Characterization of the formate (for) locus, which encodes the cytosolic serine hydroxymethyltransferase of Neurospora crassa

1992 ◽  
Vol 12 (4) ◽  
pp. 1412-1421
Author(s):  
C R McClung ◽  
C R Davis ◽  
K M Page ◽  
S A Denome
Keyword(s):  
Amino Acid ◽  
Neurospora Crassa ◽  
Amino Acid Identity ◽  
Amino Acid Sequences ◽  
Serine Hydroxymethyltransferase ◽  
Central Position ◽  
Significant Similarity ◽  
C1 Metabolism ◽  
General Amino Acid Control ◽  
Growth Requirement

Serine hydroxymethyltransferase (SHMT) occupies a central position in one-carbon (C1) metabolism, catalyzing the reaction of serine and tetrahydrofolate to yield glycine and 5,10-methylenetetrahydrofolate. Methylenetetrahydrofolate serves as a donor of C1 units for the synthesis of numerous compounds, including purines, thymidylate, lipids, and methionine. We provide evidence that the formate (for) locus of Neurospora crassa encodes cytosolic SHMT. The for+ gene was localized to a 2.8-kb BglII fragment by complementation (restoration to formate-independent growth) of a strain carrying a recessive for allele, which confers a growth requirement for formate. The for+ gene encodes a polypeptide of 479 amino acids which shows significant similarity to amino acid sequences of SHMT from bacterial and mammalian sources (47 and 60% amino acid identity, respectively). The for+ mRNA has several different start and stop sites. The abundance of for+ mRNA increased in response to amino acid imbalance induced by glycine supplementation, suggesting regulation by the N. crassa cross-pathway control system, which is analogous to general amino acid control in Saccharomyces cerevisiae. This was confirmed by documenting that for+ expression increased in response to histidine limitation (induced by 3-amino-1,2,4-triazole) and that this response was dependent on the presence of a functional cross-pathway control-1 (cpc-1) gene, which encodes CPC1, a positively acting transcription factor. There are at least five potential CPC1 binding sites upstream of the for+ transcriptional start, as well as one that exactly matches the consensus CPC1 binding site in the first intron of the for+ gene.

scholarly journals Characterization of the formate (for) locus, which encodes the cytosolic serine hydroxymethyltransferase of Neurospora crassa.

1992 ◽  
Vol 12 (4) ◽  
pp. 1412-1421 ◽  
Author(s):  
C R McClung ◽  
C R Davis ◽  
K M Page ◽  
S A Denome
Keyword(s):  
Amino Acid ◽  
Neurospora Crassa ◽  
Amino Acid Identity ◽  
Amino Acid Sequences ◽  
Serine Hydroxymethyltransferase ◽  
Central Position ◽  
Significant Similarity ◽  
C1 Metabolism ◽  
General Amino Acid Control ◽  
Growth Requirement

Serine hydroxymethyltransferase (SHMT) occupies a central position in one-carbon (C1) metabolism, catalyzing the reaction of serine and tetrahydrofolate to yield glycine and 5,10-methylenetetrahydrofolate. Methylenetetrahydrofolate serves as a donor of C1 units for the synthesis of numerous compounds, including purines, thymidylate, lipids, and methionine. We provide evidence that the formate (for) locus of Neurospora crassa encodes cytosolic SHMT. The for+ gene was localized to a 2.8-kb BglII fragment by complementation (restoration to formate-independent growth) of a strain carrying a recessive for allele, which confers a growth requirement for formate. The for+ gene encodes a polypeptide of 479 amino acids which shows significant similarity to amino acid sequences of SHMT from bacterial and mammalian sources (47 and 60% amino acid identity, respectively). The for+ mRNA has several different start and stop sites. The abundance of for+ mRNA increased in response to amino acid imbalance induced by glycine supplementation, suggesting regulation by the N. crassa cross-pathway control system, which is analogous to general amino acid control in Saccharomyces cerevisiae. This was confirmed by documenting that for+ expression increased in response to histidine limitation (induced by 3-amino-1,2,4-triazole) and that this response was dependent on the presence of a functional cross-pathway control-1 (cpc-1) gene, which encodes CPC1, a positively acting transcription factor. There are at least five potential CPC1 binding sites upstream of the for+ transcriptional start, as well as one that exactly matches the consensus CPC1 binding site in the first intron of the for+ gene.

scholarly journals Cloning and sequencing of the cDNA species for mammalian dimeric dihydrodiol dehydrogenases

1999 ◽  
Vol 342 (3) ◽  
pp. 721-728 ◽  
Author(s):  
Eiji ARIMITSU ◽  
Shinya AOKI ◽  
Syuhei ISHIKURA ◽  
Kumiko NAKANISHI ◽  
Kazuya MATSUURA ◽  
...  
Keyword(s):  
Amino Acid ◽  
Reductase Activity ◽  
Sequence Similarity ◽  
Japanese Monkey ◽  
Amino Acid Identity ◽  
Amino Acid Sequences ◽  
Amino Acid Residues ◽  
Animal Tissues ◽  
Dihydrodiol Dehydrogenase ◽  
Low Degrees

Cynomolgus and Japanese monkey kidneys, dog and pig livers and rabbit lens contain dimeric dihydrodiol dehydrogenase (EC 1.3.1.20) associated with high carbonyl reductase activity. Here we have isolated cDNA species for the dimeric enzymes by reverse transcriptase-PCR from human intestine in addition to the above five animal tissues. The amino acid sequences deduced from the monkey, pig and dog cDNA species perfectly matched the partial sequences of peptides digested from the respective enzymes of these animal tissues, and active recombinant proteins were expressed in a bacterial system from the monkey and human cDNA species. Northern blot analysis revealed the existence of a single 1.3 kb mRNA species for the enzyme in these animal tissues. The human enzyme shared 94%, 85%, 84% and 82% amino acid identity with the enzymes of the two monkey strains (their sequences were identical), the dog, the pig and the rabbit respectively. The sequences of the primate enzymes consisted of 335 amino acid residues and lacked one amino acid compared with the other animal enzymes. In contrast with previous reports that other types of dihydrodiol dehydrogenase, carbonyl reductases and enzymes with either activity belong to the aldo-keto reductase family or the short-chain dehydrogenase/reductase family, dimeric dihydrodiol dehydrogenase showed no sequence similarity with the members of the two protein families. The dimeric enzyme aligned with low degrees of identity (14-25%) with several prokaryotic proteins, in which 47 residues are strictly or highly conserved. Thus dimeric dihydrodiol dehydrogenase has a primary structure distinct from the previously known mammalian enzymes and is suggested to constitute a novel protein family with the prokaryotic proteins.

scholarly journals A Point Mutation in the Two-Component Histidine Kinase BcOS-1 Gene Confers Dicarboximide Resistance in Field Isolates of Botrytis cinerea

2002 ◽  
Vol 92 (1) ◽  
pp. 75-80 ◽  
Author(s):  
Michiyo Oshima ◽  
Makoto Fujimura ◽  
Shinpei Banno ◽  
Chigusa Hashimoto ◽  
Takayuki Motoyama ◽  
...  
Keyword(s):  
Amino Acid ◽  
Neurospora Crassa ◽  
Botrytis Cinerea ◽  
Amino Acid Substitution ◽  
Histidine Kinase ◽  
Tandem Repeats ◽  
Polymerase Chain Reaction Amplification ◽  
Amino Acid Sequences ◽  
Osmotic Sensitivity ◽  
Field Isolates

Partial DNA fragments of Botrytis cinerea field isolates encoding the putative osmosensor histidine kinase gene (BcOS1) were cloned by polymerase chain reaction amplification and the predicted amino acid sequences were compared between dicarboximide-sensitive and resistant field isolates. The predicted BcOS1p is highly homologous to osmosensor histidine kinase OS1p from Neurospora crassa including the N-terminal six tandem repeats of approximately 90 amino acids. Four dicarboximide-resistant isolates of B. cinerea (Bc-19, Bc-45, Bc-682, and Bc-RKR) contained a single base pair mutation in their BcOS1 gene that resulted in an amino acid substitution in the predicted protein. In these resistant isolates, codon 86 of the second repeat, which encodes an isoleucine residue in sensitive strains, was converted to a codon for serine. The mutation of Botrytis field resistant isolates was located on the second unit of tandem amino acid repeats of BcOS1p, whereas the point mutations of the fifth repeat of OS1p confer resistance to both dicarboximides and phenylpyrroles and also osmotic sensitivity in Neurospora crassa. These results suggest that an amino acid substitution within the second repeat of BcOS1p is responsible for phenotypes of field resistant isolates (resistant to dicarboximides but sensitive to phenylpyrroles, and normal osmotic sensitivity) in B. cinerea.

scholarly journals Vascular endothelial growth factors encoded by Orf virus show surprising sequence variation but have a conserved, functionally relevant structure

2002 ◽  
Vol 83 (11) ◽  
pp. 2845-2855 ◽  
Author(s):  
A. A. Mercer ◽  
L. M. Wise ◽  
A. Scagliarini ◽  
C. J. McInnes ◽  
M. Büttner ◽  
...  
Keyword(s):  
Amino Acid ◽  
Sequence Variation ◽  
Amino Acid Identity ◽  
Amino Acid Sequences ◽  
High Rate ◽  
Orf Virus ◽  
Vegf Receptor ◽  
Vascular Endothelial ◽  
Vegf Gene ◽  
X Ray Crystallography

The first report of a vascular endothelial growth factor (VEGF)-like gene in Orf virus included the surprising observation that the genes from two isolates (NZ2 and NZ7) shared only 41·1% amino acid sequence identity. We have examined this sequence disparity by determining the VEGF gene sequence of 21 isolates of Orf virus derived from diverse sources. Most isolates carried NZ2-like VEGF genes but their predicted amino acid sequences varied by up to 30·8% with an average amino acid identity between pairs of NZ2-like sequences of 86·1%. This high rate of sequence variation is more similar to interspecies than intraspecies variability. In contrast, only three isolates carried an NZ7-like VEGF gene and these varied from the NZ7 sequence by no more than a single nucleotide. The VEGF family are ligands for a set of tyrosine kinase receptors. The viral VEGFs are unique among the family in that they recognize VEGF receptor 2 (VEGFR-2) but not VEGFR-1 or VEGFR-3. Comparisons of the viral VEGFs with other family members revealed some correlations between conserved residues and the ability to recognize specific VEGF receptors. Despite the sequence variations, structural predictions for the viral VEGFs were very similar to each other and to the structure determined by X-ray crystallography for human VEGF-A. Structural modelling also revealed that a groove seen in the VEGF-A homodimer and believed to play a role in its binding to VEGFR-1 is blocked in the viral VEGFs. This may contribute to the inability of the viral VEGFs to bind VEGFR-1.

scholarly journals Molecular cloning of two isoforms of the murine homolog of the myeloid CD33 antigen

Blood ◽  
1994 ◽  
Vol 83 (11) ◽  
pp. 3188-3198 ◽  
Author(s):  
EZ Tchilian ◽  
PC Beverley ◽  
BD Young ◽  
SM Watt
Keyword(s):  
Amino Acid ◽  
Cell Line ◽  
Myeloid Cell ◽  
Amino Acid Identity ◽  
Amino Acid Sequences ◽  
Cdna Clones ◽  
Reading Frame ◽  
Murine Homolog ◽  
Myeloid Cell Line ◽  
Nucleotide Insertion

Abstract CD33 monoclonal antibodies recognize a 67-kD glycoprotein of unknown function that is expressed by early myeloid progenitors and their leukemic counterparts. We report here the cloning of the murine homolog of the human CD33 antigen. Two cDNA clones, differing by an 83- nucleotide insertion in the cytoplasmic region, were isolated. The insertion generated a shift in the reading frame within the cytoplasmic tail, resulting in two mouse CD33 isoforms, m33-A and m33-B, with distinct cytoplasmic domains and with predicted protein core molecular weights of 37 kD and 45 kD, respectively. The cDNAs and deduced amino acid sequences show extensive similarity with the human CD33 sequence with the highest homology occurring in the first and second lg-like domains (61% amino acid identity). The most significant divergence between the human and murine proteins occurs in their cytoplasmic portions. The murine CD33 mRNAs were detected in bone marrow, spleen, thymus, brain, liver, the multipotential progenitor cell line, A4, the myelomonocytic cell line, WEHI3B, the myeloid cell line, M1, and the macrophage cell line, P388, by Northern blot analysis. The expression pattern of the murine CD33 homolog suggests that the function of CD33 antigen in hematopoiesis may be conserved between humans and mice.

scholarly journals Chromosome-Encoded β-Lactamases TUS-1 and MUS-1 from Myroides odoratus and Myroides odoratimimus (Formerly Flavobacterium odoratum), New Members of the Lineage of Molecular Subclass B1 Metalloenzymes

2002 ◽  
Vol 46 (11) ◽  
pp. 3561-3567 ◽  
Author(s):  
Hedi Mammeri ◽  
Samuel Bellais ◽  
Patrice Nordmann
Keyword(s):  
Amino Acid ◽  
Single Species ◽  
Amino Acid Identity ◽  
Amino Acid Sequences ◽  
Intrinsic Resistance ◽  
New Members ◽  
Acid Identity ◽  
Myroides Odoratimimus ◽  
Molecular Masses ◽  
Flavobacterium Odoratum

ABSTRACT Myroides odoratus and Myroides odoratimimus (formerly designated in a single species as Flavobacterium odoratum) are gram-negative aerobes and sources of nosocomial infections in humans. They have variable susceptibility to β-lactams and a decreased susceptibility to carbapenems. Using genomic DNAs of M. odoratus CIP 103105 and M. odoratimimus CIP 103073 reference strains, shotgun cloning of β-lactamase genes was performed, followed by protein expression in Escherichia coli. The deduced amino acid sequences of these β-lactamase genes revealed that TUS-1 and MUS-1 from M. odoratus CIP 103105 and M. odoratimimus CIP 103073, respectively, shared 73% amino acid identity. Mature proteins TUS-1 and MUS-1, with pI values of 7.8 and 5.2, respectively, had relative molecular masses of ca. 26 kDa. These β-lactamases are members of the subclass B1 of metallo-β-lactamases and are distantly related to other metalloenzymes, being most closely related to IND-1 from Chryseobacterium indologenes (42% amino acid identity). However, phylogenic analysis showed that TUS-1 and MUS-1 belong to the same phylogenic lineage of subclass B1 enzymes that groups the subclass B1 β-lactamases of Flavobacterium species. Kinetic parameters of purified β-lactamases TUS-1 and MUS-1 detailed their hydrolysis spectra, which encompass most β-lactams except aztreonam. β-Lactamases TUS-1 and MUS-1 were classified in functional subgroup 3a of metalloenzymes. This work further characterizes chromosome-encoded metalloenzymes from Flavobacteriaceae species that explain at least part of their intrinsic resistance to β-lactams.

scholarly journals Oms38 Is the First Identified Pore-Forming Protein in the Outer Membrane of Relapsing Fever Spirochetes

2008 ◽  
Vol 190 (21) ◽  
pp. 7035-7042 ◽  
Author(s):  
Marcus Thein ◽  
Ignas Bunikis ◽  
Katrin Denker ◽  
Christer Larsson ◽  
Sally Cutler ◽  
...  
Keyword(s):  
Amino Acid ◽  
Outer Membrane ◽  
Signal Sequence ◽  
Amino Acid Identity ◽  
Amino Acid Sequences ◽  
Relapsing Fever ◽  
Small Water ◽  
Membrane Spanning

ABSTRACT Relapsing fever is a worldwide, endemic disease caused by several spirochetal species belonging to the genus Borrelia. During the recurring fever peaks, borreliae proliferate remarkably quickly compared to the slow dissemination of Lyme disease Borrelia and therefore require efficient nutrient uptake from the blood of their hosts. This study describes the identification and characterization of the first relapsing fever porin, which is present in the outer membranes of B. duttonii, B. hermsii, B. recurrentis, and B. turicatae. The pore-forming protein was purified by hydroxyapatite chromatography and designated Oms38, for outer membrane-spanning protein of 38 kDa. Biophysical characterization of Oms38 was done by using the black lipid bilayer method, demonstrating that Oms38 forms small, water-filled channels of 80 pS in 1 M KCl that did not exhibit voltage-dependent closure. The Oms38 channel is slightly selective for anions and shows a ratio of permeability for cations over anions of 0.41 in KCl. Analysis of the deduced amino acid sequences demonstrated that Oms38 contains an N-terminal signal sequence which is processed under in vivo conditions. Oms38 is highly conserved within the four studied relapsing fever species, sharing an overall amino acid identity of 58% and with a strong indication for the presence of amphipathic β-sheets.

Restricted activation of general amino acid control under conditions of glutamine limitation in Neurospora crassa

1990 ◽  
Vol 223 (3) ◽  
pp. 443-448 ◽  
Author(s):  
Johanna Kolanus ◽  
Jens Michalczyk ◽  
Harry J. Flint ◽  
Ilse B. Barthelmess
Keyword(s):  
Amino Acid ◽  
Neurospora Crassa ◽  
General Amino Acid Control ◽  
Acid Control ◽  
Glutamine Limitation

scholarly journals The α- and β-subunits of the Human UDP-N-acetylglucosamine:Lysosomal Enzyme Phosphotransferase Are Encoded by a Single cDNA

2005 ◽  
Vol 280 (43) ◽  
pp. 36141-36149 ◽  
Author(s):  
Mariko Kudo ◽  
Ming Bao ◽  
Anil D'Souza ◽  
Fu Ying ◽  
Huaqin Pan ◽  
...  
Keyword(s):  
Amino Acid ◽  
Catalytic Domain ◽  
Amino Acid Sequences ◽  
Subunit Structure ◽  
Bac Clone ◽  
Significant Similarity ◽  
Α Subunit ◽  
Γ Subunit ◽  
Mannose 6 Phosphate ◽  
Α And Β Subunits

Lysosomal enzymes are targeted to the lysosome through binding to mannose 6-phosphate receptors because their glycans are modified with mannose 6-phosphate. This modification is catalyzed by UDP-N-acetylglucosamine:lysosomal enzyme N-acetylglucosamine-1-phosphotransferase (GlcNAc-phosphotransferase). Bovine GlcNAc-phosphotransferase was isolated using monoclonal antibody affinity chromatography, and an α2β2γ2-subunit structure was proposed. Although cDNA encoding the γ-subunit has been described, cDNAs for the α- and β-subunits have not. Using partial amino acid sequences from the bovine α- and β-subunits, we have isolated a human cDNA that encodes both the α- and β-subunits. Both subunits contain a single predicted membrane-spanning domain. The α- and β-subunits appear to be generated by a proteolytic cleavage at the Lys928-Asp929 bond. Transfection of 293T cells with the α/β-subunits-precursor cDNA with or without the γ-subunit cDNA results in a 3.6- or 17-fold increase in GlcNAc-phosphotransferase activity in cell lysates, suggesting that the precursor cDNA contains the catalytic domain. The sequence lacks significant similarity with any described vertebrate enzyme except for two Notch-like repeats in the α-subunit. However, a 112-amino acid sequence is highly similar to a group of bacterial capsular polymerases (46% identity). A BAC clone containing the gene that spanned 85.3 kb and was composed of 21 exons was sequenced and localized to chromosome 12q23. We now report the cloning of both the cDNA and genomic DNA of the precursor of Glc-NAc-phosphotransferase. The completion of cloning all three subunits of GlcNAc-phosphotransferase allows expression of recombinant enzyme and dissection of lysosomal targeting disorders.

scholarly journals A superfamily of Arabidopsis thaliana retrotransposons.

Genetics ◽  
1991 ◽  
Vol 127 (4) ◽  
pp. 801-809 ◽  
Author(s):  
A Konieczny ◽  
D F Voytas ◽  
M P Cummings ◽  
F M Ausubel
Keyword(s):  
Arabidopsis Thaliana ◽  
Amino Acid ◽  
Reverse Transcriptase ◽  
Amino Acid Identity ◽  
Rnase H ◽  
Amino Acid Sequences ◽  
Nucleotide Sequence Analysis ◽  
Degenerate Primers ◽  
Hybridization Probes ◽  
Polymerase Chain

Abstract We describe a superfamily of Arabidopsis thaliana retrotransposable elements that consists of at least ten related families designated Ta1-Ta10. The Ta1 family has been described previously. Two genomic clones representing the Ta2 and Ta3 elements were isolated from an A. thaliana (race Landsberg erecta) lambda library using sequences derived from the reverse transcriptase region of Ta1 as hybridization probes. Nucleotide sequence analysis showed that the Ta1, Ta2 and Ta3 families share greater than 75% amino acid identity in pairwise comparisons of their reverse transcriptase and RNase H genes. In addition to Ta1, Ta2 and Ta3, we identified seven other related retrotransposon families in Landsberg erecta, Ta4-Ta10, using degenerate primers and the polymerase chain reaction to amplify a highly conserved region of retrotransposon-encoded reverse transcriptase. One to two copies of elements Ta2-Ta10 are present in the genomes of the A. thaliana races Landsberg erecta and Columbia indicating that the superfamily comprises at least 0.1% of the A. thaliana genome. The nucleotide sequences of the reverse transcriptase regions of the ten element families place them in the category of copia-like retrotransposons and phylogenetic analysis of the amino acid sequences suggests that horizontal transfer may have played a role in their evolution.

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