Recent Advances in the Expression, Evolution, and Dynamics of Prokaryotic Genomes

Arraiano, Cecília M.; Bamford, Jaana K. H.; Brüssow, Harald; Carpousis, Agamemnon J.; Pelicic, Vladimir; Pflüger, Katharina; Polard, Patrice; Vogel, Jörg

doi:10.1128/jb.00612-07

Cited by 3 publications

(3 citation statements)

References 101 publications

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“…Temperate phages, maintained as prophages in their lysogens, have been the subject of speculation concerning their benefit to the host: selective advantage, increased virulence, and other traits with varying degrees of direct and/or indirect impact on the host have been identified [ 11 , 21 - 27 ]. The challenge in this area has been how to identify phage-encoded genes that directly affect their lysogen, because many/most phage genes are annotated as encoding hypothetical proteins.…”

Section: Discussionmentioning

confidence: 99%

Identification of genes expressed in cultures of E. coli lysogens carrying the Shiga toxin-encoding prophage Φ24B

et al. 2012

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BackgroundShigatoxigenic E. coli are a global and emerging health concern. Shiga toxin, Stx, is encoded on the genome of temperate, lambdoid Stx phages. Genes essential for phage maintenance and replication are encoded on approximately 50% of the genome, while most of the remaining genes are of unknown function nor is it known if these annotated hypothetical genes are even expressed. It is hypothesized that many of the latter have been maintained due to positive selection pressure, and that some, expressed in the lysogen host, have a role in pathogenicity. This study used Change Mediated Antigen Technology (CMAT)™ and 2D-PAGE, in combination with RT-qPCR, to identify Stx phage genes that are expressed in E. coli during the lysogenic cycle.ResultsLysogen cultures propagated for 5-6 hours produced a high cell density with a low proportion of spontaneous prophage induction events. The expression of 26 phage genes was detected in these cultures by differential 2D-PAGE of expressed proteins and CMAT. Detailed analyses of 10 of these genes revealed that three were unequivocally expressed in the lysogen, two expressed from a known lysogenic cycle promoter and one uncoupled from the phage regulatory network.ConclusionPropagation of a lysogen culture in which no cells at all are undergoing spontaneous lysis is impossible. To overcome this, RT-qPCR was used to determine gene expression profiles associated with the growth phase of lysogens. This enabled the definitive identification of three lambdoid Stx phage genes that are expressed in the lysogen and seven that are expressed during lysis. Conservation of these genes in this phage genome, and other Stx phages where they have been identified as present, indicates their importance in the phage/lysogen life cycle, with possible implications for the biology and pathogenicity of the bacterial host.

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Section: Discussionmentioning

confidence: 99%

Identification of genes expressed in cultures of E. coli lysogens carrying the Shiga toxin-encoding prophage Φ24B

et al. 2012

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“…The EMBO Conference on Molecular Microbiology, Heidelberg, 2006, discussed noncoding regulatory RNA, RNases and gene expression, genomics, evolution and bacteriophages, signal transductions, protein interactions and networks, pathogenicity, virulence and endosymbiosis, chromosome dynamics, DNA uptake, and other subject matters. These presentations were published with extensive literature quotations [328]. Here is the background and the environment in which horizontally transferred genes are released and accepted.…”

Section: The Darwinian Threshold (Woese)mentioning

confidence: 99%

“…In Galveston, TX, fluoroquinolin-resistant uropathogen E. coli emerged to infect renal transplant patients; these "virulent appearing" E. coli strains remained susceptible to 3rd generation cephalosporins [357]. The EMBO conference on prokaryotic genomic evolution and gene expressions [328], dealt with the noncoding regulatory RNAs of E. coli, one of which, a sRNA, suppresses the synthesis of toxic peptides [358]. Could this mechanism neutralize toxin production in a HPI?…”

Section: The Ancient Origin Of "Virulence Genes"mentioning

confidence: 99%

Horizontal Gene Transfers with or without Cell Fusions in All Categories of the Living Matter

Sinkovics

2011

Advances in Experimental Medicine and Biology

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This article reviews the history of widespread exchanges of genetic segments initiated over 3 billion years ago, to be part of their life style, by sphero-protoplastic cells, the ancestors of archaea, prokaryota, and eukaryota. These primordial cells shared a hostile anaerobic and overheated environment and competed for survival. "Coexist with, or subdue and conquer, expropriate its most useful possessions, or symbiose with it, your competitor" remain cellular life's basic rules. This author emphasizes the role of viruses, both in mediating cell fusions, such as the formation of the first eukaryotic cell(s) from a united crenarchaeon and prokaryota, and the transfer of host cell genes integrated into viral (phages) genomes. After rising above the Darwinian threshold, rigid rules of speciation and vertical inheritance in the three domains of life were established, but horizontal gene transfers with or without cell fusions were never abolished. The author proves with extensive, yet highly selective documentation, that not only unicellular microorganisms, but the most complex multicellular entities of the highest ranks resort to, and practice, cell fusions, and donate and accept horizontally (laterally) transferred genes. Cell fusions and horizontally exchanged genetic materials remain the fundamental attributes and inherent characteristics of the living matter, whether occurring accidentally or sought after intentionally. These events occur to cells stagnating for some 3 milliard years at a lower yet amazingly sophisticated level of evolution, and to cells achieving the highest degree of differentiation, and thus functioning in dependence on the support of a most advanced multicellular host, like those of the human brain. No living cell is completely exempt from gene drains or gene insertions.

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Chapter 8 Characterizing Ribonucleases In Vitro

Arraiano

Barbas

Amblar

2008

Methods in Enzymology

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Recent Advances in the Expression, Evolution, and Dynamics of Prokaryotic Genomes

Cited by 3 publications

References 101 publications

Identification of genes expressed in cultures of E. coli lysogens carrying the Shiga toxin-encoding prophage Φ24B

Identification of genes expressed in cultures of E. coli lysogens carrying the Shiga toxin-encoding prophage Φ24B

Horizontal Gene Transfers with or without Cell Fusions in All Categories of the Living Matter

Chapter 8 Characterizing Ribonucleases In Vitro

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