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Journal of Molecular Evolution

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https://www.readbyqxmd.com/read/30456441/genomic-signatures-among-acanthamoeba-polyphaga-entoorganisms-unveil-evidence-of-coevolution
#1
Víctor Serrano-Solís, Paulo Eduardo Toscano Soares, Sávio T de Farías
The definition of a genomic signature (GS) is "the total net response to selective pressure". Recent isolation and sequencing of naturally occurring organisms, hereby named entoorganisms, within Acanthamoeba polyphaga, raised the hypothesis of a common genomic signature despite their diverse and unrelated evolutionary origin. Widely accepted and implemented tests for GS detection are oligonucleotide relative frequencies (OnRF) and relative codon usage (RCU) surveys. A common pattern and strong correlations were unveiled from OnRFs among A...
November 20, 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/30456442/genes-encoding-mammalian-oviductal-proteins-involved-in-fertilization-are-subjected-to-gene-death-and-positive-selection
#4
Carla Moros-Nicolás, Sophie Fouchécourt, Ghylène Goudet, Philippe Monget
Oviductal proteins play an important role in mammalian fertilization, as proteins from seminal fluid. However, in contrast with the latter, their phylogenetic evolution has been poorly studied. Our objective was to study in 16 mammals the evolution of 16 genes that encode oviductal proteins involved in at least one of the following steps: (1) sperm-oviduct interaction, (2) acrosome reaction, and/or (3) sperm-zona pellucida interaction. Most genes were present in all studied mammals. However, some genes were lost along the evolution of mammals and found as pseudogenes: annexin A5 (ANXA5) and deleted in malignant brain tumor 1 (DMBT1) in tarsier; oviductin (OVGP1) in megabat; and probably progestagen-associated endometrial protein (PAEP) in tarsier, mouse, rat, rabbit, dolphin, and megabat; prostaglandin D2 synthase (PTGDS) in microbat; and plasminogen (PLG) in megabat...
December 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/30456440/folding-assembly-and-persistence-the-essential-nature-and-origins-of-biopolymers
#5
Calvin M Runnels, Kathryn A Lanier, Justin Krish Williams, Jessica C Bowman, Anton S Petrov, Nicholas V Hud, Loren Dean Williams
Life as we know it requires three basic types of polymers: polypeptide, polynucleotide, and polysaccharide. Here we evaluate both universal and idiosyncratic characteristics of these biopolymers. We incorporate this information into a model that explains much about their origins, selection, and early evolution. We observe that all three biopolymer types are pre-organized, conditionally self-complementary, chemically unstable in aqueous media yet persistent because of kinetic trapping, with chiral monomers and directional chains...
December 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/30426144/delineation-of-the-genera-haemoproteus-and-plasmodium-using-rna-seq-and-multi-gene-phylogenetics
#6
Jasper Toscani Field, Josh Weinberg, Staffan Bensch, Nubia E Matta, Gediminas Valkiūnas, Ravinder N M Sehgal
Members of the order Haemosporida are protist parasites that infect mammals, reptiles and birds. This group includes the causal agents of malaria, Plasmodium parasites, the genera Leucocytozoon and Fallisia, as well as the species rich genus Haemoproteus with its two subgenera Haemoproteus and Parahaemoproteus. Some species of Haemoproteus cause severe disease in avian hosts, and these parasites display high levels of diversity worldwide. This diversity emphasizes the need for accurate evolutionary information...
December 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/30392157/the-diabetes-susceptibility-gene-slc30a8-that-encodes-the-zinc-transporter-znt8-is-a-pseudogene-in-guinea-pigs-potentially-contributing-to-low-guinea-pig-islet-zinc-content
#7
LETTER
Kristen E Syring, Karin J Bosma, James K Oeser, Masakazu Shiota, Richard M O'Brien
In most mammals pancreatic islet beta cells have very high zinc levels that promote the crystallization and storage of insulin. Guinea pigs are unusual amongst mammals in that their islets have very low zinc content. The selectionist theory of insulin evolution proposes that low environmental zinc led to the selection of a mutation in Guinea pig insulin that negated the requirement for zinc binding. In mice deletion of the Slc30a8 gene, that encodes the zinc transporter ZnT8, markedly reduces islet zinc content...
December 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/30382299/why-prokaryotes-genomes-lack-genes-with-introns-processed-by-spliceosomes
#8
EDITORIAL
Guillermo Lamolle, Héctor Musto
No abstract text is available yet for this article.
December 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/30370448/positive-selection-in-the-evolution-of-mammalian-crisps
#9
Alberto Vicens, Claudia L Treviño
Cysteine-RIch Secretory Proteins (CRISPs) constitute a versatile family, with functions in reptilian venom and mammalian reproduction. Mammals generally express three CRISPs, four in mice, and all are highly expressed in male reproductive tissues, either testis or accessory organs. Because reproductive proteins often evolve adaptively in response to post-copulatory sexual selection, we hypothesized that mammalian CRISPs, with important roles in male reproduction, could have undergone positive selection promoting their divergence...
December 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/30361751/a-non-neutral-origin-for-error-minimization-in-the-origin-of-the-genetic-code
#10
LETTER
Massimo Di Giulio
Massey (J Mol Evol 67:510-516, 2008; J Theor Biol 408:237-242, 2016; Nat Comput. https://doi.org/10.1007/s11047-017-9669-3, 2018) claims that the error minimization of the genetic code is derived by means of a neutral process and was not due to the action of natural selection. Here, I argue that this neutralist hypothesis of the origin of error minimization is not based directly on any neutral process but it could be only indirectly. On the contrary, it has been natural selection that has acted during the origin of the genetic code determining the property that similar amino acids are coded by similar codons within the genetic code table...
December 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/30327830/evolutionary-genetics-of-hypoxia-and-cold-tolerance-in-mammals
#11
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...
December 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/30306205/circular-permutation-obscures-universality-of-a-ribosomal-protein
#12
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
#13
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
#14
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
#15
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/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
#16
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/30105586/oligomerization-of-a-bimolecular-ribozyme-modestly-rescues-its-structural-defects-that-disturb-interdomain-assembly-to-form-the-catalytic-site
#17
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
#18
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
#19
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
#20
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
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