Target site specificity of the Tos17 retrotransposon shows a preference for insertion within genes and against insertion in retrotransposon-rich regions of the genome

Because retrotransposons are the major component of plant genomes, analysis of the target site selection of retrotransposons is important for understanding the structure and evolution of plant genomes. Here, we examined the target site specificity of the rice retrotransposon Tos17, which can be activated by tissue culture. We have produced 47,196 Tos17-induced insertion mutants of rice. This mutant population carries approximately 500,000 insertions. We analyzed >42,000 flanking sequences of newly transposed Tos17 copies from 4316 mutant lines. More than 20,000 unique loci were assigned on the rice genomic sequence. Analysis of these sequences showed that insertion events are three times more frequent in genic regions than in intergenic regions. Consistent with this result, Tos17 was shown to prefer gene-dense regions over centromeric heterochromatin regions. Analysis of insertion target sequences revealed a palindromic consensus sequence, ANGTT-TSD-AACNT, flanking the 5-bp target site duplication. Although insertion targets are distributed throughout the chromosomes, they tend to cluster, and 76% of the clusters are located in genic regions. The mechanisms of target site selection by Tos17, the utility of the mutant lines, and the knockout gene database are discussed. --The nucleotide sequence data were uploaded to the DDBJ, EMBL, and GenBank nucleotide sequence databases under accession numbers AG020727 to AG025611 and AG205093 to AG215049.     

Reiterative RNA folding and occupancy rate analysis for mRNA modelling

We describe computer programs that predict the most energeticallyfavorable secondary structures in growing RNA sequences, generatea sequential display of the growing structures, and monitorthe predicted participation of intramolecular sites in secondarystructure. These programs may provide insight into the relationshipsbetween messenger RNA secondary structure and expressibility. Received on August 10, 1987; accepted on October 17, 1987     

The antigenic index: a novel algorithm for predicting antigenic determinants

In this paper, we introduce a computer algorithm which can beused to predict the topological features of a protein directlyfrom its primary amino acid sequence. The computer program generatesvalues for surface accessibility parameters and combines thesevalues with those obtained for regional backbone flexibilityand predicted secondary structure. The output of this algorithm,the antigenic index, is used to create a linear surface contourprofile of the protein. Because most, if not all, antigenicsites are located within surface exposed regions of a protein,the program offers a reliable means of predicting potentialantigenic determinants. We have tested the ability of this programto generate accurate surface contour profiles and predict antigenicsites from the linear amino acid sequences of well-characterizedproteins and found a strong correlation between the predictionsof the antigenic index and known structural and biological data. Received on August 17, 1987; accepted on December 31, 1987     

Visualization of near-optimal sequence alignments

MOTIVATION: Mathematically optimal alignments do not always properly align active site residues or well-recognized structural elements. Most near-optimal sequence alignment algorithms display alternative alignment paths, rather than the conventional residue-by-residue pairwise alignment. Typically, these methods do not provide mechanisms for finding effectively the most biologically meaningful alignment in the potentially large set of options. RESULTS: We have developed Web-based software that displays near optimal or alternative alignments of two protein or DNA sequences as a continuous moving picture. A WWW interface to a C++ program generates near optimal alignments, which are sent to a Java Applet, which displays them in a series of alignment frames. The Applet aligns residues so that consistently aligned regions remain at a fixed position on the display, while variable regions move. The display can be stopped to examine alignment details.     

AUGUR: a program to predict, display and analyze the tertiary structure of B-DNA

A UGUR is a program to predict, display and analyze the three-dimensionalstructure of B-DNA. The user can choose one of six models topredict the helical parameters of a given sequence. These parametersare then used to generate the coordinates of the DNA model inthree-dimensional space (trajectory). The trajectory can bedisplayed and rotated on a graphics terminal The trajectoryand helical parameters can also be searched for bends and structuralhomologues. Received on August 17, 1987; accepted on December 31, 1987     

Functional cell surface display and controlled secretion of diverse Agarolytic enzymes by Escherichia coli with a novel ligation-independent cloning vector based on the autotransporter YfaL

Autotransporters have been employed as the anchoring scaffold for cell surface display by replacing their passenger domains with heterologous proteins to be displayed. We adopted an autotransporter (YfaL) of Escherichia coli for the cell surface display system. The critical regions in YfaL for surface display were identified for the construction of a ligation-independent cloning (LIC)-based display system. The designed system showed no detrimental effect on either the growth of the host cell or overexpressing heterologous proteins on the cell surface. We functionally displayed monomeric red fluorescent protein (mRFP1) as a reporter protein and diverse agarolytic enzymes from Saccharophagus degradans 2-40, including Aga86C and Aga86E, which previously had failed to be functional expressed. The system could display different sizes of proteins ranging from 25.3 to 143 kDa. We also attempted controlled release of the displayed proteins by incorporating a tobacco etch virus protease cleavage site into the C termini of the displayed proteins. The maximum level of the displayed protein was 6.1 × 10(4) molecules per a single cell, which corresponds to 5.6% of the entire cell surface of actively growing E. coli.     

A fixed-point alignment technique for detection of recurrent and common sequence motifs associated with biological features

A fixed-point alignment analysis technique is presented whichis designed to locate common sequence motifs in collectionsof proteins or nucleic acids. Initially a program aligns a collectionof sequences by a common sequence pattern or known biologicalfeature. The common pattern or feature (fixed-point) may bea user-specified sequence string or a known sequence positionlike mRNA start site, which may be taken directly from the annotatedfeature table of GenBank. Once all alignment markers are located,the sequences are scanned for occurrences of given oligomerswithin a specified span both upstream and downstream of thefixed-point. The occurrences may then be plotted as a functionof the position relative to the fixed-point, displayed as anactual sequence alignment or selectively summarized via variousprogram options. Applications of the technique are discussed. Received on August 17, 1987; accepted on November 17, 1987     

Graphics of RNA secondary structure; towards an object-oriented algorithm

We present a new algorithm for the display of RNA secondarystructure. The principle of the algorithm is entirely differentfrom those currently in use in that our algorithm is ‘objectoriented’ while currrent algorithms are ‘procedural’.The circular RNA molecule of chrysanthemum stunt viroid wasused as input data for demonstrating the operation of the program.The major interest of this method will be found in its potentialuse in simulation graphics of RNA folding processes. Received on October 9, 1986; accepted on February 17, 1987     

An improved algorithm for nucleic acid secondary structure display

An improved algorithm for the display of nucleic acid secondarystructures is presented. It is particularly suitable for largesequence segments and it automatically generates an aestheticallypleasing display of the structure with very limited overlapof strands. Structural similarities in different structuresare conserved in the display thus greatly aiding structuralhomology comparisons. Using the algorithm, we illustrate theeffect of ribosome translocation on the secondary structureof a rat neuropeptide messenger RNA. Received on September 21, 1987; accepted on October 22, 1987     

Susceptibility of burned black spruce (Picea mariana) forests to non-native plant invasions in interior Alaska

As climate rapidly warms at high-latitudes, the boreal forest faces the simultaneous threats of increasing invasive plant abundances and increasing area burned by wildfire. Highly flammable and widespread black spruce (Picea mariana) forest represents a boreal habitat that may be increasingly susceptible to non-native plant invasion. This study assess the role of burn severity, site moisture and time elapsed since burning in determining the invisibility of black spruce forests. We conducted field surveys for presence of non-native plants at 99 burned black spruce forest sites burned in 2004 in three regions of interior Alaska that spanned a gradient of burn severities and site moisture levels, and a chronosequence of sites in a single region that had burned in 1987, 1994, and 1999. We also conducted a greenhouse experiment where we grew invasive plants in vegetation and soil cores taken from a subset of these sites. In both our field survey and the greenhouse experiment, regional differences in soils and vegetation between burn complexes outweighed local burn severity or site moisture in determining the invasibility of burned black spruce sites. In the greenhouse experiments using cores from the 2004 burns, we found that the invasive focal species grew better in cores with soil and vegetation properties characteristic of low severity burns. Invasive plant growth in the greenhouse was greater in cores from the chronosequence burns with higher soil water holding capacity or lower native vascular biomass. We concluded that there are differences in susceptibility to non-native plant invasions between different regions of boreal Alaska based on native species regeneration. Re-establishment of native ground cover vegetation, including rapidly colonizing bryophytes, appear to offer burned areas a level of resistance to invasive plant establishment.     

A program for the graphic representation and manipulation of DNA sequences

We have developed a program for the graphic representation andmanipulation of DNA sequences. The program (named CARTE fromthe French for ‘map’) is intended as a tool in theplanning and analysis of recombinant DNA experiments. DNA sequencesare represented as standard restriction maps, using any desiredcombination of restriction enzymes. Features of interest, suchas promoters or coding sequences, can be highlighted. The sequencecan be manipulated to mimic cloning, using deletions, insertionsor replacements at specified sites. This process is facilitatedby the simultaneous display of a graphic map of the entire sequence,a detailed picture of the work in progress, and a menu of functions. Received on November 17, 1986; accepted on March 12, 1987     

Analysis of capsid portal protein and terminase functional domains: interaction sites required for DNA packaging in bacteriophage T4.

Bacteriophage DNA packaging results from an ATP-driven translocation of concatemeric DNA into the prohead by the phage terminase complexed with the portal vertex dodecamer of the prohead. Functional domains of the bacteriophage T4 terminase and portal gene 20 product (gp20) were determined by mutant analysis and sequence localization within the structural genes. Interaction regions of the portal vertex and large terminase subunit (gp17) were determined by genetic (terminase-portal intergenic suppressor mutations), biochemical (column retention of gp17 and inhibition of in vitro DNA packaging by gp20 peptides), and immunological (co-immunoprecipitation of polymerized gp20 peptide and gp17) studies. The specificity of the interaction was tested by means of a phage T4 HOC (highly antigenicoutercapsid protein) display system in which wild-type, cs20, and scrambled portal peptide sequences were displayed on the HOC protein of phage T4. Binding affinities of these recombinant phages as determined by the retention of these phages by a His-tag immobilized gp17 column, and by co-immunoprecipitation with purified terminase supported the specific nature of the portal protein and terminase interaction sites. In further support of specificity, a gp20 peptide corresponding to a portion of the identified site inhibited packaging whereas the scrambled sequence peptide did not block DNA packaging in vitro.The portal interaction site is localized to 28 residues in the central portion of the linear sequence of gp20 (524 residues). As judged by two pairs of intergenic portal-terminase suppressor mutations, two separate regions of the terminase large subunit gp17 (central and COOH-terminal) interact through hydrophobic contacts at the portal site. Although the terminase apparently interacts with this gp20 portal peptide, polyclonal antibody against the portal peptide appears unable to access it in the native structure, suggesting intimate association of gp20 and gp17 possibly internalizes terminase regions within the portal in the packasome complex. Both similarities and differences are seen in comparison to analogous sites which have been identified in phages T3 and lambda.     

Identification of a novel sequence that governs both polyadenylation and alternative splicing in region E3 of adenovirus.

Region E3 encodes four major overlapping mRNAs with different splicing patterns. There are two poly(A) sites, an upstream site called E3A and a downstream site called E3B. We have analyzed virus mutants with deletions or insertions in E3 in order to identify sequences that function in the alternative processing of E3 pre-mRNAs, and to understand what determines which poly(A) sites and which splice sites are used. In previous studies we established that the 5' boundary of the E3A poly(A) signal is at an ATTAAA sequence. We now show, using viable virus mutants, that the 3' boundary of the E3A signal is located within 47-62 nucleotides (nt) downstream of the ATTAAA (17-32 nt downstream of the last microheterogenous poly(A) addition site). Our data further suggest that the spacing between the ATTAAA, the cleavage sites, and the essential downstream sequences may be important in E3A 3' end formation. Of particular interest, these mutants suggest a novel mechanism for the control of alternative pre-mRNA processing. Mutants which are almost completely defective in E3A 3' end formation display greatly increased use of a 3' splice site located 4 nt upstream of the ATTAAA. The mRNA that uses this 3' splice site is polyadenylated at the E3B poly(A) site. We suggest, for this particular case, that alternative pre-mRNA processing could be determined by a competition between trans-acting factors that function in E3A 3' end formation or in splicing. These factors could compete for overlapping sequences in pre-mRNA.     

Position specific growth regulation of 3T3 cells in vivo.

In this study we have investigated the mechanism by which spatial growth is regulated by monitoring 3T3 cells, introduced into the developing mouse limb using exo utero surgery. The 3T3 cells were labeled with a human cell surface glycoprotein, CD8, and injected into stage 7-9 mouse limbs. At 24 and 48 hr after injection embryos were labeled with [3H]thymidine and processed for immunohistochemistry and autoradiography. The labeling index of CD8 positive cells was compared to that of neighboring limb bud cells and also to the position of the injection site within the limb. We find that the labeling index of 3T3 cells is in accord with that of the limb cells that immediately surround them; 3T3 cells display a high labeling index in limb regions of high growth and a low labeling index in limb regions of low growth. In addition, we find that both limb bud cells and injected 3T3 cells display a general proximal (low) to distal (high) gradient of growth at the stages analyzed. We conclude from these results that position-specific regulation of growth occurs in a non-cell autonomous manner and is likely to be mediated by mitogenic signals that are localized within the limb environment. In addition, our results demonstrate the usefulness of utilizing established cell lines as in vivo probes to monitor developmental mechanisms.     

Molecular analysis of a deletion polymorphism in alpha satellite of human chromosome 17: evidence for homologous unequal crossing-over and subsequent fixation.

The human alpha satellite DNA family is organized into chromosome-specific subsets characterized by distinct higher-order repeats based on a approximately 171 basepair monomer unit. On human chromosome 17, the predominant form of alpha satellite is a 16-monomer (16-mer) higher-order repeat present in 500-1000 copies per chromosome 17. In addition, less abundant 15-monomer and 14-monomer repeats are also found constitutively on chromosome 17. Polymorphisms in the form of different higher-order repeat lengths have been described for this subset, the most prominent polymorphism being a 13-monomer (13-mer) higher-order repeat present on approximately 35% of all chromosomes 17. To investigate the nature of this polymorphism, we have cloned, sequenced and compared the relevant regions of the 13-mer to the previously characterized 16-mer repeat. The results show that the repeats are virtually identical, with the principal difference being the exclusion of three monomers from the 13-mer repeat. We propose that the 13-mer is the product of an isolated homologous recombination event between two monomers of the 16-mer repeat. Sequence comparisons reveal the approximate site of recombination and flanking regions of homology. This recombination site corresponds to a position within the alphoid monomer which has been previously implicated in an independent homologous recombination event, suggesting that there may exist a preferred register for recombination in alphoid DNA. We suggest that these events are representative of an ongoing process capable of reorganizing the satellite subset of a given chromosome, thereby contributing to the establishment of chromosome-specific alpha satellite subsets.     

Non-defendable resources affect peafowl lek organization: a male removal experiment

A lekking mating system is typically thought to be non-resource based with male providing nothing to females but genes. However, males are thought to clump their display sites on areas where they are more likely to encounter females, which may depend on non-defendable resource location. We tested this hypothesis on a feral population of peacocks. In agreement, we found that, within the lek, display site proximity to food resources had an effect on female visitation rate and male mating success. The attractiveness of display sites to male intruders was explained by the distance to the feeding place and by the female visitation rate. We randomly removed 29 territorial males from their display sites. Display sites that were more attractive to male intruders before removal remained highly attractive after removal and display sites closer to the feeding area attracted the attention of intruders significantly more after removal. Similarly, display sites that were more visited by females before removal remained more visited after removal, suggesting again that the likelihood of encountering females is determined by the display site location. Overall, these results are in agreement with non-defendable resources affecting lek spatial organization in the peafowl.     

Cox17, a copper chaperone for cytochrome c oxidase: expression, purification, and formation of mixed disulphide adducts with thiol reagents

Copper chaperone for cytochrome c oxidase (Cox17) is a 7 kDa copper-binding protein, which facilitates incorporation of copper ions into Cu(A) site of cytochrome c oxidase. Cox17 contains six conserved Cys residues and occurs in three different oxidative states, which display different metal-binding properties and stability. In the present study, we have elaborated technologies for production of partially oxidized human recombinant Cox17 in a bacterial expression system and purification of fully oxidized Cox17. For this purpose we used Escherichia coli Origami strain, which is deficient in thioredoxin and thioredoxin reductase systems and allows formation of disulfide bonds in cytoplasmic proteins. Fully oxidized Cox17 was purified by a simplified two-step procedure including gel filtration and cation exchange chromatography. By using mass spectrometry we demonstrated that application of 2-mercaptoethanol (2-ME) during purification leads to formation of its mixed disulfide adducts with Cox17. Moreover, partially reduced Cox17 can form mixed disulfide adducts also with the cellular reducing agent glutathione, which abolishes copper-binding ability of partially reduced Cox17.