Sequence Analysis of Cloned cDNA and Proteolytic Fragments for Nitrate Reductase from Spinacia oleracea L.

Proteolytic fragments were obtained by limited proteolysis of120 kDa nitrate reductase from Spinacia oleracea L. using trypsinand Staphylococcus aureus V8 protease. Determination of NH₂-terminalsequences in 9 to 14 Edman degradation steps allowed the exactlocalization of the fragments within the amino-acid sequenceof spinach nitrate reductase was deduced from the nucleotidesequence of cDNA clone pSPNR117 which was initially identifiedby hybridization to squash nitrate reductase cDNA clone [Crawford,¹N. M., Campbell, W. H. and Davis, R. W. (1986) Proc. Natl. Acad.Sci. USA 83: 8073] and anti spinach nitrate reductase polyclonalantibodies. This clone has a 2324 base insert, and the aminoacid sequence deduced from its open reading frame, which contains640 residues. The predicted sizes 42.5 and 30 kDa were in reasonableagreement with previous determination of the apparent molecularsizes of the FAD-cyt-chrome b557-binding, and FAD-binding fragments,respectively. Arginine residue was the cleavage site for trypsin and glutamicacid was for S. aureus V8 protease. The amino acid residueswithin the linker regions which connect the functional domains,could be cleaved with trypsin or S. aureus V8 protease may bewell conserved in the amino acid sequences deduced from thenitrate reductase cDNA sequences. A sequence identity of 61.2-80.1 % was found in the amino acidsequences deduced from the cDNA sequences as obtained by spinachand other higher plant nitrate reductases. However, the aminoacid sequences surrounding the proteolytic cleavage sites ofnitrate reductase had poor homology. (Received March 30, 1991; Accepted July 24, 1991)     

Cloning and nucleotide sequence of cDNA for the plastid glycerol-3-phosphate acyltransferase from squash

The partial amino acid sequence and amino acid composition of acyl-(acyl-carrier-protein):glycerol-3-phosphate acyltransferase purified from squash cotyledons were determined. cDNAs encoding this enzyme were isolated from lambda gt 11 cDNA libraries made from poly(A)+ RNA of squash cotyledons by immunological selection and cross-hybridization. One of the resultant clones contained a cDNA insert of 1426 base pairs and an open reading frame of 1188 base pairs. The amino acid sequence deduced from the nucleotide sequence matched the partial amino acid sequence determined for the enzyme. The results suggest that a precursor protein of 396 amino acid residues is processed to the mature enzyme of 368 amino acid residues, losing a leader peptide of 28 amino acid residues. Relative molecular masses of the precursor and mature proteins were calculated to be 43,838 and 40,929 Da, respectively.     

Sequencing and Expression of the Gene that Encodes a 20-kDa Polypeptide of the PSI Complex from Cucumber Cotyledon

A cDNA clone encoding the polypeptide from cucumber PS I thatmigrates with an apparent molecular weight of 20 kDa on SDS-polyacrylamidegels has been isolated. The 907-bp sequence of this clone hasbeen determined and contains one large open reading frame thatencodes a 22,720-Da precursor polypeptide (207 amino acid residues).The molecular weight of the mature polypeptide was predictedto be 17,037-Da (153 amino acid residues). The deduced aminoacid sequence of this protein indicates that it is routed towardsthe stromal side of the thylakoid membrane and has no membrane-spanningregions. The sequence also confirmed the identity of the proteinas the product of the psa D gene. Chemical cross-linking offerredoxin to the PS I complex identified the 20-kDa subunitas the ferredoxin-binding protein. Northern hybridization experimentsrevealed that the mRNA of approximately 1,100 nucleotides forthe 20-kDa polypeptide was present in etiolated cucumber cotyledons,and its level increased about 5-fold during greening. The 20-kDapolypeptide was not detected by immunoblotting in etiolatedcotyledons, and it accumulated only after illumination. Labelingexperiments in vivo showed the absence of incorporation of [³⁵S]Metinto the polypeptide in etiolated cotyledons. These resultssuggest that the expression of the psa D gene is controlledat the translational level. (Received April 5, 1990; Accepted June 28, 1990)     

Characterization and sequence of a novel nitrate reductase from barley

Summary Barley (Hordeum vulgare L.) has both NADH-specific and NAD(P)H-bispecific nitrate reductases. Genomic and cDNA clones of the NADH nitrate reductase have been sequenced. In this study, a genomic clone (pMJ4.1) of a second type of nitrate reductase was isolated from barley by homology to a partial-length NADH nitrate reductase cDNA and the sequence determined. The open reading frame encodes a polypeptide of 891 amino acids and its interrupted by two small introns. The deduced amino acid sequence has 70% identity to the barley NADH-specific nitrate reductase. The non-coding regions of the pMJ4.1 gene have low homology (ca. 40%) to the corresponding regions of the NADH nitrate reductase gene. Expression of the pMJ4.1 nitrate reductase gene is induced by nitrate in root tissues which corresponds to the induction of NAD(P)H nitrate reductase activity. The pMJ4.1 nitrate reductase gene is sufficiently different from all previously reported higher plant nitrate reductase genes to suggest that it encodes the barley NAD(P)H-bispecific nitrate reductase.Scientific Paper No. 9101-14. College of Agriculture and Home Economics Research Center, Washington State University, Research Project Nos. 0233 and 0745     

Coding nucleotide sequence of rat liver malic enzyme mRNA

The nucleotide sequence of the mRNA for malic enzyme ((S)-malate NADP+ oxidoreductase (oxaloacetate-decarboxylating, EC 1.1.1.40) from rat liver was determined from three overlapping cDNA clones. Together, these clones contain 2078 nucleotides complementary to rat liver malic enzyme mRNA. The single open reading frame of 1761 nucleotides codes for a 585-amino acid polypeptide with a calculated molecular mass of about 65,460 daltons. The cloned cDNAs contain the complete 3'-noncoding region of 301 nucleotides for the major mRNA species of rat liver and 16 nucleotides of the 5'-noncoding region. Amino acid sequences of seven tryptic peptides (67 amino acids) from the purified protein are distributed through the single open reading frame and show excellent correspondence with the translated nucleotide sequence. The putative NADP-binding site for malic enzyme was identified by amino acid sequence homology with the NADP-binding site of the enoyl reductase domain of fatty acid synthetase.     

Molecular Characterization and Physiological Role of a Glyoxysome-Bound Ascorbate Peroxidase from Spinach

cDNAs encoding two cytosolic and two chloroplastic ascorbateperoxidase (AsAP) isozymes from spinach have been cloned recently[Ishikawa et al. (1995) FEBS Lett. 367: 28, (1996) FEBS Lett.384: 289]. We herein report the cloning of the fifth cDNA ofan AsAP isozyme which localizes in spinach glyoxysomes (gAsAP).The open reading frame of the 858-base pair cDNA encoded 286amino acid residues with a calculated molecular mass of 31,507Da. By determination of the latency of AsAP activity in intactglyoxysomes, the enzyme, as well as monodehydroascorbate (MDAsA)reductase, was found to be located on the external side of theorganelles. The cDNA was overexpressed in Escherichia coli (E.coli). The enzymatic properties of the partially purified recombinantgAsAP were consistent with those of the native enzyme from intactglyoxysomes. The recombinant enzyme utilized ascorbate (AsA)as its most effective natural electron donor; glutathione (GSH)and NAD(P)H could not substitute for AsA. The substrate-velocitycurves with the recombinant enzyme showed Michaelis-Menten typekinetics with AsA and hydrogen peroxide (H₂O₂); the apparentK_m values for AsA and H₂O₂were 1.89±0.05 mM and 74±4.0µM,respectively. When the recombinant enzyme was diluted with AsA-depletedmedium, the activity was stable over 180 min. We discuss theH₂O₂-scavenging system maintained by AsAP and the regenerationsystem of AsA in spinach glyoxysome. ¹Present address: Department of Biochemistry, Wakayama MedicalCollege, 27 Kyubancho, Wakayama, 640 Japan     

Purification and cDNA cloning of chloroplastic monodehydroascorbate reductase from spinach

The chloroplastic isoform of monodehydroascorbate (MDA) radical reductase was purified from spinach chloroplasts and leaves. The cDNA of chloroplastic MDA reductase was cloned, and its deduced amino acid sequence, consisting of 497 residues, showed high homology with those of putative organellar MDA reductases deduced from cDNAs of several plants. The amino acid sequence of the amino terminal of the purified enzyme suggested that the chloroplastic enzyme has a transit peptide consisting of 53 residues. A southern blot analysis suggested the occurrence of a gene encoding another isoform homologous to the chloroplastic isoform in spinach. The recombinant enzyme was highly expressed in Eschericia coli using the cDNA, and purified to a homogeneous state with high specific activity. The enzyme properties of the chloroplastic isoform are presented in comparison with those of the cytosolic form.     

The sequence of squash NADH:nitrate reductase and its relationship to the sequences of other flavoprotein oxidoreductases. A family of flavoprotein pyridine nucleotide cytochrome reductases.

Nucleotide sequences were determined for cDNA clones for squash NADH:nitrate oxidoreductase (EC 1.6.6.1), which is one of the most completely characterized forms of this higher plant enzyme. An open reading frame of 2754 nucleotides began at the first ATG. The deduced amino acid sequence contains 918 residues, with a predicted Mr = 103,376. The amino acid sequence is very similar to sequences deduced for other higher plant nitrate reductases. The squash sequence has significant similarity to the amino acid sequences of sulfite oxidase, cytochrome b5, and NADH:cytochrome b5 reductase. Alignment of these sequences with that of squash defines domains of nitrate reductase that appear to bind its 3 prosthetic groups (molybdopterin, heme-iron, and FAD). The amino acid sequence of the FAD domain of squash nitrate reductase was aligned with FAD domain sequences of other NADH:nitrate reductases, NADH:cytochrome b5 reductases, NADPH:nitrate reductases, ferredoxin:NADP+ reductases, NADPH:cytochrome P-450 reductases, NADPH:sulfite reductase flavoproteins, and Bacillus megaterium cytochrome P-450BM-3. In this multiple alignment, 14 amino acid residues are invariant, which suggests these proteins are members of a family of flavoenzymes. Secondary structure elements of the structural model of spinach ferredoxin:NADP+ reductase were used to predict the secondary structure of squash nitrate reductase and the other related flavoenzymes in this family. We suggest that this family of flavoenzymes, nearly all of which reduce a hemoprotein, be called "flavoprotein pyridine nucleotide cytochrome reductases."     

Cloning and sequence analysis of the human and Chinese hamster inosine-5'-monophosphate dehydrogenase cDNAs

Inosine-5'-monophosphate dehydrogenase, a key enzyme in the regulation of guanine nucleotide biosynthesis, was purified to homogeneity; and a polyclonal antibody directed against the purified protein was used to isolate human and Chinese hamster IMP dehydrogenase cDNA clones. These clones were sequenced and found to contain an open reading frame of a protein containing 514 amino acids. A sequence of 35 amino acids obtained by analysis of the purified protein is identical to a segment of the protein sequence deduced from the IMP dehydrogenase cDNA. The molecular mass of the deduced protein is 56 kDa, which is the observed molecular mass of the purified protein and of the immunoprecipitated in vitro translation product. Comparison of the protein sequences deduced from the human and Chinese hamster cDNA clones indicates only eight amino acid differences, suggesting that IMP dehydrogenase is a highly conserved protein.     

NAD(P)H:menadione oxidoreductase. Novel purification of enzyme cDNA and complete amino acid sequence, and gene regulation

NAD(P)H:menadione oxidoreductase induction by polycyclic hydrocarbons is known to be governed by the aromatic hydrocarbon-responsive (Ah) locus. This cytosolic enzyme was isolated from 3-methylcholanthrene-treated rat liver by a rapid two-step procedure with the use of affinity gel purification and fast-protein liquid chromatography. Polyclonal antiserum to menadione reductase was raised in rabbits. On Western (immuno) blot analysis, large increases in this hepatic menadione reductase protein (NMOR1) of 3-methylcholanthrene-treated C57BL/6N but not DBA/2N mice confirmed that induction of this enzyme by 3-methyl-cholanthrene is regulated by the Ah receptor. A cDNA expression library was constructed in lambda gt11 and screened with antiserum. Positive cDNA clones were plaque purified and further characterized by showing enhanced hybridization to 3-methylcholanthrene-induced poly(A+) RNA from rats; the longest cDNA clone (1,501 base pairs) has an open reading frame (bases 75-899) and a nucleotide sequence consistent with a new gene family. On Northern blot analysis, a single 3-methylcholanthrene-inducible rat liver mRNA (approximately 1.6 kilobases) hybridizes to the cDNA probe. On Southern blot analysis a total of 14-16 kilobases of rat genomic DNA fragments hybridize to the cDNA probe, indicating one or a small number of menadione reductase genes in this family. The amino acid sequence (274 residues) and Mr of 30,946 compare well with the size of the rat enzyme (32 kDa) estimated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The amino acid sequence of two internal fragments of the trypsin-digested purified NMOR1 protein is in complete agreement with that deduced from the cDNA nucleotide sequence. This study represents the first cloning and sequencing of a cDNA encoding a Phase II drug-metabolizing enzyme under control of the Ah locus.     

cDNA cloning of rat liver 2,4-dienoyl-CoA reductase

cDNA clones of 2,4-dienoyl-CoA reductase were isolated from rat liver cDNA libraries constructed in phages lambda gt11 and lambda gt10. Hybrid selected translation analysis revealed that 2,4-dienoyl-CoA reductase was translated as a polypeptide with a molecular weight of about 36,000, which was about 3,000 molecular weight units larger than mature reductase. Sequencing analysis revealed that the open reading frame encoded a polypeptide consisting of 335 amino acid residues (predicted molecular weight = 36,132), which contained an N-terminal extension peptide of 34 amino acid residues (presequence) in addition to the mature enzyme. Thus, 2,4-dienoyl-CoA reductase is synthesized as a larger precursor polypeptide, and the N-terminal extension peptide may be acting as the mitochondrial import signal.     

Primary structure of human poly(ADP-ribose) synthetase as deduced from cDNA sequence

Human poly(ADP-ribose) synthetase consists of three proteolytically separable domains, the first for binding of DNA, the second for automodification, and the third for binding of the substrate, NAD (Ushiro, H., Yokoyama, Y., and Shizuta, Y. (1987) J. Biol. Chem. 262, 2352-2357). We have isolated and sequenced cDNA clones for the enzyme using synthesized oligodeoxyribonucleotide probes based on the partial amino acid sequence of the protein. The open reading frame determined encodes a protein of 1,013 amino acid residues with a molecular weight of 113,203. The deduced amino acid sequence is consistent with the partial amino acid sequences of tryptic or alpha-chymotryptic peptides and the total amino acid composition of the purified enzyme. The native enzyme is relatively hydrophilic as judged from the hydrophilicity profile of the total amino acid sequence. The net charge of the NAD binding domain is neutral but the DNA binding domain and the automodification domain are considerably rich in lysine residue and quite basic. The DNA binding domain involves a homologous repeat in the sequence and exhibits a sequence homology with localized regions of transforming proteins such as c-fos and v-fos. Furthermore, this domain contains a unique sequence element which resembles the essential peptide sequences for nuclear location of SV40 and polyoma virus large T antigens. These facts suggest the possibility that the physiological function of poly(ADP-ribose) synthetase lies in its ability to bind to DNA and to control transformation of living eukaryotic cells like the cases of those oncogene products.     

The rice tapetum-specific gene RA39 encodes a type I ribosome-inactivating protein

A tapetum-specific cDNA encoded by a rice gene, RA39, was isolated by cDNA subtractive hybridization, differential screening and rapid amplification of cDNA ends. RA39 is a single-copy gene in the rice genome. mRNA in situ hybridization indicates that this gene is a tapetum-specific gene, and highly expressed in the tapetal cells at the meiosis and tetrad stages. The RA39 cDNA is 1,013 bp in length with an open reading frame encoding 298 amino acid residues. This cDNA sequence does not show significant homology to any known sequences in GenBank databases, but its deduced amino acid sequence (RA39) has between 19 and 34% sequence identity to ribosome-inactivating proteins (RIPs). Optimal alignment reveals that the five amino acid residues constituting the active site of the ricin A-chain (Tyr⁸⁰, Tyr¹²³, Glu¹⁷⁷, Arg¹⁸⁰ and Trp²¹¹), which are invariant among all RIPs published to date, are conserved in RA39. Recombinant RA39 protein expressed in Escherichia coli was purified to homogeneity. The purified protein exhibits the RNA N-glycosidase activity of RIPs. This demonstrates that RIPs occur in the reproductive organs of rice. The possible function of RA39 in anther development is discussed.     

Primary structure of rat brain prostaglandin D synthetase deduced from cDNA sequence

The amino acid sequence of rat brain prostaglandin D synthetase (Urade, Y., Fujimoto, N., and Hayaishi, O. (1985) J. Biol. Chem. 260, 12410-12415) was determined by a combination of cDNA and protein sequencing. cDNA clones specific for this enzyme were isolated from a lambda gt11 rat brain cDNA expression library. Nucleotide sequence analyses of cloned cDNA inserts revealed that this enzyme consisted of a 564- or 549-base pair open reading frame coding for a 188- or 183-amino acid polypeptide with a Mr of 21,232 or 20,749 starting at the first or second ATG. About 60% of the deduced amino acid sequence was confirmed by partial amino acid sequencing of tryptic peptides of the purified enzyme. The recognition sequence for N-glycosylation was seen at two positions of amino acid residues 51-53 (-Asn-Ser-Ser-) and 78-80 (-Asn-Leu-Thr-) counted from the first Met. Both sites were considered to be glycosylated with carbohydrate chains of Mr 3,000, since two smaller proteins with Mr 23,000 and 20,000 were found during deglycosylation of the purified enzyme (Mr 26,000) with N-glycanase. The prostaglandin D synthetase activity was detected in fusion proteins obtained from lysogens with recombinants coding from 34 and 19 nucleotides upstream and 47 and 77 downstream from the first ATG, indicating that the glycosyl chain and about 20 amino acid residues of N terminus were not essential for the enzyme activity. The amino acid composition of the purified enzyme indicated that about 20 residues of hydrophobic amino acids of the N terminus are post-translationally deleted, probably as a signal peptide. These results, together with the immunocytochemical localization of this enzyme to rough-surfaced endoplasmic reticulum and other nuclear membrane of oligodendrocytes (Urade, Y., Fujimoto, N., Kaneko, T., Konishi, A., Mizuno, N., and Hayaishi, O. (1987) J. Biol. Chem. 262, 15132-15136) suggest that this enzyme is a membrane-associated protein.