scholarly journals Characterization and Incidence of the First Member of the Genus Mitovirus Identified in the Phytopathogenic Species Fusarium oxysporum

Viruses ◽  
2020 ◽  
Vol 12 (3) ◽  
pp. 279 ◽  
Author(s):  
Almudena Torres-Trenas ◽  
Encarnación Pérez-Artés
Keyword(s):  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Genetic Code ◽  
Fusarium Oxysporum ◽  
Amino Acid Residues ◽  
Fusarium Spp ◽  
Stem Loop ◽  
Universal Genetic Code ◽  
The Family ◽  
Amino Acid Tryptophan

A novel mycovirus named Fusarium oxysporum f. sp. dianthi mitovirus 1 (FodMV1) has been identified infecting a strain of Fusarium oxysporum f. sp. dianthi from Colombia. The genome of FodMV1 is 2313 nt long, and comprises a 172-nt 5’-UTR, a 2025-nt single ORF encoding an RdRp of 675 amino acid residues, and a 113-nt 3´-UTR. Homology BlastX searches identifies FodMV1 as a novel member of the genus Mitovirus in the family Narnaviridae. As the rest of mitoviruses, the genome of FodMV1 presents a high percentage of A+U (58.8%) and contains a number of UGA codons that encode the amino acid tryptophan rather than acting as stop codons as in the universal genetic code. Another common feature with other mitoviruses is that the 5′- and 3′-UTR regions of FodMV1 can be folded into potentially stable stem-loop structures. Result from phylogenetic analysis place FodMV1 in a different clade than the rest of mitoviruses described in other Fusarium spp. Incidence of FodMV1-infections in the collection of F. oxysporum f. sp. dianthi isolates analyzed is relatively high. Of particular interest is the fact that FodMV1 has been detected infecting isolates from two geographical areas as distant as Spain and Colombia.

scholarly journals Taxonomic status of Bhanja and Kismayo viruses (family Bunyaviridae)

2012 ◽  
Vol 17 (4) ◽  
pp. 4-8
Author(s):  
A. S Klimentov ◽  
A. P Gmyl ◽  
A. M Butenko ◽  
L. V Gmyl ◽  
O. V Isaeva ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Nucleotide Sequence ◽  
Taxonomic Status ◽  
Amino Acid Sequences ◽  
The Family ◽  
L Segment

The nucleotide sequence of M= (1398 nucleotides and L= (6186 nucleotides) segments of the genome of Bhanja virus and L-segment (1297 nucleotides) of Kismayo virus has been partially determined. Phylogenetic analysis of deduced amino acid sequences showed that these viruses are novel members of the Flebovirus (Phlebovirus) genus in the family Bunyaviridae

Structure of the genetic code suggested by the hydropathy correlation between anticodons and amino acid residues

2006 ◽  
Vol 37 (1) ◽  
pp. 83-103 ◽  
Author(s):  
Sávio Torres de Farias ◽  
Carlos Henrique Costa Moreira ◽  
Romeu Cardoso Guimarães
Keyword(s):  
Amino Acid ◽  
Genetic Code ◽  
Amino Acid Residues

scholarly journals Peptidase E, a Peptidase Specific for N-Terminal Aspartic Dipeptides, Is a Serine Hydrolase

2000 ◽  
Vol 182 (9) ◽  
pp. 2536-2543 ◽  
Author(s):  
Rachel A. L. Lassy ◽  
Charles G. Miller
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Site Directed Mutagenesis ◽  
Amino Acid Residues ◽  
Serine Hydrolase ◽  
Genome Sequences ◽  
New Family ◽  
The Family ◽  
Serovar Typhimurium ◽  
Structural Classes

ABSTRACT Salmonella enterica serovar Typhimurium peptidase E (PepE) is an N-terminal Asp-specific dipeptidase. PepE is not inhibited by any of the classical peptidase inhibitors, and its amino acid sequence does not place it in any of the known peptidase structural classes. A comparison of the amino acid sequence of PepE with a number of related sequences has allowed us to define the amino acid residues that are strongly conserved in this family. To ensure the validity of this comparison, we have expressed one of the most distantly related relatives (Xenopus) in Escherichia coli and have shown that it is indeed an Asp-specific dipeptidase with properties very similar to those of serovar Typhimurium PepE. The sequence comparison suggests that PepE is a serine hydrolase. We have used site-directed mutagenesis to change all of the conserved Ser, His, and Asp residues and have found that Ser120, His157, and Asp135 are all required for activity. Conversion of Ser120 to Cys leads to severely reduced (104-fold) but still detectable activity, and this activity but not that of the parent is inhibited by thiol reagents; these results confirm that this residue is likely to be the catalytic nucleophile. These results suggest that PepE is the prototype of a new family of serine peptidases. The phylogenetic distribution of the family is unusual, since representatives are found in eubacteria, an insect (Drosophila), and a vertebrate (Xenopus) but not in the Archaea or in any of the other eukaryotes for which genome sequences are available.

scholarly journals A Novel Function of the MA-3 Domains in Transformation and Translation Suppressor Pdcd4 Is Essential for Its Binding to Eukaryotic Translation Initiation Factor 4A

2004 ◽  
Vol 24 (9) ◽  
pp. 3894-3906 ◽  
Author(s):  
Hsin-Sheng Yang ◽  
Myung-Haing Cho ◽  
Halina Zakowicz ◽  
Glenn Hegamyer ◽  
Nahum Sonenberg ◽  
...  
Keyword(s):  
Amino Acid ◽  
Translation Initiation ◽  
Binding Activity ◽  
Translation Initiation Factor ◽  
Initiation Factor ◽  
Amino Acid Residues ◽  
Eukaryotic Translation Initiation Factor ◽  
Stem Loop ◽  
Eukaryotic Translation ◽  
Eukaryotic Translation Initiation

ABSTRACT Αn α-helical MA-3 domain appears in several translation initiation factors, including human eukaryotic translation initiation factor 4G (eIF4G) and DAP-5/NAT1/p97, as well as in the tumor suppressor Pdcd4. The function of the MA-3 domain is, however, unknown. C-terminal eIF4G (eIG4Gc) contains an MA-3 domain that is located within the eIF4A-binding region, suggesting a role for eIF4A binding. Interestingly, C-terminal DAP-5/NAT1/p97 contains an MA-3 domain, but it does not bind to eIF4A. Mutation of amino acid residues conserved between Pdcd4 and eIF4Gc but not in DAP-5/NAT1/p97 to the amino acid residues found in the DAP-5/NAT1/p97 indicates that some of these amino acid residues within the MA-3 domain are critical for eIF4A-binding activity. Six Pdcd4 mutants (Pdcd4E249K, Pdcd4D253A, Pdcd4D414K, Pdcd4D418A, Pdcd4E249K,D414K, and Pdcd4D253A,D418A) lost >90% eIF4A-binding activity. Mutation of the corresponding amino acid residues in the eIF4Gc also produced similar results, as seen for Pdcd4. These results demonstrate that the MA-3 domain is important for eIF4A binding and explain the ability of Pdcd4 or eIF4Gc but not DAP-5/NAT1/p97 to bind to eIF4A. Competition experiments indicate that Pdcd4 prevents ca. 60 to 70% of eIF4A binding to eIF4Gc at a Pdcd4/eIF4A ratio of 1:1, but mutants Pdcd4D253A and Pdcd4D253A,D418A do not. Translation of stem-loop structured mRNA is susceptible to inhibition by wild-type Pdcd4 but not by Pdcd4D253A, Pdcd4D418A, or Pdcd4D235A,D418A. Together, these results indicate that not only binding to eIF4A but also prevention of eIF4A binding to the MA-3 domain of eIF4Gc contributes to the mechanism by which Pdcd4 inhibits translation.

scholarly journals Identification of isoforms of the exocytosis-sensitive phosphoprotein PP63/parafusin in Paramecium tetraurelia and demonstration of phosphoglucomutase activity

1997 ◽  
Vol 323 (1) ◽  
pp. 289-296 ◽  
Author(s):  
Karin HAUSER ◽  
Roland KISSMEHL ◽  
Jürgen LINDER ◽  
Jochen E. SCHULTZ ◽  
Friedrich LOTTSPEICH ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Genetic Code ◽  
Polyclonal Antibodies ◽  
Amino Acid Sequences ◽  
Paramecium Tetraurelia ◽  
Universal Genetic Code ◽  
Chicken Muscle ◽  
Similarity Searches ◽  
Different Sources

PP63 (parafusin) is a 63 kDa phosphoprotein which is very rapidly (within 80 ms) dephosphorylated (to P63) during triggered trichocyst exocytosis; this occurs selectively in exocytosis-competent Paramecium tetraurelia strains. In the present work, two cDNAs coding for PP63/parafusin have been isolated, one of which is a new isoform. These isoforms are 99.6% identical and are derived from two different genes. Similarity searches revealed 43-51% identity of the deduced amino acid sequences with known phosphoglucomutases from yeast and mammals. The sequences of two proteolytic peptides obtained from PP63/parafusin isolated from Paramecium are identical to parts of the amino acid sequence deduced from the major cDNA. The major cDNA was mutated from the macronuclear ciliate genetic code into the universal genetic code and expressed in Escherichia coli. The recombinant protein shows the same biochemical and immunological characteristics as the (P)P63/parafusin originally isolated from Paramecium. It has the same specific phosphoglucomutase activity as phosphoglucomutase from chicken muscle. We also show that recombinant P63-1/parafusin 1 is a substrate of an endogenous casein kinase from Paramecium, as is the originally isolated P63/parafusin. Polyclonal antibodies against recombinant P63-1/parafusin 1 were raised which recognized phosphoglucomutases from different sources. Thus we show that PP63/parafusin and phosphoglucomutase in Paramecium are identical.

scholarly journals Expression and distribution of synaptotagmin isoforms in the zebrafish retina

2020 ◽  
Author(s):  
Diane Henry ◽  
Christina Joselevitch ◽  
Gary G. Matthews ◽  
Lonnie P. Wollmuth
Keyword(s):  
Amino Acid ◽  
Large Family ◽  
Amino Acid Residues ◽  
Ribbon Synapses ◽  
The Family ◽  
Class 1 ◽  
The Central Nervous System ◽  
Asynchronous Release ◽  
The Brain

ABSTRACTSynaptotagmins belong to a large family of proteins. While various synaptotagmins have been implicated as Ca2+ sensors for vesicle replenishment and release at conventional synapses, their roles at retinal ribbon synapses remain incompletely understood. Zebrafish is a widely used experimental model for retinal research. We therefore investigated the homology between human, rat, mouse, and zebrafish synaptotagmins 1 to 10 using a bioinformatics approach. We also characterized the expression and distribution of various synaptotagmin (syt) genes in the zebrafish retina using RT-PCR and in situ hybridization, focusing on the family members whose products likely underlie Ca2+-dependent exocytosis in the central nervous system (synaptotagmins 1, 2, 5 and 7). We find that most zebrafish synaptotagmins are well conserved and can be grouped in the same classes as mammalian synaptotagmins, based on crucial amino acid residues needed for coordinating Ca2+ binding and determining phospholipid binding affinity. The only exception is synaptotagmin 1b, which lacks 34 amino acid residues in the C2B domain and is therefore unlikely to bind Ca2+ there. Additionally, the products of zebrafish syt5a and syt5b genes share identity with mammalian class 1 and 5 synaptotagmins. Zebrafish syt1, syt2, syt5 and syt7 paralogues are found in the zebrafish brain, eye, and retina, excepting syt1b, which is only present in the brain. The complementary expression pattern of the remaining paralogues in the retina suggests that syt1a and syt5a may underlie synchronous release and syt7a and syt7b may mediate asynchronous release or other Ca2+ dependent processes in different types of retinal neurons.

scholarly journals Pool of endoglucanase genes in Schizophyllum commune Fr.:Fr. (Basidiomycetes) on the territory of Ukraine

2018 ◽  
Vol 62 (1) ◽  
pp. 53-59 ◽  
Author(s):  
Sergiy M. Boiko
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Polymorphic Locus ◽  
Schizophyllum Commune ◽  
Amino Acid Residues ◽  
The Family

Pool of intracellular endoglucanases of the fungus Schizophyllum commune on the territory of Ukraine was studied. Two loci of endoglucanase (Eg1, Eg2) were found. The polymorphic locus Eg2 controls the expression of four alleles. Alleles Eg293, Eg296 and Eg2102 are rare and peculiar to certain populations. Amino acid sequence of the locus Eg2 in databases of NCBI (XP_003031634.1) and UniProt (D8Q439) was probably identified. It is classified among the family 5 (GH5) and consists of 333 amino acid residues.

scholarly journals The amino acid sequence and position of the free thiol group of a short-chain neurotoxin from common-death-adder (Acanthophis antarcticus) venom

1981 ◽  
Vol 199 (1) ◽  
pp. 211-218 ◽  
Author(s):  
H S Kim ◽  
N Tamiya
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Lethal Dose ◽  
Thiol Group ◽  
Cysteine Residue ◽  
Short Chain ◽  
Amino Acid Residues ◽  
The Family ◽  
Free Thiol Group ◽  
The Common

The amino acid sequence of a short-chain neurotoxin Acanthophis antarcticus c (toxin Aa c) from the venom of an Australian elapid snake, the common death adder (Acanthophis antarcticus, subfamily Acanthophiinae) was elucidated. Toxin Aa c is composed of 62 amino acid residues, including eight half-cystine residues and a cysteine residue. The amino acid sequence of toxin Aa c is homologous with those of other short-chain neurotoxins found in snakes of the family Elapidae, especially with those from snakes of the subfamily Hydrophiinae. The single cysteine residue was located in position 4. Toxin Aa c has a lethal dose (LD50) of 0.08 micrograms/g body weight of mouse on intramuscular injection.

scholarly journals Modern diversification of the amino acid repertoire driven by oxygen

2017 ◽  
Vol 115 (1) ◽  
pp. 41-46 ◽  
Author(s):  
Matthias Granold ◽  
Parvana Hajieva ◽  
Monica Ioana Toşa ◽  
Florin-Dan Irimie ◽  
Bernd Moosmann
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Genetic Code ◽  
Chemical Reactivity ◽  
Protein Biosynthesis ◽  
Building Blocks ◽  
Peroxyl Radicals ◽  
Basis Set ◽  
Universal Genetic Code ◽  
Amino Acid Properties

All extant life employs the same 20 amino acids for protein biosynthesis. Studies on the number of amino acids necessary to produce a foldable and catalytically active polypeptide have shown that a basis set of 7–13 amino acids is sufficient to build major structural elements of modern proteins. Hence, the reasons for the evolutionary selection of the current 20 amino acids out of a much larger available pool have remained elusive. Here, we have analyzed the quantum chemistry of all proteinogenic and various prebiotic amino acids. We find that the energetic HOMO–LUMO gap, a correlate of chemical reactivity, becomes incrementally closer in modern amino acids, reaching the level of specialized redox cofactors in the late amino acids tryptophan and selenocysteine. We show that the arising prediction of a higher reactivity of the more recently added amino acids is correct as regards various free radicals, particularly oxygen-derived peroxyl radicals. Moreover, we demonstrate an immediate survival benefit conferred by the enhanced redox reactivity of the modern amino acids tyrosine and tryptophan in oxidatively stressed cells. Our data indicate that in demanding building blocks with more versatile redox chemistry, biospheric molecular oxygen triggered the selective fixation of the last amino acids in the genetic code. Thus, functional rather than structural amino acid properties were decisive during the finalization of the universal genetic code.

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