Measurement of DNA mismatch repair activity in live cells

Large-scale preparation of fluorescence multiplex host cell reactivation (FM-HCR) reporters

Repair of DNA damage is a critical survival mechanism that affects susceptibility to various human diseases and represents a key target for cancer therapy. A major barrier to applying this knowledge in research and clinical translation has been the lack of efficient, quantitative functional assays for measuring DNA repair capacity in living primary cells. To overcome this barrier, we recently developed a technology termed 'fluorescence multiplex host cell reactivation' (FM-HCR). We describe a method for using standard molecular biology techniques to generate large quantities of FM-HCR reporter plasmids containing site-specific DNA lesions and using these reporters to assess DNA repair capacity in at least six major DNA repair pathways in live cells. We improve upon previous methodologies by (i) providing a universal workflow for generating reporter plasmids, (ii) improving yield and purity to enable large-scale studies that demand milligram quantities and (iii) reducing preparation time >ten-fold.

Fluorescence Sheds Light on DNA Damage, DNA Repair, and Mutations

DNA damage can lead to carcinogenic mutations and toxicity that promotes diseases. Therefore, having rapid assays to quantify DNA damage, DNA repair, mutations, and cytotoxicity is broadly relevant to health. For example, DNA damage assays can be used to screen chemicals for genotoxicity, and knowledge about DNA repair capacity has applications in precision prevention and in personalized medicine. Furthermore, knowledge of mutation frequency has predictive power for downstream cancer, and assays for cytotoxicity can predict deleterious health effects. Tests for all of these purposes have been rendered faster and more effective via adoption of fluorescent readouts. Here, we provide an overview of established and emerging cell-based assays that exploit fluorescence for studies of DNA damage and its consequences.

EGFRvIII upregulates DNA mismatch repair resulting in increased temozolomide sensitivity of MGMT promoter methylated glioblastoma

The oncogene epidermal growth factor receptor variant III (EGFRvIII) is frequently expressed in glioblastomas (GBM) but its impact on therapy response is still under controversial debate. Here we wanted to test if EGFRvIII influences the sensitivity towards the alkylating agent temozolomide (TMZ). Therefore, we retrospectively analyzed the survival of 336 GBM patients, demonstrating that under standard treatment, which includes TMZ, EGFRvIII expression is associated with prolonged survival, but only in patients with O6-methylguanine-DNA methyltransferase (MGMT) promoter methylated tumors. Using isogenic GBM cell lines with endogenous EGFRvIII expression we could demonstrate that EGFRvIII increases TMZ sensitivity and results in enhanced numbers of DNA double-strand breaks and a pronounced S/G2-phase arrest after TMZ treatment. We observed a higher expression of DNA mismatch repair (MMR) proteins in EGFRvIII+ cells and patient tumor samples, which was most pronounced for MSH2 and MSH6. EGFRvIII-specific knockdown reduced MMR protein expression thereby increasing TMZ resistance. Subsequent functional kinome profiling revealed an increased activation of p38- and ERK1/2-dependent signaling in EGFRvIII expressing cells, which regulates MMR protein expression downstream of EGFRvIII. In summary, our results demonstrate that the oncoprotein EGFRvIII sensitizes a fraction of GBM to current standard of care treatment through the upregulation of DNA MMR.

DNA mismatch repair is required for the host innate response and controls cellular fate after influenza virus infection

Despite the cytopathic nature of influenza A virus (IAV) replication, we recently reported that a subset of lung epithelial club cells is able to intrinsically clear virus and survive infection. However, the mechanisms that drive cell survival during a normally lytic infection remained unclear. Using a loss-of-function screening approach, we discovered that the DNA mismatch repair (MMR) pathway is essential for club cell survival of IAV infection. Repair of virally-induced oxidative damage by the DNA MMR pathway not only allowed cell survival of infection but also facilitated host gene transcription, including the expression of antiviral and stress response genes. Enhanced viral suppression of the DNA MMR pathway prevented club cell survival and increased the severity of viral disease in vivo. Altogether, these results identify previously unappreciated roles for DNA MMR as a central modulator of cellular fate and a contributor to the innate antiviral response, which together, control influenza viral disease severity.

Reporter Assays for BER Pathway

Base excision repair (BER) is one of the most active DNA repair pathways in cells correcting DNA damage from oxidation, deamination, alkylation, and damages induced by free radicals and ionizing radiation. Deregulation or deficiencies in BER mechanisms increase the level of mutations leading to carcinogenesis, and single-strand DNA break formation, which may be converted to double-strand breaks and induce apoptosis. BER deficiency is associated with development of diseases causing neurodegenerative disorders, such as Alzheimer's disease (AD) and amyotrophic lateral sclerosis (ALS). In addition, BER mechanisms can be affected by viral infections, such as HPV, HTLV-1, and HIV-1. Deficiencies in DNA repair in cells can be analyzed using a very convenient and effective approach, where mammalian cells are transfected with plasmids carrying a reporter gene of fluorescent protein that contain inactivating damages. The repair of DNA damages depends on the cellular machinery and is reflected by expression of the reporter gene measured by flow cytometry. In this chapter, we describe this plasmid-based reporter gene system to investigate in cell the repairs of DNA damages involving BER mechanisms.

Fluorescent Probes of DNA Repair

DNA repair is now understood to play a key role in a variety of disease states, most notably cancer. Tools for studying DNA have typically relied on traditional biochemical methods which are often laborious and indirect. Efforts to study the biology and therapeutic relevance of DNA repair pathways can be limited by such methods. Recently, specific fluorescent probes have been developed to aid in the study of DNA repair. Fluorescent probes offer the advantage of being able to directly assay for DNA repair activity in a simple, mix-and-measure format. This review will summarize the distinct classes of probe designs and their potential utility in varied research and preclinical settings.

Functional assessment for elimination of mismatches in nuclear and whole cell extracts obtained from mouse and human blastocysts

Preimplantation embryos may have an increased risk of having mismatches due to the rates of cell proliferation and DNA replication. Elimination of mismatches in human gametes and embryos has not been investigated. In this study we developed a sensitive functional assay to examine the repair or elimination of mismatches in both commercially available cell extracts and extracts obtained from preimplantation embryos. Heteroduplex molecules were constructed using synthetic oligonucleotides. Efficiency of the repair of mismatches was semi-quantitatively analysed by exposure to nuclear/whole cell extracts (as little as 2.5 µg) and extracts obtained from pooled mouse and human blastocysts to investigate the repair capacity in human embryos. A cell free in vitro assay was successfully developed to analyze the repair of mismatches using heteroduplex complexes. The assay was further optimized to analyze repair of mismatches in cell extracts obtained from oocytes and blastocysts using minute amounts of protein. The efficiency of mismatch repair was examined in both mouse and human blastocysts (2.5 µg). The blastocysts were observed to have a lower repair efficiency compared to commercially available nuclear and whole cell extracts. In conclusion, a sensitive, easy, and fast in vitro technique was developed to detect the repair of mismatch efficiency in embryos.

Calculating and scoring high quality multiple flexible protein structure alignments

MOTIVATION

Calculating multiple protein structure alignments (MSAs) is important for understanding functional and evolutionary relationships between protein families, and for modeling protein structures by homology. While incorporating backbone flexibility promises to circumvent many of the limitations of rigid MSA algorithms, very few flexible MSA algorithms exist today. This article describes several novel improvements to the Kpax algorithm which allow high quality flexible MSAs to be calculated. This article also introduces a new Gaussian-based MSA quality measure called 'M-score', which circumvents the pitfalls of RMSD-based quality measures.

RESULTS

As well as calculating flexible MSAs, the new version of Kpax can also score MSAs from other aligners and from previously aligned reference datasets. Results are presented for a large-scale evaluation of the Homstrad, SABmark and SISY benchmark sets using Kpax and Matt as examples of state-of-the-art flexible aligners and 3DCOMB as an example of a state-of-the-art rigid aligner. These results demonstrate the utility of the M-score as a measure of MSA quality and show that high quality MSAs may be achieved when structural flexibility is properly taken into account.

AVAILABILITY AND IMPLEMENTATION

Kpax 5.0 may be downloaded for academic use at http://kpax.loria.fr/

CONTACT

dave.ritchie@inria.fr

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Acetylation regulates DNA repair mechanisms in human cells

The p300-mediated acetylation of enzymes involved in DNA repair and replication has been previously shown to stimulate or inhibit their activities in reconstituted systems. To explore the role of acetylation on DNA repair in cells we constructed plasmid substrates carrying inactivating damages in the EGFP reporter gene, which should be repaired in cells through DNA mismatch repair (MMR) or base excision repair (BER) mechanisms. We analyzed efficiency of repair within these plasmid substrates in cells exposed to deacetylase and acetyltransferase inhibitors, and also in cells deficient in p300 acetyltransferase. Our results indicate that protein acetylation improves DNA mismatch repair in MMR-proficient HeLa cells and also in MMR-deficient HCT116 cells. Moreover, results suggest that stimulated repair of mismatches in MMR-deficient HCT116 cells is done though a strand-displacement synthesis mechanism described previously for Okazaki fragments maturation and also for the EXOI-independent pathway of MMR. Loss of p300 reduced repair of mismatches in MMR-deficient cells, but did not have evident effects on BER mechanisms, including the long patch BER pathway. Hypoacetylation of the cells in the presence of acetyltransferase inhibitor, garcinol generally reduced efficiency of BER of 8-oxoG damage, indicating that some steps in the pathway are stimulated by acetylation.

In vivo DNA mismatch repair measurement in zebrafish embryos and its use in screening of environmental carcinogens

Impairment of DNA mismatch repair (MMR) function leads to the development and progression of certain cancers. Many environmental contaminants can target DNA MMR system. Currently, measurement of MMR activity is limited to in vitro or in vivo methods at the cell line level, and reports on measurement of MMR activity at the live organism level are lacking. Here, we report an efficient method to measure DNA MMR activity in zebrafish embryos. A G-T mismatch was introduced into enhanced green fluorescent protein (EGFP) gene. Repair of the G-T mismatch to G-C in the heteroduplex plasmid generates a functional EGFP expression. The heteroduplex plasmid and a similarly constructed homoduplex plasmid were injected in parallel into the same batch of embryos at 1-cell stage and EGFP expression in EGFP positive embryos was quantified at 24 h after injection. MMR efficiency was calculated as the total fluorescence intensity of embryos injected with the heteroduplex construct divided by that of embryos injected with the homoduplex construct. Our results showed 73% reduction of MMR activity in embryos derived from MMR-deficient mlh1 mutant fish (positive control) when compared with embryos from MMR-competent wild type AB line fish, indicating feasibility of in vivo MMR activity measurement in zebrafish embryos. We further applied this novel assay for measurement of MMR efficiency in embryos exposed to environmental chemicals such as cadmium chloride (CdCl2), benzo[a]pyrene (BaP), and perfluorooctanesulphonic acid (PFOS) from 6 hpf to 24 hpf. We observed significant reductions of MMR efficiency in embryos exposed to 0.1 μM CdCl2 (52%) and 0.5 μM BaP (34%), but no effect in embryos exposed to PFOS. Our study for the first time provides a model system for in vivo measurement of DNA MMR activity at the organism level, which has important implications in risk assessment of various environmental carcinogens.

Approaches to diagnose DNA mismatch repair gene defects in cancer

The DNA repair pathway mismatch repair (MMR) is responsible for the recognition and correction of DNA biosynthetic errors caused by inaccurate nucleotide incorporation during replication. Faulty MMR leads to failure to address the mispairs or insertion deletion loops (IDLs) left behind by the replicative polymerases and results in increased mutation load at the genome. The realization that defective MMR leads to a hypermutation phenotype and increased risk of tumorigenesis highlights the relevance of this pathway for human disease. The association of MMR defects with increased risk of cancer development was first observed in colorectal cancer patients that carried inactivating germline mutations in MMR genes and the disease was named as hereditary non-polyposis colorectal cancer (HNPCC). Currently, a growing list of cancers is found to be MMR defective and HNPCC has been renamed Lynch syndrome (LS) partly to include the associated risk of developing extra-colonic cancers. In addition, a number of non-hereditary, mostly epigenetic, alterations of MMR genes have been described in sporadic tumors. Besides conferring a strong cancer predisposition, genetic or epigenetic inactivation of MMR genes also renders cells resistant to some chemotherapeutic agents. Therefore, diagnosis of MMR deficiency has important implications for the management of the patients, the surveillance of their relatives in the case of LS and for the choice of treatment. Some of the alterations found in MMR genes have already been well defined and their pathogenicity assessed. Despite this substantial wealth of knowledge, the effects of a large number of alterations remain uncharacterized (variants of uncertain significance, VUSs). The advent of personalized genomics is likely to increase the list of VUSs found in MMR genes and anticipates the need of diagnostic tools for rapid assessment of their pathogenicity. This review describes current tools and future strategies for addressing the relevance of MMR gene alterations in human disease.

Enteropathogenic Escherichia coli (EPEC): Does it have a role in colorectal tumourigenesis? A Prospective Cohort Study

BACKGROUND

Despite the characterization of many aetiologic genetic changes. The specific causative factors in the development of sporadic colorectal cancer remain unclear. This study was performed to detect the possible role of Enteropathogenic Escherichia coli (EPEC) in developing colorectal carcinoma.

PATIENTS AND METHOD

Fresh biopsy specimens have been obtained from the colonic mucosa overlying the colorectal cancer as well as from the colon of the healthy controls. Culture, genotyping and virulence of EPEC were done using (nutrient broth culture, and PCR). Strains biochemically identified as Escherichia coli were selected from the surface of a MacConkey's plate and were serogrouped by slide agglutination tests.

RESULTS

From January 2011 to June 2014, 213 colorectal cancer patients (Group 1) and 248 healthy controls (Group 2) were prospectively enrolled in this study. EPEC was positive in 108 (50.7%) in group 1 and 51 (20.6%) in group 2 (P = 0.0001). A significant difference between both groups was observed regarding serotyping, genotyping (eae gene) and virulence category (P = 0.0001). A significant difference between the 2 subgroups of colorectal cancer cases was observed regarding genotyping (eae, bfb genes) and virulence category.

CONCLUSION

The incidence EPEC was higher significantly in patients with colorectal cancer. E. coli in patients with colorectal cancer significantly differed serotypically and genotypically from the E. coli in normal population. E. coli colonization of the colonic mucosa may be a cause colorectal cancer.

Inter-individual variation in DNA repair capacity: a need for multi-pathway functional assays to promote translational DNA repair research

Why does a constant barrage of DNA damage lead to disease in some individuals, while others remain healthy? This article surveys current work addressing the implications of inter-individual variation in DNA repair capacity for human health, and discusses the status of DNA repair assays as potential clinical tools for personalized prevention or treatment of disease. In particular, we highlight research showing that there are significant inter-individual variations in DNA repair capacity (DRC), and that measuring these differences provides important biological insight regarding disease susceptibility and cancer treatment efficacy. We emphasize work showing that it is important to measure repair capacity in multiple pathways, and that functional assays are required to fill a gap left by genome wide association studies, global gene expression and proteomics. Finally, we discuss research that will be needed to overcome barriers that currently limit the use of DNA repair assays in the clinic.

The mechanism of mismatch repair and the functional analysis of mismatch repair defects in Lynch syndrome

The majority of Lynch syndrome (LS), also known as hereditary non-polyposis colorectal cancer (HNPCC), has been linked to heterozygous defects in DNA mismatch repair (MMR). MMR is a highly conserved pathway that recognizes and repairs polymerase misincorporation errors and nucleotide damage as well as functioning as a damage sensor that signals apoptosis. Loss-of-heterozygosity (LOH) that retains the mutant MMR allele and epigenetic silencing of MMR genes are associated with an increased mutation rate that drives carcinogenesis as well as microsatellite instability that is a hallmark of LS/HNPCC. Understanding the biophysical functions of the MMR components is crucial to elucidating the role of MMR in human tumorigenesis and determining the pathogenetic consequences of patients that present in the clinic with an uncharacterized variant of the MMR genes. We summarize the historical association between LS/HNPCC and MMR, discuss the mechanism of the MMR and finally examine the functional analysis of MMR defects found in LS/HNPCC patients and their relationship with the severity of the disease.

Molecular signaling mechanisms of apoptosis in hereditary non-polyposis colorectal cancer

Colorectal cancer is the second most leading cause of cancer related deaths in the western countries. One of the forms of colorectal cancer is hereditary non-polyposis colorectal cancer (HNPCC), also known as “Lynch syndrome”. It is the most common hereditary form of cancer accounting for 5%-10% of all colon cancers. HNPCC is a dominant autosomal genetic disorder caused by germ line mutations in mismatch repair genes. Human mismatch repair genes play a crucial role in genetic stability of DNA, the inactivation of which results in an increased rate of mutation and often a loss of mismatch repair function. Recent studies have shown that certain mismatch repair genes are involved in the regulation of key cellular processes including apoptosis. Thus, differential expression of mismatch repair genes particularly the contributions of MLH1 and MSH2 play important roles in therapeutic resistance to certain cytotoxic drugs such as cisplatin that is used normally as chemoprevention. An understanding of the role of mismatch repair genes in molecular signaling mechanism of apoptosis and its involvement in HNPCC needs attention for further work into this important area of cancer research, and this review article is intended to accomplish that goal of linkage of apoptosis with HNPCC. The current review was not intended to provide a comprehensive enumeration of the entire body of literature in the area of HNPCC or mismatch repair system or apoptosis; it is rather intended to focus primarily on the current state of knowledge of the role of mismatch repair proteins in molecular signaling mechanism of apoptosis as it relates to understanding of HNPCC.

DNA mismatch repair proficiency executing 5-fluorouracil cytotoxicity in colorectal cancer cells

BACKGROUND

5-fluorouracil (5FU)-based chemotherapy is the standard treatment for advanced stage colorectal cancer (CRC) patients. Several groups including ours have reported that stage II-III colorectal cancer patients whose tumors retain DNA Mismatch repair (MMR) function derive a benefit from 5FU, but patients with tumors that lost MMR function do not. Although MMR recognition of 5FU incorporated in DNA has been demonstrated biochemically, it has not been demonstrated within cells to execute 5FU cytotoxicity.

AIM

To establish an efficient construction model for 5FU within DNA and demonstrate that 5FU incorporated into DNA can trigger cellular cytotoxicity executed by the DNA MMR system.

METHODS

We constructed a 5FdU-containing heteroduplex plasmid (5FdU plasmid) and 5FdU-containing linear dsDNA (5FdU linear DNA), and transfected these into MMR-proficient, hMLH1-/- and hMSH6-/- cells. We observed cell growth characteristics of both transfectants for 5FU-induced cytotoxicity.

RESULTS

MMR- proficient cells transfected with the 5FdU plasmid but not the 5FdU linear DNA showed reduced cell proliferation by MTS and clonogenic assays, and demonstrated cell morphological change consistent with apoptosis. In MMR-deficient cells, neither the 5FdU plasmid nor 5FdU linear DNA induced cell growth or morphological changes different from controls.

CONCLUSION

5FdU as heteroduplex DNA in plasmid but not linear form triggered cytotoxicity in a MMR-dependent manner. Thus 5FU incorporated into DNA, separated from its effects on RNA, can be recognized by DNA MMR to trigger cell death.

Identification of RING finger protein 4 (RNF4) as a modulator of DNA demethylation through a functional genomics screen

DNA methylation is an important epigenetic modification involved in transcriptional regulation, nuclear organization, development, aging, and disease. Although DNA methyltransferases have been characterized, the mechanisms for DNA demethylation remain poorly understood. Using a cell-based reporter assay, we performed a functional genomics screen to identify genes involved in DNA demethylation. Here we show that RNF4 (RING finger protein 4), a SUMO-dependent ubiquitin E3-ligase previously implicated in maintaining genome stability, plays a key role in active DNA demethylation. RNF4 reactivates methylation-silenced reporters and promotes global DNA demethylation. Rnf4 deficiency is embryonic lethal with higher levels of methylation in genomic DNA. Mechanistic studies show that RNF4 interacts with and requires the base excision repair enzymes TDG and APE1 for active demethylation. This activity appears to occur by enhancing the enzymatic activities that repair DNA G:T mismatches generated from methylcytosine deamination. Collectively, our study reveals a unique function for RNF4, which may serve as a direct link between epigenetic DNA demethylation and DNA repair in mammalian cells.

A convenient spectrometric assay system for intracellular quantitative measurement of DNA glycosylase activity

Cytosine methylation is a vital biology event. However, it is also the source of genomic instability due to deamination of 5'-methylcytosine by spontaneous hydrolysis, which produces thymine and results in G:T mismatches. Thymine DNA glycosylase and methyl-CpG-binding protein 4 are major DNA glycosylases involved in the mismatch repair progress, and their activities have been measured in many related researches. In this study, we developed a convenient spectrometric assay system for specific and quantitative measurement of intracellular DNA glycosylase activity. A G:T mismatch was introduced into the upstream region of firefly luciferase-coding sequence in the pGL3-control plasmid. Only if the G:T mismatches were repaired to G:C, will luciferase be expressed in transfected cells. By measuring luciferase activity, which is simple and convenient, the intracellular DNA glycosylase activity can be determined.

Gene silencing induced by oxidative DNA base damage: association with local decrease of histone H4 acetylation in the promoter region

Oxidized DNA bases, particularly 7,8-dihydro-8-oxoguanine (8-oxoG), are endogenously generated in cells, being a cause of carcinogenic mutations and possibly interfering with gene expression. We found that expression of an oxidatively damaged plasmid DNA is impaired after delivery into human host cells not only due to decreased retention in the transfected cells, but also due to selective silencing of the damaged reporter gene. To test whether the gene silencing was associated with a specific change of the chromatin structure, we determined the levels of histone modifications related to transcriptional activation (acetylated histones H3 and H4) or repression (methylated K9 and K27 of the histone H3, and histone H1) in the promoter region and in the downstream transcribed DNA. Acetylation of histone H4 was found to be specifically decreased by 25% in the proximal promoter region of the damaged gene, while minor quantitative changes in other tested chromatin components could not be proven as significant. Treatment with an inhibitor of histone deacetylases, trichostatin A, partially restored expression of the damaged DNA, suggesting a causal connection between the changes of histone acetylation and persistent gene repression. Based on these findings, we propose that silencing of the oxidatively damaged DNA may occur in a chromatin-mediated mechanism.

From bacteria to plants: a compendium of mismatch repair assays

Mismatch repair (MMR) system maintains genome integrity by correcting mispaired or unpaired bases which have escaped the proofreading activity of DNA polymerases. The basic features of the pathway have been highly conserved throughout evolution, although the nature and number of the proteins involved in the mechanism vary from prokaryotes to eukaryotes and even between humans and plants. Cells deficient in MMR genes have been observed to display a mutator phenotype characterized by an increased rate in spontaneous mutation, instability of microsatellite sequences and illegitimate recombination between diverged DNA sequences. Studies of the mutator phenotype have demonstrated a critical role for the MMR system in mutation avoidance and genetic stability. Here, we briefly review our current knowledge of the MMR mechanism and then focus on the in vivo biochemical and genetic assays used to investigate the function of the MMR proteins in processing DNA mismatches generated during replication and mitotic recombination in Escherichia coli, Saccharomyces cerevisiae, Homo sapiens and Arabidopsis thaliana. An overview of the biochemical assays developed to study mismatch correction in vitro is also provided.

Alignment of multiple protein structures based on sequence and structure features

Comparing the structures of proteins is crucial to gaining insight into protein evolution and function. Here, we align the sequences of multiple protein structures by a dynamic programming optimization of a scoring function that is a sum of an affine gap penalty and terms dependent on various sequence and structure features (SALIGN). The features include amino acid residue type, residue position, residue accessible surface area, residue secondary structure state and the conformation of a short segment centered on the residue. The multiple alignment is built by following the 'guide' tree constructed from the matrix of all pairwise protein alignment scores. Importantly, the method does not depend on the exact values of various parameters, such as feature weights and gap penalties, because the optimal alignment across a range of parameter values is found. Using multiple structure alignments in the HOMSTRAD database, SALIGN was benchmarked against MUSTANG for multiple alignments as well as against TM-align and CE for pairwise alignments. On the average, SALIGN produces a 15% improvement in structural overlap over HOMSTRAD and 14% over MUSTANG, and yields more equivalent structural positions than TM-align and CE in 90% and 95% of cases, respectively. The utility of accurate multiple structure alignment is illustrated by its application to comparative protein structure modeling.

Attaching and effacing Escherichia coli downregulate DNA mismatch repair protein in vitro and are associated with colorectal adenocarcinomas in humans

BACKGROUND

Mucosa-associated Escherichia coli are frequently found in the colonic mucosa of patients with colorectal adenocarcinoma, but rarely in healthy controls. Chronic mucosal E. coli infection has therefore been linked to colonic tumourigenesis. E. coli strains carrying eae (encoding the bacterial adhesion protein intimin) attach intimately to the intestinal mucosa and are classed as attaching and effacing E. coli (AEEC). Enteropathogenic Escherichia coli (EPEC) are the most common form of AEEC identified in man. EPEC utilise a type III secretion system to translocate effector proteins into host cells and infection induces wide-ranging effects on the host cell proteome. We hypothesised that EPEC infection could influence molecular pathways involved in colorectal tumourigenesis.

METHODOLOGY/PRINCIPAL FINDINGS

When co-cultured with human colorectal cell lines, EPEC dramatically downregulated the expression of key DNA mismatch repair proteins MSH2 and MLH1 in an attachment specific manner. Cytochrome c staining and TUNEL analysis confirmed that this effect was not a consequence of apoptosis/necrosis. Ex vivo human colonic mucosa was co-cultured with EPEC and probed by immunofluorescence to locate adherent bacteria. EPEC entered 10% of colonic crypts and adhered to crypt epithelial cells, often in the proliferative compartment. Adenocarcinoma and normal colonic mucosa from colorectal cancer patients (n = 20) was probed by immunofluorescence and PCR for AEEC. Mucosa-associated E. coli were found on 10/20 (50%) adenocarcinomas and 3/20 (15%) normal mucosa samples (P<0.05). AEEC were detected on 5/20 (25%) adenocarcinomas, but not normal mucosa samples (P<0.05).

SIGNIFICANCE/CONCLUSIONS

The ability of EPEC to downregulate DNA mismatch repair proteins represents a novel gene-environment interaction that could increase the susceptibility of colonic epithelial cells to mutations and therefore promote colonic tumourigenesis. The potential role of AEEC in colorectal tumourigenesis warrants further investigation.

Rapid isolation of highly pure single-stranded DNA from phagemids

Single-stranded DNA (ssDNA) has many applications in molecular biology and biotechnology. The conventional method for the preparation of ssDNA from phagemids is laborious, costly, and inefficient. Here we describe an integrated protocol for consistent production of phagemid ssDNA from a bacteria/phagemid/help phage complex and rapid isolation and purification of the ssDNA with a silica column followed by duplex-specific nuclease digestion. The major advantages of our method are the expediency, low cost, and consistent yield of highly pure ssDNA that is suitable for direct sequencing and other applications. This method is especially useful for large-scale preparation of high-quality ssDNA.

Preparation of heteroduplex enhanced green fluorescent protein plasmid for in vivo mismatch repair activity assay

Preparation of heteroduplexes in large quantities with high purity is essential for the measurement of DNA mismatch repair (MMR) activity. Here we report a rapid, less labor-intensive method for the preparation of a heteroduplex plasmid that expresses the enhanced green fluorescent protein (EGFP) if the mismatch is repaired correctly. The method involves the use of a wild-type and a mutated EGFP expression plasmid and a few steps of enzymatic digestion. When the constructed heteroduplex EGFP plasmid was transfected into MMR-proficient and -deficient cell lines, the number of EGFP-expressing cells was much higher in the MMR-proficient cells than in the MMR-deficient cells, suggesting that the heteroduplex can be used for MMR activity assay in live model systems.

Rad9 plays an important role in DNA mismatch repair through physical interaction with MLH1

Rad9 is conserved from yeast to humans and plays roles in DNA repair (homologous recombination repair, and base-pair excision repair) and cell cycle checkpoint controls. It has not previously been reported whether Rad9 is involved in DNA mismatch repair (MMR). In this study, we have demonstrated that both human and mouse Rad9 interacts physically with the MMR protein MLH1. Disruption of the interaction by a single-point mutation in Rad9 leads to significantly reduced MMR activity. This disruption does not affect S/M checkpoint control and the first round of G₂/M checkpoint control, nor does it alter cell sensitivity to UV light, gamma rays or hydroxyurea. Our data indicate that Rad9 is an important factor in MMR and carries out its MMR function specifically through interaction with MLH1.

BCR/ABL inhibits mismatch repair to protect from apoptosis and induce point mutations

BCR/ABL kinase-positive chronic myelogenous leukemia (CML) cells display genomic instability leading to point mutations in various genes including bcr/abl and p53, eventually causing resistance to imatinib and malignant progression of the disease. Mismatch repair (MMR) is responsible for detecting misincorporated nucleotides, resulting in excision repair before point mutations occur and/or induction of apoptosis to avoid propagation of cells carrying excessive DNA lesions. To assess MMR activity in CML, we used an in vivo assay using the plasmid substrate containing enhanced green fluorescent protein (EGFP) gene corrupted by T:G mismatch in the start codon; therefore, MMR restores EGFP expression. The efficacy of MMR was reduced approximately 2-fold in BCR/ABL-positive cell lines and CD34(+) CML cells compared with normal counterparts. MMR was also challenged by N-methyl-N'-nitro-N-nitrosoguanidine (MNNG), which generates O(6)-methylguanine and O(4)-methylthymine recognized by MMR system. Impaired MMR activity in leukemia cells was associated with better survival, accumulation of p53 but not of p73, and lack of activation of caspase 3 after MNNG treatment. In contrast, parental cells displayed accumulation of p53, p73, and activation of caspase 3, resulting in cell death. Ouabain-resistance test detecting mutations in the Na(+)/K(+) ATPase was used to investigate the effect of BCR/ABL kinase-mediated inhibition of MMR on mutagenesis. BCR/ABL-positive cells surviving the treatment with MNNG displayed approximately 15-fold higher mutation frequency than parental counterparts and predominantly G:C-->A:T and A:T-->G:C mutator phenotype typical for MNNG-induced unrepaired lesions. In conclusion, these results suggest that BCR/ABL kinase abrogates MMR activity to inhibit apoptosis and induce mutator phenotype.

RAPIDO: a web server for the alignment of protein structures in the presence of conformational changes

Rapid alignment of proteins in terms of domains (RAPIDO) is a web server for the 3D alignment of crystal structures of different protein molecules in the presence of conformational change. The structural alignment algorithm identifies groups of equivalent atoms whose interatomic distances are constant (within a defined tolerance) in the two structures being compared and considers these groups of atoms as rigid bodies. In addition to the functionalities provided by existing tools, RAPIDO can identify structurally equivalent regions also when these consist of fragments that are distant in terms of sequence and separated by other movable domains. Furthermore, RAPIDO takes the variation in the reliability of atomic coordinates into account in the comparison of distances between equivalent atoms by employing weighting-functions based on the refined B-values. The regions identified as equivalent by RAPIDO furnish reliable sets of residues for the superposition of the two structures for subsequent detailed analysis. The RAPIDO server, with related documentation, is available at http://webapps.embl-hamburg.de/rapido.

Characterization of Trypanosoma brucei dihydroorotate dehydrogenase as a possible drug target; structural, kinetic and RNAi studies

Nucleotide biosynthesis pathways have been reported to be essential in some protozoan pathogens. Hence, we evaluated the essentiality of one enzyme in the pyrimidine biosynthetic pathway, dihydroorotate dehydrogenase (DHODH) from the eukaryotic parasite Trypanosoma brucei through gene knockdown studies. RNAi knockdown of DHODH expression in bloodstream form T. brucei did not inhibit growth in normal medium, but profoundly retarded growth in pyrimidine-depleted media or in the presence of the known pyrimidine uptake antagonist 5-fluorouracil (5-FU). These results have significant implications for the development of therapeutics to combat T. brucei infection. Specifically, a combination therapy including a T. brucei-specific DHODH inhibitor plus 5-FU may prove to be an effective therapeutic strategy. We also show that this trypanosomal enzyme is inhibited by known inhibitors of bacterial Class 1A DHODH, in distinction to the sensitivity of DHODH from human and other higher eukaryotes. This selectivity is supported by the crystal structure of the T. brucei enzyme, which is reported here at a resolution of 1.95 A. Additional research, guided by the crystal structure described herein, is needed to identify potent inhibitors of T. brucei DHODH.

An evaluation of automated homology modelling methods at low target template sequence similarity

MOTIVATION

There are two main areas of difficulty in homology modelling that are particularly important when sequence identity between target and template falls below 50%: sequence alignment and loop building. These problems become magnified with automatic modelling processes, as there is no human input to correct mistakes. As such we have benchmarked several stand-alone strategies that could be implemented in a workflow for automated high-throughput homology modelling. These include three new sequence-structure alignment programs: 3D-Coffee, Staccato and SAlign, plus five homology modelling programs and their respective loop building methods: Builder, Nest, Modeller, SegMod/ENCAD and Swiss-Model. The SABmark database provided 123 targets with at least five templates from the same SCOP family and sequence identities </=50%.

RESULTS

When using Modeller as the common modelling program, 3D-Coffee outperforms Staccato and SAlign using both multiple templates and the best single template, and across the sequence identity range 20-50%. The mean model RMSD generated from 3D-Coffee using multiple templates is 15 and 28% (or using single templates, 3 and 13%) better than those generated by Staccato and Salign, respectively. 3D-Coffee gives equivalent modelling accuracy from multiple and single templates, but Staccato and SAlign are more successful with single templates, their quality deteriorating as additional lower sequence identity templates are added. Evaluating the different homology modelling programs, on average Modeller performs marginally better in overall modelling than the others tested. However, on average Nest produces the best loops with an 8% improvement by mean RMSD compared to the loops generated by Builder.

On the relationship between sequence and structure similarities in proteomics

MOTIVATION

The underlying assumption of many sequence-based comparative studies in proteomics is that different aspects of protein structure and therefore functionality may be linked to particular sequence motifs. This holds true if sequence similarity is sufficiently high, but in general the relationship between protein sequence and structure appears complex and is not well understood.

RESULTS

Statistical analysis of multiple and pairwise structural alignments of protein structures within SCOP folds is performed. The results indicate that multiple conservation of residue identity is not common and that relationship between sequence and structure may be explained by a model based on the assumption that protein structure is tolerant to residue substitutions preserving hydropathic profile of the sequence. This model also explains the origin and specific value of the sequence similarity threshold, noticed in many previous studies, below which structural resemblance is not statistically expected.

The rise, fall and renaissance of microsatellites in eukaryotic genomes

Microsatellites are among the most versatile of genetic markers, being used in an impressive number of biological applications. However, the evolutionary dynamics of these markers remain a source of contention. Almost 20 years after the discovery of these ubiquitous simple sequences, new genomic data are clarifying our understanding of the structure, distribution and variability of microsatellites in genomes, especially for the eukaryotes. While these new data provide a great deal of descriptive information about the nature and abundance of microsatellite sequences within eukaryotic genomes, there have been few attempts to synthesise this information to develop a global concept of evolution. This review provides an up-to-date account of the mutational processes, biases and constraints believed to be involved in the evolution of microsatellites, particularly with respect to the creation and degeneration of microsatellites, which we assert may be broadly viewed as a life cycle. In addition, we identify areas of contention that require further research and propose some possible directions for future investigation.

HOXA5 regulates hMLH1 expression in breast cancer cells

Homeobox protein HOXA5 functions as a transcriptional factor for genes that are not only involved in segmentation identity but also in cell differentiation. Although HOXA5 has been shown to regulate the expression of the tumor-suppressor protein p53, its role in breast tumorigenesis is not well understood. Using yeast as a model system, we now demonstrate that overexpression of HOXA5 in yeast can be used to identify downstream target genes that are homologous in humans. One such identified gene was that of the mismatch repair pathway component MutL homolog 1. Analysis of the promoter region of the gene for human MutL homolog 1 (hMLH1) displayed several putative HOXA5-binding sites. In transient transfection experiments, the overexpression of HOXA5 transactivated the hMLH1 promoter-reporter construct. In addition, chromatin immunoprecipitation assay using a human breast cancer cell line MCF-7 demonstrated that HOXA5 binds to the hMLH1 promoter in vivo. Furthermore, we demonstrate that, in the presence of HOXA5, there is an increase in in vivo repair activity in MCF-7 cells. Taken together, our results indicate that HOXA5 is a transcriptional regulator of hMLH1 in breast cancer cells.

Generation of 3D templates of active sites of proteins with rigid prosthetic groups

MOTIVATION

With the increasing availability of protein structures, the generation of biologically meaningful 3D patterns from the simultaneous alignment of several protein structures is an exciting prospect: active sites could be better understood, protein functions and protein 3D structures could be predicted more accurately. Although patterns can already be generated at the fold and topological levels, no system produces high-resolution 3D patterns including atom and cavity positions. To address this challenge, our research focuses on generating patterns from proteins with rigid prosthetic groups. Since these groups are key elements of protein active sites, the generated 3D patterns are expected to be biologically meaningful.

RESULTS

In this paper, we present a new approach which allows the generation of 3D patterns from proteins with rigid prosthetic groups. Using 237 protein chains representing proteins containing porphyrin rings, our method was validated by comparing 3D templates generated from homologues with the 3D structure of the proteins they model. Atom positions were predicted reliably: 93% of them had an accuracy of 1.00 A or less. Moreover, similar results were obtained regarding chemical group and cavity positions. Results also suggested our system could contribute to the validation of 3D protein models. Finally, a 3D template was generated for the active site of human cytochrome P450 CYP17, the 3D structure of which is unknown. Its analysis showed that it is biologically meaningful: our method detected the main patterns of the cytochrome P450 superfamily and the motifs linked to catalytic reactions. The 3D template also suggested the position of a residue, which could be involved in a hydrogen bond with CYP17 substrates and the shape and location of a cavity. Comparisons with independently generated 3D models comforted these hypotheses.

AVAILABILITY

Alignment software (Nestor3D) is available at http://www.kingston.ac.uk/~ku33185/Nestor3D.html

Development and validation of a consistency based multiple structure alignment algorithm

SUMMARY

We introduce an algorithm that uses the information gained from simultaneous consideration of an entire group of related proteins to create multiple structure alignments (MSTAs). Consistency-based alignment (CBA) first harnesses the information contained within regions that are consistently aligned among a set of pairwise superpositions in order to realign pairs of proteins through both global and local refinement methods. It then constructs a multiple alignment that is maximally consistent with the improved pairwise alignments. We validate CBA's alignments by assessing their accuracy in regions where at least two of the aligned structures contain the same conserved sequence motif.

RESULTS

CBA correctly aligns well over 90% of motif residues in superpositions of proteins belonging to the same family or superfamily, and it outperforms a number of previously reported MSTA algorithms.

The structure and proteolytic processing of Cbln1 complexes

The hexadecapeptide cerebellin is present in the brains of many vertebrate species and is derived from a larger protein, Cbln1 (cerebellin 1 precursor protein). Although cerebellin has features of a neuropeptide, Cbln1 belongs to the C1q/tumor necrosis factor superfamily of secreted proteins, suggesting that it is the biologically active molecule and the proteolytic events that generate cerebellin serve another function. Therefore, we assessed whether Cbln1 undergoes proteolytic processing and determined what consequences the cleavage events necessary to produce cerebellin have on the structure of Cbln1. Substantial degradation of Cbln1 was evident in the synaptic compartment of cerebellum and lysates of cultured cerebellar neurons and cells transfected with Cbln1 expression vectors. However, only uncleaved Cbln1 containing the cerebellin motif was released and assembled into hexameric complexes. Using yeast two hybrid and mammalian expression systems we show that the cleavages required to produce cerebellin influence the subunit stoichiometry of Cbln1 complexes. Cleavage at the N-terminus of the cerebellin sequence in Cbln1 yields trimeric complexes by separating the trimer-mediating C-terminal C1q domain from conserved N-terminal cysteine residues that mediate higher order oligomerization. Cleavage at the C-terminus of the cerebellin motif disrupts the C1q domain and abolishes subunit interactions. Functional implications of these data are discussed.

A new progressive-iterative algorithm for multiple structure alignment

MOTIVATION

Multiple structure alignments are becoming important tools in many aspects of structural bioinformatics. The current explosion in the number of available protein structures demands multiple structural alignment algorithms with an adequate balance of accuracy and speed, for large scale applications in structural genomics, protein structure prediction and protein classification.

RESULTS

A new multiple structural alignment program, MAMMOTH-mult, is described. It is demonstrated that the alignments obtained with the new method are an improvement over previous manual or automatic alignments available in several widely used databases at all structural levels. Detailed analysis of the structural alignments for a few representative cases indicates that MAMMOTH-mult delivers biologically meaningful trees and conservation at the sequence and structural levels of functional motifs in the alignments. An important improvement over previous methods is the reduction in computational cost. Typical alignments take only a median time of 5 CPU seconds in a single R12000 processor. MAMMOTH-mult is particularly useful for large scale applications.

AVAILABILITY

http://ub.cbm.uam.es/mammoth/mult.