A new method for constructing linker scanning mutants

The mechanism of gap creation by a multifunctional nuclease during base excision repair

During base excision repair, a transient single-stranded DNA (ssDNA) gap is produced at the apurinic/apyrimidinic (AP) site. Exonuclease III, capable of performing both AP endonuclease and exonuclease activity, are responsible for gap creation in bacteria. We used single-molecule fluorescence resonance energy transfer to examine the mechanism of gap creation. We found an AP site anchor-based mechanism by which the intrinsically distributive enzyme binds strongly to the AP site and becomes a processive enzyme, rapidly creating a gap and an associated transient ssDNA loop. The gap size is determined by the rigidity of the ssDNA loop and the duplex stability of the DNA and is limited to a few nucleotides to maintain genomic stability. When the 3' end is released from the AP endonuclease, polymerase I quickly initiates DNA synthesis and fills the gap. Our work provides previously unidentified insights into how a signal of DNA damage changes the enzymatic functions.

Spectroscopic sensing and quantification of AP-endonucleases using fluorescence-enhancement by cis–trans isomerization of cyanine dyes

Apurinic/apyrimidinic (AP) endonucleases are vital DNA repair enzymes, and proposed to be a prognostic biomarker for various types of cancer in humans. Numerous DNA sensors have been developed to evaluate the extent of nuclease activity but their DNA termini are not protected against other nucleases, hampering accurate quantification. Here we developed a new fluorescence enhancement (FE)-based method as an enzyme-specific DNA biosensor with nuclease-protection by three functional units (an AP-site, Cy3 and termini that are protected from exonucleolytic cleavage). A robust FE signal arises from the fluorescent cis–trans isomerization of a cyanine dye (e.g., Cy3) upon the enzyme-triggered structural change from double-stranded (ds)DNA to single-stranded (ss)DNA that carries Cy3. The FE-based assay reveals a linear dependency on sub-nanomolar concentrations as low as 10⁻¹¹ M for the target enzyme and can be also utilized as a sensitive readout of other nuclease activities.

Apurinic/apyrimidinic (AP) endonucleases are vital DNA repair enzymes, and proposed to be a prognostic biomarker for various types of cancer in humans.

Targeted insertional mutagenesis libraries for deep domain insertion profiling

Domain recombination is a key principle in protein evolution and protein engineering, but inserting a donor domain into every position of a target protein is not easily experimentally accessible. Most contemporary domain insertion profiling approaches rely on DNA transposons, which are constrained by sequence bias. Here, we establish Saturated Programmable Insertion Engineering (SPINE), an unbiased, comprehensive, and targeted domain insertion library generation technique using oligo library synthesis and multi-step Golden Gate cloning. Through benchmarking to MuA transposon-mediated library generation on four ion channel genes, we demonstrate that SPINE-generated libraries are enriched for in-frame insertions, have drastically reduced sequence bias as well as near-complete and highly-redundant coverage. Unlike transposon-mediated domain insertion that was severely biased and sparse for some genes, SPINE generated high-quality libraries for all genes tested. Using the Inward Rectifier K⁺ channel Kir2.1, we validate the practical utility of SPINE by constructing and comparing domain insertion permissibility maps. SPINE is the first technology to enable saturated domain insertion profiling. SPINE could help explore the relationship between domain insertions and protein function, and how this relationship is shaped by evolutionary forces and can be engineered for biomedical applications.

Differential regulation of transcription by the NURR1/NUR77 subfamily of nuclear transcription factors

NURR1 is an orphan member of the nuclear receptor superfamily of transcription factors that shares close sequence homology to the orphan nuclear receptor and immediate early gene product NUR77(NGF1 beta). The physiological role of NURR1 has not been established in mammalian cells. However, the observation that NURR1 and NUR77 interact with at least one common enhancer element (AAAAGGTCA), together with their partly overlapping but differential expression patterns in mammalian tissues, suggests that these proteins may have both shared and independent transcription regulatory functions. To identify potential target genes that may be regulated by NURR1, we analyzed its DNA binding properties to potential cis-acting enhancer elements. Using point mutagenesis of the AAAAGGTCA motif, we have identified three additional sequences that bind specifically to both NURR1 and NUR77, one of which serves as a functional enhancer element. Comparative analysis of the transcription regulatory properties of NURR1 and NUR77 indicates that the proteins can display opposing transregulatory activities that are influenced by the specific cis-acting sequences to which they bind. Our results indicate that the transcriptional responses of specific target genes to the NURR1/NUR77 subfamily may be differentially regulated by the relative cellular levels of NURR1 and NUR77 and influenced by the specific enhancer sequences that mediate their activity. Finally, we have identified several potential target genes of neuronal and neuroendocrine origin whose promoters contain this element.

Elements of the rabbit uteroglobin promoter mediating its transcription in epithelial cells from the endometrium and lung

The rabbit uteroglobin gene is specifically expressed in certain epithelial cells of ontogenetically unrelated origin. In the endometrium, expression is restricted to the glandular and luminal epithelium and is inducible by progesterone and estradiol. In the lung, Clara cells lining the bronchiolar epithelium show constitutive expression of uteroglobin, which is modulated by glucocorticoids. To explore the molecular basis for this cell type specificity, we have transiently transfected the uteroglobin promoter region fused to the chloramphenicol acetyl transferase gene (CAT gene) in the endometrial cell line Ishikawa; in the human lung cell line NCI-H441, which shows morphological Clara cell characteristics; in HeLa cells; and in three fibroblast cell lines. The uteroglobin promoter efficiently drives expression of the CAT gene in Ishikawa and NCI-H441 cells, but not in HeLa and fibroblast cells. To identify the responsible elements we have analyzed progressive promoter 5'-deletion mutants and randomly generated linker scanning mutants spanning the sequence from -258 to -14 of the uteroglobin promoter. Transfection experiments reveal seven mutation-sensitive regions located around -30, -70, -95, -130, -190, -230, and -255. Several mutants display strong cell type-specific phenotypes. Most significantly, the integrity of the region around -190 is essential for full CAT gene expression in Ishikawa cells, but not in NCI-H441 cells.

Selection of novel vesicular stomatitis virus glycoprotein variants from a peptide insertion library for enhanced purification of retroviral and lentiviral vectors

The introduction of new features or functions that are not present in an original protein is a significant challenge in protein engineering. For example, modifications to vesicular stomatitis virus glycoprotein (VSV-G), which is commonly used to pseudotype retroviral and lentiviral vectors for gene delivery, have been hindered by a lack of structural knowledge of the protein. We have developed a transposon-based approach that randomly incorporates designed polypeptides throughout a protein to generate saturated insertion libraries and a subsequent high-throughput selection process in mammalian cells that enables the identification of optimal insertion sites for a novel designed functionality. This method was applied to VSV-G in order to construct a comprehensive library of mutants whose combined members have a His6 tag inserted at likely every site in the original protein sequence. Selecting the library via iterative retroviral infections of mammalian cells led to the identification of several VSV-G-His6 variants that were able to package high-titer viral vectors and could be purified by Ni-nitrilotriacetic acid affinity chromatography. Column purification of vectors reduced protein and DNA impurities more than 5,000-fold and 14,000-fold, respectively, from the viral supernatant. This substantially improved purity elicited a weaker immune response in the brain, without altering the infectivity or tropism from wild-type VSV-G-pseudotyped vectors. This work applies a powerful new tool for protein engineering to construct novel viral envelope variants that can greatly improve the safety and use of retroviral and lentiviral vectors for clinical gene therapy. Furthermore, this approach of library generation and selection can readily be extended to other challenges in protein engineering.

NMDA receptor type 2D gene as target for estrogen receptor in the brain

Although it is well known that estrogen exerts its effect in the brain, the direct target genes transcriptionally regulated by estrogen or rather estrogen receptor (ER) are almost unknown. During the search for estrogen receptor-binding sites from human CpG island library, we found one genomic DNA fragment corresponding to the putative 3'-untranslated region of human NMDA receptor subunit 2D (NR2D) gene. It contained at least four half palindromic estrogen responsive elements (hEREs) within two hundred nucleotides, which was conserved also in the rat. Interestingly, the NR2D mRNA is co-localized with ERalpha and/or ERbeta mRNA in a number of regions of rat brain. We have also demonstrated that NR2D mRNA is up-regulated in rat hypothalamus by estrogen possibly via hEREs identified here. Thus, we suggest that NR2D is one of the direct targets of estrogen receptors which are involved in reproductive as well as non-reproductive actions in the brain.

A sequence based computational identification of a Drosophila developmentally regulated TATA-less RNA polymerase II promoter and its experimental validation

Many RNA polymerase II promoters lack the characteristic TATA box sequence located -25/-30 nucleotides upstream from the transcription start. In Drosophila, half of the promoters identified so far are TATA-deficient. The yemanuclein-alpha gene whose promoter activity is restricted to oogenesis, falls in this class. A number of upstream and downstream promoter elements have been identified for some TATA-less promoters. The yem-alpha promoter contains none of the consensus elements identified so far. Our work was based on the assumption that the physical parameters of the DNA could be used to predict the location of the yem-alpha promoter. A sequence based computational analysis allowed us to determine the characteristic changes of DNA curvature and helix stability in the presumptive regulatory region. Our experimental data were in good agreement with the computational analysis. We have started to investigate the general value of this approach by analyzing other promoters.

Agonistic effect of tamoxifen is dependent on cell type, ERE-promoter context, and estrogen receptor subtype: functional difference between estrogen receptors alpha and beta

To investigate the functional differences between estrogen receptor (ER) alpha and beta subtypes, we studied the expression and the transcription stimulating activities of these receptors. RT-PCR has demonstrated that ER alpha is expressed at a high level in MCF-7 cells derived from human breast cancer. Both ER alpha and ER beta were expressed at a lower level in HOS-TE85 and Saos2 cells derived from human osteosarcoma. Chloramphenicol acetyltransferase reporter assay detected the transcriptional activation by the endogenous receptor only in MCF-7 cells. Agonistic effect of tamoxifen was observed as strong as that of 17beta-estradiol on ERE activation in MCF-7 cells at the concentration of 10(-7) M when ERE-containing reporter is constructed with beta-globin promoter. The effect of tamoxifen was not apparent when the reporter was constructed with thymidine kinase promoter, suggesting that the differential gene activation between tamoxifen and estrogen may take place depending upon ERE-promoter context. Agonistic activity of tamoxifen was also detected in COS-7 and Saos-2 cells, but not in HEC-1 cells derived from human endometrial carcinoma via exogenously expressed ER. Interestingly, this effect was ER alpha specific. Thus, we demonstrate that agonistic effect of tamoxifen depends on the cell type, ERE-promoter context, and ER subtype. These parameters would explain at least a part of the tissue specific effects of antiestrogens in vivo.

Multiple positive and negative regulatory elements in the promoter of the mouse homeobox gene Hoxb-4

Mouse Hoxb-4 (Hox-2.6) is a homeobox gene that belongs to a family which also includes Hoxa-4, Hoxc-4, and Hoxd-4 and that is related to the Deformed gene in Drosophila melanogaster. We have determined the sequence of 1.2 kb of 5' flanking DNA of mouse Hoxb-4 and by nuclease S1 and primer extension experiments identified two transcription start sites, P1 and P2, 285 and 207 nucleotides upstream of the ATG initiator codon, respectively. We have shown that this region harbors two independent promoters which drive CAT expression in several different cell lines with various efficiencies, suggesting that they are subject to cell-type-specific regulation. Through detailed mutational analysis, we have identified several cis-regulatory elements, located upstream and downstream of the transcription start sites. They include two cell-type-specific negative regulatory elements, which are more active in F9 embryonal carcinoma cells than in neuroblastoma cells (regions a and d at -226 to -186 and +169 to +205, respectively). An additional negative regulatory element has been delimited (region b between +22 and +113). Positive regulation is achieved by binding of HoxTF, a previously unknown factor, to the sequence GCCATTGG (+148 to +155) that is essential for efficient Hoxb-4 expression. We have also defined the minimal promoter sequences and found that they include two 12-bp initiator elements centered around each transcription start site. The complex architecture of the Hoxb-4 promoter provides the framework for fine-tuned transcriptional regulation during embryonic development.

Multiple positive and negative regulatory elements in the promoter of the mouse homeobox gene Hoxb-4

Mouse Hoxb-4 (Hox-2.6) is a homeobox gene that belongs to a family which also includes Hoxa-4, Hoxc-4, and Hoxd-4 and that is related to the Deformed gene in Drosophila melanogaster. We have determined the sequence of 1.2 kb of 5' flanking DNA of mouse Hoxb-4 and by nuclease S1 and primer extension experiments identified two transcription start sites, P1 and P2, 285 and 207 nucleotides upstream of the ATG initiator codon, respectively. We have shown that this region harbors two independent promoters which drive CAT expression in several different cell lines with various efficiencies, suggesting that they are subject to cell-type-specific regulation. Through detailed mutational analysis, we have identified several cis-regulatory elements, located upstream and downstream of the transcription start sites. They include two cell-type-specific negative regulatory elements, which are more active in F9 embryonal carcinoma cells than in neuroblastoma cells (regions a and d at -226 to -186 and +169 to +205, respectively). An additional negative regulatory element has been delimited (region b between +22 and +113). Positive regulation is achieved by binding of HoxTF, a previously unknown factor, to the sequence GCCATTGG (+148 to +155) that is essential for efficient Hoxb-4 expression. We have also defined the minimal promoter sequences and found that they include two 12-bp initiator elements centered around each transcription start site. The complex architecture of the Hoxb-4 promoter provides the framework for fine-tuned transcriptional regulation during embryonic development.

PAS10 is a tetratricopeptide-repeat protein that is essential for the import of most matrix proteins into peroxisomes of Saccharomyces cerevisiae

pas mutants of Saccharomyces cerevisiae are disturbed in peroxisome assembly (pas) and proliferation. Here we report the characterization of the PAS10 gene and its product (PAS10) that is essential for the import of a large subset of proteins into the peroxisomal matrix. PAS10, a protein of 69 kDa, is a member of the tetratricopeptide repeat, or snap helix, protein family, characterized by several direct repeats of a degenerate 34-amino acid motif (Sikorski, R. S., Boguski, M. S., Goebl, M. & Hieter, P. (1990) Cell 60, 307-317). Other members of this family are MAS70 (S. cerevisiae) and MOM72 (Neurospora crassa), which are mitochondrial receptors for protein import. A pas10 null mutant accumulates peroxisomal, leaflet-like membrane structures and exhibits deficient import of a number of peroxisomal matrix enzymes, particularly of proteins with an SKL-like import signal. In contrast, 3-ketoacyl-CoA thiolase associated with these membranes is resistant in vitro to degradation by proteinase K, indicating true protein import. These results suggest that PAS10 is an essential component of a peroxisomal import machinery which mediates the translocation of a specific subset of proteins to the peroxisomal matrix with an SKL-like import signal.

H2O2 and antioxidants have opposite effects on activation of NF-kappa B and AP-1 in intact cells: AP-1 as secondary antioxidant-responsive factor

We show that AP-1 is an antioxidant-responsive transcription factor. DNA binding and transactivation by AP-1 were induced in HeLa cells upon treatment with the antioxidants pyrrolidine dithiocarbamate (PDTC) and N-acetyl-L-cysteine (NAC), and upon transient expression of the antioxidative enzyme thioredoxin. While PDTC and NAC enhanced DNA binding and transactivation of AP-1 in response to phorbol ester, the oxidant H2O2 suppressed phorbol ester activation of the factor. H2O2 on its own was only a weak inducer of AP-1. Activation of AP-1 by PDTC was dependent on protein synthesis and involved transcriptional induction of c-jun and c-fos genes. Transcriptional activation of c-fos by PDTC was conferred by the serum response element, suggesting that serum response factor and associated proteins function as primary antioxidant-responsive transcription factors. In the same cell line, the oxidative stress-responsive transcription factor NF-kappa B behaved in a manner strikingly opposite to AP-1. DNA binding and transactivation by NF-kappa B were strongly activated by H2O2, while the antioxidants alone were ineffective. H2O2 potentiated the activation of NF-kappa B by phorbol ester, while PDTC and NAC suppressed PMA activation of the factor. PDTC did not influence protein kinase C (PKC) activity and PKC activation by PMA, indicating that the antioxidant acted downstream of and independently from PKC.

The C-terminal half of UvrC protein is sufficient to reconstitute (A)BC excinuclease

The UvrC protein is one of three subunits of the Escherichia coli repair enzyme (A)BC excinuclease. This subunit is thought to have at least one of the active sites for nucleophilic attack on the phosphodiester bonds of damaged DNA. To localize the active site, mutant UvrC proteins were constructed by linker-scanning and deletion mutagenesis. In vivo studies revealed that the C-terminal 314 amino acids of the 610-amino acid UvrC protein were sufficient to confer UV resistance to cells lacking the uvrC gene. The portion of the uvrC gene encoding the C-terminal half of the protein was fused to the 3' end of the E. coli malE gene (which encodes maltose binding protein), and the fusion protein MBP-C314C was purified and characterized. The fusion protein, in combination with UvrA and UvrB subunits, reconstituted the excinuclease activity that incised the eighth phosphodiester bond 5' and the fourth phosphodiester bond 3' to a psoralen-thymine adduct. These results suggest that the C-terminal 314 amino acids of UvrC constitute a functional domain capable of interacting with the UvrB-damaged DNA complex and of inducing the two phosphodiester bond incisions characteristic of (A)BC excinuclease.

Mutational analysis of the pseudoknot region in the 3' noncoding region of tobacco mosaic virus RNA

The approximately 200-nucleotide-long 3'-terminal noncoding region of tobacco mosaic virus (TMV) RNA contains a tRNA-like structure and, in its immediate upstream region, three consecutive pseudoknots, each of which is composed of two double-helical segments. To elucidate the biological functions of the pseudoknot region, we constructed several deletion mutant TMV-L (a tomato strain) RNAs by using an in vitro transcription system and tested their ability to multiply in both tobacco plants and protoplasts. When deletions were introduced just downstream of the termination codon of the coat protein gene in the 5'-to-3' direction progressively, five of six double-helical segments were dispensable for viral multiplication, indicating that the pseudoknot structures are not essential for multiplication. However, extension of the deletion into the central pseudoknot region resulted in reduction in viral multiplication, accompanied by loss of development of mosaic symptoms on systemic tobacco plants. Cessation of multiplication was observed when the sequence involved in formation of double-helical segment I just upstream of the tRNA-like structure was deleted irrespective of the start point and extent of deletion. Point mutations that destabilized double-helical segment I resulted in a loss or great reduction of viral multiplication, whereas the double mutants in which the double helix was restored by additional compensating base substitutions restored multiplication to nearly the wild-type level. Thus, double-helical segment I just upstream of the tRNA-like structure is a structural feature essential for viral multiplication.

Cell-type specificity of regulatory elements identified by linker scanning mutagenesis in the promoter of the chicken lysozyme gene

The chicken lysozyme gene is constitutively expressed in macrophages, in oviduct cells its expression is controlled by steroid hormones, and in fibroblasts the gene is not expressed. A fusion gene consisting of promoter sequences of the lysozyme gene from -208 to +15 in front of the chloramphenicol acetyltransferase (CAT) coding region was more than 50 times less active in non-expressing cells as compared to expressing cells. In order to identify the element(s) responsible for this cell-type specificity 31 different linker scanning mutations were generated within this promoter fragment and analyzed by transient transfections in the three types of chicken cells mentioned above. Three mutation sensitive regions located around position -25, -100 and between -158 and -208 were detected in each cell type, however, several LS mutations displayed clear cell-type specific differences in their phenotypic effects. Interestingly, a few LS mutations led to an increase in promoter activity in fibroblasts suggesting that the corresponding wildtype sequences represent binding sites for negatively acting transcription factors.

Site-specific degradation of Streptomyces lividans DNA during electrophoresis in buffers contaminated with ferrous iron

Streptomyces lividans DNA contains a modification which makes it susceptible to double-strand cleavage during electrophoresis in buffers contaminated with ferrous iron (which may be present in some batches of EDTA). The cleavage of the DNA is site-specific and the average fragment size resulting from limit digestion of total S. lividans DNA is about 6kb. DNA from Streptomyces coelicolor A3(2) and several other Streptomyces strains, and from E. coli, is not cleaved under the same conditions. A S. lividans mutant has been isolated which lacks the DNA modification. We suspect that many reports of "poor" preparations of S. lividans plasmids may be due to the above effect.