomic organization, diversification, and transmission remain to be elucidated. Plasmids of B. thuringiensis and other members of the Bacillus cereus group (n = 364) deposited in GenBank were screened for the presence of cry1 genes, and their genetic environment was analyzed using a comparative bioinformatic approach. The cry1 genes were identified in 27 B. thuringiensis plasmids ranging from 64 to 761 kb, and were predominantly associated with the ori44, ori60, or double orf156/orf157 and pXO1-16/pXO1-14 replication systems. In general, the cry1 genes occur individually or as a part of an insecticidal pathogenicity island (PAI), and are preceded by genes coding for an N-acetylmuramoyl-l-alanine amidase and a putative K+(Na+)/H+ antiporter. However, except in the case of the PAI, the latter gene is disrupted by the insertion of IS231B. Similarly, numerous mobile elements were recognized in the region downstream of cry1, except for cry1I that follows cry1A in the PAI. Therefore, the cassette involving cry1 and these two genes, flanked by transposable elements, named as the cry1 cassette, was the smallest cry1-carrying genetic unit recognized in the plasmids. Conservation of the genomic environment of the cry1 genes carried by various plasmids strongly suggests a common origin, possibly from an insecticidal PAI carried by B. thuringiensis megaplasmids.
Collapse
Affiliation(s)
- Krzysztof Fiedoruk
- Department of Microbiology, Medical University of Bialystok, Poland
- Corresponding author: E-mail:
| | - Tamara Daniluk
- Department of Microbiology, Medical University of Bialystok, Poland
| | - Jacques Mahillon
- Laboratory of Food and Environmental Microbiology, Earth and Life Institute, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | | | - Izabela Swiecicka
- Department of Microbiology, University of Bialystok, Poland
- Laboratory of Applied Microbiology, University of Bialystok, Poland
| |
Collapse
|
22
|
Vergnaud G, Midoux C, Blouin Y, Bourkaltseva M, Krylov V, Pourcel C. Transposition Behavior Revealed by High-Resolution Description of Pseudomonas Aeruginosa Saltovirus Integration Sites. Viruses 2018; 10:v10050245. [PMID: 29735891 PMCID: PMC5977238 DOI: 10.3390/v10050245] [Citation(s) in RCA: 3] [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] [Received: 04/09/2018] [Revised: 04/27/2018] [Accepted: 05/04/2018] [Indexed: 01/08/2023] Open
Abstract
Transposable phages, also called saltoviruses, of which the Escherichia coli phage Mu is the reference, are temperate phages that multiply their genome through replicative transposition at multiple sites in their host chromosome. The viral genome is packaged together with host DNA at both ends. In the present work, genome sequencing of three Pseudomonas aeruginosa transposable phages, HW12, 2P1, and Ab30, incidentally gave us access to the location of thousands of replicative integration sites and revealed the existence of a variable number of hotspots. Taking advantage of deep sequencing, we then designed an experiment to study 13,000,000 transposon integration sites of bacteriophage Ab30. The investigation revealed the presence of 42 transposition hotspots adjacent to bacterial interspersed mosaic elements (BIME) accounting for 5% of all transposition sites. The rest of the sites appeared widely distributed with the exception of coldspots associated with low G-C content segments, including the putative O-antigen biosynthesis cluster. Surprisingly, 0.4% of the transposition events occurred in a copy of the phage genome itself, indicating that the previously described immunity against such events is slightly leaky. This observation allowed drawing an image of the phage chromosome supercoiling into four loops.
Collapse
Affiliation(s)
- Gilles Vergnaud
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette CEDEX, France.
| | - Cédric Midoux
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette CEDEX, France.
| | - Yann Blouin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette CEDEX, France.
| | - Maria Bourkaltseva
- I. I. Mechnikov Research Institute for Vaccines & Sera, Moscow 105064, Russia.
| | - Victor Krylov
- I. I. Mechnikov Research Institute for Vaccines & Sera, Moscow 105064, Russia.
| | - Christine Pourcel
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette CEDEX, France.
| |
Collapse
|
23
|
Bertels F, Gallie J, Rainey PB. Identification and Characterization of Domesticated Bacterial Transposases. Genome Biol Evol 2017; 9:2110-2121. [PMID: 28910967 PMCID: PMC5581495 DOI: 10.1093/gbe/evx146] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/02/2017] [Indexed: 12/26/2022] Open
Abstract
Selfish genetic elements, such as insertion sequences and transposons are found in most genomes. Transposons are usually identifiable by their high copy number within genomes. In contrast, REP-associated tyrosine transposases (RAYTs), a recently described class of bacterial transposase, are typically present at just one copy per genome. This suggests that RAYTs no longer copy themselves and thus they no longer function as a typical transposase. Motivated by this possibility we interrogated thousands of fully sequenced bacterial genomes in order to determine patterns of RAYT diversity, their distribution across chromosomes and accessory elements, and rate of duplication. RAYTs encompass exceptional diversity and are divisible into at least five distinct groups. They possess features more similar to housekeeping genes than insertion sequences, are predominantly vertically transmitted and have persisted through evolutionary time to the point where they are now found in 24% of all species for which at least one fully sequenced genome is available. Overall, the genomic distribution of RAYTs suggests that they have been coopted by host genomes to perform a function that benefits the host cell.
Collapse
Affiliation(s)
- Frederic Bertels
- New Zealand Institute for Advanced Study, Massey University at Albany, Auckland, New Zealand.,Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Plön, Germany.,Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Jenna Gallie
- Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Paul B Rainey
- New Zealand Institute for Advanced Study, Massey University at Albany, Auckland, New Zealand.,Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany.,Laboratoire de Génétique de l'Evolution, Ecole Supérieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI ParisTech), PSL Research University, Paris, France
| |
Collapse
|
24
|
Jurėnas D, Garcia-Pino A, Van Melderen L. Novel toxins from type II toxin-antitoxin systems with acetyltransferase activity. Plasmid 2017; 93:30-35. [PMID: 28941941 DOI: 10.1016/j.plasmid.2017.08.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 08/24/2017] [Accepted: 08/28/2017] [Indexed: 12/21/2022]
Abstract
Type II toxin-antitoxin (TA) systems are widespread in bacterial and archeal genomes. These modules are very dynamic and participate in bacterial genome evolution through horizontal gene transfer. TA systems are commonly composed of a labile antitoxin and a stable toxin. Toxins appear to preferentially inhibit the protein synthesis process. Toxins use a variety of molecular mechanisms and target nearly every step of translation to achieve their inhibitory function. This review focuses on a recently identified TA family that includes acetyltransferase toxins. The AtaT and TacT toxins are the best-characterized to date in this family. AtaT and TacT both inhibit translation by acetylating the amino acid charged on tRNAs. However, the specificities of these 2 toxins are different as AtaT inhibits translation initiation by acetylation of the initiator tRNA whereas TacT acetylates elongator tRNAs. The molecular mechanisms of these toxins are discussed, as well as the functions and possible evolutionary origins of this diverse toxin family.
Collapse
Affiliation(s)
- Dukas Jurėnas
- Department of Biochemistry and Molecular Biology, Vilnius University Joint Life Sciences Center, Vilnius, Lithuania; Cellular and Molecular Microbiology (CM2), Faculté des Sciences, Université Libre de Bruxelles (ULB), Belgium
| | - Abel Garcia-Pino
- Cellular and Molecular Microbiology (CM2), Faculté des Sciences, Université Libre de Bruxelles (ULB), Belgium
| | - Laurence Van Melderen
- Cellular and Molecular Microbiology (CM2), Faculté des Sciences, Université Libre de Bruxelles (ULB), Belgium.
| |
Collapse
|
25
|
Kiran K, Rawal HC, Dubey H, Jaswal R, Bhardwaj SC, Prasad P, Pal D, Devanna BN, Sharma TR. Dissection of genomic features and variations of three pathotypes of Puccinia striiformis through whole genome sequencing. Sci Rep 2017; 7:42419. [PMID: 28211474 PMCID: PMC5314344 DOI: 10.1038/srep42419] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 01/10/2017] [Indexed: 01/28/2023] Open
Abstract
Stripe rust of wheat, caused by Puccinia striiformis f. sp. tritici, is one of the important diseases of wheat. We used NGS technologies to generate a draft genome sequence of two highly virulent (46S 119 and 31) and a least virulent (K) pathotypes of P. striiformis from the Indian subcontinent. We generated ~24,000-32,000 sequence contigs (N50;7.4-9.2 kb), which accounted for ~86X-105X sequence depth coverage with an estimated genome size of these pathotypes ranging from 66.2-70.2 Mb. A genome-wide analysis revealed that pathotype 46S 119 might be highly evolved among the three pathotypes in terms of year of detection and prevalence. SNP analysis revealed that ~47% of the gene sets are affected by nonsynonymous mutations. The extracellular secreted (ES) proteins presumably are well conserved among the three pathotypes, and perhaps purifying selection has an important role in differentiating pathotype 46S 119 from pathotypes K and 31. In the present study, we decoded the genomes of three pathotypes, with 81% of the total annotated genes being successfully assigned functional roles. Besides the identification of secretory genes, genes essential for pathogen-host interactions shall prove this study as a huge genomic resource for the management of this disease using host resistance.
Collapse
Affiliation(s)
- Kanti Kiran
- ICAR- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India
| | - Hukam C Rawal
- ICAR- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India
| | - Himanshu Dubey
- ICAR- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India
| | - R Jaswal
- ICAR- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India
| | - Subhash C Bhardwaj
- Indian Institute of Wheat and Barley Research, Regional Station Flowerdale, Shimla, H.P., India
| | - P Prasad
- Indian Institute of Wheat and Barley Research, Regional Station Flowerdale, Shimla, H.P., India
| | - Dharam Pal
- Indian Agricultural Research Institute, Regional Station, Shimla, H.P., India
| | - B N Devanna
- ICAR- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India
| | - Tilak R Sharma
- ICAR- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India
| |
Collapse
|
26
|
Patel S. Drivers of bacterial genomes plasticity and roles they play in pathogen virulence, persistence and drug resistance. INFECTION GENETICS AND EVOLUTION 2016; 45:151-164. [DOI: 10.1016/j.meegid.2016.08.030] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 08/26/2016] [Accepted: 08/27/2016] [Indexed: 12/11/2022]
|
27
|
Hahn J, Tsoy OV, Thalmann S, Čuklina J, Gelfand MS, Evguenieva-Hackenberg E. Small Open Reading Frames, Non-Coding RNAs and Repetitive Elements in Bradyrhizobium japonicum USDA 110. PLoS One 2016; 11:e0165429. [PMID: 27788207 PMCID: PMC5082802 DOI: 10.1371/journal.pone.0165429] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 10/11/2016] [Indexed: 11/18/2022] Open
Abstract
Small open reading frames (sORFs) and genes for non-coding RNAs are poorly investigated components of most genomes. Our analysis of 1391 ORFs recently annotated in the soybean symbiont Bradyrhizobium japonicum USDA 110 revealed that 78% of them contain less than 80 codons. Twenty-one of these sORFs are conserved in or outside Alphaproteobacteria and most of them are similar to genes found in transposable elements, in line with their broad distribution. Stabilizing selection was demonstrated for sORFs with proteomic evidence and bll1319_ISGA which is conserved at the nucleotide level in 16 alphaproteobacterial species, 79 species from other taxa and 49 other Proteobacteria. Further we used Northern blot hybridization to validate ten small RNAs (BjsR1 to BjsR10) belonging to new RNA families. We found that BjsR1 and BjsR3 have homologs outside the genus Bradyrhizobium, and BjsR5, BjsR6, BjsR7, and BjsR10 have up to four imperfect copies in Bradyrhizobium genomes. BjsR8, BjsR9, and BjsR10 are present exclusively in nodules, while the other sRNAs are also expressed in liquid cultures. We also found that the level of BjsR4 decreases after exposure to tellurite and iron, and this down-regulation contributes to survival under high iron conditions. Analysis of additional small RNAs overlapping with 3’-UTRs revealed two new repetitive elements named Br-REP1 and Br-REP2. These REP elements may play roles in the genomic plasticity and gene regulation and could be useful for strain identification by PCR-fingerprinting. Furthermore, we studied two potential toxin genes in the symbiotic island and confirmed toxicity of the yhaV homolog bll1687 but not of the newly annotated higB homolog blr0229_ISGA in E. coli. Finally, we revealed transcription interference resulting in an antisense RNA complementary to blr1853, a gene induced in symbiosis. The presented results expand our knowledge on sORFs, non-coding RNAs and repetitive elements in B. japonicum and related bacteria.
Collapse
Affiliation(s)
- Julia Hahn
- Institute of Microbiology and Molecular Biology, Justus-Liebig-University, Giessen, Germany
| | - Olga V. Tsoy
- A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Bolshoi Karetny Ln. 19, Moscow, 127051, Russia
| | - Sebastian Thalmann
- Institute of Microbiology and Molecular Biology, Justus-Liebig-University, Giessen, Germany
| | - Jelena Čuklina
- A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Bolshoi Karetny Ln. 19, Moscow, 127051, Russia
- ETH, Institute of Molecular Systems Biology, Zürich, Switzerland
| | - Mikhail S. Gelfand
- A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Bolshoi Karetny Ln. 19, Moscow, 127051, Russia
- Skolkovo Institute of Science and Technology, Nobel Str. 3, Moscow, 143026, Russia
- Faculty of Bioengineering and Bioinformatics, M. V. Lomonosov Moscow State University, Vorobyevy Gory 1–73, Moscow, 119234, Russia
- Faculty of Computer Science, Higher School of Economics, Kochnovsky Dr. 3, Moscow, 125319, Russia
- * E-mail: (EEH); (MSG)
| | - Elena Evguenieva-Hackenberg
- Institute of Microbiology and Molecular Biology, Justus-Liebig-University, Giessen, Germany
- * E-mail: (EEH); (MSG)
| |
Collapse
|
28
|
Abstract
This chapter presents an analysis of the organization and distribution of the IS200/IS605 family of insertion sequences (IS). Members of this family are widespread in both bacteria and archaea. They are unusual because they use obligatory single-strand DNA intermediates, which distinguishes them from classical IS. We summarize studies of the experimental model systems IS608 (from Helicobacter pylori) and ISDra2 (from Deinococcus radiodurans) and present biochemical, genetic, and structural data that describe their transposition pathway and the way in which their transposase (an HuH rather than a DDE enzyme) catalyzes this process. The transposition of IS200/IS605 family members can be described as a "Peel-and-Paste" mechanism. We also address the probable domestication of IS200/IS605 family transposases as enzymes involved in multiplication of repeated extragenic palindromes and as potential homing endonucleases in intron-IS chimeras.
Collapse
|
29
|
Rao C, Guyard C, Pelaz C, Wasserscheid J, Bondy-Denomy J, Dewar K, Ensminger AW. Active and adaptive Legionella CRISPR-Cas reveals a recurrent challenge to the pathogen. Cell Microbiol 2016; 18:1319-38. [PMID: 26936325 PMCID: PMC5071653 DOI: 10.1111/cmi.12586] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 02/25/2016] [Indexed: 01/04/2023]
Abstract
Clustered regularly interspaced short palindromic repeats with CRISPR‐associated gene (CRISPR‐Cas) systems are widely recognized as critical genome defense systems that protect microbes from external threats such as bacteriophage infection. Several isolates of the intracellular pathogen Legionella pneumophila possess multiple CRISPR‐Cas systems (type I‐C, type I‐F and type II‐B), yet the targets of these systems remain unknown. With the recent observation that at least one of these systems (II‐B) plays a non‐canonical role in supporting intracellular replication, the possibility remained that these systems are vestigial genome defense systems co‐opted for other purposes. Our data indicate that this is not the case. Using an established plasmid transformation assay, we demonstrate that type I‐C, I‐F and II‐B CRISPR‐Cas provide protection against spacer targets. We observe efficient laboratory acquisition of new spacers under ‘priming’ conditions, in which initially incomplete target elimination leads to the generation of new spacers and ultimate loss of the invasive DNA. Critically, we identify the first known target of L. pneumophila CRISPR‐Cas: a 30 kb episome of unknown function whose interbacterial transfer is guarded against by CRISPR‐Cas. We provide evidence that the element can subvert CRISPR‐Cas by mutating its targeted sequences – but that primed spacer acquisition may limit this mechanism of escape. Rather than generally impinging on bacterial fitness, this element drives a host specialization event – with improved fitness in Acanthamoeba but a reduced ability to replicate in other hosts and conditions. These observations add to a growing body of evidence that host range restriction can serve as an existential threat to L. pneumophila in the wild.
Collapse
Affiliation(s)
- Chitong Rao
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | | | - Carmen Pelaz
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Jessica Wasserscheid
- The McGill University and Génome Québec Innovation Centre, Montreal, Quebec, Canada
| | - Joseph Bondy-Denomy
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Ken Dewar
- The McGill University and Génome Québec Innovation Centre, Montreal, Quebec, Canada
| | - Alexander W Ensminger
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada. .,Public Health Ontario, Toronto, Ontario, Canada. .,Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.
| |
Collapse
|
30
|
Emergence of nontoxic mutants as revealed by single filament analysis in bloom-forming cyanobacteria of the genus Planktothrix. BMC Microbiol 2016; 16:23. [PMID: 26911978 PMCID: PMC4766695 DOI: 10.1186/s12866-016-0639-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 02/13/2016] [Indexed: 01/04/2023] Open
Abstract
Background Bloom-forming cyanobacteria cause toxic algae outbreaks in lakes and reservoirs. We aimed to explore and quantify mutation events occurring within the large mcy gene cluster (55 kbp) encoding microcystin (MC) biosynthesis that inactivate MC net production. For this purpose we developed a workflow to detect mutations in situ occurring anywhere within the large mcy gene cluster as amplified from one single filament of the red-pigmented cyanobacterium Planktothrix rubescens. From five lakes of the Alps eight hundred Planktothrix filaments were isolated and each individual filament was analyzed for mutations affecting the mcy genes. Results Mutations inactivating MC synthesis were either through an insertion element ISPlr1 or the partial deletion of mcy genes. Neutral mutations not affecting MC biosynthesis occurred within two intergenic spacer regions, either through the insertion of a Holliday-junction resolvase RusA or ISPlr1. Altogether, the insertions affected a few mcy genes only and their location was correlated with regions similar to repetitive extragenic palindromic DNA sequences (REPs). Taking all of the filaments together, the mutations leading to the inactivation of MC synthesis were more rare (0.5–6.9 %), when compared with the neutral mutations (7.5–20.6 %). On a spatial-temporal scale the ratio of MC synthesis-inactivating vs. neutral mutations was variable, e.g., the filament abundance carrying partial deletion of mcyD (5.2–19.4 %) and/or mcyHA (0–7.3 %) exceeded the abundance of neutral mutations. Conclusions It is concluded that insertion events occurring within the Planktothrix mcy gene cluster are predictable due to their correlation with REPs. The frequency of occurrence of the REPs within the mcy gene cluster of Planktothrix relates to the rather common mutation of mcy genes in Planktothrix. Spatial-temporal variable conditions may favor the emergence of partial mcy deletion mutants in Planktothrix, in particular a higher proportion of genotypes resulting in inactivation of MC synthesis might be caused by increased ISPlr1 activity. Electronic supplementary material The online version of this article (doi:10.1186/s12866-016-0639-1) contains supplementary material, which is available to authorized users.
Collapse
|
31
|
Rehm C, Wurmthaler LA, Li Y, Frickey T, Hartig JS. Investigation of a Quadruplex-Forming Repeat Sequence Highly Enriched in Xanthomonas and Nostoc sp. PLoS One 2015; 10:e0144275. [PMID: 26695179 PMCID: PMC4692102 DOI: 10.1371/journal.pone.0144275] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 11/16/2015] [Indexed: 12/04/2022] Open
Abstract
In prokaryotes simple sequence repeats (SSRs) with unit sizes of 1–5
nucleotides (nt) are causative for phase and antigenic variation. Although an
increased abundance of heptameric repeats was noticed in bacteria, reports about SSRs
of 6–9 nt are rare. In particular G-rich repeat sequences with the propensity
to fold into G-quadruplex (G4) structures have received little attention. In silico
analysis of prokaryotic genomes show putative G4 forming sequences to be abundant.
This report focuses on a surprisingly enriched G-rich repeat of the type
GGGNATC in Xanthomonas and cyanobacteria
such as Nostoc. We studied in detail the genomes of
Xanthomonas campestris pv. campestris ATCC 33913
(Xcc), Xanthomonas axonopodis pv.
citri str. 306 (Xac), and Nostoc
sp. strain PCC7120 (Ana). In all three organisms repeats
are spread all over the genome with an over-representation in non-coding regions.
Extensive variation of the number of repetitive units was observed with repeat
numbers ranging from two up to 26 units. However a clear preference for four units
was detected. The strong bias for four units coincides with the requirement of four
consecutive G-tracts for G4 formation. Evidence for G4 formation of the consensus
repeat sequences was found in biophysical studies utilizing CD spectroscopy. The
G-rich repeats are preferably located between aligned open reading frames (ORFs) and
are under-represented in coding regions or between divergent ORFs. The G-rich repeats
are preferentially located within a distance of 50 bp upstream of an ORF on the
anti-sense strand or within 50 bp from the stop codon on the sense strand. Analysis
of whole transcriptome sequence data showed that the majority of repeat sequences are
transcribed. The genetic loci in the vicinity of repeat regions show increased
genomic stability. In conclusion, we introduce and characterize a special class of
highly abundant and wide-spread quadruplex-forming repeat sequences in bacteria.
Collapse
Affiliation(s)
- Charlotte Rehm
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstr. 10, 78457 Konstanz, Germany
| | - Lena A Wurmthaler
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstr. 10, 78457 Konstanz, Germany
| | - Yuanhao Li
- Department of Biology, University of Konstanz, Universitätsstr. 10, 78457 Konstanz, Germany
| | - Tancred Frickey
- Department of Biology, University of Konstanz, Universitätsstr. 10, 78457 Konstanz, Germany
| | - Jörg S Hartig
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstr. 10, 78457 Konstanz, Germany
| |
Collapse
|
32
|
Gasparini R, Panatto D, Bragazzi NL, Lai PL, Bechini A, Levi M, Durando P, Amicizia D. How the Knowledge of Interactions between Meningococcus and the Human Immune System Has Been Used to Prepare Effective Neisseria meningitidis Vaccines. J Immunol Res 2015; 2015:189153. [PMID: 26351643 PMCID: PMC4553322 DOI: 10.1155/2015/189153] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 06/09/2015] [Indexed: 01/17/2023] Open
Abstract
In the last decades, tremendous advancement in dissecting the mechanisms of pathogenicity of Neisseria meningitidis at a molecular level has been achieved, exploiting converging approaches of different disciplines, ranging from pathology to microbiology, immunology, and omics sciences (such as genomics and proteomics). Here, we review the molecular biology of the infectious agent and, in particular, its interactions with the immune system, focusing on both the innate and the adaptive responses. Meningococci exploit different mechanisms and complex machineries in order to subvert the immune system and to avoid being killed. Capsular polysaccharide and lipooligosaccharide glycan composition, in particular, play a major role in circumventing immune response. The understanding of these mechanisms has opened new horizons in the field of vaccinology. Nowadays different licensed meningococcal vaccines are available and used: conjugate meningococcal C vaccines, tetravalent conjugate vaccines, an affordable conjugate vaccine against the N. menigitidis serogroup A, and universal vaccines based on multiple antigens each one with a different and peculiar function against meningococcal group B strains.
Collapse
Affiliation(s)
- R. Gasparini
- Department of Health Sciences, University of Genoa, Via Pastore 1, 16132 Genoa, Italy
| | - D. Panatto
- Department of Health Sciences, University of Genoa, Via Pastore 1, 16132 Genoa, Italy
| | - N. L. Bragazzi
- Department of Health Sciences, University of Genoa, Via Pastore 1, 16132 Genoa, Italy
| | - P. L. Lai
- Department of Health Sciences, University of Genoa, Via Pastore 1, 16132 Genoa, Italy
| | - A. Bechini
- Department of Health Sciences, University of Florence, Viale G.B. Morgagni 48, 50134 Florence, Italy
| | - M. Levi
- Department of Health Sciences, University of Florence, Viale G.B. Morgagni 48, 50134 Florence, Italy
| | - P. Durando
- Department of Health Sciences, University of Genoa, Via Pastore 1, 16132 Genoa, Italy
| | - D. Amicizia
- Department of Health Sciences, University of Genoa, Via Pastore 1, 16132 Genoa, Italy
| |
Collapse
|
33
|
Mousa WK, Raizada MN. Biodiversity of genes encoding anti-microbial traits within plant associated microbes. FRONTIERS IN PLANT SCIENCE 2015; 6:231. [PMID: 25914708 PMCID: PMC4392301 DOI: 10.3389/fpls.2015.00231] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 03/23/2015] [Indexed: 05/10/2023]
Abstract
The plant is an attractive versatile home for diverse associated microbes. A subset of these microbes produces a diversity of anti-microbial natural products including polyketides, non-ribosomal peptides, terpenoids, heterocylic nitrogenous compounds, volatile compounds, bacteriocins, and lytic enzymes. In recent years, detailed molecular analysis has led to a better understanding of the underlying genetic mechanisms. New genomic and bioinformatic tools have permitted comparisons of orthologous genes between species, leading to predictions of the associated evolutionary mechanisms responsible for diversification at the genetic and corresponding biochemical levels. The purpose of this review is to describe the biodiversity of biosynthetic genes of plant-associated bacteria and fungi that encode selected examples of antimicrobial natural products. For each compound, the target pathogen and biochemical mode of action are described, in order to draw attention to the complexity of these phenomena. We review recent information of the underlying molecular diversity and draw lessons through comparative genomic analysis of the orthologous coding sequences (CDS). We conclude by discussing emerging themes and gaps, discuss the metabolic pathways in the context of the phylogeny and ecology of their microbial hosts, and discuss potential evolutionary mechanisms that led to the diversification of biosynthetic gene clusters.
Collapse
Affiliation(s)
- Walaa K. Mousa
- Department of Plant Agriculture, University of GuelphGuelph, ON, Canada
- Department of Pharmacognosy, Faculty of Pharmacy, Mansoura UniversityMansoura, Egypt
| | - Manish N. Raizada
- Department of Plant Agriculture, University of GuelphGuelph, ON, Canada
| |
Collapse
|
34
|
Abstract
ABSTRACT
The number and diversity of known prokaryotic insertion sequences (IS) have increased enormously since their discovery in the late 1960s. At present the sequences of more than 4000 different IS have been deposited in the specialized ISfinder database. Over time it has become increasingly apparent that they are important actors in the evolution of their host genomes and are involved in sequestering, transmitting, mutating and activating genes, and in the rearrangement of both plasmids and chromosomes. This review presents an overview of our current understanding of these transposable elements (TE), their organization and their transposition mechanism as well as their distribution and genomic impact. In spite of their diversity, they share only a very limited number of transposition mechanisms which we outline here. Prokaryotic IS are but one example of a variety of diverse TE which are being revealed due to the advent of extensive genome sequencing projects. A major conclusion from sequence comparisons of various TE is that frontiers between the different types are becoming less clear. We detail these receding frontiers between different IS-related TE. Several, more specialized chapters in this volume include additional detailed information concerning a number of these.
In a second section of the review, we provide a detailed description of the expanding variety of IS, which we have divided into families for convenience. Our perception of these families continues to evolve and families emerge regularly as more IS are identified. This section is designed as an aid and a source of information for consultation by interested specialist readers.
Collapse
|
35
|
Li X, Top EM, Wang Y, Brown CJ, Yao F, Yang S, Jiang Y, Li H. The broad-host-range plasmid pSFA231 isolated from petroleum-contaminated sediment represents a new member of the PromA plasmid family. Front Microbiol 2015; 5:777. [PMID: 25628616 PMCID: PMC4290620 DOI: 10.3389/fmicb.2014.00777] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 12/18/2014] [Indexed: 11/13/2022] Open
Abstract
A self-transmissible broad-host-range (BHR) plasmid pSFA231 was isolated from petroleum-contaminated sediment in Shen-fu wastewater irrigation zone, China, using the triparental mating exogenous plasmid capture method. Based on its complete sequence the plasmid has a size of 41.5 kb and codes for 50 putative open reading frames (orfs), 29 of which represent genes involved in replication, partitioning and transfer functions of the plasmid. Phylogenetic analysis grouped pSFA231 into the newly defined PromA plasmid family, which currently includes five members. Further comparative genomic analysis shows that pSFA231 shares the common backbone regions with the other PromA plasmids, i.e., genes involved in replication, maintenance and control, and conjugative transfer. Nevertheless, phylogenetic divergence was found in specific gene products. We propose to divide the PromA group into two subgroups, PromA-α (pMRAD02, pSB102) and PromA-β (pMOL98, pIPO2T, pSFA231, pTer331), based on the splits network analysis of the RepA protein. Interestingly, a cluster of hypothetical orfs located between parA and traA of pSFA231 shows high similarity with the corresponding regions on pMOL98, pIPO2T, and pTer331, suggesting these hypothetical orfs may represent “essential” plasmid backbone genes for the PromA-β subgroup. Alternatively, they may also be accessory genes that were first acquired and then stayed as the plasmid diverged. Our study increases the available collection of complete genome sequences of BHR plasmids, and since pSFA231 is the only characterized PromA plasmid from China, our findings also enhance our understanding of the genetic diversity of this plasmid group in different parts of the world.
Collapse
Affiliation(s)
- Xiaobin Li
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences Shenyang, China ; College of Resources and Environment, University of Chinese Academy of Sciences Beijing, China
| | - Eva M Top
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies, University of Idaho Moscow, ID, USA
| | - Yafei Wang
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences Shenyang, China
| | - Celeste J Brown
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies, University of Idaho Moscow, ID, USA
| | - Fei Yao
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences Shenyang, China ; College of Resources and Environment, University of Chinese Academy of Sciences Beijing, China
| | - Shan Yang
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences Shenyang, China
| | - Yong Jiang
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences Shenyang, China
| | - Hui Li
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences Shenyang, China
| |
Collapse
|
36
|
Gómez MJ, Díaz-Maldonado H, González-Tortuero E, López de Saro FJ. Chromosomal replication dynamics and interaction with the β sliding clamp determine orientation of bacterial transposable elements. Genome Biol Evol 2014; 6:727-40. [PMID: 24614824 PMCID: PMC3971601 DOI: 10.1093/gbe/evu052] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Insertion sequences (ISs) are small transposable elements widespread in bacterial genomes, where they play an essential role in chromosome evolution by stimulating recombination and genetic flow. Despite their ubiquity, it is unclear how ISs interact with the host. Here, we report a survey of the orientation patterns of ISs in bacterial chromosomes with the objective of gaining insight into the interplay between ISs and host chromosomal functions. We find that a significant fraction of IS families present a consistent and family-specific orientation bias with respect to chromosomal DNA replication, especially in Firmicutes. Additionally, we find that the transposases of up to nine different IS families with different transposition pathways interact with the β sliding clamp, an essential replication factor, suggesting that this is a widespread mechanism of interaction with the host. Although we find evidence that the interaction with the β sliding clamp is common to all bacterial phyla, it also could explain the observed strong orientation bias found in Firmicutes, because in this group β is asymmetrically distributed during synthesis of the leading or lagging strands. Besides the interaction with the β sliding clamp, other asymmetries also play a role in the biased orientation of some IS families. The utilization of the highly conserved replication sliding clamps suggests a mechanism for host regulation of IS proliferation and also a universal platform for IS dispersal and transmission within bacterial populations and among phylogenetically distant species.
Collapse
Affiliation(s)
- Manuel J Gómez
- Department of Molecular Evolution, Centro de Astrobiología (INTA-CSIC), Madrid, Spain
| | | | | | | |
Collapse
|
37
|
Husain F, Veeranagouda Y, Boente R, Tang K, Mulato G, Wexler HM. The Ellis Island Effect: A novel mobile element in a multi-drug resistant Bacteroides fragilis clinical isolate includes a mosaic of resistance genes from Gram-positive bacteria. Mob Genet Elements 2014; 4:e29801. [PMID: 25165618 PMCID: PMC4145004 DOI: 10.4161/mge.29801] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 06/29/2014] [Accepted: 07/01/2014] [Indexed: 01/13/2023] Open
Abstract
Objectives: Bacteroides fragilis, a Gram-negative anaerobic bacterium, is alternately a gut commensal or virulent pathogen and is an important reservoir for horizontal gene transfer (HGT) of bacterial resistance and virulence genes in the human gastrointestinal tract. We identified a unique conjugative transposon (CTn) in a multidrug resistant clinical isolate of B. fragilis (BF-HMW615); we named this element CTnHyb because it included a hybrid mosaic of foreign elements. This study reports the characterization of CTnHyb and discusses the potential impact on horizontal spread of resistance genes. Results: CTnHyb contains several efflux pump genes and several genes that confer or may confer antibiotic resistance to tetracycline, kanamycin, metronidazole and spectinomycin (truncated gene). CTnHyb also contains a mosaic of mobile elements from Gram-positive organisms. CTnHyb is easily transferred from BF-HMW615 (the original isolate) to BF638R (lab strain) and integrated into the BF638R chromosome. The "foreign" (from Gram-positive bacteria) nucleotide sequences within CTnHyb were > 99% preserved indicating that the gene acquisition from the Gram-positive bacteria was very recent. Conclusion: CTnHyb is a novel CTn residing in a multidrug resistant strain of B. fragilis. The global nature and wide phylogenetic reach of HGT means that any gene in any bacterium can potentially be mobilized. Understanding the mechanisms that drive the formation and transfer of these elements and, potentially, ways to limit the transfer are necessary to prevent a devastating spread of resistance elements.
Collapse
Affiliation(s)
| | - Yaligara Veeranagouda
- GLAVAHCS; Los Angeles, CA USA ; David Geffen School of Medicine; University of California Los Angeles; Los Angeles, CA USA
| | | | - Kevin Tang
- David Geffen School of Medicine; University of California Los Angeles; Los Angeles, CA USA
| | - Gabriela Mulato
- David Geffen School of Medicine; University of California Los Angeles; Los Angeles, CA USA
| | - Hannah M Wexler
- GLAVAHCS; Los Angeles, CA USA ; David Geffen School of Medicine; University of California Los Angeles; Los Angeles, CA USA
| |
Collapse
|
38
|
Communication between binding sites is required for YqjI regulation of target promoters within the yqjH-yqjI intergenic region. J Bacteriol 2014; 196:3199-207. [PMID: 24982304 DOI: 10.1128/jb.01835-14] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The nickel-responsive transcription factor YqjI represses its own transcription and transcription of the divergent yqjH gene, which encodes a novel ferric siderophore reductase. The intergenic region between the two promoters is complex, with multiple sequence features that may impact YqjI-dependent regulation of its two target promoters. We utilized mutagenesis and DNase I footprinting to characterize YqjI regulation of the yqjH-yqjI intergenic region. The results show that YqjI binding results in an extended footprint at the yqjI promoter (site II) compared to the yqjH promoter (site I). Mutagenesis of in vivo gene reporter constructs revealed that the two YqjI binding sites, while separated by nearly 200 bp, appear to communicate in order to provide full YqjI-dependent regulation at the two target promoters. Thus, YqjI binding at both promoters is required for full repression of either promoter, suggesting that the two YqjI binding sites cooperate to control transcription from the divergent promoters. Furthermore, internal deletions that shorten the total length of the intergenic region disrupt the ability of YqjI to regulate the yqjH promoter. Finally, mutagenesis of the repetitive extragenic palindromic (REP) elements within the yqjH-yqjI intergenic region shows that these sequences are not required for YqjI regulation. These studies provide a complex picture of novel YqjI transcriptional regulation within the yqjH-yqjI intergenic region and suggest a possible model for communication between the YqjI binding sites at each target promoter.
Collapse
|
39
|
Park MK, Lee SH, Yang KS, Jung SC, Lee JH, Kim SC. Enhancing recombinant protein production with an Escherichia coli host strain lacking insertion sequences. Appl Microbiol Biotechnol 2014; 98:6701-13. [DOI: 10.1007/s00253-014-5739-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 03/27/2014] [Accepted: 03/29/2014] [Indexed: 02/07/2023]
|
40
|
Clonal relationship and differentiation among Mycobacterium abscessus isolates as determined using the semiautomated repetitive extragenic palindromic sequence PCR-based DiversiLab system. J Clin Microbiol 2014; 52:1969-77. [PMID: 24671795 DOI: 10.1128/jcm.03600-13] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mycobacterium abscessus is a rapidly growing mycobacterium that causes respiratory tract infections in predisposed patients, such as those with cystic fibrosis and nosocomial skin and soft tissue infections. In order to investigate the clonal relationships between the strains causing epidemic episodes, we evaluated the discriminatory power of the semiautomated DiversiLab (DL) repetitive extragenic palindromic sequence PCR (REP-PCR) test for M. abscessus genotyping. Since M. abscessus was shown to be composed of subspecies (M. abscessus subsp. massiliense, M. abscessus subsp. bolletii, and M. abscessus subsp. abscessus), we also evaluated the ability of this technique to differentiate subspecies. The technique was applied to two collections of clinical isolates, (i) 83 M. abscessus original isolates (43 M. abscessus subsp. abscessus, 12 M. abscessus subsp. bolletii, and 28 M. abscessus subsp. massiliense) from infected patients and (ii) 35 repeated isolates obtained over 1 year from four cystic fibrosis patients. The DL REP-PCR test was standardized for DNA extraction, DNA amplification, and electrophoresis pattern comparisons. Among the isolates from distinct patients, 53/83 (62%) isolates showed a specific pattern, and 30 were distributed in 11 clusters and 6 patterns, with 2 to 4 isolates per pattern. The clusters and patterns did not fully correlate with multilocus sequence typing (MLST) analysis results. This revealed a high genomic diversity between patients, with a discriminatory power of 98% (Simpson's diversity index). However, since some isolates shared identical patterns, this raises the question of whether it is due to transmission between patients or a common reservoir. Multiple isolates from the same patient showed identical patterns, except for one patient infected by two strains. Between the M. abscessus subspecies, the indexes were <70%, indicating that the DL REP-PCR test is not an accurate tool for identifying organisms to the subspecies level. REP-PCR appears to be a rapid genotyping method that is useful for investigating epidemics of M. abscessus infections.
Collapse
|
41
|
Abstract
Bacterial genomes are remarkably stable from one generation to the next but are plastic on an evolutionary time scale, substantially shaped by horizontal gene transfer, genome rearrangement, and the activities of mobile DNA elements. This implies the existence of a delicate balance between the maintenance of genome stability and the tolerance of genome instability. In this review, we describe the specialized genetic elements and the endogenous processes that contribute to genome instability. We then discuss the consequences of genome instability at the physiological level, where cells have harnessed instability to mediate phase and antigenic variation, and at the evolutionary level, where horizontal gene transfer has played an important role. Indeed, this ability to share DNA sequences has played a major part in the evolution of life on Earth. The evolutionary plasticity of bacterial genomes, coupled with the vast numbers of bacteria on the planet, substantially limits our ability to control disease.
Collapse
|
42
|
Siguier P, Gourbeyre E, Chandler M. Bacterial insertion sequences: their genomic impact and diversity. FEMS Microbiol Rev 2014; 38:865-91. [PMID: 24499397 PMCID: PMC7190074 DOI: 10.1111/1574-6976.12067] [Citation(s) in RCA: 380] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 01/19/2014] [Accepted: 01/22/2014] [Indexed: 01/06/2023] Open
Abstract
Insertion sequences (ISs), arguably the smallest and most numerous autonomous transposable elements (TEs), are important players in shaping their host genomes. This review focuses on prokaryotic ISs. We discuss IS distribution and impact on genome evolution. We also examine their effects on gene expression, especially their role in activating neighbouring genes, a phenomenon of particular importance in the recent upsurge of bacterial antibiotic resistance. We explain how ISs are identified and classified into families by a combination of characteristics including their transposases (Tpases), their overall genetic organisation and the accessory genes which some ISs carry. We then describe the organisation of autonomous and nonautonomous IS‐related elements. This is used to illustrate the growing recognition that the boundaries between different types of mobile element are becoming increasingly difficult to define as more are being identified. We review the known Tpase types, their different catalytic activities used in cleaving and rejoining DNA strands during transposition, their organisation into functional domains and the role of this in regulation. Finally, we consider examples of prokaryotic IS domestication. In a more speculative section, we discuss the necessity of constructing more quantitative dynamic models to fully appreciate the continuing impact of TEs on prokaryotic populations.
Collapse
Affiliation(s)
- Patricia Siguier
- Laboratoire de Microbiologie et Génétique Moléculaires, Unité Mixte de Recherche 5100, Centre National de Recherche Scientifique, Toulouse Cedex, France
| | | | | |
Collapse
|
43
|
Zhou L, Powell CA, Li W, Irey M, Duan Y. Prophage-mediated dynamics of 'Candidatus Liberibacter asiaticus' populations, the destructive bacterial pathogens of citrus huanglongbing. PLoS One 2013; 8:e82248. [PMID: 24349235 PMCID: PMC3862640 DOI: 10.1371/journal.pone.0082248] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 10/22/2013] [Indexed: 01/21/2023] Open
Abstract
Prophages are highly dynamic components in the bacterial genome and play an important role in intraspecies variations. There are at least two prophages in the chromosomes of Candidatus Liberibacter asiaticus' (Las) Floridian isolates. Las is both unculturable and the most prevalent species of Liberibacter pathogens that cause huanglongbing (HLB), a worldwide destructive disease of citrus. In this study, seven new prophage variants resulting from two hyper-variable regions were identified by screening clone libraries of infected citrus, periwinkle and psyllids. Among them, Types A and B share highly conserved sequences and localize within the two prophages, FP1 and FP2, respectively. Although Types B and C were abundant in all three libraries, Type A was much more abundant in the libraries from the Las-infected psyllids than from the Las-infected plants, and Type D was only identified in libraries from the infected host plants but not from the infected psyllids. Sequence analysis of these variants revealed that the variations may result from recombination and rearrangement events. Conventional PCR results using type-specific molecular markers indicated that A, B, C and D are the four most abundant types in Las-infected citrus and periwinkle. However, only three types, A, B and C are abundant in Las-infected psyllids. Typing results for Las-infected citrus field samples indicated that mixed populations of Las bacteria present in Floridian isolates, but only the Type D population was correlated with the blotchy mottle symptom. Extended cloning and sequencing of the Type D region revealed a third prophage/phage in the Las genome, which may derive from the recombination of FP1 and FP2. Dramatic variations in these prophage regions were also found among the global Las isolates. These results are the first to demonstrate the prophage/phage-mediated dynamics of Las populations in plant and insect hosts, and their correlation with insect transmission and disease development.
Collapse
Affiliation(s)
- Lijuan Zhou
- Horticultural Research Laboratory, Agricultural Research Service, US Department of Agriculture, Fort Pierce, Florida, United States of America
- Indian River Research and Education Center, University of Florida, Fort Pierce, Florida, United States of America
| | - Charles A. Powell
- Indian River Research and Education Center, University of Florida, Fort Pierce, Florida, United States of America
| | - Wenbin Li
- Center for Plant Health, Science and Technology, Animal and Plant health Inspection Service, US Department of Agriculture, Beltsville, Maryland, United States of America
| | - Mike Irey
- Southern Garden Citrus, U. S. Sugar Corp., Clewiston, Florida, United States of America
| | - Yongping Duan
- Horticultural Research Laboratory, Agricultural Research Service, US Department of Agriculture, Fort Pierce, Florida, United States of America
| |
Collapse
|
44
|
Okada T, Fujita K, Suzuki H, Tsuzukibashi O, Umezawa K, Nagahama F, Ikemi T, Takada K. Distribution and sequencing of enterobacterial repetitive intergenic consensus sequence elements in Streptococcus mutans serotype c. J Oral Biosci 2013. [DOI: 10.1016/j.job.2013.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
45
|
Di Nocera PP, De Gregorio E, Rocco F. GTAG- and CGTC-tagged palindromic DNA repeats in prokaryotes. BMC Genomics 2013; 14:522. [PMID: 23902135 PMCID: PMC3733652 DOI: 10.1186/1471-2164-14-522] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Accepted: 07/30/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND REPs (Repetitive Extragenic Palindromes) are small (20-40 bp) palindromic repeats found in high copies in some prokaryotic genomes, hypothesized to play a role in DNA supercoiling, transcription termination, mRNA stabilization. RESULTS We have monitored a large number of REP elements in prokaryotic genomes, and found that most can be sorted into two large DNA super-families, as they feature at one end unpaired motifs fitting either the GTAG or the CGTC consensus. Tagged REPs have been identified in >80 species in 8 different phyla. GTAG and CGTC repeats reside predominantly in microorganisms of the gamma and alpha division of Proteobacteria, respectively. However, the identification of members of both super- families in deeper branching phyla such Cyanobacteria and Planctomycetes supports the notion that REPs are old components of the bacterial chromosome. On the basis of sequence content and overall structure, GTAG and CGTC repeats have been assigned to 24 and 4 families, respectively. Of these, some are species-specific, others reside in multiple species, and several organisms contain different REP types. In many families, most units are close to each other in opposite orientation, and may potentially fold into larger secondary structures. In different REP-rich genomes the repeats are predominantly located between unidirectionally and convergently transcribed ORFs. REPs are predominantly located downstream from coding regions, and many are plausibly transcribed and function as RNA elements. REPs located inside genes have been identified in several species. Many lie within replication and global genome repair genes. It has been hypothesized that GTAG REPs are miniature transposons mobilized by specific transposases known as RAYTs (REP associated tyrosine transposases). RAYT genes are flanked either by GTAG repeats or by long terminal inverted repeats (TIRs) unrelated to GTAG repeats. Moderately abundant families of TIRs have been identified in multiple species. CONCLUSIONS CGTC REPs apparently lack a dedicated transposase. Future work will clarify whether these elements may be mobilized by RAYTs or other transposases, and assess if de-novo formation of either GTAG or CGTC repeats type still occurs.
Collapse
Affiliation(s)
- Pier Paolo Di Nocera
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II, Napoli, Via S, Pansini 5 80131, Naples, Italy.
| | | | | |
Collapse
|
46
|
Petrova M, Shcherbatova N, Gorlenko Z, Mindlin S. A new subgroup of the IS3 family and properties of its representative member ISPpy1. MICROBIOLOGY-SGM 2013; 159:1900-1910. [PMID: 23832000 DOI: 10.1099/mic.0.068676-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Recently, we described a novel insertion element, ISPpy1, isolated from a permafrost strain of Psychrobacter maritimus. In this work, we demonstrated that ISPpy1 is a member of a novel subgroup of the IS3 family of insertion sequences (ISs) that was not identified and characterized previously. IS elements of this subgroup termed the ISPpy1 subgroup are broadly distributed among different taxa of Eubacteria, including Geobacteraceae, Chlorobiaceae, Desulfobacteraceae, Methylobacteriaceae, Nitrosomonadaceae and Cyanobacteria. While displaying characteristic features of the IS3-family elements, ISPpy1 subgroup elements exhibit some unusual features. In particular, most of them have longer terminal repeats with unconventional ends and frameshifting box with an atypical organization, and, unlike many other IS3-family elements, do not exhibit any distinct IS specificity. We studied the transposition and mutagenic properties of a representative member of this subgroup, ISPpy1 and showed that in contrast to the original P. maritimus host, in a heterologous host, Escherichia coli K-12, it is able to translocate with extremely high efficiency into the chromosome, either by itself or as a part of a composite transposon containing two ISPpy1 copies. The majority of transposants carry multiple chromosomal copies (up to 12) of ISPpy1. It was discovered that ISPpy1 is characterized by a marked mutagenic activity in E. coli: its chromosomal insertions generate various types of mutations, including auxotrophic, pleiotropic and rifampicin-resistance mutations. The distribution of IS elements of the novel subgroup among different bacteria, their role in the formation of composite transposons and the horizontal transfer of genes are examined and discussed.
Collapse
Affiliation(s)
- Mayya Petrova
- Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov sq. 2, Moscow 123182, Russia
| | - Natalya Shcherbatova
- Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov sq. 2, Moscow 123182, Russia
| | - Zhosephine Gorlenko
- Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov sq. 2, Moscow 123182, Russia
| | - Sofia Mindlin
- Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov sq. 2, Moscow 123182, Russia
| |
Collapse
|
47
|
Mikheeva LE, Karbysheva EA, Shestakov SV. The role of mobile genetic elements in the evolution of cyanobacteria. ACTA ACUST UNITED AC 2013. [DOI: 10.1134/s2079059713020032] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
48
|
Rusenova N, Parvanov P, Stanilova S. Molecular typing of Paenibacillus larvae strains isolated from Bulgarian apiaries based on repetitive element polymerase chain reaction (Rep-PCR). Curr Microbiol 2013; 66:573-7. [PMID: 23361165 DOI: 10.1007/s00284-013-0318-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Accepted: 01/10/2013] [Indexed: 10/27/2022]
Abstract
The aim of the present study was to perform molecular typing of Paenibacillus larvae (P. larvae) isolates from Bulgarian apiaries with repetitive element polymerase chain reaction (rep-PCR) using BOX A1R, MBO REP1, and ERIC primers. A total of 96 isolates collected from brood combs with clinical symptoms of American foulbrood originating from apiaries located in different geographical regions of Bulgaria, a reference strain P. larvae NBIMCC 8478 and 30 commercial honey samples with Bulgarian origin were included in the study. Rep-PCR fingerprinting analysis revealed two genotypes ab and AB of P. larvae isolates from brood combs and honey samples. A combination of genotypes ab/AB was detected in one apiary and honey sample. The prevailing genotype ab was found in 78.1 % of brood combs isolates as well as in the reference strain whereas genotype AB was determined in 21.9 % of isolates. The examination of honey samples confirmed the preponderance of ab genotype which was demonstrated in 20 of 30 samples analyzed. In conclusion, the genetic epidemiology of P. larvae revealed two genotypes--ab and AB for Bulgarian strains. Developed protocols for molecular typing of P. larvae are reliable and may be used to trace the source of infection.
Collapse
Affiliation(s)
- Nikolina Rusenova
- Department of Veterinary Microbiology, Infectious and Parasitic Diseases, Faculty of Veterinary Medicine, Trakia University, 6000 Stara Zagora, Bulgaria.
| | | | | |
Collapse
|
49
|
Cepni E, Gürel F. Variation in extragenic repetitive DNA sequences in Pseudomonas syringae and potential use of modified REP primers in the identification of closely related isolates. Genet Mol Biol 2012; 35:650-6. [PMID: 23055805 PMCID: PMC3459416 DOI: 10.1590/s1415-47572012005000040] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Accepted: 04/09/2012] [Indexed: 12/02/2022] Open
Abstract
In this study, Pseudomonas syringe pathovars isolated from olive, tomato and bean were identified by species-specific PCR and their genetic diversity was assessed by repetitive extragenic palindromic (REP)-PCR. Reverse universal primers for REP-PCR were designed by using the bases of A, T, G or C at the positions of 1, 4 and 11 to identify additional polymorphism in the banding patterns. Binding of the primers to different annealing sites in the genome revealed additional fingerprint patterns in eight isolates of P. savastanoi pv. savastanoi and two isolates of P. syringae pv. tomato. The use of four different bases in the primer sequences did not affect the PCR reproducibility and was very efficient in revealing intra-pathovar diversity, particularly in P. savastanoi pv. savastanoi. At the pathovar level, the primer BOX1AR yielded shared fragments, in addition to five bands that discriminated among the pathovars P. syringae pv. phaseolicola, P. savastanoi pv. savastanoi and P. syringae pv. tomato. REP-PCR with a modified primer containing C produced identical bands among the isolates in a pathovar but separated three pathovars more distinctly than four other primers. Although REP- and BOX-PCRs have been successfully used in the molecular identification of Pseudomonas isolates from Turkish flora, a PCR based on inter-enterobacterial repetitive intergenic concensus (ERIC) sequences failed to produce clear banding patterns in this study.
Collapse
Affiliation(s)
- Elif Cepni
- Department of Molecular Biology and Genetics, Faculty of Sciences, Istanbul University, Istanbul, Turkey
| | | |
Collapse
|
50
|
Abstract
Prokaryotes are in general believed to possess small, compactly organized genomes, with repetitive sequences forming only a small part of them. Nonetheless, many prokaryotic genomes in fact contain species-specific repeats (>85 bp long genomic sequences with less than 60% identity to other species) as we have previously demonstrated. However, it is not known at present how frequent such species-specific repeats are and what their functional roles in bacterial genomes may be. Therefore, we have conducted a comprehensive survey of prokaryotic species-specific repeats and characterized them to examine as to whether there are functional classes among different repeats or not and how they are mutually related to each other. Of the 613 distinct prokaryotic species analyzed, 97% were found to contain at least one species-specific repeats. It seems interesting to note that the species-specific repeats thus identified appear to be functionally variable in different genomes: in some genomes, they are mostly associated with duplicated protein-coding genes, whereas in some other genomes with rRNA and tRNA genes. Contrary to what may be expected, only one-fourth of the species-specific repeats were found to be associated with mobile genetic elements.
Collapse
Affiliation(s)
- Triinu Koressaar
- Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.
| | | |
Collapse
|