Old versus new characters for systematics: Cautionary tales from virology

1990 ◽  
Vol 3 (1) ◽  
pp. 159
Author(s):  
A Gibbs ◽  
A Ding ◽  
J Howe ◽  
P Keese ◽  
A MacKenzie ◽  
...  
Keyword(s):  
Amino Acid ◽  
Genetic Recombination ◽  
Large Subunit ◽  
Molecular Taxonomy ◽  
Amino Acid Sequences ◽  
Sequence Information ◽  
Molecular Sequence ◽  
Taxonomic Methods ◽  
Cautionary Tales

Molecular sequence information about viruses has mostly confirmed the groupings devised by traditional taxonomic methods, but shown in addition that the genes of related species may differ in number, arrangement, orientation and in sequence homology. It has also revealed that true genetic recombination between viruses has been common, even among those with RNA genomes, indeed most virus groups seem to have arisen y recombination. Thus, there is an unexpected wealth of genetic chaos hidden behind the fatade of the phenotype, and it is possible that the difficulties that plant taxonomists have had in identifying the relationships of the major groupings of plants could have similar causes. Nonetheless, molecular taxonomy does give sensible results and this is illustrated by a classification of the large subunit Rubisco proteins of 21 plant species based on their amino acid sequences.

Molecular evolutionary analyses of the small and large subunits of ribulose-1,5-bisphosphate carboxylase/oxygenase

1992 ◽  
Vol 70 (4) ◽  
pp. 715-723 ◽  
Author(s):  
J. J. Pasternak ◽  
B. R. Glick
Keyword(s):  
Amino Acid ◽  
Molecular Evolution ◽  
Large Subunit ◽  
Distance Matrix ◽  
Small Subunit ◽  
Amino Acid Sequences ◽  
Sequence Information ◽  
Bisphosphate Carboxylase ◽  
Tree Building ◽  
Building Methods

The molecular evolution of the amino acid sequences of the mature small and large subunits of ribulose-1,5-bisphosphate carboxylase/oxygense (Rubisco) was determined. The dataset for each subunit consisted of sequences from 39 different taxa of which 22 are represented with sequence information for both subunits. Phylogenetic trees were reconstructed using distance matrix, parsimony and simultaneous alignment and phylogeny methods. For the small subunit, the latter two methods produced similar trees that differed from the topology of the distance matrix tree. For the large subunit, each of the three tree-building methods yielded a distinct tree. Except for the distance matrix small subunit tree, the tree-building methods produced topologies for the small and large subunit sequences from the nonflowering plant taxa that, for the most part, agree with current taxonomic schemes. With the full datasets, the lack of consistency both among the various trees and with conventional taxonomic relationships was most evident with the Rubisco sequences from angiosperms. It is unlikely that current tree-building methods will be able to reconstruct an unambiguous molecular evolution of either of the Rubisco subunits. Molecular trees, regardless of methodology, showed similar topologies for the small and large subunits from the 22 taxa from which both subunits have been sequenced, indicating that the subunits have changed to the same extent over time. In this case, similar trees were formed because only 4 of the 22 taxa were from dicots. Key words: ribulose-1,5-bisphosphate carboxylase/oxygenase, amino acid sequence, molecular evolution, phyletic trees.

scholarly journals Molecular Identification of Family 38 α-Mannosidase of Bacillus sp. Strain GL1, Responsible for Complete Depolymerization of Xanthan

2002 ◽  
Vol 68 (6) ◽  
pp. 2731-2736 ◽  
Author(s):  
Hirokazu Nankai ◽  
Wataru Hashimoto ◽  
Kousaku Murata
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Cell Extract ◽  
Amino Acid Sequences ◽  
Glycoside Hydrolase Family ◽  
Sequence Information ◽  
Reading Frame ◽  
A Cell ◽  
Terminal Amino ◽  
Amino Acid Sequence Information

ABSTRACT When cells of Bacillus sp. strain GL1 were grown in a medium containing xanthan as a carbon source, α-mannosidase exhibiting activity toward p-nitrophenyl-α-d-mannopyranoside (pNP-α-d-Man) was produced intracellularly. The 350-kDa α-mannosidase purified from a cell extract of the bacterium was a trimer comprising three identical subunits, each with a molecular mass of 110 kDa. The enzyme hydrolyzed pNP-α-d-Man (Km = 0.49 mM) and d-mannosyl-(α-1,3)-d-glucose most efficiently at pH 7.5 to 9.0, indicating that the enzyme catalyzes the last step of the xanthan depolymerization pathway of Bacillus sp. strain GL1. The gene for α-mannosidase cloned most by using N-terminal amino acid sequence information contained an open reading frame (3,144 bp) capable of coding for a polypeptide with a molecular weight of 119,239. The deduced amino acid sequence showed homology with the amino acid sequences of α-mannosidases belonging to glycoside hydrolase family 38.

scholarly journals cDNAs encoding the large subunit of human replication factor C

1993 ◽  
Vol 90 (23) ◽  
pp. 11014-11018 ◽  
Author(s):  
F Bunz ◽  
R Kobayashi ◽  
B Stillman
Keyword(s):  
Amino Acid ◽  
Large Subunit ◽  
Simian Virus 40 ◽  
Amino Acid Sequences ◽  
Binding Motif ◽  
Replication Factor C ◽  
Viral Origin ◽  
Replication Factor ◽  
Factor C

Replication factor C (RFC) is a multisubunit, DNA polymerase accessory protein required for the coordinated synthesis of both DNA strands during simian virus 40 DNA replication in vitro. Previous studies have shown that RFC is a DNA-dependent ATPase that binds in a structure-specific manner to the 3' end of a primer hybridized to a template DNA, an activity thought intrinsic to the 140-kDa component of this multisubunit complex. Here, the isolation and analysis of cDNAs encoding this subunit is described. Analysis of the full-length coding sequence revealed an open reading frame of 3.4 kb, encoding an 1148-amino acid protein with a predicted molecular mass of 130 kDa. A putative ATP-binding motif was observed that is similar to a motif in several of the smaller subunits of RFC and in functionally homologous replication factors of bacterial and viral origin. A "DEAD" box is also conserved among these proteins. The predicted protein shows significant identity with a DNA-binding protein of murine origin (B. Luckow, P. Lichter, and G. Schütz, personal communication). Regions of similarity were also seen between the amino acid sequences of the 140-kDa subunit of RFC, poly(ADP-ribose) polymerase, and bacterial DNA ligases--possibly representing a conserved structural feature of these proteins that bind similar DNA substrates.

A review of the damselfly genus Megalestes Selys, 1862 (Insecta: Odonata: Zygoptera: Synlestidae) using integrative taxonomic methods

Zootaxa ◽  
2020 ◽  
Vol 4851 (2) ◽  
pp. 245-270
Author(s):  
XIN YU ◽  
JUNLI XUE
Keyword(s):  
Species Diversity ◽  
Molecular Taxonomy ◽  
Species Number ◽  
Distance Analysis ◽  
Diversity Measure ◽  
Taxonomic Methods ◽  
Total Species ◽  
Genetic Distance Analysis ◽  
Molecular Characters

We used morphological and molecular characters to review the classification of damselflies in the genus Megalestes Selys, 1862 (Zygoptera: Odonata). Several methods were used for this review, including morphology, cladistics, genetic distance analysis, and molecular taxonomy. Six species were newly defined as junior synonyms (Megalestes palaceus to Megalestes haui, Megalestes chengi to Megalestes micans, Megalestes discus to Megalestes micans, Megalestes raychoudhurii to M. micans, Megalestes maai to Megalestes riccii, and Megalestes tuska to M. riccii). The total species number in Megalestes was reduced from 18 to 12. The importance of an objective species diversity measure is discussed. 

scholarly journals Consensus proposals for classification of the family Hepeviridae

2014 ◽  
Vol 95 (10) ◽  
pp. 2223-2232 ◽  
Author(s):  
Donald B. Smith ◽  
Peter Simmonds ◽  
Shahid Jameel ◽  
Suzanne U. Emerson ◽  
Tim J. Harrison ◽  
...  
Keyword(s):  
Mammalian Species ◽  
Cutthroat Trout ◽  
Hepatitis E ◽  
Amino Acid Sequences ◽  
Sequence Information ◽  
Virus Species ◽  
Wide Range ◽  
The Family ◽  
Novel Variants

The family Hepeviridae consists of positive-stranded RNA viruses that infect a wide range of mammalian species, as well as chickens and trout. A subset of these viruses infects humans and can cause a self-limiting acute hepatitis that may become chronic in immunosuppressed individuals. Current published descriptions of the taxonomical divisions within the family Hepeviridae are contradictory in relation to the assignment of species and genotypes. Through analysis of existing sequence information, we propose a taxonomic scheme in which the family is divided into the genera Orthohepevirus (all mammalian and avian hepatitis E virus (HEV) isolates) and Piscihepevirus (cutthroat trout virus). Species within the genus Orthohepevirus are designated Orthohepevirus A (isolates from human, pig, wild boar, deer, mongoose, rabbit and camel), Orthohepevirus B (isolates from chicken), Orthohepevirus C (isolates from rat, greater bandicoot, Asian musk shrew, ferret and mink) and Orthohepevirus D (isolates from bat). Proposals are also made for the designation of genotypes within the human and rat HEVs. This hierarchical system is congruent with hepevirus phylogeny, and the three classification levels (genus, species and genotype) are consistent with, and reflect discontinuities in the ranges of pairwise distances between amino acid sequences. Adoption of this system would include the avoidance of host names in taxonomic identifiers and provide a logical framework for the assignment of novel variants.

scholarly journals Functional classification of proteins based on projection of amino acid sequences: application for prediction of protein kinase substrates

2010 ◽  
Vol 11 (1) ◽  
Author(s):  
Boris Sobolev ◽  
Dmitry Filimonov ◽  
Alexey Lagunin ◽  
Alexey Zakharov ◽  
Olga Koborova ◽  
...  
Keyword(s):  
Amino Acid ◽  
Protein Kinase ◽  
Amino Acid Sequences ◽  
Functional Classification ◽  
Kinase Substrates

scholarly journals Cyclotides Isolated From Violet Plants of Cameroon Are Inhibitors of Human Prolyl Oligopeptidase

2021 ◽  
Vol 12 ◽  
Author(s):  
Jasmin Gattringer ◽  
Olivier Eteme Ndogo ◽  
Bernhard Retzl ◽  
Carina Ebermann ◽  
Christian W. Gruber ◽  
...  
Keyword(s):  
Amino Acid ◽  
De Novo ◽  
Folk Medicine ◽  
Amino Acid Sequences ◽  
Herbal Remedies ◽  
Phytochemical Analysis ◽  
Sequence Information ◽  
Prolyl Oligopeptidase ◽  
African Health ◽  
Peptide Family

Traditional medicine and the use of herbal remedies are well established in the African health care system. For instance, Violaceae plants are used for antimicrobial or anti-inflammatory applications in folk medicine. This study describes the phytochemical analysis and bioactivity screening of four species of the violet tribe Allexis found in Cameroon. Allexis cauliflora, Allexis obanensis, Allexis batangae and Allexis zygomorpha were evaluated for the expression of circular peptides (cyclotides) by mass spectrometry. The unique cyclic cystine-rich motif was identified in several peptides of all four species. Knowing that members of this peptide family are protease inhibitors, the plant extracts were evaluated for the inhibition of human prolyl oligopeptidase (POP). Since all four species inhibited POP activity, a bioactivity-guided fractionation approach was performed to isolate peptide inhibitors. These novel cyclotides, alca 1 and alca 2 exhibited IC50 values of 8.5 and 4.4 µM, respectively. To obtain their amino acid sequence information, combinatorial enzymatic proteolysis was performed. The proteolytic fragments were evaluated in MS/MS fragmentation experiments and the full-length amino acid sequences were obtained by de novo annotation of fragment ions. In summary, this study identified inhibitors of the human protease POP, which is a drug target for inflammatory or neurodegenerative disorders.

scholarly journals Bacterial lipolytic enzymes: classification and properties

1999 ◽  
Vol 343 (1) ◽  
pp. 177-183 ◽  
Author(s):  
Jean Louis ARPIGNY ◽  
Karl-Erich JAEGER
Keyword(s):  
Amino Acid ◽  
Structural Features ◽  
Biological Properties ◽  
Amino Acid Sequences ◽  
Important Class ◽  
Lipolytic Enzymes ◽  
Disulphide Bonds ◽  
Enzyme Families

Knowledge of bacterial lipolytic enzymes is increasing at a rapid and exciting rate. To obtain an overview of this industrially very important class of enzymes and their characteristics, we have collected and classified the information available from protein and nucleotide databases. Here we propose an updated and extensive classification of bacterial esterases and lipases based mainly on a comparison of their amino acid sequences and some fundamental biological properties. These new insights result in the identification of eight different families with the largest being further divided into six subfamilies. Moreover, the classification enables us to predict (1) important structural features such as residues forming the catalytic site or the presence of disulphide bonds, (2) types of secretion mechanism and requirement for lipase-specific foldases, and (3) the potential relationship to other enzyme families. This work will therefore contribute to a faster identification and to an easier characterization of novel bacterial lipolytic enzymes.

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