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Book ; Online ; Thesis: Functional genome analysis of Alcanivorax borkumensis strain SK2

Sabirova, Julia [Verfasser]

alkane metabolism, environmental adaptations and biotechnological potential

2006

Author's details	von Julia Sabirova
Keywords	Biowissenschaften, Biologie ; Life Science, Biology
Subject code	sg570
Language	English
Document type	Book ; Online ; Thesis
Database	Digital theses on the web

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Article: Enzymes Catalyzing the TCA- and Urea Cycle Influence the Matrix Composition of Biofilms Formed by Methicillin-Resistant

De Backer, Sarah / Sabirova, Julia / De Pauw, Ines / De Greve, Henri / Hernalsteens, Jean-Pierre / Goossens, Herman / Malhotra-Kumar, Surbhi

Microorganisms

2018 Volume 6, Issue 4

Abstract: In methicillin- ... ...

Abstract	In methicillin-sensitive
Language	English
Publishing date	2018-10-29
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2720891-6
ISSN	2076-2607
ISSN	2076-2607
DOI	10.3390/microorganisms6040113
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Article ; Online: Whole genome mapping as a fast-track tool to assess genomic stability of sequenced Staphylococcus aureus strains.

Sabirova, Julia S / Xavier, Basil Britto / Ieven, Margareta / Goossens, Herman / Malhotra-Kumar, Surbhi

BMC research notes

2014 Volume 7, Page(s) 704

Abstract: Background: Whole genome (optical) mapping (WGM), a state-of-the-art mapping technology based on the generation of high resolution restriction maps, has so far been used for typing clinical outbreak strains and for mapping de novo sequence contigs in ... ...

Abstract	Background: Whole genome (optical) mapping (WGM), a state-of-the-art mapping technology based on the generation of high resolution restriction maps, has so far been used for typing clinical outbreak strains and for mapping de novo sequence contigs in genome sequencing projects. We employed WGM to assess the genomic stability of previously sequenced Staphylococcus aureus strains that are commonly used in laboratories as reference standards. Results: S. aureus strains (n = 12) were mapped on the Argus™ Optical Mapping System (Opgen Inc, Gaithersburg, USA). Assembly of NcoI-restricted DNA molecules, visualization, and editing of whole genome maps was performed employing MapManager and MapSolver softwares (Opgen Inc). In silico whole genome NcoI-restricted maps were also generated from available sequence data, and compared to the laboratory-generated maps. Strains showing differences between the two maps were resequenced using Nextera XT DNA Sample Preparation Kit and Miseq Reagent Kit V2 (MiSeq, Illumina) and de novo assembled into sequence contigs using the Velvet assembly tool. Sequence data were correlated with corresponding whole genome maps to perform contig mapping and genome assembly using MapSolver. Of the twelve strains tested, one (USA300_FPR3757) showed a 19-kbp deletion on WGM compared to its in silico generated map and reference sequence data. Resequencing of the USA300_FPR3757 identified the deleted fragment to be a 13 kbp-long integrative conjugative element ICE6013. Conclusions: Frequent subculturing and inter-laboratory transfers can induce genomic and therefore, phenotypic changes that could compromise the utility of standard reference strains. WGM can thus be used as a rapid genome screening method to identify genomic rearrangements whose size and type can be confirmed by sequencing.
MeSH term(s)	Computational Biology ; Databases, Genetic ; Gene Deletion ; Gene Expression Regulation, Bacterial ; Genome, Bacterial ; Genomic Instability ; Genotype ; High-Throughput Nucleotide Sequencing ; Optical Restriction Mapping/methods ; Phenotype ; Reproducibility of Results ; Software ; Staphylococcus aureus/classification ; Staphylococcus aureus/genetics
Language	English
Publishing date	2014-10-08
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2413336-X
ISSN	1756-0500 ; 1756-0500
ISSN (online)	1756-0500
ISSN	1756-0500
DOI	10.1186/1756-0500-7-704
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Article: Roles of multiple acyl-CoA oxidases in the routing of carbon flow towards β-oxidation and polyhydroxyalkanoate biosynthesis in Yarrowia lipolytica

Haddouche, Ramdane / Delessert, Syndie / Sabirova, Julia / Neuvéglise, Cécile / Poirier, Yves / Nicaud, Jean-Marc

FEMS yeast research. 2010 Nov., v. 10, no. 7

2010

Abstract: The oleaginous yeast Yarrowia lipolytica possesses six acyl-CoA oxidase (Aox) isoenzymes encoded by genes POX1-POX6. The respective roles of these multiple Aox isoenzymes were studied in recombinant Y. lipolytica strains that express heterologous ... ...

Abstract	The oleaginous yeast Yarrowia lipolytica possesses six acyl-CoA oxidase (Aox) isoenzymes encoded by genes POX1-POX6. The respective roles of these multiple Aox isoenzymes were studied in recombinant Y. lipolytica strains that express heterologous polyhydroxyalkanoate (PHA) synthase (phaC) of Pseudomonas aeruginosa in varying POX genetic backgrounds, thus allowing assessment of the impact of specific Aox enzymes on the routing of carbon flow to β-oxidation or to PHA biosynthesis. Analysis of PHA production yields during growth on fatty acids with different chain lengths has revealed that the POX genotype significantly affects the PHA levels, but not the monomer composition of PHA. Aox3p function was found to be responsible for 90% and 75% of the total PHA produced from either C9:0 or C13:0 fatty acid, respectively, whereas Aox5p encodes the main Aox involved in the biosynthesis of 70% of PHA from C9:0 fatty acid. Other Aoxs, such as Aox1p, Aox2p, Aox4p and Aox6p, were not found to play a significant role in PHA biosynthesis, independent of the chain length of the fatty acid used. Finally, three known models of β-oxidation are discussed and it is shown that a 'leaky-hose pipe model' of the cycle can be applied to Y. lipolytica.
Keywords	yeasts ; Yarrowia lipolytica
Language	English
Dates of publication	2010-11
Size	p. 917-927.
Publisher	Blackwell Publishing Ltd
Publishing place	Oxford, UK
Document type	Article
ZDB-ID	2036775-2
ISSN	1567-1364 ; 1567-1356
ISSN (online)	1567-1364
ISSN	1567-1356
DOI	10.1111/j.1567-1364.2010.00670.x
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Article: Obtention and characterization of poly(3-hydroxybutyricacid-co-hydroxyvaleric acid)/mcl-PHA based blends

Martelli, Silvia Maria / Sabirova, Julia / Fakhoury, Farayde Matta / Dyzma, Alicja / de Meyer, Bernhard / Soetaert, Wim

Lebensmittel-Wissenschaft + [i.e. und] Technologie. 2012 July, v. 47, no. 2

2012

Abstract: The aim of this work was to evaluate the physical–chemical properties of blends of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) and a medium-chain-length polyhydroxyalkanoate (LA). Blends were obtained by casting film-solution on leveled trays. ... ...

Abstract	The aim of this work was to evaluate the physical–chemical properties of blends of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) and a medium-chain-length polyhydroxyalkanoate (LA). Blends were obtained by casting film-solution on leveled trays. Morphological analysis showed compatibility between the two polymers up to 5g/100g of LA polymer was added and phase separation in the polymeric system for compositions containing more than 5g/100g of LA polymer. TGA data and glass transition temperatures revealed some compatibility of the polymers. Moreover, there is a significant decrease of melting temperature and elasticity modulus for PHBV–LA blends with composition. Films containing 5g/100g of LA polymer showed an improvement of 50% in elongation to break (SB) when compared with pure PHBV. For other samples the SB decreased most likely due to the lack of adhesion between the two polymeric phases.
Keywords	acids ; glass transition temperature ; melting point ; modulus of elasticity ; polymers
Language	English
Dates of publication	2012-07
Size	p. 386-392.
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	241369-3
ISSN	0460-1173 ; 0023-6438
ISSN	0460-1173 ; 0023-6438
DOI	10.1016/j.lwt.2012.01.036
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Article ; Online: Employing whole genome mapping for optimal de novo assembly of bacterial genomes.

Xavier, Basil Britto / Sabirova, Julia / Pieter, Moons / Hernalsteens, Jean-Pierre / de Greve, Henri / Goossens, Herman / Malhotra-Kumar, Surbhi

BMC research notes

2014 Volume 7, Page(s) 484

Abstract: Background: De novo genome assembly can be challenging due to inherent properties of the reads, even when using current state-of-the-art assembly tools based on de Bruijn graphs. Often users are not bio-informaticians and, in a black box approach, ... ...

Abstract	Background: De novo genome assembly can be challenging due to inherent properties of the reads, even when using current state-of-the-art assembly tools based on de Bruijn graphs. Often users are not bio-informaticians and, in a black box approach, utilise assembly parameters such as contig length and N50 to generate whole genome sequences, potentially resulting in mis-assemblies. Findings: Utilising several assembly tools based on de Bruijn graphs like Velvet, SPAdes and IDBA, we demonstrate that at the optimal N50, mis-assemblies do occur, even when using the multi-k-mer approaches of SPAdes and IDBA. We demonstrate that whole genome mapping can be used to identify these mis-assemblies and can guide the selection of the best k-mer size which yields the highest N50 without mis-assemblies. Conclusions: We demonstrate the utility of whole genome mapping (WGM) as a tool to identify mis-assemblies and to guide k-mer selection and higher quality de novo genome assembly of bacterial genomes.
MeSH term(s)	Chromosome Mapping/methods ; Contig Mapping ; Genome, Bacterial/genetics ; Sequence Analysis, DNA ; Software ; Staphylococcus aureus/genetics
Language	English
Publishing date	2014-07-30
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2413336-X
ISSN	1756-0500 ; 1756-0500
ISSN (online)	1756-0500
ISSN	1756-0500
DOI	10.1186/1756-0500-7-484
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Article: Niche-specificity factors of a marine oil-degrading bacterium Alcanivorax borkumensis SK2.

Sabirova, Julia S / Chernikova, Tatyana N / Timmis, Kenneth N / Golyshin, Peter N

FEMS microbiology letters

2008 Volume 285, Issue 1, Page(s) 89–96

Abstract: Alcanivorax borkumensis strain SK2 is a cosmopolitan hydrocarbonoclastic marine bacterium, with a specialized metabolism adapted to the degradation of petroleum oil hydrocarbons. Transposon mutagenesis was used for functional genome analysis of ... ...

Abstract	Alcanivorax borkumensis strain SK2 is a cosmopolitan hydrocarbonoclastic marine bacterium, with a specialized metabolism adapted to the degradation of petroleum oil hydrocarbons. Transposon mutagenesis was used for functional genome analysis of Alcanivorax SK2 to reveal the genetic basis of other environmentally relevant phenotypes, such as biofilm formation, adaptation to UV exposure, and to growth at either low temperature or high salinity. Forty-eight relevant transposon mutants deficient in any one of these environmentally responsive functions were isolated, and the corresponding genes interrupted by the mini-Tn5 element were sequenced using inverse PCR. Several cross connections between different phenotypes (e.g. biofilm and UV stress; biofilm and UV and osmoadaptation) on signal transduction level have been revealed, pointing at complex and tightly controlled cellular interactions involving oxygen as a primary messenger and cyclic-di-GMP as a secondary messenger required for Alcanivorax responses to environmental stresses. These results provide insights into bacterial function in a complex marine environment.
MeSH term(s)	Alcanivoraceae/drug effects ; Alcanivoraceae/genetics ; Alcanivoraceae/physiology ; Alcanivoraceae/radiation effects ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Biodegradation, Environmental ; Biofilms/growth & development ; Hydrocarbons/metabolism ; Mutagenesis, Insertional ; Petroleum/metabolism ; Petroleum/microbiology ; Salts/pharmacology ; Seawater/microbiology ; Signal Transduction ; Ultraviolet Rays
Chemical Substances	Bacterial Proteins ; Hydrocarbons ; Petroleum ; Salts
Language	English
Publishing date	2008-08
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	752343-9
ISSN	1574-6968 ; 0378-1097
ISSN (online)	1574-6968
ISSN	0378-1097
DOI	10.1111/j.1574-6968.2008.01222.x
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Article ; Online: Transcriptional profiling of the marine oil-degrading bacterium Alcanivorax borkumensis during growth on n-alkanes.

Sabirova, Julia S / Becker, Anke / Lünsdorf, Heinrich / Nicaud, Jean-Marc / Timmis, Kenneth N / Golyshin, Peter N

FEMS microbiology letters

2011 Volume 319, Issue 2, Page(s) 160–168

Abstract: The marine oil-degrading bacterium Alcanivorax borkumensis SK2 has attracted significant interest due to its hydrocarbonoclastic lifestyle, its alkane-centered metabolism, and for playing an important ecological role in cleaning up marine oil spills. In ... ...

Abstract	The marine oil-degrading bacterium Alcanivorax borkumensis SK2 has attracted significant interest due to its hydrocarbonoclastic lifestyle, its alkane-centered metabolism, and for playing an important ecological role in cleaning up marine oil spills. In this study, we used microarray technology to characterize the transcriptional responses of A. borkumensis to n-hexadecane exposure as opposed to pyruvate, which led to the identification of a total of 220 differentially expressed genes, with 109 genes being upregulated and 111 genes being downregulated. Among the genes upregulated on alkanes are systems predicted to be involved in the terminal oxidation of alkanes, biofilm formation, signal transduction, and regulation.
MeSH term(s)	Alcanivoraceae/genetics ; Alcanivoraceae/growth & development ; Alcanivoraceae/isolation & purification ; Alcanivoraceae/metabolism ; Alkanes/metabolism ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Biodegradation, Environmental ; Gene Expression Profiling ; Gene Expression Regulation, Bacterial ; Molecular Sequence Data ; Seawater/microbiology ; Transcription, Genetic
Chemical Substances	Alkanes ; Bacterial Proteins
Language	English
Publishing date	2011-06
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	752343-9
ISSN	1574-6968 ; 0378-1097
ISSN (online)	1574-6968
ISSN	0378-1097
DOI	10.1111/j.1574-6968.2011.02279.x
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Article: Transcriptional profiling of the marine oil-degrading bacterium Alcanivorax borkumensis during growth on n-alkanes

Sabirova, Julia S / Becker, Anke / Lünsdorf, Heinrich / Nicaud, Jean-Marc / Timmis, Kenneth N / Golyshin, Peter N

FEMS microbiology letters. 2011 June, v. 319, no. 2

2011

Abstract	The marine oil-degrading bacterium Alcanivorax borkumensis SK2 has attracted significant interest due to its hydrocarbonoclastic lifestyle, its alkane-centered metabolism, and for playing an important ecological role in cleaning up marine oil spills. In this study, we used microarray technology to characterize the transcriptional responses of A. borkumensis to n-hexadecane exposure as opposed to pyruvate, which led to the identification of a total of 220 differentially expressed genes, with 109 genes being upregulated and 111 genes being downregulated. Among the genes upregulated on alkanes are systems predicted to be involved in the terminal oxidation of alkanes, biofilm formation, signal transduction, and regulation.
Keywords	Alcanivorax borkumensis ; bacteria ; biofilm ; cleaning ; gene expression ; gene expression regulation ; genes ; hexadecane ; lifestyle ; metabolism ; microarray technology ; oil spills ; oxidation ; pyruvic acid ; signal transduction ; transcription (genetics)
Language	English
Dates of publication	2011-06
Size	p. 160-168.
Publishing place	Blackwell Publishing Ltd
Document type	Article
ZDB-ID	752343-9
ISSN	1574-6968 ; 0378-1097
ISSN (online)	1574-6968
ISSN	0378-1097
DOI	10.1111/j.1574-6968.2011.02279.x
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Article: Engineering polyhydroxyalkanoate content and monomer composition in the oleaginous yeast Yarrowia lipolytica by modifying the ß-oxidation multifunctional protein

Haddouche, Ramdane / Poirier, Yves / Delessert, Syndie / Sabirova, Julia / Pagot, Yves / Neuvéglise, Cécile / Nicaud, Jean-Marc

Applied microbiology and biotechnology.. 2011 Sept., v. 91, no. 5

2011

Abstract: Recombinant strains of the oleaginous yeast Yarrowia lipolytica expressing the PHA synthase gene (PhaC) from Pseudomonas aeruginosa in the peroxisome were found able to produce polyhydroxyalkanoates (PHA). PHA production yield, but not the monomer ... ...

Abstract	Recombinant strains of the oleaginous yeast Yarrowia lipolytica expressing the PHA synthase gene (PhaC) from Pseudomonas aeruginosa in the peroxisome were found able to produce polyhydroxyalkanoates (PHA). PHA production yield, but not the monomer composition, was dependent on POX genotype (POX genes encoding acyl-CoA oxidases) (Haddouche et al. FEMS Yeast Res 10:917–927, 2010). In this study of variants of the Y. lipolytica β-oxidation multifunctional enzyme, with deletions or inactivations of the R-3-hydroxyacyl-CoA dehydrogenase domain, we were able to produce hetero-polymers (functional MFE enzyme) or homo-polymers (with no 3-hydroxyacyl-CoA dehydrogenase activity) of PHA consisting principally of 3-hydroxyacid monomers (>80%) of the same length as the external fatty acid used for growth. The redirection of fatty acid flux towards β-oxidation, by deletion of the neutral lipid synthesis pathway (mutant strain Q4 devoid of the acyltransferases encoded by the LRO1, DGA1, DGA2 and ARE1 genes), in combination with variant expressing only the enoyl-CoA hydratase 2 domain, led to a significant increase in PHA levels, to 7.3% of cell dry weight. Finally, the presence of shorter monomers (up to 20% of the monomers) in a mutant strain lacking the peroxisomal 3-hydroxyacyl-CoA dehydrogenase domain provided evidence for the occurrence of partial mitochondrial β-oxidation in Y. lipolytica.
Keywords	Pseudomonas aeruginosa ; Yarrowia lipolytica ; acyl coenzyme A ; acyltransferases ; fatty acids ; genes ; genotype ; proteins ; triacylglycerols ; yeasts
Language	English
Dates of publication	2011-09
Size	p. 1327-1340.
Publishing place	Springer-Verlag
Document type	Article
ZDB-ID	392453-1
ISSN	1432-0614 ; 0171-1741 ; 0175-7598
ISSN (online)	1432-0614
ISSN	0171-1741 ; 0175-7598
DOI	10.1007/s00253-011-3331-2
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