scholarly journals Arguments Reinforcing the Three-Domain View of Diversified Cellular Life

Archaea ◽  
2016 ◽  
Vol 2016 ◽  
pp. 1-11 ◽  
Author(s):  
Arshan Nasir ◽  
Kyung Mo Kim ◽  
Violette Da Cunha ◽  
Gustavo Caetano-Anollés
Keyword(s):  
Cell Movement ◽  
Protein Domain ◽  
Bacterial Cells ◽  
Domain Structures ◽  
Cellular Life ◽  
Protein Domain Structure ◽  
Gain Loss ◽  
Cellular Compartments ◽  
Origin Of Eukaryotes ◽  
Archaeal Ancestor

The archaeal ancestor scenario (AAS) for the origin of eukaryotes implies the emergence of a new kind of organism from the fusion of ancestral archaeal and bacterial cells. Equipped with this “chimeric” molecular arsenal, the resulting cell would gradually accumulate unique genes and develop the complex molecular machineries and cellular compartments that are hallmarks of modern eukaryotes. In this regard, proteins related to phagocytosis and cell movement should be present in the archaeal ancestor, thus identifying the recently described candidate archaeal phylum “Lokiarchaeota” as resembling a possible candidate ancestor of eukaryotes. Despite its appeal, AAS seems incompatible with the genomic, molecular, and biochemical differences that exist between Archaea and Eukarya. In particular, the distribution of conserved protein domain structures in the proteomes of cellular organisms and viruses appears hard to reconcile with the AAS. In addition, concerns related to taxon and character sampling, presupposing bacterial outgroups in phylogenies, and nonuniform effects of protein domain structure rearrangement and gain/loss in concatenated alignments of protein sequences cast further doubt on AAS-supporting phylogenies. Here, we evaluate AAS against the traditional “three-domain” world of cellular organisms and propose that the discovery of Lokiarchaeota could be better reconciled under the latter view, especially in light of several additional biological and technical considerations.

scholarly journals Genome-Wide Identification and Comparative Analysis of MYB Transcription Factor Family in Musa acuminata and Musa balbisiana

Plants ◽  
2020 ◽  
Vol 9 (4) ◽  
pp. 413
Author(s):  
Lin Tan ◽  
Usman Ijaz ◽  
Haron Salih ◽  
Zhihao Cheng ◽  
Nwe Ni Win Htet ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Expression Patterns ◽  
Musa Acuminata ◽  
Protein Domain ◽  
Myb Transcription Factor ◽  
Segmental Duplications ◽  
Musa Balbisiana ◽  
Functional Studies ◽  
Myb Genes ◽  
Gain Loss

MYB transcription factors (TFs) make up one of the most important TF families in plants. These proteins play crucial roles in processes related to development, metabolism, and stimulus-response; however, very few studies have been reported for the characterization of MYB TFs from banana. The current study identified 305 and 251 MYB genes from Musa acuminata and Musa balbisiana, respectively. Comprehensive details of MYBs are reported in terms of gene structure, protein domain, chromosomal localization, phylogeny, and expression patterns. Based on the exon–intron arrangement, these genes were classified into 12 gene models. Phylogenetic analysis of MYBs involving both species of banana, Oryza sativa, and Arabidopsis thaliana distributed these genes into 27 subfamilies. This highlighted not only the conservation, but also the gain/loss of MYBs in banana. Such genes are important candidates for future functional investigations. The MYB genes in both species exhibited a random distribution on chromosomes with variable densities. Estimation of gene duplication events revealed that segmental duplications represented the major factor behind MYB gene family expansion in banana. Expression profiles of MYB genes were also explored for their potential involvement in acetylene response or development. Collectively, the current comprehensive analysis of MYB genes in both species of banana will facilitate future functional studies.

scholarly journals An Algebro-Topological Description of Protein Domain Structure

PLoS ONE ◽  
2011 ◽  
Vol 6 (5) ◽  
pp. e19670 ◽  
Author(s):  
Robert Clark Penner ◽  
Michael Knudsen ◽  
Carsten Wiuf ◽  
Jørgen Ellegaard Andersen
Keyword(s):  
Domain Structure ◽  
Protein Domain ◽  
Topological Description ◽  
Protein Domain Structure

The PRIDE server for protein three-dimensional similarity

2002 ◽  
Vol 35 (5) ◽  
pp. 648-649 ◽  
Author(s):  
Kristian Vlahovicek ◽  
Oliviero Carugo ◽  
Sándor Pongor
Keyword(s):  
Similarity Search ◽  
Three Dimensional ◽  
Pairwise Comparison ◽  
Distance Matrix ◽  
Data Bank ◽  
Protein Domain ◽  
Distance Distributions ◽  
Protein Domain Structure ◽  
Structural Clustering ◽  
Structure Query

The PRIDE server is an implementation of thePRIDEalgorithm that compares protein three-dimensional structures in terms of their Cαdistance distributions. In response to queries presented as single or concatenated Protein Data Bank (PDB) files, the server can carry out (i) a pairwise comparison of two protein three-dimensional structures, (ii) a structural clustering of protein three-dimensional structures, providing a distance matrix and a dendrogram as an output; and (iii) a similarity search with a protein domain structure query against the CATH database.

scholarly journals Diversity of Fungal DNA Methyltransferases and Their Association With DNA Methylation Patterns

2021 ◽  
Vol 11 ◽  
Author(s):  
Yu-Shin Nai ◽  
Yu-Chun Huang ◽  
Ming-Ren Yen ◽  
Pao-Yang Chen
Keyword(s):  
Dna Methylation ◽  
Life Stage ◽  
Dna Methyltransferases ◽  
Fungal Species ◽  
Protein Domain ◽  
Domain Structures ◽  
Genome Wide ◽  
Fungal Dna ◽  
Fungal Genomes ◽  
Methylation Patterns

DNA methyltransferases (DNMTs) are a group of proteins that catalyze DNA methylation by transferring a methyl group to DNA. The genetic variation in DNMTs results in differential DNA methylation patterns associated with various biological processes. In fungal species, DNMTs and their DNA methylation profiles were found to be very diverse and have gained many research interests. We reviewed fungal DNMTs in terms of their biological functions, protein domain structures, and their associated epigenetic regulations compared to those known in plant and animal systems. In addition, we summarized recent reports on potential RNA-directed DNA methylation (RdDM) related to DNMT5 in fungi. We surveyed up to 40 fungal species with published genome-wide DNA methylation profiles (methylomes) and presented the associations between the specific patterns of fungal DNA methylation and their DNMTs based on a phylogenetic tree of protein domain structures. For example, the main DNMTs in Basidiomycota, DNMT1 with RFD domain + DNMT5, contributing to CG methylation preference, were distinct from RID + Dim-2 in Ascomycota, resulting in a non-CG methylation preference. Lastly, we revealed that the dynamic methylation involved in fungal life stage changes was particularly low in mycelium and DNA methylation was preferentially located in transposable elements (TEs). This review comprehensively discussed fungal DNMTs and methylomes and their connection with fungal development and taxonomy to present the diverse usages of DNA methylation in fungal genomes.

scholarly journals Eliminating redundancy among protein sequences using submodular optimization

2016 ◽  
Author(s):  
Maxwell W. Libbrecht ◽  
Jeffrey A. Bilmes ◽  
William Stafford Noble
Keyword(s):  
Protein Sequence ◽  
Sequence Data ◽  
Structural Diversity ◽  
Discrete Analogue ◽  
Protein Domain ◽  
Great Success ◽  
Optimization Approach ◽  
Clustering Methods ◽  
Submodular Optimization ◽  
Domain Structures

AbstactMotivationSubmodular optimization, a discrete analogue to continuous convex optimization, has been used with great success in many fields but is not yet widely used in biology. We apply submodular optimization to the problem of removing redundancy in protein sequence data sets. This is a common step in many bioinformatics and structural biology workflows, including creation of non-redundant training sets for sequence and structural models as well as selection of “operational taxonomic units” from metagenomics data.ResultsWe demonstrate that the submodular optimization approach results in representative protein sequence subsets with greater structural diversity than sets chosen by existing methods. In particular, we compare to a widely used, heuristic algorithm implemented in software tools such as CD-HIT, as well to as a variety of standard clustering methods, using as a gold standard the SCOPe library of protein domain structures. In this setting, submodular optimization consistently yields protein sequence subsets that include more SCOPe domain families than sets of the same size selected by competing approaches. We also show how the optimization framework allows us to design a mixture objective function that performs well for both large and small representative sets. The framework we describe is theoretically optimal under some assumptions, and it is flexible and intuitive because it applies generic methods to optimize one of a variety of objective functions. This application serves as a model for how submodular optimization can be applied to other discrete problems in biology.AvailabilitySource code is available athttps://github.com/mlibbrecht/[email protected]

Protein domain structure influences observed distribution of mutation

1988 ◽  
Vol 208 (2) ◽  
pp. 105-108 ◽  
Author(s):  
Alasdair J.E. Gordon ◽  
Barry W. Glickman
Keyword(s):  
Domain Structure ◽  
Protein Domain ◽  
Protein Domain Structure
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