Search PubMed⌕ Search

Biomedical subjects

Donald L Court

Publications and source records attributed to Donald L Court.

25 records · Page 2Linked to original sources
PubMed2003

Recombineering with overlapping single-stranded DNA oligonucleotides: testing a recombination intermediate.

A phage lambda-based recombination system, Red, can be used for high-efficiency mutagenesis, repair, and engineering of chromosomal or episomal DNA in vivo in Escherichia coli. When long linear double-stranded DNA with short flanking homologies to their targets are used for the recombination, the lambda Exo, Beta, and Gam proteins are required. The current model is: (i) Gam inhibits the host RecBCD activity, thereby protecting the DNA substrate for recombination; (ii) Exo degrades from each DNA end in a 5' --> 3' direction, creating double-stranded DNA with 3' single-stranded DNA tails; and (iii) Beta binds these 3' overhangs to protect and anneal them to complementary sequences. We have tested this model for Red recombination by using electroporation to introduce overlapping, complementary oligonucleotides that when annealed in vivo approximate the recombination intermediate that Exo should create. Using this technique we found Exo-independent recombination. Surprisingly, a similarly constructed substrate with 5' overhangs recombined more efficiently. This 5' overhang recombination required both Exo and Beta for high levels of recombination and the two oligonucleotides need to overlap by only 6 bp on their 3' ends. Results indicate that Exo may load Beta onto the 3' overhang it produces. In addition, multiple overlapping oligonucleotides were successfully used to generate recombinants in vivo, a technique that could prove useful for many genetic engineering procedures.

Bacteriophage lambda↗
PubMed2003

Phage HK022 Nun protein represses translation of phage lambda N (transcription termination/translation repression).

The N-terminal arginine-rich motif of phage HK022 Nun protein binds to NUT sequences in phage lambda nascent transcripts and induces transcription termination. Interactions between the Nun C terminus and RNA polymerase as well as the DNA template are required for termination. We have isolated Nun C-terminal point and deletion mutants that are unable to block transcription. The mutants bind NUT RNA and inhibit translation of the lambda N gene. Thus HK022 excludes lambda both by terminating transcription on the phage chromosome and by preventing translation of the essential lambda N gene. Like N autoregulation, translation repression by Nun requires host RNaseIII deficiency (rnc) or a mutation in the RNaseIII processing site (rIII) located between NUTL and the beginning of the N coding sequence. Our data support the idea that Nun bound at NUTL causes steric interference with ribosome attachment to the nearby N coding sequence. Two models, Nun acting alone or in complex with host proteins, are discussed.

Bacteriophage lambda↗
PubMed2003

A spring-loaded state of NusG in its functional cycle is suggested by X-ray crystallography and supported by site-directed mutants.

Transcription factor NusG is present in all prokaryotes, and orthologous proteins have also been identified in yeast and humans. NusG contains a 27-residue KOW motif, found in ribosomal protein L24 where it interacts with rRNA. NusG in Escherichia coli (EcNusG) is an essential protein and functions as a regulator of Rho-dependent transcription termination, phage lambda N and rRNA transcription antitermination, and phage HK022 Nun termination. Relative to EcNusG, Aquifex aeolicus NusG (AaNusG) and several other bacterial NusG proteins contain a variable insertion sequence of approximately 70 residues in the central region of the molecule. Recently, crystal structures of AaNusG in space groups P2(1) and I222 have been reported; the authors conclude that there are no conserved dimers among the contacting molecules in the crystals [Steiner, T., Kaiser, J. T., Marinkovic, S., Huber, R., and Wahl, M. C. (2002) EMBO J. 21, 4641-4653]. We have independently determined the structures of AaNusG also in two crystal forms, P2(1) and C222(1), and surprisingly found that AaNusG molecules form domain-swapped dimers in both crystals. Additionally, polymerization is also observed in the P2(1) crystal. A unique "ball-and-socket" junction dominates the intermolecular interactions within both oligomers. We believe that this interaction is a clue to the function of the molecule and propose a spring-loaded state in the functional cycle of NusG. The importance of the ball-and-socket junction for the function of NusG is supported by the functional analysis of site-directed mutants.

Amino Acid Sequence↗
PubMed2002

The global regulator RNase III modulates translation repression by the transcription elongation factor N.

Efficient expression of most bacteriophage lambda early genes depends upon the formation of an antiterminating transcription complex to overcome transcription terminators in the early operons, p(L) and p(R). Formation of this complex requires the phage-encoded protein N, the first gene product expressed from the p(L) operon. The N leader RNA contains, in this order: the NUTL site, an RNase III-sensitive hairpin and the N ribosome-binding site. N bound to NUTL RNA is part of both the antitermination complex and an autoregulatory complex that represses the translation of the N gene. In this study, we show that cleavage of the N leader by RNase III does not inhibit antitermination but prevents N-mediated translation repression of N gene expression. In fact, by preventing N autoregulation, RNase III activates N gene translation at least 200-fold. N-mediated translation repression is extremely sensitive to growth rate, reflecting the growth rate regulation of RNase III expression itself. Given N protein's critical role in lambda development, the level of RNase III activity therefore serves as an important sensor of physiological conditions for the bacteriophage.

5' Untranslated Regions↗
PubMed2002

Genetic engineering using homologous recombination.

In the past few years, in vivo technologies have emerged that, due to their efficiency and simplicity, may one day replace standard genetic engineering techniques. Constructs can be made on plasmids or directly on the Escherichia coli chromosome from PCR products or synthetic oligonucleotides by homologous recombination. This is possible because bacteriophage-encoded recombination functions efficiently recombine sequences with homologies as short as 35 to 50 base pairs. This technology, termed recombineering, is providing new ways to modify genes and segments of the chromosome. This review describes not only recombineering and its applications, but also summarizes homologous recombination in E. coli and early uses of homologous recombination to modify the bacterial chromosome. Finally, based on the premise that phage-mediated recombination functions act at replication forks, specific molecular models are proposed.

Bacteriophage lambda↗
PubMed2002

Bex, the Bacillus subtilis homolog of the essential Escherichia coli GTPase Era, is required for normal cell division and spore formation.

The Bacillus subtilis bex gene complemented the defect in an Escherichia coli era mutant. The Bex protein showed 39 percent identity and 67 percent similarity to the E. coli Era GTPase. In contrast to era, bex was not essential in all strains. bex mutant cells were elongated and filled with diffuse nucleoid material. They grew slowly and exhibited severely impaired spore formation.

Bacillus subtilis↗