High-level expression of staphylococcal nuclease R gene in Escherichia coli

Effect of N-terminal deletions on the foldability, stability, and activity of staphylococcal nuclease

The effect of N-terminally successive deletions on the foldability, stability, and activity of staphylococcal nuclease was examined. The structural changes in the nuclease caused by the deletions follow a hierarchical pattern: N-terminal truncation of the nuclease by up to nine residues clearly perturbs the conformation of the N-terminal beta-subdomain but does not affect the C-terminal alpha-subdomain; deletion of 11 or 12 residues perturbs the C-terminal alpha-subdomain, resulting in formation of a molten globule state; deletion of 13 residues causes the nuclease to become highly unfolded. N-terminally deleted nuclease delta11 retains the ability to fold but delta12 is not able to fold into an enzymatically active conformation, suggesting that 11 residues is the maximum length that can be deleted from the N-terminus while still retaining the folding competence of the nuclease. Further, the results suggest that proper folding of the C-terminal alpha-subdomain probably relies on the integrity of the N-terminal beta-subdomain.

The effects of amino acid replacements of glycine 20 on conformational stability and catalysis of staphylococcal nuclease

Staphylococcal nuclease (SNase) is a well-established model for protein folding studies. Its three-dimensional structure has been determined. The enzyme, Ca2+, and DNA or RNA substrate form a ternary complex. Glycine 20 is the second position of the first beta-turn of SNase, which may serve as the folding initiation site for the SNase polypeptide. To study the role of Gly20 in the conformational stability and catalysis of SNase, three mutants, in which Gly20 was replaced by alanine, valine, or isoleucine, were constructed and studied by using circular dichroism spectra, intrinsic and ANS-binding fluorescence spectra, stability and activity assays. The mutations have little effect on the conformational integrity of the mutants. However, the catalytic activity is reduced drastically by the mutations, and the stability of the protein is progressively decreased in the order G20A<G20V<G20I. Kinetic analysis indicates that the mutant enzymes G20A and G20V show almost 20-fold higher KmCa values than the wild-type enzyme, and the value for G20I is more than 50-fold higher. KACa values indicate more than 17.5-fold weaker binding of Ca2+ to the G20A and G20V mutants, and more than 39-fold weaker to the G20I mutant, compared to wild-type SNase. The above results suggest that the substitutions at Gly20 cause significantly weaker binding of Ca2+ in both the binary enzyme-Ca2+ complex and the ternary complex. However, there is little difference in the values of KmDNA and KSDNA between the mutants and the wild-type enzyme, suggesting that the substitutions at Gly20 have little effect on the binding of DNA substrates to the enzyme. Consistent with the changes in KmCa and KACa, the mutant enzymes G20A, G20V and G20I show about 10(3)-, 10(4)- and 10(5)-fold lower KCat values than the wild-type enzyme, respectively. These results suggest that Gly20 plays an important role in maintaining a suitable conformation at the active site of the enzyme.

Conformational adjustments of SNase R and its N-terminal fragments probed by monoclonal antibodies

Two monoclonal antibodies specific for staphylococcal nuclease R (SNase R) (McAb2C9 and McAb1B8) were prepared and used to probe protein folding during peptide elongation, by measuring antibody binding to seven N-terminal fragments (SNR141, SNR135, SNR121, SNR110, SNR102, SNR79 and SNR52) of SNase R. Comparative studies of the conformations of the N-terminal fragments have shown that all seven fragments of SNase R have a certain amount of residual structure, indicating that folding may occur during elongation of the nascent peptide chain. We show that the binding abilities of the intact enzyme and its seven fragments to the monoclonal antibodies are not simply proportional to the length of the peptide chain, suggesting that there may be continuous conformational adjustment in the nascent peptide chain as new C-terminal amino acids are added. A folding intermediate close in structure to the native state but with structural features in common with SNR121 is highly populated in 0.6 M GuHCl, and is also formed transiently during folding.

An in vitro peptide folding model suggests the presence of the molten globule state during nascent peptide folding

Although molten globules have been widely accepted as a general intermediate in protein folding, there is no clear evidence to show their presence during nascent peptide folding. This paper concentrates on whether the molten globule state occurs, and if it does, when does it form during nascent peptide folding, by comparing the changes in conformation during peptide chain extension of staphylococcal nuclease R. The results show that a large N-terminal fragment of staphylococcal nuclease, SNR121, which already contains more than 80% amino acid sequence of the nuclease, is found to fulfill all the criteria for the molten globule state, suggesting that the molten globule should occur at a later stage of peptide elongation. At this stage the hydrophobic collapse of the polypeptide chain occurs driven by the hydrophobic force, which leads to the formation of a solvent-accessible non-polar core, characterized by the high ANS-binding fluorescence. The nascent peptide folding of the nuclease is a hierarchical process that at the very least includes the following steps: secondary structure accumulation, pre-molten globule state, molten globule state, post-molten globule state and finally the native state. Constant conformation adjustment is necessary for correct folding and active expression of the protein.

Cloning of mnuA, a membrane nuclease gene of Mycoplasma pulmonis, and analysis of its expression in Escherichia coli

Membrane nucleases of mycoplasmas are believed to play important roles in growth and pathogenesis, although no clear evidence for their importance has yet been obtained. As a first step in defining the function of this unusual membrane activity, studies were undertaken to clone and analyze one of the membrane nuclease genes from Mycoplasma pulmonis. A novel screening strategy was used to identify a recombinant lambda phage expressing nuclease activity, and its cloned fragment was analyzed. Transposon mutagenesis was used to identify an open reading frame of 1,410 bp, which coded for nuclease activity in Escherichia coli. This gene coded for a 470-amino-acid polypeptide of 53,739 Da and was designated mnuA (for "membrane nuclease"). The MnuA protein contained a prolipoprotein signal peptidase II recognition sequence along with an extensive hydrophobic region near the amino terminus, suggesting that the protein may be lipid modified or that it is anchored in the membrane by this membrane-spanning region. Antisera raised against two MnuA peptide sequences identified an M. pulmonis membrane protein of approximately 42 kDa by immunoblotting, which corresponded to a trypsin-sensitive nucleolytic band of the same size. Maxicell experiments with E. coli confirmed that mnuA coded for a nuclease of unknown specificity. Hybridization studies showed that mnuA sequences are found in few Mycoplasma species, suggesting that mycoplasma membrane nucleases display significant sequence variation within the genus Mycoplasma.

Conformational features of a truncated staphylococcal nuclease R (SNR135) and their implications for catalysis

Conformational features of a truncated (14 amino acid residues deleted from the C-terminus) staphylococcal nuclease R (SNR135) and the ternary complex of SNR135-Ca2+-pdTp were studied using circular dichroism (CD) spectra and 1-anilinonaphthalene-8-sulfonate (ANS)-binding fluorescence spectra under different conditions. Kinetic parameters such as KDNAM, KDNAS, KCaM, KCaA, and KpdTpd of SNR135 were also determined. The results show that SNR135 contains some residual secondary structure and some tertiary structure elements as indicated by far-UV and near-UV CD spectra and that it has the ability to fold into a native-like state in the presence of pdTp and Ca2+, but there are obvious differences both in secondary structure and in tertiary structure between the SNR135-Ca2+-pdTp complex and SNase R. The unfolding curves in Gdn-HCl show that the stability of the native-like conformation of the SNR135-Ca2+-pdTp complex is much less than that of SNase R though the ligand (Ca2+, pdTp) binding increases the stability of the SNR135-Ca2+-pdTp complex to some extent. Comparison of the kinetic parameters of SNR135 with those of the full-length nuclease shows that both SNR135 and SNase R have the same value of KpdTpd and very similar values of KCaM and KCaA, but SNR135 has larger values of KDNAM and KDNAS than SNase R. Such results indicate that the C-terminal deletion for SNR135 does not greatly affect the ligand (Ca2+, pdTp) binding and decreases the binding affinity of the DNA substrate to the nuclease, implying that the amino acid residues at the ligand binding sites in SNR135 are probably arranged in a similar topology to those in SNase R and that effective binding of the DNA substrate to the enzyme needs the conformational integrity of the entire enzyme molecule. Furthermore, it is suggested that the binding sites of pdTp and DNA substrate may overlap but are not exactly the same. This paper also provides evidence obtained by monitoring ANS-binding fluorescence that the partially unfolded conformation of SNR135 is not in the molten globule state.

Folding of SNase R begins early during synthesis: the conformational feature of two short N-terminal fragments of staphylococcal nuclease R

To further understand the folding of nascent peptide during the early course of peptide synthesis, two short N-terminal fragments of staphylococcal nuclease R (SNase R), SNR52 and SNR79, were made by deleting 97 and 70 amino acid residues from the C-terminus. The conformations of SNR52 and SNR79 were studied by FTIR and far-ultraviolet CD. The results demonstrate that even the short N-terminal fragments of SNase R still have a certain amount of residual ordered secondary structure in the physiological condition. The ordered secondary structures were mainly assigned as beta-strands and turns, which corresponds well to the structures of the N-terminal part in the native protein. The conformational changes during unfolding and refolding in different concentrations of guanidine hydrochloride (GuHCl), monitored by far-ultraviolet CD and intrinsic fluorescence, show that the interaction between amino acid residues, which governs the formation of their conformation are not random. Considered together with earlier studies (Jing et al., Biochim Biophys Acta 1995;1250:189-196; Zhou et al., J Biochem 1996:120: 881-888), the results suggest that the folding of nascent peptide chains begins early in the synthesis process and that the amount of ordered structure increases with increasing peptide chain length until the conformation of the biologically active protein is generated.

Free luciferase may acquire a more favorable conformation than ribosome-associated luciferase for its activity expression

A variant of firefly luciferase in which the C-terminal end was extended with 44 amino acid residues served as a model protein in this study. After transcription and translation in vitro, the enzyme activity was measured when still attached to the ribosome and when released from the ribosome by incubation with RNase A or puromycin. It was found that the C-terminally extended luciferase already had activity when linked to the ribosome, but its activity was greatly increased when released from the ribosome. These results indicate that the luciferase is folded during synthesis on the ribosome; however, some conformational adjustments occur after its release from the ribosome which are required for the full expression of its enzymatic activity.

Comparative studies of the conformation of the N-terminal fragments of staphylococcal nuclease R in solution

In order to elucidate the folding of nascent peptide, five peptide fragments of staphylococcal nuclease R starting from N-terminal end and of different chain lengths are made by deletion of 47, 39, 28, 14 and 8 amino-acid residues from its C-terminal end, respectively. Changes in conformation of the N-terminal fragments have been compared by using Fourier-transform infrared spectra, far-ultraviolet circular dichroism spectra and analysis of surface hydrophobicity. The experiments indicate that all the five fragments have certain amounts of residual structure; in general, with increasing the peptide chain, the contents of secondary structure and the enzyme's activity of the peptide increase, and the exposed hydrophobic side chains brought about by the deletion of C-terminal residues are gradually buried in the interior of the nuclease. However, the ordered secondary structures do not always increase with increasing the peptide chain. Further growth of the length of the peptide chain could have an important effect on the conformation of the peptide fragment already synthesized, suggesting some structural adjustments should be necessary in order for the newly synthesized polypeptide to attain its final native conformation. These results support Tsou's nascent peptide folding hypothesis (Tsou, C.-L. (1988) Biochemistry 27, 1809-1812).