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Journal of Molecular Evolution

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https://www.readbyqxmd.com/read/30327830/evolutionary-genetics-of-hypoxia-and-cold-tolerance-in-mammals
#1
Kangli Zhu, Deyan Ge, Zhixin Wen, Lin Xia, Qisen Yang
Low oxygen and fluctuant ambient temperature pose serious challenges to mammalian survival. Physiological adaptations in mammals to hypoxia and low temperatures have been intensively investigated, yet their underlying molecular mechanisms need further exploration. Independent invasions of high-altitude plateaus, subterranean burrows and marine environments by different mammals provide opportunities to conduct such analyses. Here, we focused on six genes in the hypoxia inducible factor (HIF) pathway and two non-shivering thermogenesis (NST)-related genes [PPAR co-activator 1 (PGC-1) and uncoupling protein 1 (UCP1)] in representative species of pikas and other mammals to understand whether these loci were targeted by natural selection during independent invasions to conditions characterized by hypoxia and temperature fluctuations by high-altitude, subterranean and marine mammals...
October 16, 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/30218341/computational-models-of-polymer-synthesis-driven-by-dehydration-rehydration-cycles-repurination-in-simulated-hydrothermal-fields
#2
Mason Hargrave, Spencer K Thompson, David Deamer
Cycles of biologically relevant reactions are an alternative to an origin of life emerging from a steady state away from equilibrium. The cycles involve a rate at which polymers are synthesized and accumulate in microscopic compartments called protocells, and two rates in which monomers and polymers are chemically degraded by hydrolytic reactions. Recent experiments have demonstrated that polymers are synthesized from mononucleotides and accumulate during cycles of hydration and dehydration, which means that the rate of polymer synthesis during the dehydrated phase of the cycle is balanced (but not dominated) by the rate of polymer hydrolysis during the hydrated phase of the cycle...
September 15, 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/30206667/three-finger-toxin-diversification-in-the-venoms-of-cat-eye-snakes-colubridae-boiga
#3
Daniel Dashevsky, Jordan Debono, Darin Rokyta, Amanda Nouwens, Peter Josh, Bryan G Fry
The Asian genus Boiga (Colubridae) is among the better studied non-front-fanged snake lineages, because their bites have minor, but noticeable, effects on humans. Furthermore, B. irregularis has gained worldwide notoriety for successfully invading Guam and other nearby islands with drastic impacts on the local bird populations. One of the factors thought to allow B. irregularis to become such a noxious pest is irditoxin, a dimeric neurotoxin composed of two three-finger toxins (3FTx) joined by a covalent bond between two newly evolved cysteines...
September 12, 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/30206666/identification-and-analysis-of-ovate-family-members-from-genome-of-the-early-land-plants-provide-insights-into-evolutionary-history-of-ofp-family-and-function
#4
Meenakshi Dangwal, Sandip Das
Mosses, liverworts, hornworts and lycophytes represent transition stages between the aquatic to terrestrial/land plants. Several morphological and adaptive novelties driven by genomic components including emergence and expansion of new or existing gene families have played a critical role during and after the transition, and contributed towards successful colonization of terrestrial ecosystems. It is crucial to decipher the evolutionary transitions and natural selection on the gene structure and function to understand the emergence of phenotypic and adaptive diversity...
September 11, 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/30306205/circular-permutation-obscures-universality-of-a-ribosomal-protein
#5
Nicholas A Kovacs, Petar I Penev, Amitej Venapally, Anton S Petrov, Loren Dean Williams
Functions, origins, and evolution of the translation system are best understood in the context of unambiguous and phylogenetically based taxonomy and nomenclature. Here, we map ribosomal proteins onto the tree of life and provide a nomenclature for ribosomal proteins that is consistent with phylogenetic relationships. We have increased the accuracy of homology relationships among ribosomal proteins, providing a more informative picture of their lineages. We demonstrate that bL33 (bacteria) and eL42 (archaea/eukarya) are homologs with common ancestry and acute similarities in sequence and structure...
October 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/30302501/ancestral-and-compensatory-mutations-that-promote-antiviral-resistance-in-influenza-n1-neuraminidase-revealed-by-a-phylonumerics-approach
#6
Elma H Akand, Kevin M Downard
Implementation of a new phylonumerics approach to construct a mass tree representing over 6000 H1N1 human influenza strains has enabled ancestral and compensatory descendant mutations to be identified in N1 neuraminidase that promote antiviral resistance and restore viral fitness. Adjacent to the H275Y resistance mutation site, mutations S299A and S247N, respectively, lead the evolution of oseltamivir-resistant strains and restore viral fitness to those strains thereafter. Importantly the mass tree phylonumerics approach can identify such mutations globally, without any positional bias, so that functionally linked or compensatory mutations remote in the sequence or structure of the protein can be identified and interrogated...
October 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/30283979/an-analysis-of-is630-tc1-mariner-transposons-in-the-genome-of-a-pacific-oyster-crassostrea-gigas
#7
M V Puzakov, L V Puzakova, S V Cheresiz
Transposable elements represent the DNA fragments capable of increasing their copy number and moving within the genome. Class II mobile elements represents the DNA transposons, which transpose via excision and the subsequent reinsertion at random genomic loci. The increase of their copy number occurs only when the transposition event is coupled with the replication. IS630/Tc1/mariner DNA transposon superfamily is one of the largest and widely distributed among the Class II elements. In this work, we provide a detailed analysis of IS630/Tc1/mariner DNA transposons from the Pacific oyster, Crassostrea gigas...
October 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/30238312/the-ammonium-channel-nod26-is-the-evolutionary-innovation-that-drives-the-emergence-consolidation-and-dissemination-of-nitrogen-fixing-symbiosis-in-angiosperms
#8
Romina Frare, Nicolás Ayub, Karina Alleva, Gabriela Soto
Increasing evidence indicates that N-fixing symbiosis has evolved several times in the N-fixing clade of angiosperms and that this evolution is driven by a single evolutionary innovation. However, the genetics of this ancestral predisposition to N-fixing symbiosis remains unclear. A natural candidate for such molecular innovation is the ammonium channel NOD26, the main protein component of the symbiosome membrane, which facilitates the plant uptake of the nitrogen fixed by symbiotic bacteria. Here, in concordance with the emergence of N-fixing symbiosis in angiosperms but not in ancestral plants, phylogenetic analysis showed that NOD26 belongs to an angiosperm-exclusive subgroup of aquaporins...
October 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/30105586/oligomerization-of-a-bimolecular-ribozyme-modestly-rescues-its-structural-defects-that-disturb-interdomain-assembly-to-form-the-catalytic-site
#9
Md Motiar Rahman, Shigeyoshi Matsumura, Yoshiya Ikawa
The emergence of cellular compartmentalization was a crucial step in the hypothetical RNA world and its evolution because it would not only prevent the extinction of RNA self-replication systems due to dispersion/diffusion of their components but also facilitate ribozyme reactions by molecular crowding effects. Here, we proposed and examined self-assembly of RNA components as a primitive cellular-like environment, which may have the ability to mimic cellular compartmentalization and crowding effects. We engineered a bimolecular group I ribozyme to form a one-dimensional (1D)-ribozyme assembly...
August 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/30099590/cotranscriptional-3-end-processing-of-t7-rna-polymerase-transcripts-by-a-smaller-hdv-ribozyme
#10
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 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/30066019/scratching-the-surface-of-an-itch-molecular-evolution-of-aculeata-venom-allergens
#11
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...
August 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/30062554/investigation-on-the-evolutionary-relation-of-diverse-polyhydroxyalkanoate-gene-clusters-in-betaproteobacteria
#12
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...
August 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
#13
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...
August 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/30022295/evolutionary-perspectives-of-genotype-phenotype-factors-in-leishmania-metabolism
#14
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...
August 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
#15
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
#16
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/29974176/evolution-of-the-biosynthetic-pathway-for-cyanogenic-glucosides-in-lepidoptera
#17
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
#18
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
#19
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/29934734/concurrent-duplication-of-drosophila-cid-and-cenp-c-genes-resulted-in-accelerated-evolution-and-male-germline-biased-expression-of-the-new-copies
#20
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
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