The DNA Damage Response: Making It Safe to Play with Knives

Cellular responses to DNA damage are mediated by a number of protein kinases, including ATM (ataxia telangiectasia mutated) and ATR (ATM and Rad3-related). The outlines of the signal transduction portion of this pathway are known, but little is known about the physiological scope of the DNA damage response (DDR). We performed a large-scale proteomic analysis of proteins phosphorylated in response to DNA damage on consensus sites recognized by ATM and ATR and identified more than 900 regulated phosphorylation sites encompassing over 700 proteins. Functional analysis of a subset of this data set indicated that this list is highly enriched for proteins involved in the DDR. This set of proteins is highly interconnected, and we identified a large number of protein modules and networks not previously linked to the DDR. This database paints a much broader landscape for the DDR than was previously appreciated and opens new avenues of investigation into the responses to DNA damage in mammals.

/pdf/atm-and-atr-substrate-analysis-reveals-extensive-protein-1sj3dzzn7g.pdf

ATM and ATR substrate analysis reveals extensive protein networks responsive to DNA damage

MYC on the Path to Cancer

https://www.cell.com/cell/pdf/S0092-8674(00)80371-2.pdf

CRM1 Is an Export Receptor for Leucine-Rich Nuclear Export Signals

▪ Abstract The compartmentation of eukaryotic cells requires all nuclear proteins to be imported from the cytoplasm, whereas, for example, transfer RNAs, messenger RNAs, and ribosomes are made in the nucleus and need to be exported to the cytoplasm. Nuclear import and export proceed through nuclear pore complexes and can occur along a great number of distinct pathways, many of which are mediated by importin β-related nuclear transport receptors. These receptors shuttle between nucleus and cytoplasm, and they bind transport substrates either directly or via adapter molecules. They all cooperate with the RanGTPase system to regulate the interactions with their cargoes. Another focus of our review is nuclear export of messenger RNA, which apparently largely relies on export mediators distinct from importin β-related factors. We discuss mechanistic aspects and the energetics of transport receptor function and describe a number of pathways in detail.

Transport between the cell nucleus and the cytoplasm.

The BRCT repeats of the breast and ovarian cancer predisposition protein BRCA1 are essential for tumor suppression. Phosphopeptide affinity proteomic analysis identified a protein, Abraxas, that directly binds the BRCA1 BRCT repeats through a phospho-Ser-X-X-Phe motif. Abraxas binds BRCA1 to the mutual exclusion of BACH1 (BRCA1-associated C-terminal helicase) and CtIP (CtBP-interacting protein), forming a third type of BRCA1 complex. Abraxas recruits the ubiquitin-interacting motif (UIM)–containing protein RAP80 to BRCA1. Both Abraxas and RAP80 were required for DNA damage resistance, G2-M checkpoint control, and DNA repair. RAP80 was required for optimal accumulation of BRCA1 on damaged DNA (foci) in response to ionizing radiation, and the UIM domains alone were capable of foci formation. The RAP80-Abraxas complex may help recruit BRCA1 to DNA damage sites in part through recognition of ubiquitinated proteins.

/pdf/abraxas-and-rap80-form-a-brca1-protein-complex-required-for-1mdhafky4l.pdf

Abraxas and RAP80 Form a BRCA1 Protein Complex Required for the DNA Damage Response

The MYC proto-oncogene encodes a transcription factor that has been implicated in the genesis of many human tumours Here, we used a bar-code short hairpin RNA (shRNA) screen to identify multiple genes that are required for MYC function One of these genes encodes USP28, an ubiquitin-specific protease USP28 is required for MYC stability in human tumour cells USP28 binds to MYC through an interaction with FBW7alpha, an F-box protein that is part of an SCF-type ubiquitin ligase Therefore, it stabilizes MYC in the nucleus, but not in the nucleolus, where MYC is degraded by FBW7gamma High expression levels of USP28 are found in colon and breast carcinomas, and stabilization of MYC by USP28 is essential for tumour-cell proliferation

The ubiquitin-specific protease USP28 is required for MYC stability

A Role for the Deubiquitinating Enzyme USP28 in Control of the DNA-Damage Response

In the yeast commitment complex and the mammalian E complex, there is an important base-pairing interaction between the 5′ end of U1 snRNA and the conserved 5′ splice site region of pre-mRNA. But no protein contacts between splicing proteins and the pre-mRNA substrate have been defined in or near this region of early splicing complexes. To address this issue, we used 4-thiouridine-substituted 5′ splice site-containing RNAs as substrates and identified eight cross-linked proteins, all of which were identified previously as commitment complex components. The proteins were localized to three domains: the exon, the six nucleotides of the 5′ ss region, and the downstream intron. The results indicate that the 5′ splice site region and environs are dense with protein contacts in the commitment complex and suggest that some of them make important contributions to formation or stability of the U1 snRNP–pre-mRNA complex.

/pdf/identification-of-eight-proteins-that-cross-link-to-pre-mrna-565o7gaibb.pdf

Identification of eight proteins that cross-link to pre-mRNA in the yeast commitment complex

Recently, cannabinoids, such as cannabidiol (CBD) and Δ9 -tetrahydrocannabinol (THC), have been the subject of intensive research and heavy scrutiny. Cannabinoids encompass a wide array of organic molecules, including those that are physiologically produced in humans, synthesized in laboratories, and extracted primarily from the Cannabis sativa plant. These organic molecules share similarities in their chemical structures as well as in their protein binding profiles. However, pronounced differences do exist in their mechanisms of action and clinical applications, which will be briefly compared and contrasted in this review. The mechanism of action of CBD and its potential applications in cancer therapy will be the major focus of this review article.

https://www.mdpi.com/2072-6694/12/11/3203/pdf

Dong Zhang

Papers

Abraxas and RAP80 Form a BRCA1 Protein Complex Required for the DNA Damage Response

The ubiquitin-specific protease USP28 is required for MYC stability

A Role for the Deubiquitinating Enzyme USP28 in Control of the DNA-Damage Response

Identification of eight proteins that cross-link to pre-mRNA in the yeast commitment complex

Cannabidiol (CBD) as a Promising Anti-Cancer Drug