Molecular characterization in the dpy-14 region identifies the adenosylhomocysteine hydrolase gene in Caenorhabditis elegans

Caenorhabditis elegans dpy-14: an essential collagen gene with unique expression profile and physiological roles in early development

We describe the molecular characterisation of Caenorhabditis elegans dpy-14, a gene encoding an essential cuticular collagen annotated as col-59. Expression of dpy-14 starts at the 16 E cell stage, making it the earliest-expressing collagen reported to date. SAGE data and dpy-14 promoter::GFP reporter constructs indicate that the gene is transcribed mainly during embryogenesis, specifically in ciliated neurons and hypoderm. Water permeability assays and lectin staining showed that a mutation in the DPY-14 collagen results in defects in the channels of the amphids, which are a class of ciliated neuron, while the amphids appear morphologically normal by dye filling methods. Behavioural assays showed that the ciliated neurons expressing the gene are functional in dpy-14 mutants. All together, our data suggest that ciliated neurons and their hypodermal support cells collaborate in the transcription and synthesis of DPY-14, which then becomes a component of the amphid channels but not of the amphids proper. Interestingly, seam cells of dpy-14 mutants do not properly fuse to form a syncytium. This novel phenotype due to collagen mutations further stresses that dpy-14 plays a fundamental role in C. elegans physiology, since it is required for the proper development of the hypoderm.

Expression, purification, and characterization of recombinant S-adenosylhomocysteine hydrolase from the thermophilic archaeon Sulfolobus solfataricus

S-Adenosylhomocysteine hydrolase from Sulfolobus solfataricus was expressed in Escherichia coli by inserting the genomic fragment containing the gene encoding for S-adenosylhomocysteine hydrolase downstream the isopropyl-beta-d-thiogalactoside-inducible promoter of pTrc99A expression vector. An ATG positioned 25 bp upstream of the gene which is in frame with a stop codon was utilized as the initiation codon. This construct was used to transform E. coli RB791 and E. coli JM105 strains. The recombinant protein, purified by a fast and efficient two-step procedure (yield of 0.4 mg of enzyme per gram of cells), does not appear homogeneous on SDS-PAGE because of the presence of a protein contaminant corresponding to a "truncated" S-adenosylhomocysteine hydrolase subunit lacking the first 24 amino acid residues. The recombinant enzyme shows the same molecular mass, optimum temperature, and kinetic features of S-adenosylhomocysteine hydrolase isolated from S. solfataricus but it is less thermostable. To construct a vector which presents a correct distance between the ribosome-binding site and the start codon of S-adenosylhomocysteine hydrolase gene, a NcoI site was created at the translation initiation codon using site-directed mutagenesis. The expression of the homogeneous mutant S-adenosylhomocysteine hydrolase was achieved at high level (1.7 mg of mutant protein per gram of cells). The mutant S-adenosylhomocysteine hydrolase and the native one were indistinguishable in all physicochemical and kinetic properties including thermostability, indicating that the interactions involving the NH(2)-terminal sequence of the protein play a role in the thermal stability of S. solfataricus S-adenosylhomocysteine hydrolase.

Chemical modification and site-directed mutagenesis of cysteine residues in human placental S-adenosylhomocysteine hydrolase

Human placental S-adenosylhomocysteine (AdoHcy) hydrolase (EC 3.3.1. 1) was inactivated by 5',5-dithiobis(2-nitrobenzoic acid) following pseudo-first-order kinetics. Modification of three of the 10 cysteine residues per enzyme subunit resulted in complete inactivation of the enzyme. The three modified cysteine residues were identified as Cys113, Cys195, and Cys421, respectively, by protein sequencing after modification with [1-14C]iodoacetamide. Of the three modifiable cysteines, Cys113 and Cys195 could be protected from modification in the presence of the substrate adenosine (Ado), which also protected the enzyme from inactivation. On the other hand, Cys421 was not protected by Ado, and modification of Cys421 alone did not affect the enzyme activity. To verify whether some of these cysteine residues are important for the enzyme catalysis, these three cysteine residues were replaced by either serine or aspartic acid using site-directed mutagenesis. Mutants of both Cys113 (C113S and C113D) and Cys421 (C421S and C421D) had enzyme activities similar to that of the wild-type enzyme, and only slight changes were observed in the steady-state kinetics measured in both the synthetic and hydrolytic directions. However, mutants of Cys195 (C195D and C195S) displayed drastically reduced enzyme activities, and kcat values were only 7 and 12% of that of the wild-type enzyme, respectively, resulting in a calculated loss in binding energy (DeltaDeltaG) of approximate 1 Kcal/mol. The Cys195 mutants were capable of catalyzing both the 3'-oxidative and 5'-hydrolytic reactions, as evidenced by the reduction of E.NAD+ to NADH and formation of the 5'-hydrolytic product when incubated with (E)-5', 6'-didehydro-6'-deoxy-6'-chlorohomoadenosine at rates comparable with those catalyzed by the wild-type enzyme. However, mutations of the Cys195 severely altered the 3'-reduction potential as evidenced by the drastic reduction in the rate of [2,8-3H]Ado release from the E-NADH.[2,8-3H]3'-keto-Ado complex. Circular dichroism studies of the Cys195 mutants confirmed that the observed effects are not due to changes in secondary structure. These results suggested that the Cys195 is involved in the catalytic center and may play an important role in maintaining the 3'-reduction potential for effective release of the reaction products and regeneration of the active form (NAD+ form) of the enzyme; the Cys113 is located in or near the substrate binding site, but plays no role beneficial to the catalysis; and the Cys421 is a nonessential residue, which also explains why Cys421 does not occur in any other known AdoHcy hydrolases.

Cloning and sequencing of the gene coding for S-adenosylhomocysteine hydrolase in the thermophilic archaeon Sulfolobus solfataricus

The gene from the thermophilic archaeon Sulfolobus solfataricus (Ss), encoding the S-adenosylhomocysteine hydrolase (AdoHcyHD), has been cloned. Two degenerate oligodeoxyribonucleotide (oligo) probes, synthesized on the basis of amino acid (aa) sequence of cyanogen bromide-peptide fragments of the purified protein, were used to screen a genomic library of Ss cloned into the pGEM7Zf(+) vector. The AdoHcyHD gene (adohcyhd) comprises 1254 nucleotides (nt) and encodes a polypeptide of 417 aa with a deduced molecular mass of 46 kDa, in good agreement with the value directly measured for the purified enzyme. The identity of more than 32% of the deduced aa sequence was confirmed by Edman degradation of peptides. Putative regulatory elements which are in good agreement with the archaeal promoter consensus sequences were identified in the flanking regions. Comparison of the aa sequences of AdoHcyHD from different sources shows a remarkable degree of conservation. Surprisingly, several aa residues, thought important in substrate binding and catalysis, show non-conserved replacements in Ss AdoHcyHD.

Photoaffinity labeling of human placental S-adenosylhomocysteine hydrolase with [2-3H]8-azido-adenosine

The potential photoaffinity probe 8-azido-adenosine (8-N3-Ado) was shown to serve as a substrate for the 3'-oxidative activity of human S-adenosylhomocysteine (AdoHcy) hydrolase (Aiyar, V. N., and Hershfield, M. S. (1985) Biochem. J. 232, 643-650). In this study, we have determined the equilibrium binding properties of 8-N3-Ado with AdoHcy hydrolase (NAD+ form) and identified the specific amino acid residues that are covalently modified. After irradiation of the reaction mixture of [2-3H]8-N3-Ado and AdoHcy hydrolase (NAD+ form) and followed by tryptic digestion, peptides specifically photolabeled by [2-3H]3'-keto-8-N3-Ado were effectively separated from peptides nonspecifically labeled with [2-3H]8-N3-Ado using boronate affinity chromatography. After purification by reverse phase high performance liquid chromatography, two photolabeled peptides were isolated and identified as Val175-Lys186 and Val319-Arg327, in which Ala177 and Ile321 were associated with radioactivity. The specificity of the photoaffinity labeling with [2-3H]3'-keto-8-N3-Ado was demonstrated by the observation that these photolabeled peptides were not isolated when [2-3H]8-N3-Ado was incubated with apo AdoHcy hydrolase and irradiated. The two photolabeled peptides are assumed to be parts of the adenine-binding domain for substrates. They are both within well conserved regions of AdoHcy hydrolases. The peptide Val175-Lys186 is located very close to Cys195 and Glu197. Ser198, both of which were indicated to be located in the active site of the enzyme by chemical modification and limited proteolysis methods. The peptide Val319-Arg327 is adjacent to Leu330, which is proposed by a computer graphics model to interact with the C-6-NH2 group of Ado.

The gene and pseudogenes of rat S-adenosyl-L-homocysteine hydrolase

Two rat liver genomic DNA libraries constructed in lambda DASH and lambda Charon 4A were screened for sequences with similarity to S-adenosyl-L-homocysteine (AdoHcy) hydrolase cDNA. Of 36 clones purified, two contained the AdoHcy hydrolase gene sequence and 34 contained pseudogene sequences. The AdoHcy hydrolase gene, which has been sequenced in its entirety, spans approximately 15 kb and consists of 10 exons. Primer extension and S1 experiments show that transcription is initiated from two major initiation sites located at positions -63 and -62 from the starting codon and from several minor sites. The promoter region is located in a CpG island, sequence TATTTAAA is present 23 bases upstream from the transcription start site, and an inverted CCAAT box is located 285 bp upstream from the transcription start site. Other potential transcription-factor binding sites including SP1, AP-2, GRE and Oct-1 sites were identified in the 5'-flanking region. Several different processed pseudogenes were found and analyzed.

glh-1, a germ-line putative RNA helicase from Caenorhabditis, has four zinc fingers

We have cloned a family of putative RNA helicases from the free-living nematode Caenorhabditis elegans. One of these, a cDNA that we call glh-1, most closely matches in sequence and expression the previously described germ-line helicases PL10 from mouse and vasa from Drosophila. The amino terminus of the predicted protein of glh-1 contains a set of glycine-rich repeats similar in location and sequence to those in the predicted vasa protein. However, unlike all other putative RNA helicases, glh-1 also contains four retroviral-type zinc fingers. The RNA expression pattern of this Caenorhabditis helicase correlates with the presence of germ-line tissue in the parasitic nematode Ascaris lumbricoides var. suum and with the presence of germ cells in wild type and several germ-line mutants of Caenorhabditis. In the germ-line mutants glp-4 and glp-1, additional larger species of glh-1 RNA exist, which correspond to different adenylylated forms of the glh-1 transcript; these may be specified by motifs in the 3' untranslated region of glh-1 that are similar to adenylylation control elements and nos response elements.