Laser cross-linking of proteins to nucleic acids. II. Interactions of the bacteriophage T4 DNA replication polymerase accessory proteins complex with DNA

SPRTN metalloprotease participates in repair of ROS-mediated DNA-protein crosslinks

Exposure to reactive oxygen species (ROS) can induce DNA-protein crosslinks (DPCs), unusually bulky DNA lesions that block replication and transcription and play a role in aging, cancer, cardiovascular disease, and neurodegenerative disorders. Repair of DPCs depends on the coordinated efforts of proteases and DNA repair enzymes to cleave the protein component of the lesion to smaller DNA-peptide crosslinks which can be processed by tyrosyl-DNA phosphodiesterases 1 and 2, nucleotide excision and homologous recombination repair pathways. DNA-dependent metalloprotease SPRTN plays a role in DPC repair, and SPRTN-deficient mice exhibit an accelerated aging phenotype and develop liver cancer early in life. We investigated the role of the SPRTN enzyme in the repair of DPCs produced by a free radical mechanism. Sprtn-deficient MEF cells treated with ionizing radiation had higher levels of total DPCs and exhibited greater sensitivity upon exposure to hydrogen peroxide and other crosslinking agents including cisplatin, phosphoramide mustard, and 1,2,3,4-diepoxybutane. Using a sensitive and accurate nanoLC-ESI+-MS/MS assay, we specifically measured the radical-induced crosslinking of thymidine in DNA crosslinking of thymidine in DNA to tyrosine in proteins (dT-Tyr) in the tissues of SPRTN hypomorphic (SprtnH/H) and wild type mice. Genomic DNA isolated from the tissues of SPRTN hypomorphic (SprtnH/H) mice exhibited higher levels of dT-Tyr in the liver, brain, heart, and kidney than wild-type animals. Overall, our results are consistent with the understanding that SPRTN has a role in maintaining genomic integrity upon exposure to ionizing radiation and endogenous reactive oxygen species.

Synthesis and polymerase bypass studies of DNA-peptide and DNA-protein conjugates

DNA-peptide (DpCs) and DNA-protein cross-links (DPCs) are DNA lesions formed when polypeptides and nuclear proteins become covalently trapped on DNA strands. DNA-protein cross-links are of enormous size and hence pose challenges to cell survival by blocking DNA replication, transcription, and repair. However, DPCs can undergo proteolytic degradation via various pathways to give shorter polypeptide chains (DpCs). The resulting DpC lesions are efficiently bypassed by translesion synthesis (TLS) DNA polymerases like κ, η, δ, etc., although polymerase bypass efficiency as well as correct base insertion depends heavily on size, sequence context, and position of peptides in DpCs. This chapter explores various synthetic methods to generate these lesions including detailed experimental procedures for the construction of DpCs and DPCs via reductive amination and oxime ligation. Further we describe biochemical experiments to investigate the effects of these lesions on DNA polymerase activity and fidelity.

The m6A landscape of polyadenylated nuclear (PAN) RNA and its related methylome in the context of KSHV replication

Polyadenylated nuclear (PAN) RNA is a long noncoding transcript involved in Kaposi's sarcoma-associated herpesvirus (KSHV) lytic reactivation and regulation of cellular and viral gene expression. We have previously shown that PAN RNA has dynamic secondary structure and protein binding profiles that can be influenced by epitranscriptomic modifications. N6-methyladenosine (m6A) is one of the most abundant chemical signatures found in viral RNA genomes and virus-encoded RNAs. Here, we combined antibody-independent next-generation mapping with direct RNA sequencing to address the epitranscriptomic status of PAN RNA in KSHV infected cells. We showed that PAN m6A status is dynamic, reaching the highest number of modifications at the late lytic stages of KSHV infection. Using a newly developed method, termed selenium-modified deoxythymidine triphosphate (SedTTP)-reverse transcription (RT) and ligation assisted PCR analysis of m6A (SLAP), we gained insight into the fraction of modification at identified sites. By applying comprehensive proteomic approaches, we identified writers and erasers that regulate the m6A status of PAN, and readers that can convey PAN m6A phenotypic effects. We verified the temporal and spatial subcellular availability of the methylome components for PAN modification by performing confocal microscopy analysis. Additionally, the RNA biochemical probing (SHAPE-MaP) outlined local and global structural alterations invoked by m6A in the context of full-length PAN RNA. This work represents the first comprehensive overview of the dynamic interplay that takes place between the cellular epitranscriptomic machinery and a specific viral RNA in the context of KSHV infected cells.

Y-box proteins combine versatile cold shock domains and arginine-rich motifs (ARMs) for pleiotropic functions in RNA biology

Y-box proteins are single-strand DNA- and RNA-binding proteins distinguished by a conserved cold shock domain (CSD) and a variable C-terminal domain organized into alternating short modules rich in basic or acidic amino acids. A huge literature depicts Y-box proteins as highly abundant, staggeringly versatile proteins that interact with all mRNAs and function in most forms of mRNA-specific regulation. The mechanisms by which Y-box proteins recognize mRNAs are unclear, because their CSDs bind a jumble of diverse elements, and the basic modules in the C-terminal domain are considered to bind nonspecifically to phosphates in the RNA backbone. A survey of vertebrate Y-box proteins clarifies the confusing names for Y-box proteins, their domains, and RNA-binding motifs, and identifies several novel conserved sequences: first, the CSD is flanked by linkers that extend its binding surface or regulate co-operative binding of the CSD and N-terminal and C-terminal domains to proteins and RNA. Second, the basic modules in the C-terminal domain are bona fide arginine-rich motifs (ARMs), because arginine is the predominant amino acid and comprises 99% of basic residues. Third, conserved differences in AA (amino acid) sequences between isoforms probably affect RNA-binding specificity. C-terminal ARMs connect with many studies, demonstrating that ARMs avidly bind sites containing specific RNA structures. ARMs crystallize insights into the under-appreciated contributions of the C-terminal domain to site-specific binding by Y-box proteins and difficulties in identifying site-specific binding by the C-terminal domain. Validated structural biology techniques are available to elucidate the mechanisms by which YBXprot (Y-box element-binding protein) CSDs and ARMs identify targets.

Mass Spectrometry-Based Tools to Characterize DNA-Protein Cross-Linking by Bis-Electrophiles

DNA-protein cross-links (DPCs) are unusually bulky DNA adducts that form in cells as a result of exposure to endogenous and exogenous agents including reactive oxygen species, ultraviolet light, ionizing radiation, environmental agents (e.g. transition metals, formaldehyde, 1,2-dibromoethane, 1,3-butadiene) and common chemotherapeutic agents. Covalent DPCs are cytotoxic and mutagenic due to their ability to interfere with faithful DNA replication and to prevent accurate gene expression. Key to our understanding of the biological significance of DPC formation is identifying the proteins most susceptible to forming these unusually bulky and complex lesions and quantifying the extent of DNA-protein cross-linking in cells and tissues. Recent advances in bottom-up mass spectrometry-based proteomics have allowed for an unbiased assessment of the whole protein DPC adductome after in vitro and in vivo exposures to cross-linking agents. This MiniReview summarizes current and emerging methods for DPC isolation and analysis by mass spectrometry-based proteomics. We also highlight several examples of successful applications of these novel methodologies to studies of DPC lesions induced by bis-electrophiles such as formaldehyde, 1,2,3,4-diepoxybutane, nitrogen mustards and cisplatin.

The replication clamp-loading machine at work in the three domains of life

Sliding clamps are ring-shaped proteins that tether DNA polymerases to DNA, which enables the rapid and processive synthesis of both leading and lagging strands at the replication fork. The clamp-loading machinery must repeatedly load sliding-clamp factors onto primed sites at the replication fork. Recent structural and biochemical analyses provide unique insights into how these clamp-loading ATPase machines function to load clamps onto the DNA. Moreover, these studies highlight the evolutionary conservation of the clamp-loading process in the three domains of life.

Solution study of the NF-kappaB p50-DNA complex by UV laser protein-DNA cross-linking

In this study, we describe a new approach for studying protein-DNA interactions in solution. The approach is based on mapping the UV laser-induced protein-DNA cross-links between the amino acids of the protein and the DNA bases that are in direct contact. The approach was applied for studying the solution structure of the human necrosis factor (NF)-kappaB p50 homodimer bound to a 37 base pair DNA. Several points of contact identical to those observed in the NF-kappaB-DNA crystal structure were found between the two biomolecules. Evidence is provided for the occurrence of two new contact points, one for each DNA strand. These new points of contact are located symmetrically a base apart from the extremity of the binding sequence.

Differential remodeling of the HIV-1 nucleosome upon transcription activators and SWI/SNF complex binding

Here we have examined HIV-1 nucleosome remodeling upon the binding of transcription factors and the SWI/SNF complex using a novel approach. The approach combines UV laser protein-DNA crosslinking, electrophoretic mobility-shift analysis and DNase I protection analysis with immunochemical techniques. It was found that single activator-bound HIV-1 nucleosomes exhibit very weak perturbation in histone NH(2) tail-DNA interactions. However, the simultaneous binding of the transcription activators Sp1, NF-kB1, LEF-1 and USF synergistically increased the release of histone NH(2) tails from nucleosomal DNA. In contrast, the binding of SWI/SNF complex to HIV-1 nucleosome disrupted structured histone domain-DNA contacts, but not histone NH(2) tail-DNA interactions. Stable remodeled nucleosomes, (obtained after detachment of SWI/SNF), displayed identical structural alterations with those bound to SWI/SNF. These results demonstrate a different in vitro remodeling of the HIV-1 nucleosome upon the binding of multiple transcription activators and of SWI/SNF complex.

Structural analyses of gp45 sliding clamp interactions during assembly of the bacteriophage T4 DNA polymerase holoenzyme. I. Conformational changes within the gp44/62-gp45-ATP complex during clamp loading

A multisubunit ring-shaped protein complex is used to tether the polymerase to the DNA at the primer-template junction in most DNA replication systems. This "sliding clamp" interacts with the polymerase, completely encircles the DNA duplex, and is assembled onto the DNA by a specific clamp loading complex in an ATP-driven process. Site-specific mutagenesis has been used to introduce single cysteine residues as reactive sites for adduct formation within each of the three subunits of the bacteriophage T4-coded sliding clamp complex (gp45). Two such mutants, gp45S19C and gp45K81C, are reacted with the cysteine-specific photoactivable cross-linker TFPAM-3 and used to track the changes in the relative positioning of the gp45 subunits with one another and with the other components of the clamp loading complex (gp44/62) in the various stages of the loading process. Cross-linking interactions performed in the presence of nucleotide cofactors show that ATP binding and hydrolysis, interaction with primer-template DNA, and release of ADP all result in significant conformational changes within the clamp loading cycle. A structural model is presented to account for the observed rearrangements of intersubunit contacts within the complex during the loading process.

Nuclear recruitment of A1p145 subunit of replication factor C in the early G1 phase of the cell cycle in Faza 567 hepatoma cell line and hepatocyte primary cultures

Using a combination of immunoprecipitation and Western blotting with Faza 567 hepatoma cell extracts revealed that the large subunit of replication factor C (A1p145; mRFC140) was in a complex with proliferating cell nuclear antigen (PCNA). Western blotting showed that A1p145 was more abundant in nuclear extracts from butyrate-treated hepatoma cells which blocks the cells in the G1 phase of the cell cycle than from routinely cultured cells. Indirect immunoperoxidase analysis of G1 blocked Faza hepatoma cells localized A1p145 protein predominantly in the nucleoli. When hepatoma cells were stimulated to progress toward the S phase, A1p145 protein was then observed in both the cytoplasm and the nucleoplasm of these cells. Studies with early cultured normal hepatocytes which are progressing from G0 towards G1, also showed a nucleolus distribution for A1p145. This is the first demonstration in mammalian cells that the large subunit of replication factor C is associated with PCNA in the nucleus and that its distribution within cells changes during the cell cycle.

Transcriptional activation by a DNA-tracking protein: structural consequences of enhancement at the T4 late promoter

Transcriptional initiation at bacteriophage T4 late promoters is activated from enhancer-like distal sites by the T4 gene 44, 62, and 45 DNA polymerase accessory proteins (gp44, gp62, and gp45, respectively). Enhancement is ATP hydrolysis-dependent and requires protein tracking along DNA. The structural analysis of the enhanced transcription initiation complex shows gp45 located at the upstream end of this promoter complex in the vicinity of its transcriptional coactivator, the T4 gene 33 protein. The ATP-cleaving gene 44 protein-gene 62 protein complex serves as the assembly factor for gp45, but does not stably associate with the enhanced promoter complex. Transcriptional enhancement quantitatively favors, but does not qualitatively change, DNA strand separation in the transcription bubble. A model of the transcriptional activation that rationalizes its DNA-tracking and activation-polarity properties is presented.

DNA replication: enzymology and mechanisms

Research into the enzymology of DNA replication has seen a multitude of highly significant advances during the past year, in both prokaryotic and eukaryotic systems. The scope of this article is limited to chromosomal replicases and origins of initiation. The multiprotein chromosomal replicases of prokaryotes and eukaryotes appear to be strikingly similar in structure and function, although future work may reveal their differences. Recent developments, elaborating the activation of origins in several systems, have begun to uncover mechanisms of regulation. The enzymology of eukaryotic origins has, until now, been limited to viral systems, but over the past few years, enzymology has caught a grip on the cellular origins of yeast.