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Differential expression analysis of Escherichia coli proteins using a novel software for relative quantitation of LC-MS/MS data
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
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2006 (English)In: Proteomics, ISSN 1615-9853, E-ISSN 1615-9861, Vol. 6, no 16, 4475-4485 p.Article in journal (Refereed) Published
Abstract [en]

The study of changes in protein levels between samples derived from cells representing different biological conditions is a key to the understanding of cellular function. There are two main methods available that allow both for global scanning for significantly varying proteins and targeted profiling of proteins of interest. One method is based on 2-D gel electrophoresis and image analysis of labelled proteins. The other method is based on LC-MS/MS analysis of either unlabelled peptides or peptides derived from isotopically labelled proteins or peptides. In this study, the non-labelling approach was used involving a new software, DeCydei (TM) S Differential Analysis Software (DeCyder MS) intended for automated detection and relative quantitation of unlabelled peptides in LC-MS/MS data. Total protein extracts of E. coli strains expressing varying levels of dihydrofolate reductase and integron integrase were digested with trypsin and analyzed using a nanoscale liquid chromatography system, Ettan (TM) MDLC, online connected to an LTQ (TM) linear ion-trap mass spectrometer fitted with a nanospray interface. Acquired NIS data were subjected to DeCyder NIS analysis where 2-D representations of the peptide patterns from individual LC-MS/MS analyses were matched and compared. This approach to unlabelled quantitative analysis of the E. coli proteome resulted in relative protein abundances that were in good agreement with results obtained from traditional methods for measuring protein levels.

Place, publisher, year, edition, pages
2006. Vol. 6, no 16, 4475-4485 p.
Keyword [en]
DeCycler MS, DHFR, integrase, label-free quantitation, LC-MS/MS
National Category
Medical and Health Sciences
URN: urn:nbn:se:uu:diva-95310DOI: 10.1002/pmic.200500921ISI: 000240036100005PubMedID: 16858737OAI: oai:DiVA.org:uu-95310DiVA: diva2:169477
Available from: 2007-01-02 Created: 2007-01-02 Last updated: 2011-06-21Bibliographically approved
In thesis
1. Mechanisms and DNA Specificity in Site-specific Recombination of Integron Cassettes
Open this publication in new window or tab >>Mechanisms and DNA Specificity in Site-specific Recombination of Integron Cassettes
2007 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Bacterial resistance to antibiotics has become a serious problem. This is due to the remarkable ability of bacteria to respond and rapidly adapt to environmental changes. Integrons are elements with the capacity for gene capture by an integron-encoded site-specific recombinase called IntI. IntI binds and acts at the recombination sites, attI and attC resulting in excision and integration of short DNA elements called gene cassettes carrying an attC site in the 3’ end. Several families of antibiotic resistance genes are borne on gene cassettes in integrons connected to mobile elements. Other cassettes reside in the larger and ancestral superintegrons located on chromosomes in both pathogenic and environmental bacteria. Due to their close connection with lateral gene transfer systems, it is possible that integrons are functionally dependent on those networks. This work presents arguments for such connections. The attC of the aadA1-qacE cassette junction in Tn21 was characterized in detail. Like other attC sites, it contains two pairs of inverted repeats and is almost palindromic. By using electrophoretic mobility shift assays, this study showed that IntI1 binds only to the bottom strand of attC. Upon folding the strand into a hairpin, a few chiral hairpin distortions define both the strand choice and also the appropriate orientation of the highly symmetrical site. Structural recognition also explains the wide sequence variation among attC sites. We have documented the initial cleavage step in recombination in IntI extracts and integrase levels in extracts were evaluated by a new method. Mutagenesis and homology modelling were performed to find amino acid residues in IntI1 that are important for recognition of attC hairpin-DNA. Comparisons were made with other tyrosine family members to explain how integron integrases differ in site-recognition and also in their mechanism of strand exchange.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2007. 65 p.
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Medicine, ISSN 1651-6206 ; 214
Microbiology, lateral gene transfer, site-specific recombination, tyrosine recombinase, integron, single-stranded, DNA hairpin, Mikrobiologi
Research subject
Pharmaceutical Microbiology
urn:nbn:se:uu:diva-7429 (URN)978-91-554-6767-8 (ISBN)
Public defence
2007-01-24, C10:301, BMC, Husargatan 3, Uppsala, 09:15
Available from: 2007-01-02 Created: 2007-01-02Bibliographically approved

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Johansson, CarolinaSundström, Lars
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