In Silico Screening of Inhibitors of the Venezuelan Equine Encephalitis Virus Nonstructural Protein 2 Cysteine Protease

The Venezuelan equine encephalitis virus (VEEV) nonstructural protein 2 (nsP2) cysteine protease (EC 3.4.22.B79) is essential for viral replication. High throughput in silico/in vitro screening using a focused set of known cysteine protease inhibitors identified two epoxysuccinyl prodrugs, E64d and CA074 methyl ester (CA074me) and a reversible oxindole inhibitor. Here, we determined the X-ray crystal structure of the CA074-inhibited nsP2 protease and compared it with our E64d-inhibited structure. We found that the two inhibitors occupy different locations in the protease. We designed hybrid inhibitors with improved potency. Virus yield reduction assays confirmed that the viral titer was reduced by >5 logs with CA074me. Cell-based assays showed reductions in viral replication for CHIKV, VEEV, and WEEV, and weaker inhibition of EEEV by the hybrid inhibitors. The most potent was NCGC00488909-01 which had an EC₅₀ of 1.76 µM in VEEV-Trd-infected cells; the second most potent was NCGC00484087 with an EC₅₀ = 7.90 µM. Other compounds from the NCATS libraries such as the H1 antihistamine oxatomide (>5-log reduction), emetine, amsacrine an intercalator (NCGC0015113), MLS003116111-01, NCGC00247785-13, and MLS00699295-01 were found to effectively reduce VEEV viral replication in plaque assays. Kinetic methods demonstrated time-dependent inhibition by the hybrid inhibitors of the protease with NCGC00488909-01 (K_i = 3 µM) and NCGC00484087 (K_i = 5 µM). Rates of inactivation by CA074 in the presence of 6 mM CaCl₂, MnCl₂, or MgCl₂ were measured with varying concentrations of inhibitor, Mg²⁺ and Mn²⁺ slightly enhanced inhibitor binding (3 to 6-fold). CA074 inhibited not only the VEEV nsP2 protease but also that of CHIKV and WEEV.

Gas chromatography coupled-to Fourier transform orbitrap mass spectrometer for enantioselective amino acid analyses: Application to pre-cometary organic analog

Gas chromatography (GC) is a separation technique commonly developed for targeted in situ analyses in planetary space missions. It is coupled with low-resolution mass spectrometry to obtain additional structural information and allow compound identification. However, ground-based analyses of extraterrestrial samples have shown the presence of large molecular diversities. For future targeted in situ analyses, it is therefore essential to develop new technologies. High resolution mass spectrometry (HRMS) is currently being spatialized using FT-orbitrap-MS technology. In this contribution, the coupling of gas chromatography with FT-orbitrap-MS is studied for targeted amino acid analyses. The method for enantioselective separation of amino acids was optimized on a standard mixture comprising 47 amino acid enantiomers. Different ionization modes were optimized, chemical ionization with three different reactive gasses (NH₃, CH₄ and NH₃/CH₄) and electron impact ionization at different electron energies. Single ion and full scan monitoring modes were compared, and detection and quantification limits were estimated by internal calibration under the optimized conditions. The GC-FT-orbitrap-MS demonstrated its ability to separate 47 amino acid enantiomers with minimal co-elution. Furthermore, due to the high mass resolution and accuracy of FT-orbitrap-MS, with mass extraction, the S/N is close to zero, allowing average LOD values of 10⁻⁷ M, orders of magnitude lower than conventional GC-MS techniques. Finally, these conditions were tested for enantioselective analysis of amino acids on an analog of a pre-cometary organic material showing similarities to that of extraterrestrial materials.

Lactation performance of dairy cows fed yeast-derived microbial protein in low- and high-forage diets

The objective of this study was to investigate the effect of substituting soybean meal products with yeast-derived microbial protein (YMP) on lactation performance in diets containing 2 forage-to-concentrate ratios. Sixteen Holstein cows (4 primiparous and 12 multiparous) were randomly assigned to multiple 4 × 4 Latin squares with a 2 × 2 factorial arrangement of treatments. Diets contained low (LF; 45% of diet DM) or high forage (HF; 65% of diet DM) and YMP at 0 (NYMP) or 2.25% (WYMP) of the diet. The forage mix consisted of 67% corn silage and 33% alfalfa hay on a DM basis. No interactions of forage and YMP were noted for any of the production parameters measured. Feed efficiency (energy-corrected milk/dry matter intake) was greater for cows fed NYMP compared with WYMP. Regardless of the addition of YMP, cows fed LF had greater dry matter intake and produced more milk than cows fed HF. In addition, cows fed LF produced more energy-corrected milk than those fed HF. Milk fat percentage was lower in cows fed LF compared with HF, whereas fat yield was similar between forage concentrations. Fat yield tended to decrease with feeding YMP. Interactions of forage and YMP were observed for propionate concentration, acetate and propionate proportion, and acetate-to-propionate ratio. A tendency for an interaction of forage and YMP was also noted for ruminal pH. Cows fed HF diets had greater ruminal ammonia and butyrate concentrations, as well as proportion of butyrate. Arterial concentrations of Ile, Leu, Met, Thr, and Val were greater in cows fed LF. Cows fed NYMP had greater arterial concentrations of Ile, Lys, Trp, and Val than cows fed WYMP. Substitution of soybean proteins with YMP did not improve performance or feed efficiency of high-producing dairy cows regardless of the forage-to-concentrate ratio of the diet.

Feeding fat from distillers dried grains with solubles to dairy heifers: I. Effects on growth performance and total-tract digestibility of nutrients

The objective of this study was to determine if increased dietary fat from dried distillers grains with solubles (DDGS) in diets of growing heifers affected dry matter intake, average daily gain (ADG), growth performance, and nutrient digestibility. Thirty-three Holstein heifers (133±18 d old) were used in a 24-wk randomized complete block design. Treatments were (1) control (CON) containing ground corn and soybean products, (2) low-fat (LFDG) containing low-fat, high-protein DDGS and ground corn, and (3) high-fat (HFDG) with traditional DDGS. All diets contained 39.8% grass hay, 24.8% corn silage, and 1.5% vitamins and minerals. The HFDG diet was formulated to contain 4.8% fat compared with 2.8% in the CON and LFDG diets, which were greater in nonfibrous carbohydrate. Diets had a net energy gain of 1.0Mcal/kg of dry matter and were limit-fed at 2.45% of body weight. Heifers were weighed every 2wk and rations were adjusted accordingly. Heart girth, hip and wither heights, body length, and body condition score were recorded every 2wk. Total-tract digestion of nutrients was evaluated during wk16 using fecal grab sampling and an external marker. No treatments by time interactions were found. Dry matter intakes, body weights, ADG, and gain-to-feed ratio were similar among treatments; however, ADG averaged 0.96kg/d among treatments, which is greater than recommended. All body frame measurements and body condition scores were similar among treatments. Total-tract digestibilities of dry matter and organic matter were not different among treatments. However, crude protein and neutral detergent fiber digestibility were increased in the HFDG diet compared with the CON and LFDG diets. These results demonstrate that using DDGS or low-fat DDGS with corn in growing heifer rations can maintain performance. Utilizing the fat in DDGS as a dietary energy source in replacement of starch from corn did not influence growth performance or negatively affect nutrient digestion.

Short communication: Feeding fat from distillers dried grains with solubles to dairy heifers: III. Effects on posttrial reproductive and lactation performance

The objective of this research was to determine the subsequent effects on lactation and reproductive performance from feeding fat from distillers dried grains with solubles (DDGS) to growing dairy heifers. During the prepubertal growth phase, 33 Holstein heifers (133±18 d old) were used in a 24-wk randomized complete block design. Treatments included (1) a control diet (CON) containing ground corn and soybean products, 2) a diet with low-fat DDGS (LFDG), and (3) a higher-fat diet with traditional DDGS (HFDG). All diets contained 39.8% grass hay, 24.8% corn silage, and 1.5% vitamins and minerals. Previous results demonstrated that growth performance was maintained across treatments, but plasma cholesterol and fatty acids were greater and puberty may occur earlier in heifers fed HFDG. It was hypothesized that differences among treatments in metabolic profile and puberty may influence reproductive and first-lactation performance. Posttrial data on reproductive performance and milk production for the first 4 mo of lactation were collected for each heifer from dairy herd records. At 3wk prepartum and at calving, body weights, body condition scores, and body measurements were taken. No differences were observed among treatments for age at conception or age at calving. At calving, heifers fed the HFDG were shorter in withers height compared with heifers fed the other diets. Milk yields and components were similar or improved in heifers fed the distillers grains diets compared with heifers fed CON. Heifers fed LFDG had greater milk production and a tendency for greater milk protein yields compared with the heifers fed CON. Energy-corrected milk yields were similar among treatments. Feeding increased dietary fat from DDGS during the prepubertal growth phase did not negatively affect milk production, despite earlier attainment of puberty compared with other treatments. The overall ADG for all 3 treatments was 0.96kg/d during the prepubertal period, which is greater than recommended and may have compromised milk yield across treatments. Based on these findings, producers can feed either DDGS or LFDG with corn in replacement of soybean products and corn to prepubertal heifers and maintain or enhance subsequent reproductive and lactation performance. Dietary fat from DDGS can replace starch from corn as an energy source for prepubertal heifers without detriment to later performance.

Feeding fat from distillers dried grains with solubles to dairy heifers: II. Effects on metabolic profile

The objective of this study was to determine if increased dietary fat from dried distillers grains with solubles (DDGS) in diets of growing heifers affected metabolic profile, plasma fatty acid profile, and reproductive maturation. Thirty-three Holstein heifers (133±18 d of age) were used in a 24-wk randomized complete block design with 3 treatment diets. Treatment diets were (1) control (CON) containing ground corn (15.9% of DM) and soybean products (17.9%), (2) low-fat (LFDG) containing low-fat DDGS (21.9%) and ground corn (11.9%), or (3) high-fat (HFDG) with traditional DDGS (33.8%). Diets were isonitrogenous and isocaloric, but the HFDG diet was formulated to contain 4.8% fat compared with 2.8% in the CON and LFDG diets. All 3 diets were limit-fed to 2.45% of body weight on a dry matter basis, and resulted in a mean average daily gain of 0.96kg/d across treatments. Every 4wk, jugular blood was collected for analysis of metabolites and metabolic hormones. During wk20 of the feeding period, blood samples were collected for analysis of plasma fatty acid profiles. When heifers weighed between 200 and 300kg of body weight, coccygeal blood samples were taken twice weekly for analysis of progesterone to determine if puberty had been reached. Plasma concentrations of nonesterified fatty acids were similar among treatments and consistent over the duration of the study. Plasma concentrations of β-hydroxybutyrate, insulin, insulin-like growth factor-1, and leptin were similar among heifers fed each treatment diet, but increased over the duration of the feeding period. Serum concentrations of glucose tended to be less in heifers fed HFDG compared with heifers fed the CON diet. Glucose concentrations fluctuated throughout the feeding period, but no treatment by time interactions were noted. Plasma urea N concentrations were less in heifers fed LFDG compared with heifers fed HFDG and CON diets. The concentrations of plasma urea N increased over the duration of the feeding period, with no treatment by week interaction. Total plasma cholesterol was greater in heifers fed HFDG compared with the CON and LFDG diets, and a significant week effect and a week by treatment interaction were observed. Fatty acid profiles also differed among treatments based on the supply of fatty acids from the diet. Progesterone analysis indicated that heifers fed HFDG tended to be pubertal at a younger age than heifers on CON. These results demonstrate that dietary fat from DDGS can be used in high-plane of nutrition rations for growing heifers and maintain metabolic energy status compared with starch from corn, but alters the concentrations of different blood lipids.

Soybean meal substitution with a yeast-derived microbial protein source in dairy cow diets

The objective of this study was to examine the effects substituting soybean meal with a yeast-derived microbial protein (YMP) on rumen and blood metabolites, dry matter intake, and milk production of high-producing dairy cows. Sixteen Holstein cows (12 multiparous and 4 primiparous), 93 ± 37 DIM (mean ± SD) at the beginning of the experiment, were used in a 4×4 Latin square design with four 28-d periods. Cows were blocked by parity and production, with 1 square consisting of 4 animals fitted with rumen cannulas. Basal diets, formulated for 16.1% crude protein and 1.56 Mcal/kg of net energy for lactation, contained 40% corn silage, 20% alfalfa hay, and 40% concentrate mix. During each period, cows were fed 1 of 4 treatment diets corresponding to YMP (DEMP; Alltech Inc., Nicholasville, KY) concentrations of 0, 1.14, 2.28, and 3.41% DM. Soybean meal (44% CP) was replaced by YMP to attain isonitrogenous and isoenergetic diets. Dietary treatments had no effect on pH and on most ruminal volatile fatty acid concentrations, with the exception of isovalerate, which decreased linearly with the addition of YMP. Rumen ammonia concentration decreased linearly, whereas free amino acids, total amino acid nitrogen, and soluble proteins weighing more than 10 kDa showed a cubic response on rumen N fractionation. A quadratic response was observed in oligopeptides that weighed between 3 and 10 kDa and peptides under 3kDa when expressed as percentages of total amino acids and total nitrogen. Although nonesterified fatty acid concentration in blood did not differ between treatments, β-hydroxybutyrate and plasma glucose increased linearly as YMP increased. Dry matter intake showed a cubic effect, where cows fed 1.14, and 3.41% YMP had the highest intake. Milk production was not affected by YMP, whereas a trend was observed for a quadratic increase for 4% fat-corrected milk and energy-corrected milk. Medium- and long-chain fatty acid concentrations in milk increased quadratically, which elicited similar effects on milk fat concentration and yield. Total solids percentage and yield, and milk urea nitrogen also showed quadratic effects as YMP increased in the diet. No effects were observed on feed efficiency, milk protein, and lactose percentage or yield. A complementary in vitro study demonstrated a quadratic tendency for apparent and true dry matter digestibility as YMP was added to the diet. It was concluded that the substitution of soybean meal with YMP increased the percentage of total solids in milk and tended to improve energy-corrected and fat-corrected milk production in high-producing dairy cows consuming high-forage diets.

Ensiling characteristics of wet distillers grains mixed with soybean hulls and evaluation of the feeding value for growing Holstein heifers

Two experiments were conducted to evaluate the fermentation characteristics of ensiled wet corn distillers grains with solubles (WDG) alone or mixed with soybean hulls (SH) and the ability of the mixture to maintain growth performance in dairy heifers. The first experiment was an ensiling study using laboratory silos. Ensiled blends were 100% WDG, 85% WDG with 15% SH, and 70% WDG with 30% SH on an as-fed basis. Silos were opened for analysis on d 0, 3, 7, and 21. The pH was less in the 100% WDG compared with other treatments (P < 0.01), but all treatments had a pH near 4. Lactic acid concentration was greater in 100% WDG compared with the blends of WDG and SH (P < 0.01). Acetic acid was not found in 100% WDG and increased over time in the 2 blends (P < 0.01). Other differences between blends, such as DM, CP, ammonia N, fiber, and fat, were reflective of the different concentrations of WDG and SH in the blends. In the second experiment, the 70% WDG and 30% SH (as-fed) blend was ensiled in a silo bag and then evaluated as a feed for growing dairy heifer diets. Twenty-four heifers were used in a randomized complete block design and assigned to be fed 1 of 3 diets: 1) control, 2) low inclusion of WDGSH, and 3) a high inclusion of WDGSH. All treatment diets consisted of 50% brome grass hay on a DM basis. The control diet had 50% of the diet (DM basis) as a grain mix, which was composed of corn, soybean meal, and minerals. The low WDGSH diet contained 24.4% of the blend and 25.6% grain mix. The high WDGSH diet contained 48.7% of the blend and 1.3% mineral mix. Average daily gain and most of the body growth measures were similar among treatments. However, DMI decreased linearly (P < 0.01) as the WDGSH blends were fed, resulting in improved (P = 0.02) G:F. Results from these experiments indicated that WDG can be effectively ensiled with SH and sustain adequate growth rate when fed to growing dairy heifers.

Use of dynamically coated capillaries for the routine analysis of methamphetamine, amphetamine, MDA, MDMA, MDEA, and cocaine using capillary electrophoresis

A rapid, accurate, precise, reproducible, economical, and environmentally gentle method using capillary electrophoresis (CE) is presented for the routine analysis of methamphetamine, amphetamine, MDA, MDMA, MDEA, and cocaine in seized drugs. The methodology uses a 32 cm by 50 microm capillary (length to detector 23.5 cm) with a commercially available buffer kit and diode array UV detection. Dynamic coating of the capillary surface is accomplished by flushing with base for 1 min, a proprietary polycation for 1 min, and then a proprietary polyanion for 2 min. This approach provides a relatively high and stable electroosmotic flow (EOF), even at low pHs. The background electrolyte (BGE) contains 75 mM phosphate buffer (pH 2.5) with the same polyanion as above. Using this methodology, amphetamine, methamphetamine, MDA, MDMA, MDEA, and an internal standard (n-butylamphetamine) are baseline resolved in less than 5 min. The run-to-run migration time %RSDs and peak area %RSDs are typically <0.3% and <2.1%, respectively. The day-to-day and capillary-to-capillary migration time %RSDs are <1.5% and <2.1%, respectively. The %RSDs of the relative migration times compared with the internal standard on a day-to-day and capillary-to-capillary basis are <0.2% and <0.06%, respectively. The linear dynamic range using peak areas range from 0.003 to 0.10 mg/mL. The correlation coefficients are >0.9998, with all calibration curves passing at or near the origin. Similar data are obtained for cocaine and its internal standard henyltoloxamine. None of the compounds usually encountered in illicit samples interfere with the target compound (e.g., methamphetamine and cocaine) or the internal standard. Quantitative results for synthetic mixtures and seized exhibits are in good agreement with actual values, and also with results obtained from other techniques. The relatively high EOF for the dynamically coated capillary system allows for the screening of basic, acidic, and neutral adulterants in drug seizures; identification is facilitated by the use of automated UV library searches.

Repression of vaccinia virus Holliday junction resolvase inhibits processing of viral DNA into unit-length genomes

The vaccinia virus A22R gene encodes a protein that is homologous to the bacterial enzyme RuvC and specifically cleaves and resolves four-way DNA Holliday junctions into linear duplex products. To investigate the role of the vaccinia virus Holliday junction resolvase during an infection, we constructed two recombinant viruses: vA22-HA, which has a short C-terminal epitope tag appended to the A22R open reading frame, and vA22i, in which the original A22R gene is deleted and replaced by an inducible copy. Polyacrylamide gel electrophoresis and Western blot analysis of extracts and purified virions from cells infected with vA22-HA revealed that the resolvase was expressed after the onset of DNA replication and incorporated into virion cores. vA22i exhibited a conditional replication defect. In the absence of an inducer, (i) viral protein synthesis was unaffected, (ii) late-stage viral DNA replication was reduced, (iii) most of the newly synthesized viral DNA remained in a branched or concatemeric form that caused it to be trapped at the application site during pulsed-field gel electrophoresis, (iv) cleavage of concatemer junctions was inhibited, and (v) virion morphogenesis was arrested at an immature stage. These data indicated multiple roles for the vaccinia virus Holliday junction resolvase in the replication and processing of viral DNA into unit-length genomes.

Tumor necrosis factor (TNF) receptor superfamily member TACI is a high affinity receptor for TNF family members APRIL and BLyS

An expression cloning approach was employed to identify the receptor for B-lymphocyte stimulator (BLyS) and identified the tumor necrosis factor receptor superfamily member TACI as a BLyS-binding protein. Expression of TACI in HEK293T cells confers on the cells the ability to bind BLyS with subnanomolar affinity. Furthermore, a TACI-Fc fusion protein recognizes both the cleaved, soluble form of BLyS as well as the membrane BLyS present on the cell surface of a recombinant cell line. TACI mRNA is found predominantly in B-cells and correlates with BLyS binding in a panel of B-cell lines. We also demonstrate that TACI interacts with nanomolar affinity with the BLyS-related tumor necrosis factor homologue APRIL for which no clear in vivo role has been described. BLyS and APRIL are capable of signaling through TACI to mediate NF-kappaB responses in HEK293 cells. We conclude that TACI is a receptor for BLyS and APRIL and discuss the implications for B-cell biology.

Bacterial-type DNA holliday junction resolvases in eukaryotic viruses

Homologous DNA recombination promotes genetic diversity and the maintenance of genome integrity, yet no enzymes with specificity for the Holliday junction (HJ)-a key DNA recombination intermediate-have been purified and characterized from metazoa or their viruses. Here we identify critical structural elements of RuvC, a bacterial HJ resolvase, in uncharacterized open reading frames from poxviruses and an iridovirus. The putative vaccinia virus resolvase was expressed as a recombinant protein, affinity purified, and shown to specifically bind and cleave a synthetic HJ to yield nicked duplex molecules. Mutation of either of two conserved acidic amino acids abrogated the catalytic activity of the A22R protein without affecting HJ binding. The presence of bacterial-type enzymes in metazoan viruses raises evolutionary questions.

Interaction of EF-C/RFX-1 with the inverted repeat of viral enhancer regions is required for transactivation

The hepatitis B virus (HBV) and polyomavirus (Py) enhancer regions contain multiple cis-acting elements that contribute to enhancer activity. The EF-C binding site was previously shown to be an important functional component of each enhancer region. EF-C is a ubiquitous binding activity that interacts with an inverted repeat sequence in the HBV and Py enhancer regions. Although the EF-C binding site is required for optimal enhancer function, the EF-C site does not possess intrinsic enhancer activity when assayed in the absence of flanking elements. With both the HBV and Py enhancer regions, EF-C stimulates the activity of adjacent enhancer elements in a synergistic manner. EF-C corresponds to RFX-1, a protein that binds to a conserved and functionally important site in major histocompatibility complex (MHC) class II antigen promoter regions. Interestingly, the RFX-1 binding site in MHC class II promoters only contains an EF-C half-site, maintaining one arm of the inverted repeat in an EF-C binding site. We have investigated the binding of purified EF-C and RFX-1 to sites in the Py and HBV enhancer regions that carry mutations that either disrupt one arm of the EF-C inverted repeat, or alter the spacing between the repeats. Our results show that the interaction of EF-C and RFX-1 with an intact inverted repeat is required for functional activity of these viral enhancer regions. Chemical footprinting and modification interference assays show that the interaction of EF-C and RFX-1 with the DRA MHC class II promoter truly represents half-site interaction, and that this binding is unstable. In contrast, the binding of EF-C and RFX-1 to the viral inverted repeats is stable. These results suggest that an additional activity may be required to stabilize EF-C/RFX-1 interaction with the MHC class II promoter, and that viral enhancer regions have evolved high affinity binding sites to sequester dimeric EF-C/RFX-1.

Functional interaction of nuclear factors EF-C, HNF-4, and RXR alpha with hepatitis B virus enhancer I

Hepatitis B virus (HBV) enhancer I contains cis-acting elements that are both sufficient and essential for liver-specific enhancer function. The EF-C binding site was previously shown to be a key element in enhancer I. EF-C binding activity is evident in hepatic and nonhepatic cells. Although the EF-C binding site is required for efficient HBV enhancer I function, the EF-C site does not possess intrinsic enhancer activity when assayed in the absence of flanking elements. We have defined a novel region in HBV enhancer I, termed the GB element, that is adjacent to and functions in conjunction with the EF-C binding site. The GB element and EF-C site confer interdependent liver-specific enhancer activity in the absence of flanking HBV enhancer sequences. The nucleotide sequence of the GB element is similar to sequences of the DNA binding sites for members of the steroid receptor superfamily. Among these proteins, we demonstrate that HNF-4, RXR (retinoid X receptor), and COUP-TF bind to the GB element in vitro. HNF-4 transactivates a promoter linked to a multimerized GB/EF-C domain via the GB element in vivo in a manner that is dependent on the integrity of the adjacent EF-C binding site. RXR alpha also transactivates promoter expression via the GB element in vivo in response to retinoic acid but in a largely EF-C-independent manner. Finally, we show that COUP-TF antagonizes the activity of the GB element in human liver cells.

Analysis of the human regulators of complement activation (RCA) gene cluster with yeast artificial chromosomes (YACs)

The human regulators of complement activation gene cluster (RCA cluster) have been partially characterized with yeast artificial chromosomes (YACs). While the data confirm many points previously elucidated, the finer resolution of YAC mapping has allowed the discovery and/or localization of partial gene duplications, the determination of gene orientations, and the measurement of gaps between known genes. Here nine overlapping YACs that encompass a genomic region of 800 kb, encoding four RCA genes and three gene-like elements, are described. The encoded genes and two of the gene-like elements share the same orientation and are ordered (5' to 3') DAF, CR2, CR1, MCP-like, CR1-like, and MCP. A C4bp-like region lies upstream from DAF and is likely to correspond to one recently observed by F. Pardo-Manuel, J. Rey-Campos, A. Hillarp, B. Dahlback, and S. Rodriguez de Cordoba (1990, Proc. Natl. Acad. Sci. USA 87: 4529-4533). MCP-like, a new genetic element, was discovered and found to be homologous to the 5' portion of the MCP gene. Two large gaps of 85 kb (between CR2 and DAF) and 110 kb (between DAF and the C4bp-like element) could carry additional RCA genes. The arrangement of CR1, MCP-like, CR1-like, and MCP, in that order, strongly suggests that this region was generated by a single duplication of neighboring CR1/CR1-like and MCP/MCP-like forerunners. The RCA YACs will now serve as convenient DNA sources for the subcloning and further characterization of this region.

Methylation-dependent and -independent DNA binding of nuclear factor EF-C

Nuclear factor EF-C binds to important functional sites in the hepatitis B virus and polyomavirus enhancer regions. In this paper, we have characterized new and divergent EF-C binding sites in several viral regulatory regions. We also have demonstrated that EF-C binds to certain DNA sites only when CpG dinucleotide base pairs are methylated (m5C). EF-C binds to other sites in a methylation-independent manner. Based on similar binding properties and identical binding sites, it is very likely that EF-C corresponds to the nuclear protein MDBP previously identified by virtue of binding to methylated DNA.

A discrete region centered 22 base pairs upstream of the initiation site modulates transcription of Drosophila tRNAAsn genes

We have studied the mechanism by which 5'-flanking sequences modulate the in vitro transcription of eucaryotic tRNA genes. Using deletion and linker substitution mutagenesis, we have found that the 5'-flanking sequences responsible for the different in vitro transcription levels of three Drosophila tRNA5Asn genes are contained within a discrete region centered 22 nucleotides upstream from the transcription initiation site. In conjunction with the A-box intragenic control region, this upstream transcription-modulatory region functions in the selection mechanism for the site of transcription initiation. Since the transcription-modulatory region directs the position of the start site and the actual sequence of the transcription-modulatory region determines the level of tRNAAsn gene transcription, the possibility is raised that the transcription-modulatory region directs a transcription initiation event similar to open complex formation at procaryotic promoters.

Transcription of the Drosophila melanogaster 5S RNA gene requires an upstream promoter and four intragenic sequence elements

Linker-scanning (LS) mutations were constructed spanning the length of the Drosophila melanogaster 5S RNA gene. In vitro transcription analysis of the LS 5S DNAs revealed five transcription control regions. One control region essential for transcription initiation was identified in the 5'-flanking sequence. The major sequence determinants of this upstream promoter region were located between coordinates -39 and -26 (-30 region), but important sequences extended to the transcription start site at position 1. Since mutations in the upstream promoter did not alter the ability of 5S DNA to sequester transcription factors into a stable transcription complex, it appears that this control region involved the interaction of RNA polymerase III. Active 5S DNA transcription additionally required the four intragenic control regions (ICRs) located between coordinates 3 and 18 (ICR I), 37 and 44 (ICR II), 48 and 61 (ICR III), and 78 and 98 (ICR IV). LS mutations in each ICR decreased the ability of 5S DNA to sequester transcription factors. ICR III, ICR IV, and the spacer sequence between were similar in sequence and position to the determinant elements of the multipartite ICR of Xenopus 5S DNA. The importance of ICR III and ICR IV in transcription initiation and in sequestering transcription factors suggests the presence of an activity in D. melanogaster similar to transcription factor TFIIIA of Xenopus laevis and HeLa cells. Transcription initiation of Drosophila 5S DNA was not eliminated by LS mutations in the spacer region even though these mutations reduced the ability of the TFIIIA-like activity to bind. The previously unidentified control regions ICR I and ICR II appear to be important for the interaction of a transcription factor activity, or multiple-factor activities, distinct from the TFIIIA-like activity. The interaction of this activity with ICR I directed the selection of the transcription start site.

Formation of an active transcription complex in the Drosophila melanogaster 5S RNA gene is dependent on an upstream region

We constructed deletion-substitution and linker-scanning mutations in the 5'-flanking region of the Drosophila melanogaster 5S RNA gene. In vitro transcription of these templates in Drosophila and HeLa cell extracts revealed the presence of an essential control region (-30 region) located between nucleotides -39 and -26 upstream of the transcription initiation site: deletion of sequences upstream of nucleotide position -39 had no detectable effect on the wild-type level of in vitro transcription, whereas mutations extending between positions -39 and 1 resulted in templates with decreased transcriptional levels; specifically, deletion and linker-scanning mutations in the -34 to -26 region (-30 region) resulted in loss of transcription. The -30 region is essential for transcription and therefore forms part of the Drosophila 5S RNA gene transcription promoter. Compared with the activity of the wild-type gene, mutant 5S DNAs exhibited no impairment in the ability to sequester limiting transcription factors in a template exclusion competition assay. While we do not know which transcription factor(s) interacts with the -30 region, the possible involvement of RNA polymerase III at this region is discussed.