Independent folding of individual components in hybrid proteins. Evidence that the carboxy-terminal 135 residues of the LexA repressor constitute a single autonomous domain

Accurate insertional inactivation of lacZalpha: construction of pTrueBlue and M13TrueBlue cloning vectors

Color selection plasmid and phage vectors based on insertional inactivation of the lacZalpha gene fragment have been in wide use for nearly two decades. The originals (the pUC and M13mp series) and all subsequent derivatives of these vectors contain the same mechanism for insertional inactivation of lacZalpha placing the sites for gene interruption between the initiator ATG codon and codon 7, a region that encodes a functionally nonessential part of the lacZalpha-complementation peptide. Numerous observations found in the literature and made in our laboratory suggest that the color selection process in these vectors does not function reliably and that erroneous conclusions about the success of cloning experiments are frequently drawn. We have studied the efficiency of lacZalpha inactivation by performing insertions at different intervals along the entire length of the proximal 60-amino-acid (aa)-coding region of the lacZ gene (lacZalpha). Our results show that accurate and reliable inactivation of lacZalpha occurs only when insertions are made within the DNA region that encodes aa 11-36. Based on these results, novel color selection plasmid and phage vectors, pTrueBlue and M13TrueBlue, have been constructed. Application of these vectors for gap-free shotgun sequencing of genomic DNA is discussed.

Ribosome-mediated translational pause and protein domain organization

Because regions on the messenger ribonucleic acid differ in the rate at which they are translated by the ribosome and because proteins can fold cotranslationally on the ribosome, a question arises as to whether the kinetics of translation influence the folding events in the growing nascent polypeptide chain. Translationally slow regions were identified on mRNAs for a set of 37 multidomain proteins from Escherichia coli with known three-dimensional structures. The frequencies of individual codons in mRNAs of highly expressed genes from E. coli were taken as a measure of codon translation speed. Analysis of codon usage in slow regions showed a consistency with the experimentally determined translation rates of codons; abundant codons that are translated with faster speeds compared with their synonymous codons were found to be avoided; rare codons that are translated at an unexpectedly higher rate were also found to be avoided in slow regions. The statistical significance of the occurrence of such slow regions on mRNA spans corresponding to the oligopeptide domain termini and linking regions on the encoded proteins was assessed. The amino acid type and the solvent accessibility of the residues coded by such slow regions were also examined. The results indicated that protein domain boundaries that mark higher-order structural organization are largely coded by translationally slow regions on the RNA and are composed of such amino acids that are stickier to the ribosome channel through which the synthesized polypeptide chain emerges into the cytoplasm. The translationally slow nucleotide regions on mRNA possess the potential to form hairpin secondary structures and such structures could further slow the movement of ribosome. The results point to an intriguing correlation between protein synthesis machinery and in vivo protein folding. Examination of available mutagenic data indicated that the effects of some of the reported mutations were consistent with our hypothesis.

Construction and functional characterization of recombinant fusion proteins of human lipoprotein lipase and apolipoprotein CII

The hydrolysis of triacylglycerols of chylomicrons and very low density lipoproteins by lipoprotein lipase (LPL) requires the presence of apolipoprotein (apo) CII as a cofactor. To obtain further information on the interaction of apo CII and LPL, we generated two fusion proteins consisting of the complete LPL molecule and the mature form of apo CII. The cDNAs of both proteins were either connected directly or by a segment encoding a 16-amino-acid linker peptide. The fused cDNAs were stably expressed in human embryonic kidney (HEK) 293 cells and the enzymic properties of the recombinant proteins were examined. The fusion proteins hydrolysed both emulsified long-chain (lipase) triacyglycerol substrate and a water-soluble short-chain (esterase) fatty acid ester substrate (p-nitrophenylbutyrate), regardless of whether or not they contained the linker peptide. In the absence of exogenous apo CII, the fusion proteins had up to 3.5-times higher basal activity than wild-type LPL. Similar to wild-type LPL, the fusion proteins were inhibited by 1 M NaCl, however less than wild-type LPL. A polyclonal antibody specific for apo CII impaired their ability to hydrolyse triacylglycerol emulsions. A similar effect was seen when the tetrapeptide KGEE was used as inhibitor, which corresponds to the carboxy-terminal four amino acids of apo CII.

Construction and characterization of two lexA mutants of Salmonella typhimurium with different UV sensitivities and UV mutabilities

Salmonella typhimurium has a SOS regulon which resembles that of Escherichia coli. recA mutants of S. typhimurium have already been isolated, but no mutations in lexA have been described yet. In this work, two different lexA mutants of S. typhimurium LT2 have been constructed on a sulA background to prevent cell death and further characterized. The lexA552 and lexA11 alleles contain an insertion of the kanamycin resistance fragment into the carboxy- and amino-terminal regions of the lexA gene, respectively. SOS induction assays indicated that both lexA mutants exhibited a LexA(Def) phenotype, although SOS genes were apparently more derepressed in the lexA11 mutant than in the lexA552 mutant. Like lexA(Def) of E. coli, both lexA mutations only moderately increased the UV survival of S. typhimurium, and the lexA552 strain was as mutable as the lexA+ strain by UV in the presence of plasmids encoding MucAB or E. coli UmuDC (UmuDCEc). In contrast, a lexA11 strain carrying any of these plasmids was nonmutable by UV. This unexpected behavior was abolished when the lexA11 mutation was complemented in trans by the lexA gene of S. typhimurium. The results of UV mutagenesis correlated well with those of survival to UV irradiation, indicating that MucAB and UmuDCEc proteins participate in the error-prone repair of UV damage in lexA552 but not in lexA11. These intriguing differences between the mutagenic responses of lexA552 and lexA11 mutants to UV irradiation are discussed, taking into account the different degrees to which the SOS response is derepressed in these mutants.

Physical and kinetic effects on induction of various linker regions in beta-galactosidase/galactose dehydrogenase fusion enzymes

To examine the role of the connecting region in the artificial bifunctional enzyme beta-galactosidase/galactose dehydrogenase, linkers of different length were inserted between the catalytic units. The specific activity of the galactose dehydrogenase part of the complex was increased when longer linkers (9 and 13 amino acids) were used as connectors. These bifunctional enzymes were predominantly found to comprise hexamers, however, complexes of higher molecular weight were also formed. The sequential reaction was carried out more efficiently when hybrid enzymes with the longer linkers were used as demonstrated both in vitro by using purified protein preparations as well as in vivo by determining the growth rates of recombinant E. coli cells on a minimal medium containing lactose.

Deletions, fusions and domain rearrangements

The techniques of protein engineering are proving to be powerful analytical tools for the study of the structure and function of complex multidomain proteins. In particular, the overexpression of individual functional modules is providing proteins for three-dimensional structural analyses. Progress is also being made in the design and construction of novel multidomain proteins with potential therapeutic applications.