TY  - JOUR
A1  - Schneider, György
A1  - Dobrindt, Ulrich
A1  - Middendorf, Barbara
A1  - Hochhut, Bianca
A1  - Szijártó, Valeria
A1  - Emódy, Levente
A1  - Hacker, Jörg
T1  - Mobilisation and remobilisation of a large archetypal pathogenicity island of uropathogenic \(Escherichia\) \(coli\) \(in\) \(vitro\) support the role of conjugation for horizontal transfer of genomic islands
JF  - BMC Microbiology
N2  - Background: 

A substantial amount of data has been accumulated supporting the important role of genomic islands (GEIs) - including pathogenicity islands (PAIs) - in bacterial genome plasticity and the evolution of bacterial pathogens. Their instability and the high level sequence similarity of different (partial) islands suggest an exchange of PAIs between strains of the same or even different bacterial species by horizontal gene transfer (HGT). Transfer events of archetypal large genomic islands of enterobacteria which often lack genes required for mobilisation or transfer have been rarely investigated so far. 

Results: 
To study mobilisation of such large genomic regions in prototypic uropathogenic E. coli (UPEC) strain 536, PAI II(536) was supplemented with the mob(RP4) region, an origin of replication (oriV(R6K)), an origin of transfer (oriT(RP4)) and a chloramphenicol resistance selection marker. In the presence of helper plasmid RP4, conjugative transfer of the 107-kb PAI II(536) construct occured from strain 536 into an E. coli K-12 recipient. In transconjugants, PAI II(536) existed either as a cytoplasmic circular intermediate (CI) or integrated site-specifically into the recipient's chromosome at the leuX tRNA gene. This locus is the chromosomal integration site of PAI II(536) in UPEC strain 536. From the E. coli K-12 recipient, the chromosomal PAI II(536) construct as well as the CIs could be successfully remobilised and inserted into leuX in a PAI II(536) deletion mutant of E. coli 536. 

Conclusions: 
Our results corroborate that mobilisation and conjugal transfer may contribute to evolution of bacterial pathogens through horizontal transfer of large chromosomal regions such as PAIs. Stabilisation of these mobile genetic elements in the bacterial chromosome result from selective loss of mobilisation and transfer functions of genomic islands.
KW  - Recombination directionality factor
KW  - Staphylococcus-aureus
KW  - Yersinia-pseudotuberculosis
KW  - Pseudomonas-aeruginosa
KW  - Bacterial conjugation
KW  - Suicide vector
KW  - Gene-transfer
KW  - Excision
KW  - Family
KW  - Evolution
Y1  - 2011
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-140975
VL  - 11
ER  - 
TY  - JOUR
A1  - Arhondakis, Stilianos
A1  - Frousios, Kimon
A1  - Iliopoulos, Costas S.
A1  - Pissis, Solon P.
A1  - Tischler, German
A1  - Kossida, Sophia
T1  - Transcriptome map of mouse isochores
JF  - BMC Genomics
N2  - Background: 

The availability of fully sequenced genomes and the implementation of transcriptome technologies have increased the studies investigating the expression profiles for a variety of tissues, conditions, and species. In this study, using RNA-seq data for three distinct tissues (brain, liver, and muscle), we investigate how base composition affects mammalian gene expression, an issue of prime practical and evolutionary interest. 

Results: 

We present the transcriptome map of the mouse isochores (DNA segments with a fairly homogeneous base composition) for the three different tissues and the effects of isochores' base composition on their expression activity. Our analyses also cover the relations between the genes' expression activity and their localization in the isochore families. 

Conclusions: 

This study is the first where next-generation sequencing data are used to associate the effects of both genomic and genic compositional properties to their corresponding expression activity. Our findings confirm previous results, and further support the existence of a relationship between isochores and gene expression. This relationship corroborates that isochores are primarily a product of evolutionary adaptation rather than a simple by-product of neutral evolutionary processes.
KW  - Biased gene conversion
KW  - Human genome
KW  - GC-Content
KW  - Mammalian genomes
KW  - Base composition
KW  - Expresses genes
KW  - Higher rates
KW  - RNA-SEQ
KW  - Evolution
KW  - Rodents
Y1  - 2011
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-142773
VL  - 12
IS  - 511
ER  -