A flexible new computer program for handling DNA sequence data

The genome of budgerigar fledgling disease virus, an avian polyomavirus

Budgerigar fledgling disease virus (BFDV) represents the first avian member of the Polyomavirus family. In contrast to mammalian polyomaviruses BFDV exhibits unique biological properties, in particular it is able to cause an acute disease with distinct organ manifestations in affected birds. Here we present the complete nucleotide sequence of the BFDV genome, consisting of 4980 bp. When compared to published nucleotide sequences of other polyomaviruses, the BFDV genome exposes a number of very similar structural features, and undoubtedly qualifies as a member of that family of viruses. The most important differences include a large T antigen remarkably reduced in size, and an origin of replication region with fundamental deviations from the origin structure of all other polyomaviruses. The specific characteristics of the BFDV genome may be used to place this virus into a distinct subgroup within the Polyomavirus family and may give a clue to the elucidation of its extraordinary biological properties.

Plastocyanin is encoded by an uninterrupted nuclear gene in spinach

Plastocyanin is a member of photosynthetic electron transport chains that transfers electrons from cytochrome f to the oxidized P700 chlorophyll a pigment of the photosystem I reaction center. We have isolated and characterized cDNA- and genomic clones from spinach (Spinacia oleracea) encoding the complete plastocyanin-precursor polypeptide. The amino acid sequence derived from the nucleotide sequence shows that the precursor consists of 168 amino acid residues including a transit sequence of 69 residues. The precursor polypeptide has a predicted Mr of 16,917, the mature protein of 10,413. The available data indicate that plastocyanin derives probably from a single-copy gene. The coding region contains no intron. The size of the mRNA as determined by S1 nuclease protection experiments is approximately 660 nucleotides, although analysis of different cDNA clones suggests that longer RNA species do exist, approaching the size of the mRNA (850 bases) estimated by Northern blot techniques.

Structure and evolution of two related transcription units of Epstein-Barr virus carrying small tandem repeats

Two regions of the Epstein-Barr virus (EBV) genome carrying partially homologous clusters of short tandem repeats (NotI and PstI repeats) flanked by 1044 and 1045 base pairs with almost complete homology (DL and DR, left and right duplication, respectively) were most abundantly transcribed into poly(A)+ mRNA after induction with the tumor promoter 12-O-tetradecanoyl-phorbol-13-acetate. The nucleotide sequence of both repeat clusters and the conserved upstream regulatory sequences from the M-ABA EBV strain are presented. Nearly the whole part of the sequences coding for the RNAs is covered by the NotI and PstI repeats, respectively. The regulatory sequences for these genes are located in the homologous regions of 1044 and 1045 base pairs (DL and DR, respectively). A CAAT box, a TATA box, and other herpes simplex virus-like elements were identified for both transcription units. The initiation points and the 3' ends of both inducible RNAs were mapped by S1 nuclease analysis. Both genes have open reading frames and may potentially code for proteins with repetitive amino acid compositions. The structure of these two inducible EBV genes is discussed, and an evolutionary model is proposed for the generation of gene duplication in the M-ABA strain of EBV.

Complete DNA sequence of lymphotropic papovavirus: prototype of a new species of the polyomavirus genus

Lymphotropic papovavirus (LPV) is a new member of the polyomavirus genus. Its host range in vitro is restricted to transformed cells of B-lymphocyte origin. Here the complete 5270-bp DNA sequence of LPV is presented. The LPV early region can encode a large T and a small t antigen but no middle T antigen and the late region can encode the three structural proteins VP1, VP2, and VP3. Based on sequence conservation of shared proteins LPV is equally related to both mouse polyomavirus (Py) and simian virus 40 (SV40) and represents a new distinct species of the polyomavirus genus. Sequence comparisons of LPV, SV40, and Py point out essential conserved sequence features of the polyomavirus genus more clearly than the comparison of only SV40 and Py. The most conserved proteins are VP1 with 42% and large T antigen with 28% of the amino acids conserved among the three viruses. Although least conserved the noncoding DNA sequences of LPV show significant homologies both to SV40 and Py (origin of viral DNA replication and putative early promoter). A 63-bp tandem repeat at the late side of the replication origin possibly represents a LPV enhancer element.

The ribosomal RNA genes from chloroplasts of mustard (Sinapis alba L.): mapping and sequencing of the leader region

The genes coding for rRNAs from mustard chloroplasts were mapped within the inverted repeat regions of intact ctDNA and on ctDNA fragments cloned in pBR322. R-loop analysis and restriction endonuclease mapping show that the genes for 16S rRNA map at distances of 17 kb from the junctions of the repeat regions with the large unique region. The genes for 23S rRNA are located at distances of 2.8 kb from the junctions with the small unique region. Genes for 4.5S and 5S rRNA are located in close proximity to the 23S rRNA genes towards the small unique region. DNA sequencing of portions of the 5' terminal third from the mustard 16S rRNA gene shows 96-99% homology with the corresponding regions of the maize, tobacco and spinach chloroplast genes. Sequencing of the region proximal to the 16S rRNA gene reveals the presence of a tRNA(Val) gene in nearly the same position and with identical sequence as in maize, tobacco and spinach. Somewhat less but still strong homology is also observed for the tDNA (Val)/16S rDNA intercistronic regions and for the regions upstream of the tRNA(Val) gene. However, due to many small and also a few larger deletions and insertions in the leader region, common reading frames coding for homologous peptides larger than 44 amino acids can not be detected; it is therefore unlikely that this region contains a protein coding gene.

Plasmid RP4 encodes two forms of a DNA primase

The pri gene locus of the conjugative broad host range plasmid RP4 maps between coordinates 40.3 and 43.5 and encodes two antigenically related forms of a DNA primase with a molecular mass of 118 and 80 kDa (kilodalton). Genesis of these two products has been examined using Pri+-recombinant plasmids. As shown by deletion analysis, the primase polypeptides are tow separate translation products which arise from an in-phase overlapping gene arrangement. It is suggested that transcription of a set of RP4 genes including the pri gene starts at a promoter site within the Tra1 region. In vivo, RP4 mutant primase can apparently substitute for Escherichia coli primase as demonstrated by measuring suppression of the dnaG3 (ts) mutant.

Simplified computer programs for search of homology within nucleotide sequences

Four new computer programs for search of homology within nucleotide sequences are presented. The main scope of the program design is flexibility, independence of sequence length and the capability to be used by any molecular biologist without any prior computer experience. The programs offer a linear search, a search for maximal identity, an alignment along a given sequence and a search based on homology within the amino acid coding capacity of nucleotide sequences. The language is Fortran V. Copies are available on request.

Structure of the chloroplast gene for the precursor of the Mr 32,000 photosystem II protein from mustard (Sinapis alba L.)

The nucleotide sequence of the mustard chloroplast gene for the precursor of the Mr 32,000 photosystem II protein is presented. A comparison with the corresponding genes from spinach and Nicotiana debneyi (14) reveals less than 5% nucleotide divergence in the coding region. The derived protein of mustard differs from the corresponding proteins by three amino acid positions at the C-terminus. We have defined the presumed transcription start and termination sites of the mustard gene. Upstream from the start site are sequences typical of a prokaryotic promoter and, also, a sequence that resembles the eukaryotic 'TATA' box. A search for intrastrand base pairing revealed stem-loop secondary structure at the transcription start and termination sites and in the region preceding the presumed promoter. This latter region is a 69-base-pair sequence element unique to the 5'flanking sequence of the mustard gene.

Extension of a flexible computer program for handling DNA sequence data

Our previously (Nucl. Acids Res. 10, 229 (1982] described program is largely extended. Maintaining the program architecture we are now able to present the same program with a highly increased comfort. The number of nucleotides per line is variable and the option for calculating restriction enzyme fragments is included. A four digit code guides through the program. The program is selfdefining and may be used without any prior computer experience. Copies are available on request.

Two distant clusters of partially homologous small repeats of Epstein-Barr virus are transcribed upon induction of an abortive or lytic cycle of the virus

The two regions of the Epstein-Barr virus genome carrying partially homologous clusters of short tandem repeats (DSL and DSR [duplicated sequences, left and right, respectively] ) are transcribed into polyadenylated RNA upon spontaneous or chemical induction of the lytic virus cycle. In Raji, an Epstein-Barr virus genome carrying a nonproducer cell line, transcription of DSL and DSR is only observed upon induction of an abortive life cycle of the virus. In the nonproducer cell line Raji, the polyadenylated transcripts of DSL and DSR are about 2,500 and 2,700 bases, respectively, in length. Four different spontaneous Epstein-Barr virus producer lines, M-ABA, CC34-5, QIMR-WIL, and B95-8, differ in the length of their DSL and/or DSR regions by different numbers of tandem repeats. The size of the RNAs corresponds in all cases to the size of the respective cluster of repeats, indicating that a large part of each RNA species is colinearly transcribed from the entire tandem repeat arrays. Both the DSL and the DSR RNAs have the same polarity proceeding from right to left on the Epstein-Barr virus genome. DNA sequence analysis of the DSR repeat revealed that translation of the RNA would be possible in three open reading frames within the repeat cluster. Short homologies to herpes simplex virus IR-TR sequences and to immunoglobulin switch region sequences (IgH-S) are discussed.

A zein gene of maize is transcribed from two widely separated promoter regions

The zein proteins are the major storage proteins of maize endosperm. They are made from large amounts of zein RNAs of several distinct sizes, ranging from the small 900 base final size RNA to precursor forms of over 3800 bases. The 900 base mRNA and the smallest precursor mRNA of 1800 bases are transcribed from two distinct promoter regions, P1 and P2. In vitro transcription of a maize genomic clone containing a zein gene pML 1 allowed both promoters to be mapped. The sequence of pML 1, covering the two promoter regions, contained consensus transcription start sequences at both of the predicted promoters. S1 mapping with RNA prepared from maize endosperm showed that both P1 and P2 are active in vivo as double starts.

The uteroglobin gene region: hormonal regulation, repetitive elements and complete nucleotide sequence of the gene

Differential uteroglobin induction represents an appropriate model for the molecular analysis of the mechanism by which steroid hormones control gene expression in mammals. We have analyzed the structure and hormonal regulation of a 35 Kb region of genomic DNA in which the uteroglobin gene is located. The complete sequence of 3,700 nucleotides including the uteroglobin gene and its flanking regions has been determined, and the limits of the gene established by S1 nuclease mapping. Several regions containing repeated sequences were mapped by blot hybridization, one of which is located within the large intron in the uteroglobin gene. Analysis of the RNAs extracted from endometrium, lung and liver, after treatment with estrogen and/or progesterone shows that within the 35 Kb region, the uteroglobin gene is the only DNA segment whose transcription into stable RNA is induced by progesterone.

DNA sequence and genome organization of genital human papillomavirus type 6b

The complete nucleotide sequence of the circular double-stranded DNA of the genital human papillomavirus type 6b (HPV6b) comprising 7902 bp was determined and compared with the DNA sequences of human papillomavirus type 1a (HPV1a) and bovine papillomavirus type 1 (BPV1). All major open reading frames are located on one DNA strand only. Their arrangement reveals that the genomic organization of HPV6b is similar to that of HPV1a and BPV1. The putative early region includes two large open reading frames E1 and E2 with marked amino acid sequence homologies to HPV1a and BPV1 which are flanked by several smaller frames. The internal part of E2 completely overlaps with another open reading frame E4. The putative late region contains two large open reading frames L1 and L2. The L1 amino acid sequences are highly conserved among analyzed papillomavirus types. By sequence comparison, potential promoter, splicing and polyadenylation signals can be localized in HPV6b DNA suggesting possible mechanisms of genital papillomavirus gene expression.

A chain of interlinked genes in the ninR region of bacteriophage lambda

The 3612-bp DNA sequence of the phage lambda P-Q (ninR) region contains a series of nine open reading frames in a distinctly overlapping pattern: ATGA sequence modules occur at the boundaries of consecutive genes and are able to serve both as terminator (TGA) and (re)initiator (ATG) codons for most of the adjacent frames. Together with genes O, P, and Q, the newly detected ren and ninA through ninH constitute a series of twelve closely linked genes in the pR operon. Based upon the available evidence for several of the nin proteins, and on plasmid expression data, we conclude that at least the larger nin genes, and probably all of the newly detected open reading frames code for proteins. The nin5 deletion of 2803 bp is a frame-to-frame fusion of ren and ninH, and covers the t R2 termination signal located near its left boundary, immediately behind the ren gene. The possible significance of the observed chain of closely interlinked genes for the regulation of Q expression is discussed.

The rex region of bacteriophage lambda: two genes under three-way control

The nucleotide sequence of the phage lambda rex region consists of 1428 bp and codes for two genes, rexA and rexB. Hence the complete lambda immunity region codes for four genes and covers 2664 bp of sequence unique to lambda, as defined by the left and right boundaries of the imm434 region. Coordinate expression of both rexA and rexB, which are co-regulated with the cI repressor gene from promoters p rm and p re is responsible for the Rex phenotype, i.e. exclusion of a wide variety of superinfecting phage such as T4rII. The position of a third promoter, p lit, which overlaps the carboxy-terminal end of the rexA coding region, permits expression of rexB without rexA, from the resulting 470 nucleotide lit RNA. The lit transcript, therefore, must act as messenger for rexB in the noncoordinate expression of the rex genes that occurs late in lambda lytic infection. The coordinate and noncoordinate expression of rexB and rexA suggests a dual role for the very hydrophobic rexB protein. Studies of lambda early and late DNA replication implicate rexB as having auxiliary functions in both lysogenisation and lytic infection.