scholarly journals The archaeal RecJ-like proteins: nucleases and ex-nucleases with diverse roles in replication and repair

2018 ◽  
Vol 2 (4) ◽  
pp. 493-501
Author(s):  
Stuart A. MacNeill

RecJ proteins belong to the DHH superfamily of phosphoesterases that has members in all three domains of life. In bacteria, the archetypal RecJ is a 5′ → 3′ ssDNA exonuclease that functions in homologous recombination, base excision repair and mismatch repair, while in eukaryotes, the RecJ-like protein Cdc45 (which has lost its nuclease activity) is a key component of the CMG (Cdc45–MCM–GINS) complex, the replicative DNA helicase that unwinds double-stranded DNA at the replication fork. In archaea, database searching identifies genes encoding one or more RecJ family proteins in almost all sequenced genomes. Biochemical analysis has confirmed that some but not all of these proteins are components of archaeal CMG complexes and has revealed a surprising diversity in mode of action and substrate preference. In addition to this, some archaea encode catalytically inactive RecJ-like proteins, and others a mix of active and inactive proteins, with the inactive proteins being confined to structural roles only. Here, I summarise current knowledge of the structure and function of the archaeal RecJ-like proteins, focusing on similarities and differences between proteins from different archaeal species, between proteins within species and between the archaeal proteins and their bacterial and eukaryotic relatives. Models for RecJ-like function are described and key areas for further study highlighted.

2021 ◽  
Vol 22 (5) ◽  
pp. 2472
Author(s):  
Carl Randall Harrell ◽  
Valentin Djonov ◽  
Vladislav Volarevic

Mesenchymal stem cells (MSCs) are self-renewable, rapidly proliferating, multipotent stem cells which reside in almost all post-natal tissues. MSCs possess potent immunoregulatory properties and, in juxtacrine and paracrine manner, modulate phenotype and function of all immune cells that participate in tissue repair and regeneration. Additionally, MSCs produce various pro-angiogenic factors and promote neo-vascularization in healing tissues, contributing to their enhanced repair and regeneration. In this review article, we summarized current knowledge about molecular mechanisms that regulate the crosstalk between MSCs and immune cells in tissue repair and regeneration.


1999 ◽  
Vol 274 (9) ◽  
pp. 5637-5648 ◽  
Author(s):  
Angelos Constantinou ◽  
Daniela Gunz ◽  
Elizabeth Evans ◽  
Philippe Lalle ◽  
Paul A. Bates ◽  
...  

2015 ◽  
Vol 290 (34) ◽  
pp. 21067-21075 ◽  
Author(s):  
John M. Hinz ◽  
Peng Mao ◽  
Daniel R. McNeill ◽  
David M. Wilson

Non-coding apurinic/apyrimidinic (AP) sites are generated at high frequency in genomic DNA via spontaneous hydrolytic, damage-induced or enzyme-mediated base release. AP endonuclease 1 (APE1) is the predominant mammalian enzyme responsible for initiating removal of mutagenic and cytotoxic abasic lesions as part of the base excision repair (BER) pathway. We have examined here the ability of wild-type (WT) and a collection of variant/mutant APE1 proteins to cleave at an AP site within a nucleosome core particle. Our studies indicate that, in comparison to the WT protein and other variant/mutant enzymes, the incision activity of the tumor-associated variant R237C and the rare population variant G241R are uniquely hypersensitive to nucleosome complexes in the vicinity of the AP site. This defect appears to stem from an abnormal interaction of R237C and G241R with abasic DNA substrates, but is not simply due to a DNA binding defect, as the site-specific APE1 mutant Y128A, which displays markedly reduced AP-DNA complex stability, did not exhibit a similar hypersensitivity to nucleosome structures. Notably, this incision defect of R237C and G241R was observed on a pre-assembled DNA glycosylase·AP-DNA complex as well. Our results suggest that the BER enzyme, APE1, has acquired distinct surface residues that permit efficient processing of AP sites within the context of protein-DNA complexes independent of classic chromatin remodeling mechanisms.


2020 ◽  
Vol 48 (6) ◽  
pp. 3014-3028 ◽  
Author(s):  
Niu Li ◽  
Jian Wang ◽  
Susan S Wallace ◽  
Jing Chen ◽  
Jia Zhou ◽  
...  

Abstract The NEIL3 DNA glycosylase is a base excision repair enzyme that excises bulky base lesions from DNA. Although NEIL3 has been shown to unhook interstrand crosslinks (ICL) in Xenopus extracts, how NEIL3 participants in ICL repair in human cells and its corporation with the canonical Fanconi anemia (FA)/BRCA pathway remain unclear. Here we show that the NEIL3 and the FA/BRCA pathways are non-epistatic in psoralen-ICL repair. The NEIL3 pathway is the major pathway for repairing psoralen-ICL, and the FA/BRCA pathway is only activated when NEIL3 is not present. Mechanistically, NEIL3 is recruited to psoralen-ICL in a rapid, PARP-dependent manner. Importantly, the NEIL3 pathway repairs psoralen-ICLs without generating double-strand breaks (DSBs), unlike the FA/BRCA pathway. In addition, we found that the RUVBL1/2 complex physically interact with NEIL3 and function within the NEIL3 pathway in psoralen-ICL repair. Moreover, TRAIP is important for the recruitment of NEIL3 but not FANCD2, and knockdown of TRAIP promotes FA/BRCA pathway activation. Interestingly, TRAIP is non-epistatic with both NEIL3 and FA pathways in psoralen-ICL repair, suggesting that TRAIP may function upstream of the two pathways. Taken together, the NEIL3 pathway is the major pathway to repair psoralen-ICL through a unique DSB-free mechanism in human cells.


2020 ◽  
Vol 48 (12) ◽  
pp. 6530-6546 ◽  
Author(s):  
Shunlei Duan ◽  
Xuerui Han ◽  
Mansour Akbari ◽  
Deborah L Croteau ◽  
Lene Juel Rasmussen ◽  
...  

Abstract OGG1 initiated base excision repair (BER) is the major pathway for repair of oxidative DNA base damage 8-oxoguanine (8-oxoG). Here, we report that RECQL4 DNA helicase, deficient in the cancer-prone and premature aging Rothmund-Thomson syndrome, physically and functionally interacts with OGG1. RECQL4 promotes catalytic activity of OGG1 and RECQL4 deficiency results in defective 8-oxoG repair and increased genomic 8-oxoG. Furthermore, we show that acute oxidative stress leads to increased RECQL4 acetylation and its interaction with OGG1. The NAD+-dependent protein SIRT1 deacetylates RECQL4 in vitro and in cells thereby controlling the interaction between OGG1 and RECQL4 after DNA repair and maintaining RECQL4 in a low acetylated state. Collectively, we find that RECQL4 is involved in 8-oxoG repair through interaction with OGG1, and that SIRT1 indirectly modulates BER of 8-oxoG by controlling RECQL4–OGG1 interaction.


2010 ◽  
Vol 2 (2) ◽  
pp. 91-104 ◽  
Author(s):  
Ewa Tomkowiak ◽  
Joanna Romana Pienkowska

SummaryAquaporins (AQPs) or water channels are some of the most ubiquitous integral membrane proteins, and are present in all living organisms. Their presence in the lipid bilayer of cell membranes considerably increases their permeability to water and, in some cases, to other small solutes. All AQPs, identified thus far, share the same structure, comprising of six transmembrane segments and two conserved regions forming the pore. Depending on the transported solutes, AQPs can be divided into two classes: ‘classical’ aquaporins (permeable only to water) and aquaglyceroporins (permeable also to glycerol and/or other solutes). Many subtypes of AQPs coexist in a single organism. Localization of particular subtypes of AQPs is tissue-specific. AQPs have been well characterized in almost all vertebrate classes. However, little is known about their counterparts in invertebrates. Most of the water channels characterized in invertebrates are found in insects. Therefore, the knowledge of aquaporins in invertebrates is generally limited to the information concerning water channels in this class of organism. Insects are characterized by an astonishing variety of physiological adaptations, notable in their feeding strategies or survival strategies in hostile environments. An example of such, is feeding on blood, or tolerating extreme cold or drought. It is likely that many of these adaptation patterns emerged due to the expression and regulation of particular aquaporins. Here we review the current state of knowledge of invertebrate AQPs (of insects and nematodes) and compare their structure and function with mammalian water channels


Author(s):  
Dawit Kidane

Infections contribute to carcinogenesis through inflammation-related mechanisms. It is well established that H. pylori infection is an etiological factor in gastric carcinogenesis. However, the mechanism through which H. pylori infection contributes to the development of gastric cancer has not been fully elucidated. H. pylori-associated chronic inflammation is linked to genomic instability via reactive oxygen and nitrogen species (RONS). In this article, we summarize the current knowledge of H. pylori-induced double strand breaks (DSBs). Further, we will provide mechanistic insight into how processing of oxidative DNA damage via base excision repair (BER) leads to double strand breaks (DSBs). We review the recent progress how H. pylori infection triggers NF-kB /iNOS versus NF-kB/nucleotide excision repair (NER) axis mediated DSBs to drive genomic instability. Taken together, this review discusses current findings related to DSBs and their implications for the mechanisms of DSB repair.


2021 ◽  
Author(s):  
Romeo Cosimo Arrigo Dubini ◽  
Eva Korytiaková ◽  
Thea Schinkel ◽  
Pia Heinrichs ◽  
Thomas Carell ◽  
...  

5-carboxycytosine (5caC) is a rare epigenetic modification found in nucleic acids of all domains of life. Despite its sparse genomic abundance, 5caC is presumed to play essential regulatory roles in transcription, maintenance and base-excision processes in DNA. In this work, we utilize nuclear magnetic resonance (NMR) spectroscopy to address the effects of 5caC incorporation into canonical DNA strands at multiple pH and temperature conditions. Our results demonstrate that 5caC has a pH-dependent global destabilizing and a base-pair mobility enhancing local impact on dsDNA, albeit without any detectable influence on the ground-state B-DNA structure. Measurement of hybridization thermodynamics and kinetics of 5caC-bearing DNA duplexes highlighted how acidic environment (pH 5.8 and 4.7) destabilizes the double-stranded structure by ≈10-20 kJ mol-1 at 37 °C when compared to the same sample at neutral pH. Protonation of 5caC results in a lower activation energy for the dissociation process and a higher barrier for annealing. Studies on conformational exchange on the µs time scale regime revealed a sharply localized base-pair motion involving exclusively the modified site and its immediate surroundings. By direct comparison with canonical and 5-formylcytosine (5fC)-edited strands, we were able to address the impact of the two most oxidized naturally occurring cytosine derivatives in the genome. These insights on 5caC's subtle sensitivity to acidic pH contribute to the long standing questions of its capacity as a substrate in base excision repair processes and its purpose as an independent, stable epigenetic mark.


2016 ◽  
Vol 2016 ◽  
pp. 1-14 ◽  
Author(s):  
Laura Narciso ◽  
Eleonora Parlanti ◽  
Mauro Racaniello ◽  
Valeria Simonelli ◽  
Alessio Cardinale ◽  
...  

There is a growing body of evidence indicating that the mechanisms that control genome stability are of key importance in the development and function of the nervous system. The major threat for neurons is oxidative DNA damage, which is repaired by the base excision repair (BER) pathway. Functional mutations of enzymes that are involved in the processing of single-strand breaks (SSB) that are generated during BER have been causally associated with syndromes that present important neurological alterations and cognitive decline. In this review, the plasticity of BER during neurogenesis and the importance of an efficient BER for correct brain function will be specifically addressed paying particular attention to the brain region and neuron-selectivity in SSB repair-associated neurological syndromes and age-related neurodegenerative diseases.


Blood ◽  
2013 ◽  
Vol 122 (21) ◽  
pp. 1248-1248
Author(s):  
Subodh Kumar ◽  
Jagannath Pal ◽  
Jialan Shi ◽  
Puru Nanjappa ◽  
Maria Gkotzamanidou ◽  
...  

Abstract We have previously shown that endonuclease activity is deregulated in myeloma and suppression of base excision repair (BER) associated apurinic/apyrimidinic endonuclease (APE) activity, mediated chemically or transgenically, reduces homologous recombination (HR) and genomic instability in multiple myeloma (MM). The purpose of this study was to investigate the role of BER-specific AP nucleases APE1 and APE2, separately or together, in the activation of HR pathway following exposure of MM cells to different DNA damaging agents and unravel possible mechanism/s and translational significance of this cross talk between two repair pathways in MM. We transduced MM cells with lentivirus-based shRNAs, either control (CS) or those targeting APE1, APE2, or both (APE1/2; double knockdown) and selected the transduced cells in puromycin. Knockdowns were confirmed by Western blotting and Q-PCR. Using evaluation by Q-PCR we observed that whereas APE2 was suppressed by 80% in APE2- as well as double-knockdown cells, it was upregulated by 70% in APE1 knock down cells. These data indicate that certain level of AP nuclease activity is probably required by MM cell to function and is consistent with a 25-30% reduced proliferation rate of double-knockdown cells under spontaneous condition. To study the impact of these modulations on ability of cells to activate HR-mediated repair pathway in response to DNA damage, the cells were exposed to either UV (20 J/m2) and incubated for 2 and 48 hrs or melphalan (2.5 µM) treatment for 24 hrs, and then incubation for further 1 and 24 hrs and evaluated for RAD51 and γ-H2AX foci. Following UV treatment, RAD51 foci were detected in 91%, 48%, 49%, and 28% of cells transduced with control, APE1, APE2, or both shRNAs, respectively. Similary melphalan treatment induced RAD51 foci in 76% of control shRNA transduced cells whereas only in 46%, 47%, and 27% of APE1, APE2, and APE1/2-knockdown cells. These data show that AP nuclease activity is involved in DNA damaging agent-induced activation of HR repair pathway. Impact of the suppression of AP nucleases was also assessed on cell proliferation at 48 hrs after treatment with melphalan. Viability of cells lacking APE1, APE2, and APE1/2 relative to control shRNA-transduced cells was reduced by 28%, 26%, and 43% (P<0.00005), respectively, within 48 hrs of treatment. In summary, we show that: 1) AP nuclease activity plays a critical role in the activation of HR-mediated DNA repair and survival of MM cells following DNA damage; 2) Although suppression of APE1 or APE2 alone does not significantly affect spontaneous proliferation rates, simultaneous suppression of both reduces proliferation by ∼25-30%; 3) Suppression of APE1 leads to induction of APE2, indicating that certain level of AP nuclease activity (from either APE1 or APE2) is required by MM cell to function and is consistent with the reduced proliferation rate of double-knockdown cells; 4) Simultaneous suppression of both AP nucleases impairs the activation of HR repair following DNA damage. These data combined with our previous observations conclude that AP nucleases (APE1 and APE2) play critical role in HR-mediated repair and survival of MM cells following DNA damage and are important targets to reduce genomic instability as well as to sensitize MM cells to radio/chemotherapy. Disclosures: No relevant conflicts of interest to declare.


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