scholarly journals Correction to: Testing assembly strategies of Francisella tularensis genomes to infer an evolutionary conservation analysis of genomic structures

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Kerstin Neubert ◽  
Eric Zuchantke ◽  
Robert Maximilian Leidenfrost ◽  
Röbbe Wünschiers ◽  
Josephine Grützke ◽  
...  
Keyword(s):  
Francisella Tularensis ◽  
Evolutionary Conservation ◽  
Conservation Analysis ◽  
Testing Assembly

scholarly journals Testing assembly strategies of Francisella tularensis genomes to infer an evolutionary conservation analysis of genomic structures

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Kerstin Neubert ◽  
Eric Zuchantke ◽  
Robert Maximilian Leidenfrost ◽  
Roebbe Wuenschiers ◽  
Josephine Grützke ◽  
...  
Keyword(s):  
Francisella Tularensis ◽  
High Throughput Sequencing ◽  
Genomic Structure ◽  
Evolutionary Conservation ◽  
Pathogenicity Islands ◽  
Insertion Sequences ◽  
Hybrid Assembly ◽  
Short Read ◽  
Conservation Analysis ◽  
Long Read

Abstract Background We benchmarked sequencing technology and assembly strategies for short-read, long-read, and hybrid assemblers in respect to correctness, contiguity, and completeness of assemblies in genomes of Francisella tularensis. Benchmarking allowed in-depth analyses of genomic structures of the Francisella pathogenicity islands and insertion sequences. Five major high-throughput sequencing technologies were applied, including next-generation “short-read” and third-generation “long-read” sequencing methods. Results We focused on short-read assemblers, hybrid assemblers, and analysis of the genomic structure with particular emphasis on insertion sequences and the Francisella pathogenicity island. The A5-miseq pipeline performed best for MiSeq data, Mira for Ion Torrent data, and ABySS for HiSeq data from eight short-read assembly methods. Two approaches were applied to benchmark long-read and hybrid assembly strategies: long-read-first assembly followed by correction with short reads (Canu/Pilon, Flye/Pilon) and short-read-first assembly along with scaffolding based on long reads (Unicyler, SPAdes). Hybrid assembly can resolve large repetitive regions best with a “long-read first” approach. Conclusions Genomic structures of the Francisella pathogenicity islands frequently showed misassembly. Insertion sequences (IS) could be used to perform an evolutionary conservation analysis. A phylogenetic structure of insertion sequences and the evolution within the clades elucidated the clade structure of the highly conservative F. tularensis.

Mouse Beta-Mannosidase: cDNA Cloning, Expression, and Chromosomal Localization

2001 ◽  
Vol 21 (3) ◽  
pp. 315-323 ◽  
Author(s):  
Tommaso Beccari ◽  
Lucia Bibi ◽  
Sofia Stinchi ◽  
John Laing Stirling ◽  
Aldo Orlacchio
Keyword(s):  
Chromosomal Localization ◽  
Human Gene ◽  
Evolutionary Conservation ◽  
Northern Blotting ◽  
Northern Analysis ◽  
Gene Encoding ◽  
Lysosomal Disorder ◽  
Conservation Analysis ◽  
High Degree ◽  
Differential Tissue

β-mannosidase is an exoglycosidase involved in the degradation of N-linked oligosacharides moieties of glycoproteins. Lack of β-mannosidase activity leads to the lysosomal disorder β-mannosidosis (MIM 248510). We have isolated and sequenced the gene encoding the mouse β-mannosidase. Comparison of the deduced amino acid sequence of mouse, human, bovine, and goat β-mannosidase showed 64% identity, reflecting a high degree of evolutionary conservation. Analysis of a multiple tissue northern blotting revealed a major transcript of about 3.7 kb in all tissues examined. The northern analysis also demonstrates that there is differential tissue mRNA expression. The mouse β-mannosidase gene (Bmn) was mapped to the distal end of Chromosome (Chr) 3, in a region that is homologous with a segment of human Chr 4 containing the orthologous human gene.

scholarly journals Molecular dynamics and protein frustration analysis of human fused in Sarcoma protein variants in Amyotrophic Lateral Sclerosis type 6: An In Silico approach

PLoS ONE ◽  
2021 ◽  
Vol 16 (9) ◽  
pp. e0258061
Author(s):  
L. F. S. Bonet ◽  
J. P. Loureiro ◽  
G. R. C. Pereira ◽  
A. N. R. Da Silva ◽  
J. F. De Mesquita
Keyword(s):  
Molecular Dynamics ◽  
Amyotrophic Lateral Sclerosis ◽  
Protein Stability ◽  
Motor Neurons ◽  
Evolutionary Conservation ◽  
Nucleotide Polymorphisms ◽  
Conservation Analysis ◽  
Prediction Algorithms ◽  
Fused In Sarcoma ◽  
Lateral Sclerosis

Amyotrophic lateral sclerosis (ALS) is the most frequent adult-onset motor neuron disorder. The disease is characterized by degeneration of upper and lower motor neurons, leading to death usually within five years after the onset of symptoms. While most cases are sporadic, 5%-10% of cases can be associated with familial inheritance, including ALS type 6, which is associated with mutations in the Fused in Sarcoma (FUS) gene. This work aimed to evaluate how the most frequent ALS-related mutations in FUS, R521C, R521H, and P525L affect the protein structure and function. We used prediction algorithms to analyze the effects of the non-synonymous single nucleotide polymorphisms and performed evolutionary conservation analysis, protein frustration analysis, and molecular dynamics simulations. Most of the prediction algorithms classified the three mutations as deleterious. All three mutations were predicted to reduce protein stability, especially the mutation R521C, which was also predicted to increase chaperone binding tendency. The protein frustration analysis showed an increase in frustration in the interactions involving the mutated residue 521C. Evolutionary conservation analysis showed that residues 521 and 525 of human FUS are highly conserved sites. The molecular dynamics results indicate that protein stability could be compromised in all three mutations. They also affected the exposed surface area and protein compactness. The analyzed mutations also displayed high flexibility in most residues in all variants, most notably in the interaction site with the nuclear import protein of FUS.

scholarly journals The Structure of Clostridioides difficile SecA2 ATPase Exposes Regions Responsible for Differential Target Recognition of the SecA1 and SecA2-Dependent Systems

2020 ◽  
Vol 21 (17) ◽  
pp. 6153
Author(s):  
Nataša Lindič ◽  
Jure Loboda ◽  
Aleksandra Usenik ◽  
Robert Vidmar ◽  
Dušan Turk
Keyword(s):  
Protein Translocation ◽  
Target Recognition ◽  
Evolutionary Conservation ◽  
Nosocomial Pathogen ◽  
Nucleotide Hydrolysis ◽  
Conservation Analysis ◽  
Clostridioides Difficile ◽  
Open Conformation ◽  
Secretory System

SecA protein is a major component of the general bacterial secretory system. It is an ATPase that couples nucleotide hydrolysis to protein translocation. In some Gram-positive pathogens, a second paralogue, SecA2, exports a different set of substrates, usually virulence factors. To identify SecA2 features different from SecA(1)s, we determined the crystal structure of SecA2 from Clostridioides difficile, an important nosocomial pathogen, in apo and ATP-γ-S-bound form. The structure reveals a closed monomer lacking the C-terminal tail (CTT) with an otherwise similar multidomain organization to its SecA(1) homologues and conserved binding of ATP-γ-S. The average in vitro ATPase activity rate of C. difficile SecA2 was 2.6 ± 0.1 µmolPi/min/µmol. Template-based modeling combined with evolutionary conservation analysis supports a model where C. difficile SecA2 in open conformation binds the target protein, ensures its movement through the SecY channel, and enables dimerization through PPXD/HWD cross-interaction of monomers during the process. Both approaches exposed regions with differences between SecA(1) and SecA2 homologues, which are in agreement with the unique adaptation of SecA2 proteins for a specific type of substrate, a role that can be addressed in further studies.

scholarly journals ConPlex: a server for the evolutionary conservation analysis of protein complex structures

2010 ◽  
Vol 38 (Web Server) ◽  
pp. W450-W456 ◽  
Author(s):  
Y. S. Choi ◽  
S. K. Han ◽  
J. Kim ◽  
J.-S. Yang ◽  
J. Jeon ◽  
...  
Keyword(s):  
Protein Complex ◽  
Evolutionary Conservation ◽  
Complex Structures ◽  
Conservation Analysis
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