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J Pustell

Publications and source records attributed to J Pustell.

8 recordsLinked to original sources

The legumin gene family: structure of a B type gene of Vicia faba and a possible legumin gene specific regulatory element.

The field bean, Vicia faba L. var. minor, possesses two sub-families of 11 S legumin genes named A and B. We isolated from a genomic library a B-type gene (LeB4) and determined its primary DNA sequence. Gene LeB4 codes for a 484 amino acid residue prepropolypeptide, encompassing a signal peptide of 22 amino acid residues, an acidic, very hydrophilic alpha-chain of 281 residues and a basic, somewhat hydrophobic beta-chain of 181 residues. The latter two coding regions are immediately contiguous, but each is interrupted by a short intron. Type A legumin genes from soybean and pea are known to have introns in the same two positions, in addition to an extra intron (within the alpha-coding sequence). Sequence comparisons of legumin genes from these three plants revealed a highly conserved sequence element of at least 28 bp, centered at approximately 100 bp upstream of each cap site. The element is absent from the equivalent position of all non-legumin and other plant and fungal genes examined. We tentatively name this element "legumin box" and suggest that it may have a function in the regulation of legumin gene expression.

Amino Acid Sequence↗

A convenient and adaptable microcomputer environment for DNA and protein sequence manipulation and analysis.

We describe the further development of a widely used package of DNA and protein sequence analysis programs for microcomputers (1,2,3). The package now provides a screen oriented user interface, and an enhanced working environment with powerful formatting, disk access, and memory management tools. The new GenBank floppy disk database is supported transparently to the user and a similar version of the NBRF protein database is provided. The programs can use sequence file annotation to automatically annotate printouts and translate or extract specified regions from sequences by name. The sequence comparison programs can now perform a 5000 X 5000 bp analysis in 12 minutes on an IBM PC. A program to locate potential protein coding regions in nucleic acids, a digitizer interface, and other additions are also described.

Amino Acid Sequence↗

The 3' ends of two genes in the Balbiani ring c locus of Chironomus thummi.

The 3'-end sequences of two nonallelic genes derived from the Balbiani ring c (BRc) locus of Chironomus thummi are described. Only one of the genes appears to be transcribed abundantly in normal late larval salivary glands. The two sequences are highly similar, even in the 3' untranslated regions, but sharply diverge beyond the polyadenylation site. Together with evidence from the 3' ends of BR1 and BR2 genes of C. pallidivittatus and C. tentans, independently characterized by others, this result suggests the existence of a sequence-homogenization mechanism that operates across the 3' ends of all BR genes characterized to date. The 3'-terminal coding region of each BRc gene is divided into two portions by a short intron. The upstream portion is homologous to and continuous with the tandem repeats that make up the internal core of each BR gene; however, that portion is variant in sequence relative to the core, and apparently is not subject to the homogenization process that operates on the core repeats. The portion downstream of the intron encodes a unique, 111-residue polypeptide highly different from the rest of the BRc product. The evolution of the various segments of the BRc genes is discussed.

Animals↗

Coding and potential regulatory sequences of a cluster of chorion genes in Drosophila melanogaster.

We have characterized at the nucleotide level a 4.8-kilobase pair segment of the third chromosome of Drosophila melanogaster, which contains a cluster of three chorion genes, s18-1, s15-1 and s19-1. These genes are tandemly oriented and share the same basic organization: a small and a large exon separated by a short intron in the signal peptide region. In the coding region, limited similarities at the DNA and protein level suggest a common but distant evolutionary origin. The flanking sequences were searched for elements that might be involved in controlling the tissue-specific and temporally regulated expression and the selective amplification of the chorion genes. A good candidate for a cis-regulatory element is the hexamer, TCACGT, which is found in all three genes in a highly significant position, 23 to 27 nucleotides upstream of the TATA-box, accompanied by additional, less exact similarities. Palindromes and short inverted repeats that are found in the vicinity of their complement are non-uniformly distributed: they are most concentrated in the 3' flanking part of all three genes, in and near regions of unusually high A and T content. The highest number of dyad symmetries, reminiscent of sequences that function as viral replication origins, is found associated with the T- and A-rich regions between genes s18-1 and s15-1.

Amino Acid Sequence↗

A convenient and adaptable package of computer programs for DNA and protein sequence management, analysis and homology determination.

We describe the further development of a widely used package of DNA/protein sequence analysis programs (1). Important revisions have been made based on user experience, and new features, multi-user capability, and a set of large scale homology programs have been added. The programs are very user friendly, economical of time and memory, and extremely transportable. They are written in a version of FORTRAN which will compile, with a few defined changes, as FORTRAN 66, FORTRAN 77, FORTRAN IV, FORTRAN IV+, and others. They are running on a variety of microcomputers, minicomputers, and mainframes, in both single user and multi-user configurations.

Amino Acid Sequence↗

Balbiani ring DNA: sequence comparisons and evolutionary history of a family of hierarchically repetitive protein-coding genes.

All known types of Balbiani ring (BR) genes consist of multiple, tandemly arranged, ca. 180 to 300-bp repeat units that can be divided into a constant region and a subrepeat region. The latter region includes short tandem subrepeats (SRs). Comparison of all available BR sequences using computer methods has enabled us (a) to define more precisely the constant and subrepeat regions, (b) to infer the evolutionary relationships among the various types of BR repeats, (c) to derive a consensus approximation of an ancestral sequence from a small segment of which the highly diverse present-day SRs may have originated, and (d) to detect an underlying substructure in the constant region, evident in the consensus but not in the present-day sequences and possibly corresponding to an original 39-bp DNA segment from which the extant, giant BR sequences may have evolved. We discuss the processes of reduplication, diversification, and homogenization within the hierarchically repetitive BR sequences as examples of how a simple DNA element may evolve into a diverse family of large, protein-coding genes.

Animals↗

A high speed, high capacity homology matrix: zooming through SV40 and polyoma.

We present a new homology matrix program which owes its basic conception to the two-dimensional dot matrices previously described (1,2), but has important improvements and new features. It scores sequence homology over an adjustable range and plots the scores which are above an operator-determined filtration level. Its powerful noise-filtration system, capacity for compression without much loss of information, and speed of execution make this program a valuable tool in the analysis of homologies, internal direct repeats and reverse repeats, including palindromic sequences. The properties of the program are exemplified by analysis of SV40 and polyoma DNA sequences.

Base Composition↗

A convenient and adaptable package of DNA sequence analysis programs for microcomputers.

We describe a package of DNA data handling and analysis programs designed for microcomputers. The package is convenient for immediate use by persons with little or no computer experience, and has been optimized by trial in our group for a year. By typing a single command, the user enters a system which asks questions or gives instructions in English. The system will enter, alter, and manage sequence files or a restriction enzyme library. It generates the reverse complement, translates, calculates codon usage, finds restriction sites, finds homologies with various degrees of mismatch, and graphs amino acid composition or base frequencies. A number of options for data handling and printing can be used to produce figures for publication. The package will be available in ANSI Standard FORTRAN for use with virtually any FORTRAN compiler.

Amino Acid Sequence↗