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Journal of Molecular Evolution

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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
#1
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...
April 20, 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29623351/primitive-dark-phase-cycle-of-photosynthesis-at-the-origin-of-life
#2
LETTER
Michel Koenig
Simple phosphorylation, isomerization, and aldolisation reactions starting from glyceraldehyde have the potential to lead to the synthesis of pre-ribonucleotide polymers through a primitive form of the Calvin cycle (dark phase of photosynthesis) involving the unusual formation of phospho-nonulose phosphate and phospho-deculose phosphate, as key intermediates. These reactions involve activated phosphates which are generated from schreibersite minerals, geochemically available in Hadean times.
April 5, 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29623350/group-selection-may-explain-cancer-predisposition-and-other-human-traits-evolution
#3
EDITORIAL
Konstantinos Voskarides
Group selection is a matter of acute controversy among evolutionary biologists. The most well-publicized debate in this regard is that between Edward O. Wilson and Richard Dawkins. As is widely known, Edward O. Wilson is very excited about the idea of social selection and eusociality; by contrast Richard Dawkins favors the idea of gene selection. As is often the case, the truth is somewhere in the middle. Evolution is most likely a multilevel procedure, where selection forces act on genes, individuals, and groups...
April 5, 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29594426/mineral-grains-dimples-and-hot-volcanic-organic-streams-dynamic-geological-backstage-of-macromolecular-evolution
#4
Nikolai E Skoblikow, Andrei A Zimin
The hypothesis of hot volcanic organic stream as the most probable and geologically plausible environment for abiogenic polycondensation is proposed. The primary synthesis of organic compounds is considered as result of an explosive volcanic (perhaps, meteorite-induced) eruption. The eruption was accompanied by a shock wave propagating in the primeval atmosphere and resulting in the formation of hot cloud of simple organic compounds-aldehydes, alcohols, amines, amino alcohols, nitriles, and amino acids-products, which are usually obtained under the artificial conditions in the spark-discharge experiments...
March 28, 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29574604/evolution-of-melanoma-antigen-a11-magea11-during-primate-phylogeny
#5
Christopher S Willett, Elizabeth M Wilson
Melanoma antigen-A11 (MAGE-A11) is an X-linked and primate-specific steroid hormone receptor transcriptional coregulator and proto-oncogenic protein whose increased expression promotes the growth of prostate cancer. The MAGEA11 gene is expressed at low levels in normal human testis, ovary, and endometrium, and at highest levels in castration-resistant prostate cancer. Annotated genome predictions throughout the surviving primate lineage show that MAGEA11 acquired three 5' coding exons unique within the MAGEA subfamily during the evolution of New World monkeys (NWM), Old World monkeys (OWM), and apes...
March 24, 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29564489/first-report-of-a-mitochondrial-pseudogene-in-agnathan-vertebrates-cyclostomata-petromyzontidae
#6
LETTER
Rex Meade Strange, Kimberly J Delaney
We report herein the characterization of a nuclear paralog of a fragment of the mitochondrial genome (a numt) in two closely related species of lampreys (Ichthyomyzon spp.). Although numts have been characterized in several vertebrate taxa, numts have yet to be reported for fishes in general. Given the phylogenetic position of lampreys relative to other vertebrates, the presence of numts within the lamprey genome is either evidence of an ancestral trait lost in other fishes but uniquely retained in agnathans and amniotes, or (more intriguingly) a product of the genome rearrangements these animals undergo during development...
March 21, 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29556741/application-of-chloroplast-phylogenomics-to-resolve-species-relationships-within-the-plant-genus-amaranthus
#7
Erika Viljoen, Damaris A Odeny, Martin P A Coetzee, Dave K Berger, David J G Rees
Amaranthus species are an emerging and promising nutritious traditional vegetable food source. Morphological plasticity and poorly resolved dendrograms have led to the need for well resolved species phylogenies. We hypothesized that whole chloroplast phylogenomics would result in more reliable differentiation between closely related amaranth species. The aims of the study were therefore: to construct a fully assembled, annotated chloroplast genome sequence of Amaranthus tricolor; to characterize Amaranthus accessions phylogenetically by comparing barcoding genes (matK, rbcL, ITS) with whole chloroplast sequencing; and to use whole chloroplast phylogenomics to resolve deeper phylogenetic relationships...
March 19, 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29556740/horizontal-gene-transfer-building-prokaryote-genomes-genes-related-to-exchange-between-cell-and-environment-are-frequently-transferred
#8
Apuã C M Paquola, Huma Asif, Carlos Alberto de Bragança Pereira, Bruno César Feltes, Diego Bonatto, Wanessa Cristina Lima, Carlos Frederico Martins Menck
Horizontal gene transfer (HGT) has a major impact on the evolution of prokaryotic genomes, as it allows genes evolved in different contexts to be combined in a single genome, greatly enhancing the ways evolving organisms can explore the gene content space and adapt to the environment. A systematic analysis of HGT in a large number of genomes is of key importance in understanding the impact of HGT in the evolution of prokaryotes. We developed a method for the detection of genes that potentially originated by HGT based on the comparison of BLAST scores between homologous genes to 16S rRNA-based phylogenetic distances between the involved organisms...
March 19, 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29536136/genomic-insights-into-evolution-of-adpa-family-master-regulators-of-morphological-differentiation-and-secondary-metabolism-in-streptomyces
#9
Mariia Rabyk, Oleksandr Yushchuk, Ihor Rokytskyy, Maria Anisimova, Bohdan Ostash
The AdpA protein from a streptomycin producer Streptomyces griseus is a founding member of the AdpA family of pleiotropic regulators, known to be ubiquitously present in streptomycetes. Functional genomic approaches revealed a huge number of AdpA targets, leading to the claim that the AdpA regulon is the largest one in bacteria. The expression of adpA is limited at the level of translation of the rare leucyl UUA codon. All known properties of AdpA regulators were discovered on a few streptomycete strains. There are open questions about the true abundance and diversity of AdpA across actinobacterial taxa (and beyond) and about the possible evolutionary forces that shape the AdpA orthologous group in Streptomyces...
March 13, 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29460038/the-performance-of-two-supertree-schemes-compared-using-synthetic-and-real-data-quartet-input
#10
Eliran Avni, Zahi Yona, Reuven Cohen, Sagi Snir
Despite impressive advancements in technological and theoretical tools, construction of phylogenetic (evolutionary) trees is still a challenging task. The availability of enormous quantities of molecular data has made large-scale phylogenetic reconstruction involving thousands of species, a more viable goal. For this goal, separate trees over different, overlapping subsets of species, representing histories of various markers of these species, are collected. These trees, typically with conflicting signals, are subsequently combined into a single tree over the full set, an operation denoted as supertree construction...
February 19, 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29455279/divergent-selection-of-pattern-recognition-receptors-in-mammals-with-different-ecological-characteristics
#11
Ran Tian, Meixiu Chen, Simin Chai, Xinghua Rong, Bingyao Chen, Wenhua Ren, Shixia Xu, Guang Yang
Pattern recognition receptors (PRRs) are specialized receptors that represent a key component of the host innate immune system. Whether molecular evolutionary history of different PRR classes have involved different genetic mechanisms underlying diverse pathogen environment in mammals, and whether distinct ecology of mammals may have imposed divergent selective pressures on the evolution of the PRRs, remained unknown. To test these hypotheses, we investigated the characterization of 20 genes belonging to four PRR classes in mammals...
February 17, 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29429061/iterative-calibration-a-novel-approach-for-calibrating-the-molecular-clock-using-complex-geological-events
#12
Tzitziki Loeza-Quintana, Sarah J Adamowicz
During the past 50 years, the molecular clock has become one of the main tools for providing a time scale for the history of life. In the era of robust molecular evolutionary analysis, clock calibration is still one of the most basic steps needing attention. When fossil records are limited, well-dated geological events are the main resource for calibration. However, biogeographic calibrations have often been used in a simplistic manner, for example assuming simultaneous vicariant divergence of multiple sister lineages...
February 10, 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29379986/ancient-diversification-of-three-finger-toxins-in-micrurus-coral-snakes
#13
Daniel Dashevsky, Bryan G Fry
Coral snakes, most notably the genus Micrurus, are the only terrestrial elapid snakes in the Americas. Elapid venoms are generally known for their potent neurotoxicity which is usually caused by Three-Finger Toxin (3FTx) proteins. These toxins can have a wide array of functions that have been characterized from the venom of other elapids. We examined publicly available sequences from Micrurus 3FTx to show that they belong to 8 monophyletic clades that diverged as deep in the 3FTx phylogenetic tree as the other clades with characterized functions...
January 27, 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29356848/artificial-gene-amplification-in-escherichia-coli-reveals-numerous-determinants-for-resistance-to-metal-toxicity
#14
Kenric J Hoegler, Michael H Hecht
When organisms are subjected to environmental challenges, including growth inhibitors and toxins, evolution often selects for the duplication of endogenous genes, whose overexpression can provide a selective advantage. Such events occur both in natural environments and in clinical settings. Microbial cells-with their large populations and short generation times-frequently evolve resistance to a range of antimicrobials. While microbial resistance to antibiotic drugs is well documented, less attention has been given to the genetic elements responsible for resistance to metal toxicity...
February 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29349600/beneficial-mutations-from-evolution-experiments-increase-rates-of-growth-and-fermentation
#15
Aysha L Sezmis, Martino E Malerba, Dustin J Marshall, Michael J McDonald
A major goal of evolutionary biology is to understand how beneficial mutations translate into increased fitness. Here, we study beneficial mutations that arise in experimental populations of yeast evolved in glucose-rich media. We find that fitness increases are caused by enhanced maximum growth rate (R) that come at the cost of reduced yield (K). We show that for some of these mutants, high R coincides with higher rates of ethanol secretion, suggesting that higher growth rates are due to an increased preference to utilize glucose through the fermentation pathway, instead of respiration...
February 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29344693/triplet-based-codon-organization-optimizes-the-impact-of-synonymous-mutation-on-nucleic-acid-molecular-dynamics
#16
Gregory A Babbitt, Erin E Coppola, Jamie S Mortensen, Patrick X Ekeren, Cosmo Viola, Dallan Goldblatt, André O Hudson
Since the elucidation of the genetic code almost 50 years ago, many nonrandom aspects of its codon organization remain only partly resolved. Here, we investigate the recent hypothesis of 'dual-use' codons which proposes that in addition to allowing adjustment of codon optimization to tRNA abundance, the degeneracy in the triplet-based genetic code also multiplexes information regarding DNA's helical shape and protein-binding dynamics while avoiding interference with other protein-level characteristics determined by amino acid properties...
January 17, 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29349599/evolution-of-eukaryal-and-archaeal-pseudouridine-synthase-pus10
#17
Elisabeth Fitzek, Archi Joardar, Ramesh Gupta, Matt Geisler
In archaea, pseudouridine (Ψ) synthase Pus10 modifies uridine (U) to Ψ at positions 54 and 55 of tRNA. In contrast, Pus10 is not found in bacteria, where modifications at those two positions are carried out by TrmA (U54 to m5 U54) and TruB (U55 to Ψ55). Many eukaryotes have an apparent redundancy; their genomes contain orthologs of archaeal Pus10 and bacterial TrmA and TruB. Although eukaryal Pus10 genes share a conserved catalytic domain with archaeal Pus10 genes, their biological roles are not clear for the two reasons...
January 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29330556/evolution-of-the-phosphatidylcholine-biosynthesis-pathways-in-green-algae-combinatorial-diversity-of-methyltransferases
#18
Takashi Hirashima, Masakazu Toyoshima, Takashi Moriyama, Naoki Sato
Phosphatidylcholine (PC) is one of the most common phospholipids in eukaryotes, although some green algae such as Chlamydomonas reinhardtii are known to lack PC. Recently, we detected PC in four species in the genus Chlamydomonas: C. applanata NIES-2202, C. asymmetrica NIES-2207, C. debaryana NIES-2212, and C. sphaeroides NIES-2242. To reveal the PC biosynthesis pathways in green algae and the evolutionary scenario involved in their diversity, we analyzed the PC biosynthesis genes in these four algae using draft genome sequences...
January 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29260254/from-molecules-to-life-quantifying-the-complexity-of-chemical-and-biological-systems-in-the-universe
#19
Thomas Böttcher
Life is a complex phenomenon and much research has been devoted to both understanding its origins from prebiotic chemistry and discovering life beyond Earth. Yet, it has remained elusive how to quantify this complexity and how to compare chemical and biological units on one common scale. Here, a mathematical description of molecular complexity was applied allowing to quantitatively assess complexity of chemical structures. This in combination with the orthogonal measure of information complexity resulted in a two-dimensional complexity space ranging over the entire spectrum from molecules to organisms...
January 2018: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29248946/elastic-multi-scale-mechanisms-computation-and-biological-evolution
#20
Juan G Diaz Ochoa
Explanations based on low-level interacting elements are valuable and powerful since they contribute to identify the key mechanisms of biological functions. However, many dynamic systems based on low-level interacting elements with unambiguous, finite, and complete information of initial states generate future states that cannot be predicted, implying an increase of complexity and open-ended evolution. Such systems are like Turing machines, that overlap with dynamical systems that cannot halt. We argue that organisms find halting conditions by distorting these mechanisms, creating conditions for a constant creativity that drives evolution...
January 2018: Journal of Molecular Evolution
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