A new host-vector system allowing selection for foreign DNA inserts in bacteriophage lambda gtWES

Pre-early functions of bacteriophage T5 and its relatives

Coliphage T5 injects its DNA in 2 steps: the first step transfer (FST) region 7.9% is injected and its genes are expressed and only then does the remainder (second step transfer, SST) of its DNA enter the cell. In the FST region, only 2 essential genes (A1 and A2) have been identified and a third (dmp) non-essential gene codes for a deoxyribonucleotide 5' monophosphatase. Thirteen additional putative ORFs are present in the FST region. Numerous properties have been attributed to FST region, including SST, host DNA degradation, inhibition of host RNA and protein synthesis, restriction insensitivity and protection of T5 DNA. These effects do not occur following infection with an A1 mutant. The A2 gene seems only to be involved in SST transfer. This is puzzling since there are more seemingly unrelated effects than there are essential genes to accomplish them and it is possible that some important genes were not identified. This review attempts to analyze these problems that were first identified in the 1970-80 s. In particular, an attempt is made to determine which potential ORFs are conserved in evolution (and thus likely to be important); by comparing T5 to 10 newly isolated and completely sequenced T5-like phages. A similar approach is used to identify conserved repeats, inverted repeats and palindromes that occur in all T5-like phages in the region containing the injection stop signal (iss) and the terminase substrate. Finally, an attempt is made to re-analyze the mechanism whereby T5 protects itself from the enzymes that degrade host DNA, from the RecBCD nuclease and from restriction enzymes. For all of these FST effects new hypotheses and possible new genetic and biochemical approaches are envisaged.

Comparison of the lignin-degrading white rot fungi Phanerochaete chrysosporium and Sporotrichum pulverulentum at the DNA level

DNA-hybridisation studies showed a close relationship between Phanerochaete chrysosporium ME446, most used in lignin degradation studies, and Sporotrichum pulverulentum Novobranova, the other standard lignin degrading strain. Two other strains of P. chrysosporium were both less related. We show that P. chrysosporium ME446 and S. pulverulentum Novobranova both have a GC-content of 59% for chromosomal DNA with the rRNA genes present as an AT-rich satellite; the mitochondrial DNA has a GC-content of 33%. The genome size estimated for P. chrysosporium ME446 is about 4-5 × 10(7) bp.

The first-step transfer-DNA injection-stop signal of bacteriophage T5

Bacteriophage T5 is different from most phages in that its DNA is injected in two steps during infection. The region containing the injection stop signal (iss) has been cloned and sequenced and found to contain numerous large repeats and inverted repeats which may be part of the iss. The most impressive of these are the 31-bp repeat units (rb) which are present three times in 99 bp. The rb repeats, themselves, contain inverted repeats so that mutually exclusive stem-and-loop structures may potentially form, not only within the repeats, but also between them. Another pair of repeats (21 bp each) contains two sequences resembling DnaA protein-binding sites. The region sequenced also contains one of the T5 site-specific strand interruptions and this was found to lie at the base of a perfect 9-bp palindrome.

Vectors with restriction-site banks. I. pJRD158, a 3903-bp plasmid containing 28 unique cloning sites

A DNA fragment has been constructed that contains many unique cloning sites not present in currently used Escherichia coli plasmid cloning vehicles. Insertion of this fragment into a modified version of pBR322 results in an AmpRTetR vector (pJRD158) of 3903 bp containing 28 unique cloning sites, four "almost unique" cloning sites, and eight unassigned unique 6-bp palindromes. The plasmid has the additional advantages of very high copy number and altered incompatibility. The latter permits it to be stably maintained in the same host as pBR322.

Direction of transcription in bacteriophage T5 first-step transfer DNA

The transcription of the T5 first-step transfer genes A2 and A3 has been shown to proceed from right to left (i.e., from A3 to A2) on the T5 DNA molecule.

Cloning of bacteriophage T5 DNA fragments. II. Isolation of recombinants carrying T5 PstI fragments

The adjacent PstI-J, I and G fragments of the phage T5 DNA molecule (4.4, 4.6 and 7.2 kb, respectively) have been cloned in plasmid pBR322 and their locations verified by Southern blot analysis. The PstI I and G fragments overlap the previously cloned HindIII-P and G fragments and like those, contain no known genetic markers. In addition, one of the 12 newly isolated T5 mutants maps in this PstI-IG region. Thus, the size of the "empty" region between genes D15 and D17, which we have previously observed on the genetic map, extends to at least 11.8 kb. In contrast, the PstI-J fragment carried part of the D12 gene and the intact D14 and D15 genes. This clone is of particular interest since the D15 gene product is a nuclease and is responsible for the positive control of late gene transcription. The orientation of these genes relative to the T5 DNA molecule has been determined by a combination of restriction, deletion and complementation analyses.

Cloning of bacteriophage T5 DNA fragments. III. Expression in Escherichia coli mini-cells

Use has been made of the mini-cell system to study polypeptide synthesis from cloned EcoRI, HindIII and PstI fragments of T5 DNA. The correlation of certain gene products with known genes has been established, as well as the physical mapping of genes not yet identified genetically. In some cases, it has been possible to demonstrate the presence of T5 promoters on the cloned DNA fragments. The design of experiments to avoid certain artifacts inherent in the use of the mini-cell system is discussed.

Cloning and characterization of the integrated viral DNA from three lines of SV40-transformed mouse cells

Recombinant DNA techniques have been used to isolate the integrated viral DNA, together with flanking cellular sequences, from three independently isolated lines of SV40-transformed BALB/c 3T3 cells. We have determined the structures of these cloned segments and their relationships to one another by restriction enzyme mapping, electron microscopic heteroduplex analysis and transfer hybridization experiments. Our data indicate that the structure of the integrated viral DNA is consistent with the idea that integration involves a tandemly repeated intermediate, that extensive amplification and rearrangement of viral and adjacent cellular sequences occurs after integration and that the majority of viral DNA insertions do not contain an intact early transcription unit. The altered templates presumably encode the truncated and super T antigens found in these cells. Either they are interrupted in the middle of the early region, in which case they generally retain the region in which tsA mutations map, or they contain tandem duplications of the tsA region. Further structural analysis will allow the prediction of the precise structures of these unusual T antigens, and the availability of the corresponding templates opens the way to an analysis of the functions of these proteins.

Cloning and expression of Trypanosoma brucei kinetoplast DNA in Escherichia coli

The kinetoplast DNA of Trypanosoma brucei is made of two components: mini-circles (1 kb, 90% of total kDNA) and maxi-circles (20 kb, 10%) of total kDNA). These are interlocked to form a network of about 10 000 kb. In order to analyse the components of such a network structure, we have cloned individual mini-circle molecules and two of the three EcoRI maxi-circle fragments in E. coli. Cloned mini-circles are somewhat heterogeneous in size and their restriction patterns are completely different. Despite this heterogeneity all are found to contain a homologous region(s) defined by DNA/DNA hybridization. The maxi-circles probably correspond to the mitochondrial DNA of other organisms and, in contrast to mini-circles, do not show sequence heterogeneity. One of the two cloned maxi-circle EcoRI fragments is able to direct the synthesis of two polypeptides of 10 300 and 13 500 daltons in E. coli mini-cells. Detailed analysis of this phenomenon shows that both structural genes and promoter(s) are located within the cloned maxi-circle fragment.

Cloning of bacteriophage T5 DNA fragments in plasmid pBR322 and bacteriophage lambda gtWES

Bacteriophage T5 was digested with the restriction endonucleases HindIII and EcoRI and the resulting fragments were inserted into the plasmid pBR322 and the bacteriophage lambda gtWES as vectors. Approx. 15% of the phage genome was recovered in recombinant clones. The recombinants were characterized by restriction analysis, DNA/DNA hybridization employing Southern blots, and ability to complement or recombine with amber mutants of T5. The results obtained allow revisions of the physical map of the T5 genome and partial correlation of the physical map with the genetic map.