Heat shock proteins and DNA repair mechanisms: an updated overview

Abstract

Heat shock proteins (HSPs), also known as molecular chaperones, participate in important cellular processes, such as protein aggregation, disaggregation, folding, and unfolding. HSPs have cytoprotective functions that are commonly explained by their antiapoptotic role. Their involvement in anticancer drug resistance has been the focus of intense research efforts, and the relationship between HSP induction and DNA repair mechanisms has been in the spotlight during the past decades. Because DNA is permanently subject to damage, many DNA repair pathways are involved in the recognition and removal of a diverse array of DNA lesions. Hence, DNA repair mechanisms are key to maintain genome stability. In addition, the interactome network of HSPs with DNA repair proteins has become an exciting research field and so their use as emerging targets for cancer therapy. This article provides a historical overview of the participation of HSPs in DNA repair mechanisms as part of their molecular chaperone capabilities.

Keywords: DNA damage response; DNA repair; Heat shock proteins; Molecular chaperones.

Fig. 1

Sources of DNA damage and repair mechanisms. Endogenous and exogenous agents constantly impact on DNA. They may cause many different forms of DNA damage. The scheme shows the five major DNA repair mechanisms operating in the nucleus of mammalian cells capable of removing a wide range of DNA lesions: direct damage reversal, base excision repair (BER), nucleotide excision repair (NER), mismatch repair (MMR), homologous recombination (HR), and non-homologous end joining (NHEJ). The BER system may also be found in the mitochondria. ROS reactive oxygen species, IR ionizing radiation, TOPOII topoisomerase II

Fig. 2

HSPs and the DNA damage response (DDR). Complex processes and signaling pathways take place in the cell in response to DNA single-strand breaks (SSBs) and double strand breaks (DSBs). SSBs are detected by RPA and DSBs by the MRN complex (MRE11-RAD50-NBS1). RPA and MRN mediate the recruitment of ATM and ATR, respectively. ATR is bound by the ATR-interacting protein (ATRIP), which interacts with RPA. Both ATM and ATR can phosphorylate (P) the histone variant H2AX on Ser139 (γH2AX) in the damaged DNA region. p53-binding protein 1 (53BP1) participates in the nuclear foci organization, promotes ATM activation, and facilitates the phosphorylation of specific substrates by ATM. The DNA damage signaling cascade continues with the phosphorylation of the cell cycle checkpoint kinases CHK1 and CHK2, which activate the downstream effectors: the tumor suppressor protein p53 or the CDC25 protein phosphatase. As a result, cell cycle progression is interrupted to allow DNA repair, senescence, or, in cases where DNA damage is too severe, apoptosis. The solid arrows show the DDR activation pathway. The dotted lines indicate the relationship between DDR and HSPs

Fig. 3

Participation of HSPs in the main steps of the base excision repair pathway. In human cells, BER mechanisms are achieved by two subpathways, short or long patch. The figure shows the main steps of the short-patch BER, which usually removes specific base damages. The recognition is initiated by specific DNA glycosylases (partially overlapping between them), which flip out the damaged base to form an abasic apurinic/apyrimidinic (AP) site in the DNA. An AP endonuclease (APE1 in mammalian cells) cleaves the 5′ phosphodiester bond, generating 3′OH and 5′dRP terminus, then produces the excision of the 3′ abasic fragment to form a gap that is filled by DNA polymerase β (Polβ). Finally, DNA ligase 3 (LIG3) performs the ligation step in association with XRCC1 (X-ray repair cross-complementing protein 1). Single-strand breaks, generated by ionizing radiation or OH radical, may also be corrected by the short-patch BER with the participation of the PARP1/XRCC1 complex. The figure also shows the involvement of HSPA1A and HSPC1 in BER steps

Fig. 4

HSPs and the mismatch repair system (MMR). The heterodimer composed by the proteins MSH2 and MSH6 (referred to as MutSα, E. coli MutS homolog) recognizes base-base mismatches and IDLs of one or two extrahelical nucleotides. The repair of larger IDLs is initiated by MutSβ, a heterodimer of MSH2 and MSH3 (not shown). MutLα, a heterodimer of MLH1 and PMS2, is also a core complex. The MutSα-MutLα complex remains bound to the mismatch and initiates the repair reaction in coordination with other factors: PCNA (proliferating cell nuclear antigen), RFC (replication factor C), RPA (replication protein A), EXO1 (exonuclease 1), DNA polymerase δ and/or DNA polymerase ε, and DNA ligase I. Dotted lines indicate the relationship between HSPs and MMR components

Fig. 5

HSPs and nucleotide excision repair (NER). NER can be divided in two subpathways, GG-NER and TC-NER. GG-NER is mediated by the XPC-HR23B-Centrine 2 heterodimer, which senses distortions. XPC (xeroderma pigmentosum C) is a DNA binding protein with high affinity for damaged DNA. HR23B (human homolog of the yeast protein Rad23) and Centrine 2 stabilize the complex. Additional factors then interact to form a multiprotein complex composed of XPA, RPA, transcription factor IIH (TFIIH), XPG, and XPF. RPA and TFIIH facilitate the unwinding of the double helix. RPA also binds to single-strand DNA. In the next step, the damaged strand is excised by two endonucleases. XPG cuts at the 3′ side, and XPF/ERCC1 (excision repair cross-complementing 1) cuts at the 5′ side, generating an incision 15 to 24 nucleotides away. The resulting gap is filled by DNA polymerase δ and ε, RFC and PCNA, and sealed by DNA ligase 1 or ligase 3-XRCC1. TC-NER removes lesions from the transcribed strand of active genes. GG-NER and TC-NER differ in the recognition step. RNA polymerase II stalls at damages sites. CSA and CSB proteins (Cockayne syndrome A and B, respectively) interact and cooperate with RNA polymerase II and with XPG. All downstream steps are common to both pathways. The implications of HSPB1 and HSPA1A are highlighted in the figure

Fig. 6

HSPs and double strand break repair. Double strand breaks (DSB) are repaired by two major mechanisms: homologous recombination repair (HR) and non-homologous end joining (NHEJ). HR operates after replication, when a second identical DNA copy is available. The pathway begins with the recruitment of the MRN complex (MRE11-NBS1-RAD50) to the DSB. ATM, ATR, and the MRN complex act as damage sensors. MRE11 has DNA exonuclease and DNA unwinding activity. RAD50 contains motifs for nucleotide binding. BRCA1 interacts with p53, BRCA2, RAD51, MRN complex, p21, and cyclin B to form multisubunit complexes. hSNM1B/Apollo is a DNA 5′ exonuclease with a preference for single-stranded substrates. The resection of 5′ DNA on either side of the DSB is accomplished by a BRCA1-dependent process, resulting in the exposure of two regions of single-stranded DNA (ssDNA). BRCA2 localizes the DNA recombinase RAD51 to the exposed ssDNA regions. RAD51 forms a nucleoprotein filament that can invade the DNA double helix and pair with undamaged homologous sequences. DNA polymerases δ/ε use the homologous DNA sequence as a template and synthesize new DNA. After DNA synthesis occurs, recombination between chromatids can be resolved by endonucleases and the nicks sealed by DNA ligase 1. Meanwhile, the NHEJ system ligates two broken ends without a sequence homology and when DSB is affecting a short region (1 to 6 bp). The first step consists in the DNA binding of the Ku70/Ku80 heterodimer, protecting the DNA from exonuclease digestion. The Ku heterodimer then binds to the catalytic subunit of DNA-PK (DNA-dependent protein kinase), activating the enzyme, and Artemis stabilizes the ends. After juxtaposition of the two DNA ends, DNA-PK autophophorylates and DNA ligation is performed by the DNA ligase 4 (LIG4)-XRCC4. When end processing is required, DNA polymerase μ (Pol μ) and DNA polymerase λ (Pol λ) can fill in 5′-single-strand extensions, which are sealed by the LIG4-XRCC4 complex. The participation of HSPs is indicated with dotted lines