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Journal of Molecular Evolution

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https://www.readbyqxmd.com/read/30099590/cotranscriptional-3-end-processing-of-t7-rna-polymerase-transcripts-by-a-smaller-hdv-ribozyme
#1
Arvin Akoopie, Ulrich F Müller
In vitro run-off transcription by T7 RNA polymerase generates heterogeneous 3'-ends because the enzyme tends to add untemplated adenylates. To generate homogeneous 3'-termini, HDV ribozymes have been used widely. Their sequences are added to the 3'-terminus such that co-transcriptional self-cleavage generates homogeneous 3'-ends. A shorter HDV sequence that cleaves itself efficiently would be advantageous. Here we show that a recently discovered, small HDV ribozyme is a good alternative to the previously used HDV ribozyme...
August 11, 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/30066019/scratching-the-surface-of-an-itch-molecular-evolution-of-aculeata-venom-allergens
#2
Kate Baumann, Daniel Dashevsky, Kartik Sunagar, Bryan Fry
Hymenopteran insects are infamous for their sting, and their ability to cause severe anaphylaxis and in some cases death. This allergic reaction is a result of allergens present in the venom. Hymenopterans have many common venom allergens, the most widespread of which include phospholipase A1 , phospholipase A2 , acid phosphatase, hyaluronidase, serine protease and antigen 5. While there have been studies that look at the phylogenetic histories of allergens within closely related species, to our knowledge, this is the first study using evolutionary analyses to compare across Hymenoptera the types of selection that are occurring on allergens...
July 31, 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/30062554/investigation-on-the-evolutionary-relation-of-diverse-polyhydroxyalkanoate-gene-clusters-in-betaproteobacteria
#3
Gurusamy Kutralam-Muniasamy, Rodolfo Marsch, Fermín Pérez-Guevara
Products of numerous genes (phaC, phaA, phaB, phaP, phaR, and phaZ) are involved in the synthesis and degradation processes of the ubiquitous prokaryotic polyhydroxyalkanoate (PHA) intracellular reserve storage system. In this study, we performed a bioinformatics analysis to identify PHA-related genes and proteins in the genome of 66 selected organisms (class: Betaproteobacteria) that occur in various habitats; besides, evolutionary trajectories of the PHA system are reported here. The identified PHA-related genes were organized into clusters, and the gene arrangement was highly diverse...
July 31, 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/30056594/sequential-molecular-events-of-functional-trade-offs-in-5-hydroxyisourate-hydrolase-before-and-after-gene-duplication-led-to-the-evolution-of-transthyretin-during-chordate-diversification
#4
Kiyoshi Yamauchi, Kentaro Kasai
Transthyretin (TTR), a plasma thyroid hormone distributor protein (THDP), emerged from 5-hydroxyisourate hydrolase (HIUHase), an enzyme involved in urate metabolism, by gene duplication at a stage of chordate evolution. Comparison of amino acid sequences revealed the presence of two His-rich segments in the primitive TTRs. Using several HIUHase and TTR mutants, we investigated 5-hydroxyisourate (HIU) hydrolysis activity and thyroid hormone (TH) binding activity to elucidate how a novel function as a THDP arose...
July 28, 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/30022295/evolutionary-perspectives-of-genotype-phenotype-factors-in-leishmania-metabolism
#5
Abhishek Subramanian, Ram Rup Sarkar
The sandfly midgut and the human macrophage phagolysosome provide antagonistic metabolic niches for the endoparasite Leishmania to survive and populate. Although these environments fluctuate across developmental stages, the relative changes in both these environments across parasite generations might remain gradual. Such environmental restrictions might endow parasite metabolism with a choice of specific genotypic and phenotypic factors that can constrain enzyme evolution for successful adaptation to the host...
July 19, 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29992348/retroelements-and-dna-methylation-could-contribute-to-diversity-of-5s-rdna-in-agave-l
#6
Y J Tamayo-Ordóñez, J A Narváez-Zapata, M C Tamayo-Ordóñez, L F Sánchez-Teyer
Agave L. is a genus of economic importance, and many of the 166 species in the American plant genus Agave L. inhabit high-stress environments, which makes the genus promising for facing global climate change. However, sustainable use of economically important species without interfering with their ecology and evolution requires generating knowledge about the factors responsible for their genetic variation and diversity and, on this basis, their adaptation and speciation. Few genetic studies exploring the evolutionary relationships, speciation processes, genetic variability and diversity within species of Agave are currently available...
July 10, 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29987491/haplogroup-context-is-less-important-in-the-penetrance-of-mitochondrial-dna-complex-i-mutations-compared-to-mt-trna-mutations
#7
Hannah O'Keefe, Rachel A Queen, Surita Meldau, Phillip Lord, Joanna L Elson
Mitochondrial diseases are a highly complex, heterogeneous group of disorders. Mitochondrial DNA variants that are linked to disease can exhibit variable expression and penetrance. This has an implication for mitochondrial diagnostics as variants that cause disease in one individual may not in another. It has been suggested that the sequence context in which a variant arises could influence the genotype-phenotype relationship. However, the consequence of sequence variation between different haplogroups on the expression of disease is not well understood...
July 9, 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29934734/concurrent-duplication-of-drosophila-cid-and-cenp-c-genes-resulted-in-accelerated-evolution-and-male-germline-biased-expression-of-the-new-copies
#8
José R Teixeira, Guilherme B Dias, Marta Svartman, Alfredo Ruiz, Gustavo C S Kuhn
Despite their essential role in the process of chromosome segregation in eukaryotes, kinetochore proteins are highly diverse across species, being lost, duplicated, created, or diversified during evolution. Based on comparative genomics, the duplication of the inner kinetochore proteins CenH3 and Cenp-C, which are interdependent in their roles of establishing centromere identity and function, can be said to be rare in animals. Surprisingly, the Drosophila CenH3 homolog Cid underwent four independent duplication events during evolution...
June 23, 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29926120/genes-relocated-between-drosophila-chromosome-arms-evolve-under-relaxed-selective-constraints-relative-to-non-relocated-genes
#9
Margaret L I Hart, Ban L Vu, Quinten Bolden, Keith T Chen, Casey L Oakes, Lejla Zoronjic, Richard P Meisel
Gene duplication creates a second copy of a gene either in tandem to the ancestral locus or dispersed to another chromosomal location. When the ancestral copy of a dispersed duplicate is lost from the genome, it creates the appearance that the gene was "relocated" from the ancestral locus to the derived location. Gene relocations may be as common as canonical dispersed duplications in which both the ancestral and derived copies are retained. Relocated genes appear to be under more selective constraints than the derived copies of canonical duplications, and they are possibly as conserved as single-copy non-relocated genes...
June 21, 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29974176/evolution-of-the-biosynthetic-pathway-for-cyanogenic-glucosides-in-lepidoptera
#10
Mika Zagrobelny, Mikael Kryger Jensen, Heiko Vogel, René Feyereisen, Søren Bak
Cyanogenic glucosides are widespread defence compounds in plants, and they are also found in some arthropods, especially within Lepidoptera. The aliphatic linamarin and lotaustralin are the most common cyanogenic glucosides in Lepidoptera, and they are biosynthesised de novo, and/or sequestered from food plants. Their biosynthetic pathway was elucidated in the burnet moth, Zygaena filipendulae, and consists of three enzymes: two cytochrome P450 enzymes, CYP405A2 and CYP332A3, and a glucosyl transferase, UGT33A1...
July 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29959476/the-standard-genetic-code-facilitates-exploration-of-the-space-of-functional-nucleotide-sequences
#11
Shubham Tripathi, Michael W Deem
The standard genetic code is well known to be optimized for minimizing the phenotypic effects of single-nucleotide substitutions, a property that was likely selected for during the emergence of a universal code. Given the fitness advantage afforded by high standing genetic diversity in a population in a dynamic environment, it is possible that selection to explore a large fraction of the space of functional proteins also occurred. To determine whether selection for such a property played a role during the emergence of the nearly universal standard genetic code, we investigated the number of functional variants of the Escherichia coli PhoQ protein explored at different time scales under translation using different genetic codes...
July 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29955898/correlated-selection-on-amino-acid-deletion-and-replacement-in-mammalian-protein-sequences
#12
Yichen Zheng, Dan Graur, Ricardo B R Azevedo
A low ratio of nonsynonymous and synonymous substitution rates (dN/dS) at a codon is an indicator of functional constraint caused by purifying selection. Intuitively, the functional constraint would also be expected to prevent such a codon from being deleted. However, to the best of our knowledge, the correlation between the rates of deletion and substitution has never actually been estimated. Here, we use 8595 protein-coding region sequences from nine mammalian species to examine the relationship between deletion rate and dN/dS...
July 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29947946/evolutionary-dynamics-of-copy-number-and-meiotic-recombination-in-murine-5s-rdna-possible-involvement-of-natural-selection
#13
Miyu Isobe, Mitsuo Nunome, Ken Katakura, Hitoshi Suzuki
We investigated evolutionary trends of the 5S ribosomal RNA gene in the house mouse, Mus musculus. First, we assessed the 5S cluster and copy numbers in eight laboratory strains by pulsed-field gel electrophoresis. The copy numbers in seven lines were estimated to be around 130-170 copies per cluster, with 63 copies in the remaining strain, implying that the copy number can change drastically and has been maintained under certain evolutionary constraints at ~ 140 copies. Second, we addressed the frequency of meiotic recombination mediated by the 5S cluster by performing a mating experiment with laboratory strains, and found that the 5S cluster did not accelerate recombination events...
June 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29943091/correction-to-transposable-elements-activity-is-positively-related-to-rate-of-speciation-in-mammals
#14
Marco Ricci, Valentina Peona, Etienne Guichard, Cristian Taccioli, Alessio Boattini
The original version of the article unfortunately contained tagging error in Given and Surname of all the authors.
June 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29855654/transposable-elements-activity-is-positively-related-to-rate-of-speciation-in-mammals
#15
Marco Ricci, Valentina Peona, Etienne Guichard, Cristian Taccioli, Alessio Boattini
Transposable elements (TEs) play an essential role in shaping eukaryotic genomes and generating variability. Speciation and TE activity bursts could be strongly related in mammals, in which simple gradualistic models of differentiation do not account for the currently observed species variability. In order to test this hypothesis, we designed two parameters: the Density of insertion (DI) and the Relative rate of speciation (RRS). DI is the ratio between the number of TE insertions in a genome and its size, whereas the RRS is a conditional parameter designed to identify potential speciation bursts...
June 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29748740/exploration-of-rna-sequence-space-in-the-absence-of-a-replicase
#16
Madhan R Tirumalai, Quyen Tran, Maxim Paci, Dimple Chavan, Anuradha Marathe, George E Fox
It is generally considered that if an RNA World ever existed that it would be driven by an RNA capable of RNA replication. Whether such a catalytic RNA could emerge in an RNA World or not, there would need to be prior routes to increasing complexity in order to produce it. It is hypothesized here that increasing sequence variety, if not complexity, can in fact readily emerge in response to a dynamic equilibrium between synthesis and degradation. A model system in which T4 RNA ligase catalyzes synthesis and Benzonase catalyzes degradation was constructed...
June 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29725703/chiral-monomers-ensure-orientational-specificity-of-monomer-binding-during-polymer-self-replication
#17
Hemachander Subramanian, Robert A Gatenby
Biomolecular homochirality is universally observed in living systems but the molecular and evolutionary dynamics that led to its emergence are unknown. In fact, there are significant disadvantages in using chiral monomers for polymerization, which include enantiomeric cross-inhibition in racemic medium and under-utilization of available resources for self-replication in the primordial environment. Nevertheless, most investigations of homochirality in living systems assume that the individual primordial monomers were chiral prior to the formation of self-replicating polymer and therefore focus on identifying a symmetry-breaking mechanism that might choose one enantiomer over the other in a racemic medium...
June 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29721580/domain-specific-proteogenomic-analysis-of-collagens-to-evaluate-de-novo-sequencing-results-and-database-information
#18
Anne J Kleinnijenhuis, Frédérique L van Holthoon
Collagen is an important structural protein and the most abundant protein in mammals. In several research fields, structural analysis of collagens is performed. Fibrillar collagens almost entirely consist of continuous repeats of GXY, where G is glycine, X is often proline or alanine and Y is often hydroxyproline or alanine. In the present study, the collagen structure was investigated in detail at the nucleotide, codon group, amino acid and target peptide level using sequence analyses. One of the most important findings was that a selection of codon groups is predominantly involved in amino acid changes between closely related collagens and that other change routes come up when collagens are less related...
June 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29691606/phylogenetic-reconstruction-shows-independent-evolutionary-origins-of-mitochondrial-transcription-factors-from-an-ancient-family-of-rna-methyltransferase-proteins
#19
LETTER
Aj Harris, Aaron David Goldman
Here, we generate a robust phylogenetic framework for the rRNA adenine N(6)-methyltransferase (RAMTase) protein family that shows a more ancient and complex evolutionary history within the family than previously reported. RAMTases occur universally by descent across the three domains of life, and typical orthologs within the family perform methylation of the small subunits of ribosomal RNA (rRNA). However, within the RAMTase family, two different groups of mitochondrial transcription factors, mtTFB1 and mtTFB2, have evolved in eukaryotes through neofunctionalization...
June 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29679096/protein-evolution-is-potentially-governed-by-protein-stability-directed-evolution-of-an-esterase-from-the-hyperthermophilic-archaeon-sulfolobus-tokodaii
#20
Ryo Kurahashi, Satoshi Sano, Kazufumi Takano
The study of evolution is important to understand biological phenomena. During evolutionary processes, genetic changes confer amino acid substitutions in proteins, resulting in new or improved functions. Unfortunately, most mutations destabilize proteins. Thus, protein stability is a significant factor in evolution; however, its role remains unclear. Here, we simply and directly explored the association between protein activity and stability in random mutant libraries to elucidate the role of protein stability in evolutionary processes...
June 2018: Journal of Molecular Evolution
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