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 Roles of the C-Terminal Amino Acids of Non-Hexameric Helicases: Insights from Escherichia coli UvrD

2021 ◽  
Vol 22 (3) ◽  
pp. 1018
Author(s):  
Hiroaki Yokota
Keyword(s):  
Escherichia Coli ◽  
Amino Acids ◽  
Amino Acid ◽  
Single Molecule ◽  
Underlying Mechanism ◽  
Amino Acid Sequences ◽  
E Coli ◽  
X Ray Crystallography ◽  
Terminal Amino

Helicases are nucleic acid-unwinding enzymes that are involved in the maintenance of genome integrity. Several parts of the amino acid sequences of helicases are very similar, and these quite well-conserved amino acid sequences are termed “helicase motifs”. Previous studies by X-ray crystallography and single-molecule measurements have suggested a common underlying mechanism for their function. These studies indicate the role of the helicase motifs in unwinding nucleic acids. In contrast, the sequence and length of the C-terminal amino acids of helicases are highly variable. In this paper, I review past and recent studies that proposed helicase mechanisms and studies that investigated the roles of the C-terminal amino acids on helicase and dimerization activities, primarily on the non-hexermeric Escherichia coli (E. coli) UvrD helicase. Then, I center on my recent study of single-molecule direct visualization of a UvrD mutant lacking the C-terminal 40 amino acids (UvrDΔ40C) used in studies proposing the monomer helicase model. The study demonstrated that multiple UvrDΔ40C molecules jointly participated in DNA unwinding, presumably by forming an oligomer. Thus, the single-molecule observation addressed how the C-terminal amino acids affect the number of helicases bound to DNA, oligomerization, and unwinding activity, which can be applied to other helicases.

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 Viral Vascular Endothelial Growth Factor Plays a Critical Role in Orf Virus Infection

2000 ◽  
Vol 74 (22) ◽  
pp. 10699-10706 ◽  
Author(s):  
Loreen J. Savory ◽  
Steven A. Stacker ◽  
Stephen B. Fleming ◽  
Brian E. Niven ◽  
Andrew A. Mercer
Keyword(s):  
Vascular Endothelial Growth Factor ◽  
Growth Factor ◽  
Virus Infection ◽  
Vascular Endothelial Cells ◽  
Critical Role ◽  
Skin Lesions ◽  
Orf Virus ◽  
Vegf Receptor ◽  
Vascular Endothelial ◽  
Endothelial Growth Factor

ABSTRACT Infection by the parapoxvirus orf virus causes proliferative skin lesions in which extensive capillary proliferation and dilation are prominent histological features. This infective phenotype may be linked to a unique virus-encoded factor, a distinctive new member of the vascular endothelial growth factor (VEGF) family of molecules. We constructed a recombinant orf virus in which the VEGF-like gene was disrupted and show that inactivation of this gene resulted in the loss of three VEGF activities expressed by the parent virus: mitogenesis of vascular endothelial cells, induction of vascular permeability, and activation of VEGF receptor 2. We used the recombinant orf virus to assess the contribution of the viral VEGF to the vascular response seen during orf virus infection of skin. Our results demonstrate that the viral VEGF, while recognizing a unique profile of the known VEGF receptors (receptor 2 and neuropilin 1), is able to stimulate a striking proliferation of blood vessels in the dermis underlying the site of infection. Furthermore, the data demonstrate that the viral VEGF participates in promoting a distinctive pattern of epidermal proliferation. Loss of a functional viral VEGF resulted in lesions with markedly reduced clinical indications of infection. However, viral replication in the early stages of infection was not impaired, and only at later times did it appear that replication of the recombinant virus might be reduced.

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 Bovine papular stomatitis virus encodes a functionally distinct VEGF that binds both VEGFR-1 and VEGFR-2

2007 ◽  
Vol 88 (3) ◽  
pp. 781-791 ◽  
Author(s):  
Marie K. Inder ◽  
Norihito Ueda ◽  
Andrew A. Mercer ◽  
Stephen B. Fleming ◽  
Lyn M. Wise
Keyword(s):  
Cell Function ◽  
Amino Acid Identity ◽  
Biologically Active ◽  
The Other ◽  
Active Member ◽  
Vegf Receptor ◽  
Vascular Endothelial ◽  
Monocyte Migration ◽  
Bovine Papular Stomatitis Virus ◽  
Endothelial Growth Factor

Bovine papular stomatitis virus (BPSV), a member of the genus Parapoxvirus, causes proliferative dermatitis in cattle and humans. Other species of the genus cause similar lesions, the nature of which has been attributed, at least in part, to a viral-encoded vascular endothelial growth factor (VEGF) that induces vascularization and dermal oedema through VEGF receptor-2 (VEGFR-2). The results of this study showed that BPSV strain V660 encodes a novel VEGF and that the predicted BPSV protein showed only 33–52 % amino acid identity to VEGFs encoded by the other species of the genus. BPSV VEGF showed higher identity to mammalian VEGF-A (51 %) than the other parapoxviral VEGFs (31–46 %). Assays of the purified BPSV VEGF (BPSVV660VEGF) demonstrated that it was also functionally more similar to VEGF-A, as it showed significant binding to VEGFR-1 and induced monocyte migration. Like VEGF-A and the other viral VEGFs, BPSVV660VEGF bound VEGFR-2 with high affinity. Sequence analysis and structural modelling of BPSVV660VEGF revealed specific residues, outside the known receptor-binding face, that are predicted either to influence VEGF structure or to mediate binding directly to the VEGFRs. These results indicate that BPSVV660VEGF is a biologically active member of the VEGF family and that, via its interaction with VEGFR-2, it is likely to contribute to the proliferative and highly vascularized nature of BPSV lesions. This is also the first example of a viral VEGF acting via VEGFR-1 and influencing haematopoietic cell function. These data suggest that BPSVV660VEGF is an evolutionary and functional intermediate between VEGF-A and the other parapoxviral VEGFs.

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 Galactan-binding antibodies. Diversity and structure of idiotypes.

1983 ◽  
Vol 158 (5) ◽  
pp. 1385-1400 ◽  
Author(s):  
S Rudikoff ◽  
M Pawlita ◽  
J Pumphrey ◽  
E Mushinski ◽  
M Potter
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Molecular Basis ◽  
Sequence Variation ◽  
Amino Acid Sequences ◽  
Repair Enzymes ◽  
Nucleotide Addition ◽  
Recombination Processes ◽  
Strong Homology ◽  
Primary Amino

A group of eight IgM hybridoma proteins induced with beta(1,6)-D-galactan-containing antigens has been characterized in terms of primary amino acid sequence and idiotype expression. The H chain amino acid sequences reveal very strong homology in the VH segment although several substitutions are seen that suggest the occurrence of somatic mutation in these IgM molecules. Significant sequence variation was observed in CDR-3, the region generated by the D segment, and the two recombination events, VH-D and D-JH. The number of amino acids in this region contributed by the D segment was found to vary from two to six, yet the overall length of CDR-3 was precisely maintained by the addition of amino acids on either side of D during the recombination processes. These additional amino acids are suggested to result from nucleotide addition by repair enzymes. Idiotypic analysis of these proteins, in conjunction with an assessment of the H chain sequences, has permitted an identification of the molecular basis of both cross-reacting and unique idiotypic determinants expressed by these molecules.

Synopses from the poster exhibition organized by I. M. Kerr, 1. Interferon: a tertiary structure predicted from amino acid sequences

1982 ◽  
Vol 299 (1094) ◽  
pp. 125-127 ◽  
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Tertiary Structure ◽  
Three Dimensional ◽  
Amino Acid Sequences ◽  
Dimensional Structure ◽  
X Ray ◽  
Three Dimensional Structure ◽  
X Ray Crystallography ◽  
Functional Studies

Functional studies on interferon would be helped by a three-dimensional structure for the molecule. However, it may be several years before the structure of the protein is determined by X-ray crystallography. We have therefore used available methods for predicting the secondary - and the tertiary - structure of a protein from its amino acid sequence to propose a tertiary model involving the packing of four a-helices. Details of this work have been published elsewhere (Sternberg & Cohen 1982).

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.

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