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Determination of Temperature Sensitive Plasmid Copy Number in Escherichia coli by Absolute and Relative Real Time Quantitation PCR. Jundishapur J Microbiol 2017. [DOI: 10.5812/jjm.14600] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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2
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Yousef T, Abu El-Reash G, Al-Jahdali M, El-Rakhawy EBR. Structural and biological evaluation of some metal complexes of vanillin-4N-(2-pyridyl) thiosemicarbazone. J Mol Struct 2013. [DOI: 10.1016/j.molstruc.2013.08.034] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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3
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El-Ayaan U. Transition metal complexes of 3-acetylpyridine 4 N-(2-pyridyl)thiosemicarbazone (HAPS); structural, spectroscopic, and biological studies. J COORD CHEM 2012. [DOI: 10.1080/00958972.2012.658381] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
- Usama El-Ayaan
- a Department of Chemistry, Faculty of Science , Mansoura University , Mansoura 35516 , Egypt
- b Department of Chemistry , College of Science, King Faisal University , P.O. Box 380, Hofuf 31982 , Saudi Arabia
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4
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Synthesis, DNA affinity, and antimicrobial activity of 4-substituted phenyl-2,2′-bichalcophenes and aza-analogues. Med Chem Res 2011. [DOI: 10.1007/s00044-011-9964-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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5
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Mußmann M, Hu FZ, Richter M, de Beer D, Preisler A, Jørgensen BB, Huntemann M, Glöckner FO, Amann R, Koopman WJH, Lasken RS, Janto B, Hogg J, Stoodley P, Boissy R, Ehrlich GD. Insights into the genome of large sulfur bacteria revealed by analysis of single filaments. PLoS Biol 2007; 5:e230. [PMID: 17760503 PMCID: PMC1951784 DOI: 10.1371/journal.pbio.0050230] [Citation(s) in RCA: 136] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2007] [Accepted: 06/26/2007] [Indexed: 11/19/2022] Open
Abstract
Marine sediments are frequently covered by mats of the filamentous Beggiatoa and other large nitrate-storing bacteria that oxidize hydrogen sulfide using either oxygen or nitrate, which they store in intracellular vacuoles. Despite their conspicuous metabolic properties and their biogeochemical importance, little is known about their genetic repertoire because of the lack of pure cultures. Here, we present a unique approach to access the genome of single filaments of Beggiatoa by combining whole genome amplification, pyrosequencing, and optical genome mapping. Sequence assemblies were incomplete and yielded average contig sizes of approximately 1 kb. Pathways for sulfur oxidation, nitrate and oxygen respiration, and CO2 fixation confirm the chemolithoautotrophic physiology of Beggiatoa. In addition, Beggiatoa potentially utilize inorganic sulfur compounds and dimethyl sulfoxide as electron acceptors. We propose a mechanism of vacuolar nitrate accumulation that is linked to proton translocation by vacuolar-type ATPases. Comparative genomics indicates substantial horizontal gene transfer of storage, metabolic, and gliding capabilities between Beggiatoa and cyanobacteria. These capabilities enable Beggiatoa to overcome non-overlapping availabilities of electron donors and acceptors while gliding between oxic and sulfidic zones. The first look into the genome of these filamentous sulfur-oxidizing bacteria substantially deepens the understanding of their evolution and their contribution to sulfur and nitrogen cycling in marine sediments.
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Affiliation(s)
- Marc Mußmann
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- * To whom correspondence should be addressed. E-mail: (MM); (FOG); (GDE)
| | - Fen Z Hu
- Center for Genomic Sciences, Allegheny General Hospital/Allegheny-Singer Research Institute, Pittsburgh, Pennsylvania, United States of America
| | - Michael Richter
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- School of Engineering and Sciences, Jacobs University Bremen, Bremen, Germany
| | - Dirk de Beer
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - André Preisler
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Bo B Jørgensen
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Marcel Huntemann
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- School of Engineering and Sciences, Jacobs University Bremen, Bremen, Germany
| | - Frank Oliver Glöckner
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- School of Engineering and Sciences, Jacobs University Bremen, Bremen, Germany
- * To whom correspondence should be addressed. E-mail: (MM); (FOG); (GDE)
| | - Rudolf Amann
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Werner J. H Koopman
- Department of Membrane Biochemistry, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Roger S Lasken
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Benjamin Janto
- Center for Genomic Sciences, Allegheny General Hospital/Allegheny-Singer Research Institute, Pittsburgh, Pennsylvania, United States of America
| | - Justin Hogg
- Center for Genomic Sciences, Allegheny General Hospital/Allegheny-Singer Research Institute, Pittsburgh, Pennsylvania, United States of America
| | - Paul Stoodley
- Center for Genomic Sciences, Allegheny General Hospital/Allegheny-Singer Research Institute, Pittsburgh, Pennsylvania, United States of America
| | - Robert Boissy
- Center for Genomic Sciences, Allegheny General Hospital/Allegheny-Singer Research Institute, Pittsburgh, Pennsylvania, United States of America
| | - Garth D Ehrlich
- Center for Genomic Sciences, Allegheny General Hospital/Allegheny-Singer Research Institute, Pittsburgh, Pennsylvania, United States of America
- * To whom correspondence should be addressed. E-mail: (MM); (FOG); (GDE)
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6
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Pollock S, Thomas DY, Jansen G. PCR-based unidirectional deletion method for creation of comprehensive cDNA libraries. Biochim Biophys Acta Gen Subj 2005; 1723:265-9. [PMID: 15780982 DOI: 10.1016/j.bbagen.2005.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2004] [Revised: 11/25/2004] [Accepted: 02/01/2005] [Indexed: 11/20/2022]
Abstract
A new strategy for the rapid creation of DNA deletion libraries using a simple PCR-based method is presented. Unidirectional deletion fragments are created and may be cloned into any vector system without the constraint of using restriction enzymes. Our strategy combines methodologies from DNA sequencing, PCR, and homologous recombination (either in vivo or in vitro) to allow for the creation of a library containing fragments representing all possible deletions of a given cDNA. Using this strategy we have successfully constructed a deletion library of the cDNA encoding for the lumenal domain of yeast Ire1p, and have shown that resulting fragments range from 100 bp to the full length cDNA (1557 bp). This method is simple, inexpensive, and can easily be adapted for automated high-throughput research.
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Affiliation(s)
- Stephanie Pollock
- Biochemistry Department, Faculty of Medicine, McGill University, McIntyre Medical Sciences Building, 3655 Promenade Sir William Osler, Montréal, Québec, Canada, H3G 1Y6
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7
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Trevors J. Molecular evolution in bacteria: genome size, cell size, restriction-modification and recognition. ACTA ACUST UNITED AC 1998. [DOI: 10.1016/s0020-2452(98)80026-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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8
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Kleman GL, Horken KM, Tabita FR, Strohl WR. Overproduction of recombinant ribulose 1,5-bisphosphate carboxylase/oxygenase from Synechococcus sp. strain PCC6301 in glucose-controlled high-cell-density fermentations by Escherichia coli K-12. Appl Environ Microbiol 1996; 62:3502-7. [PMID: 8795245 PMCID: PMC168151 DOI: 10.1128/aem.62.9.3502-3507.1996] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
A predictive and feedback glucose feed controller, previously developed for nutrient-sufficient growth of Escherichia coli to high cell densities, was used to produce large quantities of a heterologous, cyanobacterial recombinant hexadecameric (L8S8) protein, ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) in E. coli. Culture and plasmid stability conditions were optimized to yield the production of approximately 1 g of soluble, active recombinant RubisCO per liter. Recombinant RubisCO also was produced in lactose-induced high-cell-density fermentation of E. coli K-12.
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Affiliation(s)
- G L Kleman
- Department of Microbiology, Ohio State University, Columbus 43210, USA
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Abstract
This manuscript examines genome size in bacteria. The opposing capability of bacteria to alter their genome sizes and order of genes within limits yet remain somewhat constant provides a mechanisms for diversity and evolution in bacterial populations. Bacteria may have evolved by increasing their genome size and changing gene orders with the assistance of restriction endonucleases cleaving foreign DNA and providing a diverse pool of DNA sequences for recombination. These aspects and selected information on physically mapping bacterial genomes will be discussed.
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Affiliation(s)
- J T Trevors
- Department of Environmental Biology, University of Guelph, Ontario, Canada.
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Leblond P, Francou F, Simonet JM, Decaris B. Pulsed-field gel electrophoresis analysis of the genome ofStreptomyces ambofaciensstrains. FEMS Microbiol Lett 1990. [DOI: 10.1111/j.1574-6968.1990.tb03866.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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11
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Birch A, Häusler A, Vögtli M, Krek W, Hütter R. Extremely large chromosomal deletions are intimately involved in genetic instability and genomic rearrangements in Streptomyces glaucescens. MOLECULAR & GENERAL GENETICS : MGG 1989; 217:447-58. [PMID: 2770699 DOI: 10.1007/bf02464916] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Genetic instability in Streptomyces glaucescens characteristically involves the occurrence of gross genomic rearrangements including high-level sequence amplification and extensive deletion. We investigated the relationship of the unstable melC and strS loci and a 100 kb region of the chromosome which frequently gives rise to intense heterogeneous DNA amplification. Standard chromosome walking using a cosmid bank in conjunction with a "reverse-blot" procedure enabled us to construct a contiguous genomic BamHI map of the unstable region exceeding 900 kb. The unstable genes and the amplifiable region (AUD locus) are physically linked within a 600 kb segment of the chromosome. The previously characterized deletions which affect these loci are merely components of much larger deletions ranging from 270 to over 800 kb which are polar in nature, effecting the sequential loss of the strS and melC loci. The more extensive deletions terminate either adjacent to, or in the vicinity of DNA reiterations at the AUD locus. Additionally, a deletion junction fragment and the corresponding deletion ends were cloned and analysed at the sequence level.
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Affiliation(s)
- A Birch
- Mikrobiologisches Institut, Eidgenössische Technische Hochschule, Zürich, Switzerland
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12
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Baylis HA, Bibb MJ. Transcriptional analysis of the 16S rRNA gene of the rrnD gene set of Streptomyces coelicolor A3(2). Mol Microbiol 1988; 2:569-79. [PMID: 2460716 DOI: 10.1111/j.1365-2958.1988.tb00065.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The nucleotide sequence of 2.5 kb of the Streptomyces coelicolor A3(2) rRNA gene set rrnD, extending from upstream of the 16S rRNA gene to the putative 5' end of the 23S rRNA gene, has been determined (Baylis and Bibb, 1987; this paper). In addition to locating the 5' end of the 16S rRNA gene, nuclease S1 mapping identified seven RNA 5' end-points upstream of the 16S rRNA gene; four of these were coincident with transcriptional initiation points for S. coelicolor A3(2) RNA polymerase in vitro and were consequently regarded as in vivo transcription start points for promoters p1 to p4. One end-point identified by nuclease S1 mapping localized a putative processing site analogous to those found upstream of 16S rRNA genes in other eubacteria. Sequence motifs similar to those discovered in low G+C Gram-positive bacteria were found associated with two of the promoters and the processing site. A probable protein coding region was observed upstream of the promoter region.
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MESH Headings
- Base Sequence
- Cloning, Molecular
- DNA, Bacterial
- Genes, Bacterial
- Molecular Sequence Data
- Plasmids
- Promoter Regions, Genetic
- RNA Processing, Post-Transcriptional
- RNA, Bacterial/genetics
- RNA, Ribosomal/genetics
- RNA, Ribosomal, 16S/genetics
- Restriction Mapping
- Streptomyces/genetics
- Transcription, Genetic
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Affiliation(s)
- H A Baylis
- John Innes Institute of Plant Science Research, Norwich, UK
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Sinclair RB, Bibb MJ. The repressor gene (c) of the Streptomyces temperate phage phi c31: nucleotide sequence, analysis and functional cloning. MOLECULAR & GENERAL GENETICS : MGG 1988; 213:269-77. [PMID: 3185504 DOI: 10.1007/bf00339591] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The nucleotide sequence of the 3.4 kb SphI-G fragment that contained the repressor gene (c) of the temperate Streptomyces phage phi c31 was determined. Analysis of this sequence revealed a large open reading frame with protein coding character and sequence changes in c gene point and deletion mutants identified this as the coding region of the repressor. Two of the mutants studied had undergone deletions of 1.1 kb and 1.4 kb that had occurred across short direct repeats of 6 bp and 11 bp, respectively. Coupled in vitro transcription-translation experiments using the cloned SphI-G fragment and Streptomyces lividans cell free extracts identified a protein product of approximately 72 kDa, in close agreement with that predicted from the nucleotide sequence. A strongly predicted helix-turn-helix motif that may be involved in DNA binding occurred towards the carboxy-terminus of the amino acid sequence. Initial attempts to clone the SphI-G fragment in Streptomyces failed; using information gained from the sequence analysis a smaller segment of this DNA fragment was cloned in S. lividans and conferred immunity to a clear plaque mutant (c1) of phi c31.
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14
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Baylis HA, Bibb MJ. Organisation of the ribosomal RNA genes in Streptomyces coelicolor A3(2). MOLECULAR & GENERAL GENETICS : MGG 1988; 211:191-6. [PMID: 2832699 DOI: 10.1007/bf00330593] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Using Southern hybridisation of radiolabelled purified ribosomal RNAs to genomic DNA the ribosomal RNA genes of Streptomyces coelicolor A3(2) were shown to be present in six gene sets. Each gene set contains at least one copy of the 5 S, 16 S and 23 S sequences and in at least two cases these are arranged in the order 16 S - 23 S - 5 S. Three gene sets, rrnB, rrnD and rrnF, were isolated by screening a lambda library of S. coelicolor A3(2) DNA. The restriction map of one of these, rrnD, was determined and the nucleotide sequences corresponding to the three rRNAs were localised by Southern hybridisation. The gene order in rrnD is 16 S - 23 S - 5 S.
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Mendez C, Chater KF. Cloning of whiG, a gene critical for sporulation of Streptomyces coelicolor A3(2). J Bacteriol 1987; 169:5715-20. [PMID: 3680175 PMCID: PMC214075 DOI: 10.1128/jb.169.12.5715-5720.1987] [Citation(s) in RCA: 59] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
In whiG mutants of Streptomyces coelicolor A3(2), aerial hyphae do not show any sign of sporulation. A library of S. coelicolor DNA was prepared in a phi C31 temperate phage vector (KC516), and one recombinant phage (KC750) that could restore the wild-type phenotype to a collection of whiG mutants when integrated into their genomes was found. Subcloning experiments with low- and high-copy-number Streptomyces plasmid vectors allowed partial localization of whiG in the cloned DNA and revealed that hypersporulation was associated with the presence of extra copies of whiG.
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Affiliation(s)
- C Mendez
- John Innes Institute, Norwich, England
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