Application of an electrochemical NAD+ recycling system involving a string-like carbon fiber to an enzyme reactor.

A string-like carbon fiber was found to be very suitable as a working electrode material for direct electrochemical oxidation of ß-nicotinamide adenine dinucleotide reduced form (NADH), and direct use of it for an enzyme reactor was possible. The electrochemical NAD+ recycling system was applied to glucose dehydrogenase (GDH) and to the recombinant formate dehydrogenase (RFDH) reactors. The maximum oxidation current value increased to 3.9 mA in the case of the GDH reactor. The remaining GDH activity after the reaction for 10 h amounted to 57% of the initial level. The remaining NAD+ activity amounted to 78% of the initial level. The current efficiency was calculated to be 80%. Furthermore, RFDH, which was more stable than GDH, was applied to the system. The maximum current value reached 5.9 mA. The remaining RFDH activity after reaction for 10 h amounted to 81% of the initial level. The remaining NAD+ activity was 78% of the initial level. The current efficiency was calculated to be 73%. Based on these results, both the enzyme and NAD+ were found to be acceptably stable in the electrochemical NAD+ recycling system.

Self-catalyzing functions of DNA.

We already reported that 281 bp DNA was degraded to 5'-dNMP by treatment at 70 degrees C and pH 7.5 for 1 h in the presence of 10 mM Mn ions, and the detailed results are published on Biosci. Biotechnol. Biochem., Vol. 71, 2670-2679 (2007). The degradation was accelerated by 100 mM NaCl. More than 80 bp DNA prepared by PCR using human ZNF 219 cDNA as the template were degraded into 5'- dNMP. Fifty bp DNA prepared by PCR us- ing the synthetic F and R primers of 22 mer was degraded into unknown material besides dNMP. Single-strand 281 b DNA prepared by Strandase (Novagen) was suggested not to be degraded into dNMP but to be degraded into the unknown material. Only double-strand DNA is presumed to be degraded into dNMP, therefore the double-strand structure is considered to be necessary for the degradation into dNMP. Furthermore, the unknown material was found in the ppt. fraction after centrifugation of the reaction mixture in the case of 34mer only G oligomer, while 5'-dGMP were found not to be degraded into any material. The m/z of the unknown material prepared from 34mer only G oligomer was determined to be 266 by LC-TOFMS. The elucidation of the conversion mechanism is under investigation.

Degradation of DNA into 5'-monodeoxyribonucleotides in the presence of Mn(2+) ions.

DNA is known to be aggregated by metal ions including Mn(2+) ions, but analysis of the aggregation process from a chemical viewpoint, which means identification of the product yielded during the process, has not been performed yet. On examination of the kinds of degraded materials that were in the supernatant obtained on centrifugation of a DNA mixture aggregated under conditions of 10 mM Mn(2+) ions ([Mn]/[P] = 46.3) at 70 degrees C for 1 h, the degradation products were found to be dAMP, dCMP, dGMP, and TMP. These dNMPs were purified by HPLC on TSKgel ODS-80Ts and identified by LC-TOF/MS. The degradation activity was lost on pretreatment of the DNA with a phenol-chloroform mixture, and the activity was recovered by pretreatment with a mixture of DMSO and a buffer containing surfactants. Mn(2+), Co(2+), Ni(2+), Cu(2+), Zn(2+), and Cd(2+), as transition element metal ions, were effective as to the degradation into dNMP. Mg(2+), Ca(2+), Sr(2+), and Ba(2+), as alkali earth element metal ions, were not effective as to the degradation. Monovalent anions such as Cl(-), CH(3)OO(-), and NO(3)(-) were found to increase the degradation rate. Sixty mug of the 120 mug of the starting DNA in 450 mul was degraded into dNMP on reaction for 1 h in the presence of 100 mM NaCl and 10 mM Mn(2+) ions. In this process, aggregation did not occur, and thus was not considered to be necessary for degradation. The degradation was found not to occur at pH 7.0, and to be very sensitive to pH. The OH(-) ion should have a critical role in cleavage of the phosphodiester linkages in this case. The dNMP obtained in the degradation process was found to be only 5'-NMP, based on the H(1)NMR spectra. This prosess should prove to be a new process for the production of 5'-dNMP in addtion to the exonuclease.

Photocontrol of kinesin ATPase activity using an azobenzene derivative.

Azobenzene is a photochromic molecule that undergoes rapid and reversible isomerization between the cis- and trans-forms in response to ultraviolet (UV) and visible (VIS) light irradiation, respectively. Here, we introduced the sulfhydryl-reactive azobenzene derivative 4-phenylazophenyl maleimide (PAM) into the functional region of kinesin to reversibly regulate the ATPase activity of kinesin by photoirradiation. We prepared five kinesin motor domain mutants, A247C, L249C, A252C, G272C and S275C, which contained a single reactive cysteine residue in loops L11 and L12. These loops are considered to be key regions for the functioning of kinesin as a motor protein. PAM was stoichiometrically incorporated into the cysteine residues in the loops of the mutants. The PAM-modified S275C mutant exhibited reversible alterations in ATPase activity accompanied by cis-trans isomerization upon UV and VIS light irradiation. The ATPase activity exhibited by the cis-isomer of the PAM bound to the mutant was two times higher than that of the trans-isomer. Further, the PAM-modified L249C mutant exhibited reversible alterations in ATPase activity on UV-VIS light irradiation but exhibited the opposite effect on UV and VIS light irradiation. Using a photochromic azobenzene derivative, we have demonstrated that the ATPase activity of the motor protein kinesin is photoregulated.

Conformational dynamics of loops L11 and L12 of kinesin as revealed by spin-labeling EPR.

The EPR spectra of the spin labels attached to loops L11 and L12 of kinesin were resolved into slow (rotational correlation time, tau=10-45 ns) and fast (tau=2 ns) components. The fraction of the slow component increased considerably when kinesin was complexed with a microtubule (MT). On MT binding and in the presence of nucleotides ADP and AMPPNP, the spin labels on L11, particularly at A252C and L249C, significantly decreased the fraction of the slow component. Moreover, dipolar EPR detected a wide distribution in distance range, 1-2 nm between the two spin labels attached to T242C/A252C or A247C/A252C; this distribution was slightly narrower in the presence of MTs than in their absence. These results suggested that the L11 residues undergo conformational transition on the binding of nucleotides and MT, while these residues remained to fluctuate over a nanometer range.

Self-cleavage of DNA in the presence of metal ions.

DNA is well known to be aggregated by metal ions including Mn ions, however, analysis of the aggregation process from a chemical aspect, which means identification of the product yielded during the process, has not been performed yet. On determination of what kinds of degraded materials were in the supernatant obtained on centrifugation of a DNA mixture aggregated under the conditions of 10 mM Mn ions ([Mn]/[P]=46.3) at 70 degrees C for 1 h, dAMP, dCMP, dGMP, and TMP produced through self-cleavage of DNA were found in the water-soluble part. These mononucleotides were purified by HPLC using TSKgel ODS-80Ts, and identified by LC-TOF/MS. The self-cleavage was effectively occurred under the conditions of more than 5 mM Mn ions, a reaction temperature of more than 70 degrees C, a reaction time of more than 30 min, and the use of DNA with a molecular weight of more than 140 bp. The self-cleavage was affected by the molecular size of the DNA.

Identification of the DNA binding specificity of the human ZNF219 protein and its function as a transcriptional repressor.

The ZNF219 gene is a member of the Kruppel-like zinc finger gene family that is involved in a diverse range of biological processes. The ZNF219 gene encodes a 77-kDa nuclear protein containing nine sets of C2H2 zinc finger structures. By using a random oligonucleotide selection assay and the electromobility gel shift assay, we have revealed that the ZNF219 protein recognizes two copies of CCCCCA. The DNA binding core element is CCCCC. 3' flanking A residues enhance binding of the ZNF219 protein. Use of the various truncated ZNF219 constructs demonstrated that zinc finger 1 to 3 or zinc finger 5 and 6 domains are sufficient to allow specific DNA binding. Both domains independently recognized the same consensus sequence, CCCCCA. Proteins expressed from human cDNA clones KIAA0390 and KIAA0222, which have partial similarities to ZNF219, also showed specific binding to the same core DNA sequence. Potential ZNF219 binding sites were found in the HMGN1 promoter. To examine the function of ZNF219 in the modulation of transcription, we constructed Gal4 DNA binding domain (DBD)/ZNF219 fusion proteins and demonstrated that ZNF219 functioned as a transcriptional repressor for the HMGN1 promoter. Experiments with the truncated ZNF219 constructs suggest that the proline-rich sequence (226-272 a.a., proline content 49%) was responsible for part of the observed repression. These findings provide us with an important start point in our understanding of the functional role of ZNF219 in vivo.

Isolation from Nocardioides sp. strain CT16, purification, and characterization of a deoxycytidine deaminase extremely thermostable in the presence of D,L-dithiothreitol.

A deoxycytidine deaminase that was extremely thermostable in the presence of dithiothreitol was found in a mesophilic bacterium isolated from soil. The bacterium was classified as a Nocardioides sp. The enzyme was purified to a homogeneous protein by treatment at 100 degrees C, ammonium sulfate precipitation, and chromatography on DEAE-Toyopearl, hydroxyapatite, and then Sephacryl S-100. Twenty micrograms of the pure enzyme was obtained from 811 mg of the starting crude protein. After treatment at 50 degrees C for 15 min in the absence of dithiothreitol, enzyme activity was 44% of the starting activity; after treatment at 100 degrees C for 2 h in the presence of 50 mm dithiothreitol, activity was 56% of the starting activity. Dithiothreitol greatly stabilized the enzyme. Activity was maximum at 99 degrees C. The Km values for deoxycytidine, cytidine, and methyl-deoxycytidine were 55.2, 140, and 130 microM, respectively. The molecular mass was estimated to be 52 kDa by gel permeation chromatography. The enzyme molecule was dissociated into two subunits each of 18 kDa subunit when reduced with mercaptoethanol.