Thursday, January 15, 2009

Changing each other’s lives and transcription

One of the challenges of biology is that life does not function as a vacuum, but rather constantly influences and is influenced by other organisms and the environment. Therefore, in order to unravel some of the mysteries of the functions and evolution of living things, one must examine not only the organism itself, but also those things that may be influencing it. For bacteria, horizontal gene transfer (HGT) is a key process by which a bacterium is influenced by its environment and the genetic organization of neighboring bacteria. Through HGT a bacterium can acquire plasmids that confer upon the bacterial host new phenotypic traits. In the case of plasmid pCAR1, hosts receive the genetic information necessary to degrade carbazole and therefore use it as a carbon source. However, the gain or loss of a plasmid and its inherent phenotypic properties are not the extent of how plasmids and bacteria influence one another. As the authors of this paper pointed out, the host’s chromosomal transcriptome can be influenced by the presence of a plasmid and that, conversely, transcription of plasmid backbone and accessory genes are affected by the chromosome of the host in which the plasmid finds itself.

Past research by these authors showed that pCAR1 could successfully transfer to and function in Pseudomonas putida KT2440 from its original host, Pseudomonas resinovorans CA10. They also found that the introduction of the pCAR1 affected chromosomal transcription. In this study, they pursued the question of if and how plasmid transcription of pCAR1 is affected by different host chromosomes, again using P. putida KT2440 and P. resinovorans CA10. To do this they used a microarray to map and quantify PCAR1 transcripts in the two hosts when grown on succinate or carbazole as the only available carbon source. They also verified their results from the microarrays through real-time PCR. Through these two methods, the authors verified that growth on carbazole induced the catabolic operons antA and antR to the same extent, regardless of the host. However, other genes, such as the car operons, were expressed at significantly different levels depending on which host the plasmid was acting in.

This article adds to the growing body of evidence that the expression of genomes are not static bodies with occasional changes due only to mistakes made from one generation of cells to another, but is rather a dynamic entity that is, like the organism itself, influenced by its immediate environment at any given time.

Primary article:

Miyakoshi M, H Nishida, M Shintani, H Yamane, H Nojiri. (2009). High-resolution mapping of plasmid transcriptomes in different host bacteria. BMC Genomics, 10:12.

Additional reading:

Frost LS, Leplae R, Summers AO, Toussaint A. (2005). Mobile genetic elements: the agents of open source evolution. Nat Rev Microbiol 3:722-32.

Harr B, Schlötterer C. (2006). Gene expression analysis indicates extensive genotype-specific crosstalk between the conjugative F-plasmid and the E. coli chromosome. BMC Microbiol 6:80.

Miyakoshi M, Sintani M, Terabayashi T, Kai S, Yamane H, Nojiri H. (2007). Transcriptome analysis of Pseudomonas putida KT2440 harboring the completely sequenced IncP-7 plasmid pCAR1. Bacteriol. 189: 6849-60.

Ramos JL, Marqués S, Timmis KN. (1997). Transcriptional control of the Pseudomonas TOL plasmid catabolic operons is achieved through an interplay of host factors and plasmid-encoded regulators. Annu Rec Microbiol. 51: 341-72.

Thomas CM. (2006). Transcription regulatory circuits in bacterial plasmids. Biochem Soc Trans. 34:1072-4.

Julie M. Hughes
University of Idaho

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