Welcome to ZOMEBase, the information center for the three PCI Zomes: COP9 Signalosome, the regulatory lid of the 26S proteasome and eIF3

What is a ZOME?

A "ZOME" is any one of three related multi-protein complexes:

the Cop9 Signalosome

the Regulatory Lid of the 26S proteasome

eIF3

These complexes were grouped together on the basis of similarities in their subunit composition and predicted structure. While subunits between the complexes share little primary sequence similarity, six subunits of all three complexes contain a PCI (Proteasome, CSN, eIF3) motif, while two subunits carry an MPN (Mpr1, Pad1, N-terminal) motif. This conserved six PCI / two MPN structure (among most higher eukaryotes) strongly suggests a common ancestor for these complexes. (1)

ZOMES, individually and in concert, affect proteome composition.

In ZOMEBase you can find

Information about each invidual Zome, including:
- Detailed subunit information for each complex
- Lists of interacting proteins for each complex
- Description of mutants
- InterZomal interactions
Information about past and future ZOMES conferences.
A very short ZomeHistory
ZomesResearchers

Want to contribute to ZOMEBase?

All Zomers are welcome and invited to contribute to and modify ZOMEBase using the Twiki editor on each page. To edit, you'll need a username and password. Please contact dannyc@tauex.tau.ac.il . As a contributer you can edit and add to exisiting content including making new pages.

Pages that need to be worked on

ZOMEBase Utilities

ATasteOfTWiki - A quick overview of Twiki
TWikiTutorial is a 20-minute tour of TWiki essentials.
WebTopicList - all__ZOMEBase__ topics in alphabetical order
WebChanges - recent topic changes in this web
WebNotify - subscribe to an e-mail alert sent when ZOMEBase topics change
WebRss, WebAtom - RSS and ATOM news feeds of ZOMEBase topic changes
WebStatistics - listing popular topics and top contributors
WebPreferences - preferences of this web

Recent ZOMES articles

pubmed: cop9 or "proteasome ...

NCBI: db=pubmed; Term=cop9 or "proteasome lid" or eIF3 or jab1

Determination of reliable reference genes for multi-generational gene expression analysis on C. elegans exposed to abused drug nicotine.

Determination of reliable reference genes for multi-generational gene expression analysis on C. elegans exposed to abused drug nicotine.

Psychopharmacology (Berl). 2013 May 17;

Authors: Taki FA, Zhang B

Abstract
RATIONAL: More research has recently been focused on multigenerational toxicogenomics impacts. Such studies rely on behavioral as well as genetic and epigenetic analyses using various biotechniques. Of these technologies, quantitative reverse transcriptase PCR is considered as a mature discovery and validation tool. Nevertheless, the interpretation of the resulting gene expression necessitates the establishment of reliable internal controls for normalization. No study has been performed to identify reliable reference genes in multigenerational settings. OBJECTIVES: The primary aim was to evaluate the stability of 16 reference gene candidates in Caenorhabditis elegans exposed to nicotine and their two subsequent generations for determining the most reliable reference genes for multigenerational study. METHODS: We exposed C. elegans to nicotine in the F0 generation and investigated the relative stabilities of 16 housekeeping genes in L4 larvae across three generations (F0, F1, and F2) using five statistical approaches (geNorm, ∆Ct method, NormFinder, BestKeeper, and RefFinder). RESULTS: geNorm shows that CDC-42 and Y45F10D.4 were the most stable reference genes. Based on NormFinder, TBA-1, EIF3.C, ARP-6, CDC-42, and MDH2 may serve as the top reliable reference genes. Comparative ∆Ct method ranked TBA-1, CDC-42, EIF3.C, ARP-6, and Y45F10D.4 as the most stable reference genes. BestKeeper shows that Y45F10D.4, F35G12.2, TBA-1, CDC-42, and CSQ-1were better reference genes. Overall, TBA-1, CDC-42, EIF3.C, ARP-6, and Y45F10D.4 were the most reliable reference genes for mutigenerational nicotine-exposed study. CONCLUSIONS: Of the 16 tested gene candidates, TBA-1 and CDC-42 were the two most stable reference genes for performing reliable gene expression normalization in the multigenerational impact of nicotine exposure.

PMID: 23681163 [PubMed - as supplied by publisher]

Notes

1 : Hofmann, K., and Bucher, P. (1998). The pci domain: A common theme in three multi-protein complexes. Trends Biochem Sci 23, 204-205.;Aravind, L., and Ponting, C.P. (1998). Homologues of 26S proteasome subunits are regulators of transcription and translation. Protein Sci 7, 1250-1254.; Kim, T.-H., Hofmann, K., von Arnim, A.G., and Chamovitz, D.A. (2001). The pci complexes:pretty complex interations in diverse signaling pathways. Trend Plant Sciences 6, 379-386.

r21 - 02 Aug 2010 - 12:15:05 - IdoGan

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