SOT 2009 - Cytochrome P450 genes in zebrafish development

Cytochrome P450 genes in zebrafish development.
Goldstone, J., M. Jonsson, T. Parente, J. Zanette, A.G. McArthur, B.R. Woodin, D.R. Nelson, & J.J. Stegeman. 2009.
Presentation at the Society of Toxicology 48th Annual Meeting, Baltimore, Maryland.


This presentation summarizes observations on the full complement of CYP genes in zebrafish, a non-mammalian model for pharmacological, toxicological and carcinogenesis research. A total of 88 CYP genes were identified in zebrafish. Homologies between zebrafish and human CYP were inferred from amino acid sequence identity and molecular phylogeny. Functions and regulation of most zebrafish CYP are not known. For CYP that are likely involved principally in endogenous functions there is clear orthology between human genes and their zebrafish counterparts, although there are differences in numbers of genes in some families. Relative to the human CYP complement there is expansion or enhanced diversity in zebrafish CYP families 1, 2 and 3 thought to be most involved in xenobiotic metabolism. There are five CYP1 genes, five CYP3s, and 42 CYP2s in 11 subfamilies. Only two of the zebrafish CYP2s (CYP2R and CYP2U) warrant the same designation as in humans based on sequence identity. However, syntenic analysis reveals that there are some 11 genes in the zebrafish CYP2N, 2P, 2V, and 2AD subfamilies, all of which occur in tandem in a cluster that has shared synteny with the single human CYP2J2, indicating orthology. Studies of CYP2Ns and CYP2Ps in other species indicate functional similarity with human CYP2J2. The multiple CYP2Ks share synteny with CYP2W, but the CYP2Xs and CYP2AAs do not obviously share synteny with any human CYP2 genes. The five zebrafish CYP1s occur in four subfamilies, divided into 2 clades. Zebrafish CYP1s show organ, cell and developmental stage differences in transcript expression and in inducibility by aryl hydrocarbon receptor agonists. CYP1D1, which is most closely related to CYP1A, is distinctly not induced by AH receptor agonists. Oligonucleotide microarrays targeted to all zebrafish CYPs reveal that many CYPs, including 17 CYP2s, are expressed during early zebrafish development.

Why the name?

In the last post I said the robot name of cytochromes P450 would be explained later. Now is the time! For that I will remount you back to the time whem CYPs were not even discovered.The presence of a weird pigment in liver microsomes, which presented a sharp absorvance peak at 450nm when ligated to CO,  were detected by Klingenberg in 1958. The nature of this peak remained unclear until Omura & Sato discovered in 1964 that it was due to the absorbance of an heme-protein. Not knowing which protein was that, they gave them the provisory name of Cytochromes P450 - because they absorbed light (CYtochromes) with a Peak (P) of absorbance at 450nm (450). This absorbance peak is now known as the Soret peak (http://en.wikipedia.org/wiki/Soret_peak).

                       Ryo Sato                              Tsuneo Omura

At that time, no one could imagine how diverse this family would be in terms of either forms, functions and widespread in biodiversity.
A year later, in 1965, a group leaded by Ronald Estabrook published in science the first described function for a P450 - it was the hydroxylation of the 17-hydroxyprogesterone to deoxycorticosterone.

more infos about that might be found at:
M. Klingenberg, Arch.Biochem.Biophys.75:376 (1958)
T. Omura, and R. Sato,J.Biol.Chem.239:2370 (1964)
D.Y.Cooper, S.Levin, S.Narasimhulu, O.Rosenthal and R.W.Estabrook, Science 147:400 (1965) 
http://www.issx.org/i4a/pages/index.cfm?pageid=3352 

What is this CYP?

CYPs, is the short form CYTOCHROME P450. The origins for the short form (CYP) I belive is CYtochromesP450. Agreed that it is not a very good short form but that is the only explanation I have heard and could think about. It will be awesome if anyone post the real and probably better explanation for that. The origins for the robotic name of Cytochromes P450 will be discussed on a later post.
Anyway, the CYPs forms a gene family which until Aug 2009 had more that 11000 described genes divided into 977 families and 2519 sub-families (http://drnelson.utmem.edu/CytochromeP450.html) widespread in all the three domains of life (and even on viruses particles!!!). Plants, with 4266 different genes, are responsable for most of its diversity; followed by animals (3282), fungi (2570), bacteria (905), protists (247), archea (22) and viruses (2). Insects, with 1675 genes, have more the half of all animals CYP genes. The huge CYP diversity in plants and insects is believed to be the result of an evolutionary battle between prey vs predator: the insect-plant chemical warfare (unmissable reference: Molecular mechanisms of metabolic resistance to synthetic and natural xenobiotics.
Annu Rev Entomol. 2007;52:231-53.)
But, what are all those forms doing???? That is a point! We still do not know what does each one do. Anyway, from what we currently know, they play several different important roles in order to maintain the homeostasis. In this regard, a short, general and fascinating paper is the one by Stegeman & Livingstone 1998 (Comp Biochem Physiol C Pharmacol Toxicol Endocrinol. 1998 Nov;121(1-3):1-3.). They genially summarizes in a single figure most of the roles the CYPs are involved with. Once ago John gifted me with a previous and colored version of these figure, which you can see above.

So, a great number of CYPs participates in endogenous pathways such as biosynthesis of hormones, while another great number are involved with the metabolism of foreigners compounds (namely xenobiotics, non endogenous and non nutrient substances absorbed by an organism - like drugs and pollutants).
But what are CYPs originally meant to be and do? Why do we have so many of them? We can only speculate about the answers for those questions yet. In fact, discussions about these speculations has all the potential to became the first topic of intense debate in this blog - so, let's start posting ours comments! One thing that is known is that CYP origin dates millions years back in time, when the atmosphere was not yet saturated with oxygen and the first primitive cells was starting to develop. This ancestral CYP is supposed to be more similar to the now-a-days CYP51, which are the unique family found in biological kingdoms and possesses an endogenous function.

THE PURPOSES

The main purpose of this blog is to create a full time forum to debate about one of the nature's most diverse and widespread gene family: the CYTOCHROMES P450, also known as CYPs! All and any topic involving CYP will be covered - ranging from CYP origins, evolution and diversification to involvement of CYPs in human diseases passing through CYP applications in biotechnology. Usually, I will use this forum to advertise and comment what I find to be the most outstanding up-to-date publications in the field.
As CYP publications are reaching absurd numbers per day, a huge percentage of the outstanding articles will not be discussed. However, I count on the YOU (the readers) to send comments not only discussing my current post but also linking to others excellent papers that might not be directly related to the current post. Senior CYP scientists will eventually be invited to write very brief reviews or about priority research on the field. Also, any CYP scientist/student are encouraged to write short posts and send it to me. These posts will be posted in the blog and credits will be given to the author(s).
Sure this blog is also a great place for high-school and undergraduate students to learn about these very interesting enzymes and all the metabolic and physiologic processes they are involved in. Despite CYP importance and the number of scientific papers published on it, this is (as far as I am aware) the first blog devoted entirely to the CYPs.
In sum, I hope CYP scientists can find here a forum to discuss all aspects of our favorite proteins: the CYPs. By doing it, we will be always in touch and not limit to few days each year during some of ours CYP meetings. More over, we will meet here CYP specialists that works on different parts of the CYP universe, which the odds to meet elsewhere are very low. This will expand our limited vision and can potentially help each of us to better understand the small part of this huge universe we are studying. Finally, it is meant to open the eyes of younger students to this amazingly diverse gene/protein/enzyme family.

WELCOME TO THE CYPblog!

Cheers,
Thiago Parente