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Jørgensen TS, Mohite O, Sterndorff E, Alvarez-Arevalo M, Blin K, Booth T, Charusanti P, Faurdal D, Hansen T, Nuhamunada M, Mourched AS, Palsson B, Weber T. A treasure trove of 1034 actinomycete genomes. Nucleic Acids Res 2024; 52:7487-7503. [PMID: 38908028 PMCID: PMC11260486 DOI: 10.1093/nar/gkae523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 04/30/2024] [Accepted: 06/04/2024] [Indexed: 06/24/2024] Open
Abstract
Filamentous Actinobacteria, recently renamed Actinomycetia, are the most prolific source of microbial bioactive natural products. Studies on biosynthetic gene clusters benefit from or require chromosome-level assemblies. Here, we provide DNA sequences from >1000 isolates: 881 complete genomes and 153 near-complete genomes, representing 28 genera and 389 species, including 244 likely novel species. All genomes are from filamentous isolates of the class Actinomycetia from the NBC culture collection. The largest genus is Streptomyces with 886 genomes including 742 complete assemblies. We use this data to show that analysis of complete genomes can bring biological understanding not previously derived from more fragmented sequences or less systematic datasets. We document the central and structured location of core genes and distal location of specialized metabolite biosynthetic gene clusters and duplicate core genes on the linear Streptomyces chromosome, and analyze the content and length of the terminal inverted repeats which are characteristic for Streptomyces. We then analyze the diversity of trans-AT polyketide synthase biosynthetic gene clusters, which encodes the machinery of a biotechnologically highly interesting compound class. These insights have both ecological and biotechnological implications in understanding the importance of high quality genomic resources and the complex role synteny plays in Actinomycetia biology.
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Affiliation(s)
- Tue Sparholt Jørgensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Søltofts Plads, building 220, 2800 Kgs. Lyngby, Denmark
| | - Omkar S Mohite
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Søltofts Plads, building 220, 2800 Kgs. Lyngby, Denmark
| | - Eva B Sterndorff
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Søltofts Plads, building 220, 2800 Kgs. Lyngby, Denmark
| | - Maria Alvarez-Arevalo
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Søltofts Plads, building 220, 2800 Kgs. Lyngby, Denmark
| | - Kai Blin
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Søltofts Plads, building 220, 2800 Kgs. Lyngby, Denmark
| | - Thomas J Booth
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Søltofts Plads, building 220, 2800 Kgs. Lyngby, Denmark
| | - Pep Charusanti
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Søltofts Plads, building 220, 2800 Kgs. Lyngby, Denmark
| | - David Faurdal
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Søltofts Plads, building 220, 2800 Kgs. Lyngby, Denmark
| | - Troels Ø Hansen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Søltofts Plads, building 220, 2800 Kgs. Lyngby, Denmark
| | - Matin Nuhamunada
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Søltofts Plads, building 220, 2800 Kgs. Lyngby, Denmark
| | - Anna-Sophie Mourched
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Søltofts Plads, building 220, 2800 Kgs. Lyngby, Denmark
| | - Bernhard Ø Palsson
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Søltofts Plads, building 220, 2800 Kgs. Lyngby, Denmark
- Department of Bioengineering, University of California, 417 Powell-Focht Bioengineering Hall, San Diego, La Jolla, CA 92093-0412, USA
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Søltofts Plads, building 220, 2800 Kgs. Lyngby, Denmark
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2
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Bury-Moné S, Thibessard A, Lioy VS, Leblond P. Dynamics of the Streptomyces chromosome: chance and necessity. Trends Genet 2023; 39:873-887. [PMID: 37679290 DOI: 10.1016/j.tig.2023.07.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/26/2023] [Accepted: 07/28/2023] [Indexed: 09/09/2023]
Abstract
Streptomyces are prolific producers of specialized metabolites with applications in medicine and agriculture. Remarkably, these bacteria possess a large linear chromosome that is genetically compartmentalized: core genes are grouped in the central part, while the ends are populated by poorly conserved genes including antibiotic biosynthetic gene clusters. The genome is highly unstable and exhibits distinct evolutionary rates along the chromosome. Recent chromosome conformation capture (3C) and comparative genomics studies have shed new light on the interplay between genome dynamics in space and time. Here, we review insights that illustrate how the balance between chance (random genome variations) and necessity (structural and functional constraints) may have led to the emergence of spatial structuring of the Streptomyces chromosome.
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Affiliation(s)
- Stéphanie Bury-Moné
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
| | | | - Virginia S Lioy
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Pierre Leblond
- Université de Lorraine, INRAE, DynAMic, F-54000 Nancy, France
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3
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Hawkey J, Cottingham H, Tokolyi A, Wick RR, Judd LM, Cerdeira L, de Oliveira Garcia D, Wyres KL, Holt KE. Linear plasmids in Klebsiella and other Enterobacteriaceae. Microb Genom 2022; 8. [PMID: 35416146 PMCID: PMC9453081 DOI: 10.1099/mgen.0.000807] [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] [Indexed: 11/20/2022] Open
Abstract
Linear plasmids are extrachromosomal DNA elements that have been found in a small number of bacterial species. To date, the only linear plasmids described in the family Enterobacteriaceae belong to Salmonella, first found in Salmonella enterica Typhi. Here, we describe a collection of 12 isolates of the Klebsiella pneumoniae species complex in which we identified linear plasmids. Screening of assembly graphs assembled from public read sets identified linear plasmid structures in a further 13 K. pneumoniae species complex genomes. We used these 25 linear plasmid sequences to query all bacterial genome assemblies in the National Center for Biotechnology Information database, and discovered an additional 61 linear plasmid sequences in a variety of Enterobacteriaceae species. Gene content analysis divided these plasmids into five distinct phylogroups, with very few genes shared across more than two phylogroups. The majority of linear plasmid-encoded genes are of unknown function; however, each phylogroup carried its own unique toxin–antitoxin system and genes with homology to those encoding the ParAB plasmid stability system. Passage in vitro of the 12 linear plasmid-carrying Klebsiella isolates in our collection (which include representatives of all five phylogroups) indicated that these linear plasmids can be stably maintained, and our data suggest they can transmit between K. pneumoniae strains (including members of globally disseminated multidrug-resistant clones) and also between diverse Enterobacteriaceae species. The linear plasmid sequences, and representative isolates harbouring them, are made available as a resource to facilitate future studies on the evolution and function of these novel plasmids.
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Affiliation(s)
- Jane Hawkey
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria 3004, Australia
| | - Hugh Cottingham
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria 3004, Australia
| | - Alex Tokolyi
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Ryan R Wick
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria 3004, Australia
| | - Louise M Judd
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria 3004, Australia
| | | | | | - Kelly L Wyres
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria 3004, Australia
| | - Kathryn E Holt
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria 3004, Australia.,Department of Infection Biology, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
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4
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Barry CP, Gillane R, Talbo GH, Plan M, Palfreyman R, Haber-Stuk AK, Power J, Nielsen LK, Marcellin E. Multi-omic characterisation of Streptomyces hygroscopicus NRRL 30439: detailed assessment of its secondary metabolic potential. Mol Omics 2022; 18:226-236. [PMID: 34989730 DOI: 10.1039/d1mo00150g] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The emergence of multidrug-resistant pathogenic bacteria creates a demand for novel antibiotics with distinct mechanisms of action. Advances in next-generation genome sequencing promised a paradigm shift in the quest to find new bioactive secondary metabolites. Genome mining has proven successful for predicting putative biosynthetic elements in secondary metabolite superproducers such as Streptomycetes. However, genome mining approaches do not inform whether biosynthetic gene clusters are dormant or active under given culture conditions. Here we show that using a multi-omics approach in combination with antiSMASH, it is possible to assess the secondary metabolic potential of a Streptomyces strain capable of producing mannopeptimycin, an important cyclic peptide effective against Gram-positive infections. The genome of Streptomyces hygroscopicus NRRL 30439 was first sequenced using PacBio RSII to obtain a closed genome. A chemically defined medium was then used to elicit a nutrient stress response in S. hygroscopicus NRRL 30439. Detailed extracellular metabolomics and intracellular proteomics were used to profile and segregate primary and secondary metabolism. Our results demonstrate that the combination of genomics, proteomics and metabolomics enables rapid evaluation of a strain's performance in bioreactors for industrial production of secondary metabolites.
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Affiliation(s)
- Craig P Barry
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, 4072 St. Lucia, Australia.
| | - Rosemary Gillane
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, 4072 St. Lucia, Australia.
| | - Gert H Talbo
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, 4072 St. Lucia, Australia. .,The Queensland Node of Metabolomics Australia, AIBN, The University of Queensland, 4072 St. Lucia, Australia
| | - Manual Plan
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, 4072 St. Lucia, Australia. .,The Queensland Node of Metabolomics Australia, AIBN, The University of Queensland, 4072 St. Lucia, Australia
| | - Robin Palfreyman
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, 4072 St. Lucia, Australia. .,The Queensland Node of Metabolomics Australia, AIBN, The University of Queensland, 4072 St. Lucia, Australia
| | | | - John Power
- Zoetis, 333 Portage Street, Kalamazoo, MI 49007, USA
| | - Lars K Nielsen
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, 4072 St. Lucia, Australia. .,The Queensland Node of Metabolomics Australia, AIBN, The University of Queensland, 4072 St. Lucia, Australia.,The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Esteban Marcellin
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, 4072 St. Lucia, Australia. .,The Queensland Node of Metabolomics Australia, AIBN, The University of Queensland, 4072 St. Lucia, Australia
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5
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Novakova R, Rückert C, Knirschova R, Feckova L, Busche T, Csolleiova D, Homerova D, Rezuchova B, Javorova R, Sevcikova B, Kalinowski J, Kormanec J. The linear plasmid pSA3239 is essential for the replication of the Streptomyces lavendulae subsp. lavendulae CCM 3239 chromosome. Res Microbiol 2021; 172:103870. [PMID: 34487842 DOI: 10.1016/j.resmic.2021.103870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 07/16/2021] [Accepted: 07/22/2021] [Indexed: 10/20/2022]
Abstract
We previously reported the complete genome of Streptomyces lavendulae subsp. lavendulae CCM 3239, containing the linear chromosome and the large linear plasmid pSA3239. Although the chromosome exhibited replication features characteristic for the archetypal end-patching replication, it lacked the tap/tpg gene pair for two proteins essential for this process. However, this archetypal tpgSa-tapSa operon is present in pSA3239. Complete genomic sequence of the S. lavendulae Del-LP strain lacking this plasmid revealed the circularization of its chromosome with a large deletion of both arms. These results suggest an essential role of pSA3239-encoded TapSa/TpgSa in the end-patching replication of the chromosome.
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Affiliation(s)
- Renata Novakova
- Institute of Molecular Biology, Slovak Academy of Sciences, 845 51 Bratislava, Slovak Republic.
| | - Christian Rückert
- Center for Biotechnology (CeBiTec), Universität Bielefeld, Bielefeld, Germany.
| | - Renata Knirschova
- Institute of Molecular Biology, Slovak Academy of Sciences, 845 51 Bratislava, Slovak Republic.
| | - Lubomira Feckova
- Institute of Molecular Biology, Slovak Academy of Sciences, 845 51 Bratislava, Slovak Republic.
| | - Tobias Busche
- Center for Biotechnology (CeBiTec), Universität Bielefeld, Bielefeld, Germany.
| | - Dominika Csolleiova
- Institute of Molecular Biology, Slovak Academy of Sciences, 845 51 Bratislava, Slovak Republic.
| | - Dagmar Homerova
- Institute of Molecular Biology, Slovak Academy of Sciences, 845 51 Bratislava, Slovak Republic.
| | - Bronislava Rezuchova
- Institute of Molecular Biology, Slovak Academy of Sciences, 845 51 Bratislava, Slovak Republic.
| | - Rachel Javorova
- Institute of Molecular Biology, Slovak Academy of Sciences, 845 51 Bratislava, Slovak Republic.
| | - Beatrica Sevcikova
- Institute of Molecular Biology, Slovak Academy of Sciences, 845 51 Bratislava, Slovak Republic.
| | - Jörn Kalinowski
- Center for Biotechnology (CeBiTec), Universität Bielefeld, Bielefeld, Germany.
| | - Jan Kormanec
- Institute of Molecular Biology, Slovak Academy of Sciences, 845 51 Bratislava, Slovak Republic.
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6
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Spatial rearrangement of the Streptomyces venezuelae linear chromosome during sporogenic development. Nat Commun 2021; 12:5222. [PMID: 34471115 PMCID: PMC8410768 DOI: 10.1038/s41467-021-25461-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 08/12/2021] [Indexed: 12/13/2022] Open
Abstract
Bacteria of the genus Streptomyces have a linear chromosome, with a core region and two ‘arms’. During their complex life cycle, these bacteria develop multi-genomic hyphae that differentiate into chains of exospores that carry a single copy of the genome. Sporulation-associated cell division requires chromosome segregation and compaction. Here, we show that the arms of Streptomyces venezuelae chromosomes are spatially separated at entry to sporulation, but during sporogenic cell division they are closely aligned with the core region. Arm proximity is imposed by segregation protein ParB and condensin SMC. Moreover, the chromosomal terminal regions are organized into distinct domains by the Streptomyces-specific HU-family protein HupS. Thus, as seen in eukaryotes, there is substantial chromosomal remodelling during the Streptomyces life cycle, with the chromosome undergoing rearrangements from an ‘open’ to a ‘closed’ conformation. Streptomyces bacteria have a linear chromosome and a complex life cycle, including development of multi-genomic hyphae that differentiate into mono-genomic exospores. Here, Szafran et al. show that the chromosome of Streptomyces venezuelae undergoes substantial remodelling during sporulation, from an ‘open’ to a ‘closed’ conformation.
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7
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Pan HY, Chen CW, Huang CH. A highly efficient targeted recombination system for engineering linear chromosomes of industrial bacteria Streptomyces. J GEN APPL MICROBIOL 2018; 64:167-173. [PMID: 29669960 DOI: 10.2323/jgam.2017.11.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Soil bacteria Streptomyces are the most important producers of secondary metabolites, including most known antibiotics. These bacteria and their close relatives are unique in possessing linear chromosomes, which typically harbor 20 to 30 biosynthetic gene clusters of tens to hundreds of kb in length. Many Streptomyces chromosomes are accompanied by linear plasmids with sizes ranging from several to several hundred kb. The large linear plasmids also often contain biosynthetic gene clusters. We have developed a targeted recombination procedure for arm exchanges between a linear plasmid and a linear chromosome. A chromosomal segment inserted in an artificially constructed plasmid allows homologous recombination between the two replicons at the homology. Depending on the design, the recombination may result in two recombinant replicons or a single recombinant chromosome with the loss of the recombinant plasmid that lacks a replication origin. The efficiency of such targeted recombination ranges from 9 to 83% depending on the locations of the homology (and thus the size of the chromosomal arm exchanged), essentially eliminating the necessity of selection. The targeted recombination is useful for the efficient engineering of the Streptomyces genome for large-scale deletion, addition, and shuffling.
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Affiliation(s)
- Hung-Yin Pan
- Graduate Institution of Engineering Technology, National Taipei University of Technology
| | - Carton W Chen
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University
| | - Chih-Hung Huang
- Institute of Biochemical and Biomedical Engineering, National Taipei University of Technology
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8
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Mingyar E, Novakova R, Knirschova R, Feckova L, Bekeova C, Kormanec J. Unusual features of the large linear plasmid pSA3239 from Streptomyces aureofaciens CCM 3239. Gene 2017; 642:313-323. [PMID: 29155332 DOI: 10.1016/j.gene.2017.11.046] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 11/13/2017] [Accepted: 11/15/2017] [Indexed: 11/17/2022]
Abstract
We previously identified the aur1 gene cluster, responsible for the production of the angucycline antibiotic auricin in Streptomyces aureofaciens CCM 3239. Pulse-field gel electrophoresis showed a single, 241kb linear plasmid, pSA3239, in this strain, and several approaches confirmed the presence of the aur1 cluster in this plasmid. We report here the nucleotide sequence of this 241,076-bp plasmid. pSA3239 contains an unprecedentedly small (13bp) telomeric sequence CCCGCGGAGCGGG, which is identical to the conserved Palindrome I sequence involved in the priming of end-patching replication. A bioinformatics analysis revealed 234 open reading frames with high number (28) of regulatory genes from various families. In contrast to most other linear plasmids, pSA3239 contains a pair of replication initiation genes (sa76 and sa75) located at its extreme left end, adjacent to the telomere. Together with similar proteins from several other linear plasmids (pFRL2, pSLA2-M, pSV2, pSDA1, and SAP1), they constitute a new family of replication initiation proteins. This left end also contains two genes, tpgSa and tapSa, encoding the terminal protein and the telomere associated-protein involved in telomere end-patching replication. pSA3239 also contains two genes homologous to the parAB partitioning system, and deletion of the parA homologue (sa43) affects structural stability of the plasmid. pSA3239 carries five potential secondary metabolite gene clusters. In addition to aur1 and a non-ribosomal peptide synthase (NRPS) gene cluster for the blue pigment indigoidine, it also contains a partial type II polyketide synthase (PKS) gene cluster, a partial type I PKS gene cluster, and a NRPS/PKSI gene cluster for unknown secondary metabolites. The last gene cluster contains a subcluster of seven genes (sa91-sa97), highly similar to part of the valanimycin biosynthetic cluster vlm. A S. aureofaciens strain lacking pSA3239 was prepared. This deletion did not substantially affect growth and differentiation. A comparative analysis of secondary metabolites between both strains did not identify any product, except auricin and indigoidine, which is dependent upon pSA3239. Thus, the other three identified gene clusters are likely silent under these conditions.
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Affiliation(s)
- Erik Mingyar
- Institute of Molecular Biology, Slovak Academy of Sciences, 845 51 Bratislava, Slovak Republic
| | - Renata Novakova
- Institute of Molecular Biology, Slovak Academy of Sciences, 845 51 Bratislava, Slovak Republic
| | - Renata Knirschova
- Institute of Molecular Biology, Slovak Academy of Sciences, 845 51 Bratislava, Slovak Republic
| | - Lubomira Feckova
- Institute of Molecular Biology, Slovak Academy of Sciences, 845 51 Bratislava, Slovak Republic
| | - Carmen Bekeova
- Institute of Molecular Biology, Slovak Academy of Sciences, 845 51 Bratislava, Slovak Republic
| | - Jan Kormanec
- Institute of Molecular Biology, Slovak Academy of Sciences, 845 51 Bratislava, Slovak Republic.
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9
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Yang CC, Tseng SM, Pan HY, Huang CH, Chen CW. Telomere associated primase Tap repairs truncated telomeres of Streptomyces. Nucleic Acids Res 2017; 45:5838-5849. [PMID: 28369604 PMCID: PMC5449611 DOI: 10.1093/nar/gkx189] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 03/11/2017] [Indexed: 01/01/2023] Open
Abstract
Replication of the linear chromosomes of soil bacteria Streptomyces proceeds from an internal origin towards the telomeres, followed by patching of the resulting terminal single-strand overhangs by DNA synthesis using terminal proteins as the primer, which remains covalently bound to the 5΄ ends of the DNA. In most Streptomyces chromosomes, the end patching requires the single-strand overhangs, terminal protein Tpg, and terminal associated protein Tap. The telomere overhangs contain several palindromic sequences capable of forming stable hairpins. Previous in vitro deoxynucleotidylation studies indicated that Tap adds the Palindrome I sequence to Tpg, which is extended by a polymerase to fill the gap. In this study, the stringency of Palindrome I sequence was examined by an in vitro deoxynucleotidylation system and in vivo replication. Several nt in Palindrome I were identified to be critical for priming. While the first 3 G on the template were required for deoxynucleotidylation in vitro, deletions of them could be suppressed by the presence of dGTP. In vivo, deletions of these G were also tolerated, and the telomere sequence was restored in the linear plasmid DNA. Our results indicated that the truncated telomeres were repaired by extension synthesis by Tap on the foldback Palindrome I sequence.
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Affiliation(s)
- Chien-Chin Yang
- Department of Chemistry, Chung-Yuan Christian University, Chung-li, Taiwan
- To whom correspondence should be addressed. Tel: +886 3 2653303; Fax: +886 3 2653399;
| | - Shu-Min Tseng
- Department of Chemistry, Chung-Yuan Christian University, Chung-li, Taiwan
| | - Hung-Yin Pan
- Institute of Biochemical and Biomedical Engineering, National Taipei University of Technology, Taipei, Taiwan
| | - Chih-Hung Huang
- Institute of Biochemical and Biomedical Engineering, National Taipei University of Technology, Taipei, Taiwan
| | - Carton W. Chen
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan
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10
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Feijoo-Siota L, Rama JLR, Sánchez-Pérez A, Villa TG. Considerations on bacterial nucleoids. Appl Microbiol Biotechnol 2017; 101:5591-5602. [PMID: 28664324 DOI: 10.1007/s00253-017-8381-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 06/01/2017] [Accepted: 06/02/2017] [Indexed: 12/21/2022]
Abstract
The classic genome organization of the bacterial chromosome is normally envisaged with all its genetic markers linked, thus forming a closed genetic circle of duplex stranded DNA (dsDNA) and several proteins in what it is called as "the bacterial nucleoid." This structure may be more or less corrugated depending on the physiological state of the bacterium (i.e., resting state or active growth) and is not surrounded by a double membrane as in eukayotic cells. The universality of the closed circle model in bacteria is however slowly changing, as new data emerge in different bacterial groups such as in Planctomycetes and related microorganisms, species of Borrelia, Streptomyces, Agrobacterium, or Phytoplasma. In these and possibly other microorganisms, the existence of complex formations of intracellular membranes or linear chromosomes is typical; all of these situations contributing to weakening the current cellular organization paradigm, i.e., prokaryotic vs eukaryotic cells.
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Affiliation(s)
- Lucía Feijoo-Siota
- Department of Microbiology, Biotechnology Unit, Faculty of Pharmacy, University of Santiago de Compostela, 15706, Santiago de Compostela, Spain
| | - José Luis R Rama
- Department of Microbiology, Biotechnology Unit, Faculty of Pharmacy, University of Santiago de Compostela, 15706, Santiago de Compostela, Spain
| | - Angeles Sánchez-Pérez
- Discipline of Physiology and Bosch Institute, School of Medical Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Tomás G Villa
- Department of Microbiology, Biotechnology Unit, Faculty of Pharmacy, University of Santiago de Compostela, 15706, Santiago de Compostela, Spain.
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