Monday, January 18, 2010

Protein dancing partners, yeast as our allies, and more, in my Picks of the Week from RB

Another week has gone by and some very interesting molbio blog posts have been aggregated to Every week [see my opening post on the matter], I'll select some blog posts I consider particularly interesting in the field of molecular biology [see here to get a sense of the criteria that will be used], briefly describe them and list them here for you to check out.

Note that I'm only taking into consideration the molbio-related blog posts aggregated under "Biology".

Congratulations to everyone who got their post selected.

1) By making use of what was known about the galactose-mediated induction of gene expression in yeast (one of the earliest model systems for studying transcriptional regulation), and of studies showing the modular nature of the DNA-binding and activation domains of transcriptional activators, the Fields lab published in 1989 the first report of the yeast two-hybrid system, an approach for assessing protein-protein interactions in vivo. LabRat describes, in very simple terms, the logic behind this technique, in light of a recent review which discusses recent modifications this system has suffered in the last few years in order for it to be a more powerful source of biological information.

2) The genomes of humans and chimpanzees, as a whole, are practically identical: indeed, as stated in the article reporting the initial sequence of the chimpanzee genome, "nearly all of the bases are identical by descent and sequences can be readily aligned except in recently derived, large repetitive regions".

A recent report suggests this scenery dramatically changes when only the Y chromosomes are the subject of comparison. Apparently, there have been stark changes between the chimp and human Y chromosomes, particularly due to gene loss in the chimp, gene gain in the human and rearrangements of large portions of the chromosome.

"Thirty percent of our Y-chromosome sequences have no counterpart in the chimpanzee. As the authors say that's the sort of divergence you'd expect to see between humans and chickens, which are separated by 310 million years of evolution not humans and chimps which only split 6 million years ago!"
The Atavism discusses this article from an evolutionary point of view, commenting on possible mechanisms that could account for the amazing evolutionary rate the Y chromosome displays, compared to the rest of the genome.

"So, the burning question is what is behind that evolutionary rate? There is probably no single answer to that question but it's safe to assume it results from some of the unique features of the Y-chromosome; a lack of genetic recombination, the presence of those large repetitive sections of DNA and the preponderance of male specific genes"
3) In a sort of shameless self-promotion, I’d also like to highlight the two-article series on Yeast Recombinational cloning (YRC), an alternative to “classic cloning”, posted on our blog last week. These posts have been widely read, so I decided to select them for this week’s picks.

So, what is YRC?
"Just to refresh your memory, and in a nutshell, the idea is to co-transform the DNA segment to be cloned into yeast along with the linearized target plasmid, provided that this DNA segment bears homology to defined plasmid sequences. By homologous recombination, yeast machinery will directly “ligate” your DNA segment into the linearized vector."
The first post explains the methodology and how it relates to my own research, and the second one, explains how we get the resulting plasmid out of yeast in order to transform our model organism of choice.
This is way cheaper than using In Fusion ;-)

That's it for this week. Stay tuned for more MolBio Research Highlights!

ResearchBlogging.orgSome of the articles discussed in this week's selected posts:

Brückner A, Polge C, Lentze N, Auerbach D, & Schlattner U (2009). Yeast two-hybrid, a powerful tool for systems biology. International journal of molecular sciences, 10 (6), 2763-88 PMID: 19582228

Hughes, J., Skaletsky, H., Pyntikova, T., Graves, T., van Daalen, S., Minx, P., Fulton, R., McGrath, S., Locke, D., Friedman, C., Trask, B., Mardis, E., Warren, W., Repping, S., Rozen, S., Wilson, R., & Page, D. (2010). Chimpanzee and human Y chromosomes are remarkably divergent in structure and gene content Nature DOI: 10.1038/nature08700

Oldenburg KR, Vo KT, Michaelis S, & Paddon C (1997). Recombination-mediated PCR-directed plasmid construction in vivo in yeast. Nucleic acids research, 25 (2), 451-2 PMID: 9016579

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1 Comment:

David said...

Hi Alejandro,

Thanks for the link! I'll have to read up on your Yeast cloning articles :)