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Journal of Molecular Evolution

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https://www.readbyqxmd.com/read/29192334/putative-independent-evolutionary-reversals-from-genotypic-to-temperature-dependent-sex-determination-are-associated-with-accelerated-evolution-of-sex-determining-genes-in-turtles
#1
Robert Literman, Alexandria Burrett, Basanta Bista, Nicole Valenzuela
The evolutionary lability of sex-determining mechanisms across the tree of life is well recognized, yet the extent of molecular changes that accompany these repeated transitions remain obscure. Most turtles retain the ancestral temperature-dependent sex determination (TSD) from which multiple transitions to genotypic sex determination (GSD) occurred independently, and two contrasting hypotheses posit the existence or absence of reversals back to TSD. Here we examined the molecular evolution of the coding regions of a set of gene regulators involved in gonadal development in turtles and several other vertebrates...
December 1, 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29189888/on-the-early-evolution-of-catabolic-pathways-a-comparative-genomics-approach-i-the-cases-of-glucose-ribose-and-the-nucleobases-catabolic-routes
#2
Mario Rivas, Arturo Becerra, Antonio Lazcano
Compared with the large corpus of published work devoted to the study of the origin and early development of anabolism, little attention has been given to the discussion of the early evolution of catabolism in spite of its significance. In the present study, we have used comparative genomics to explore the evolution and phylogenetic distribution of the enzymes that catalyze the extant catabolic pathways of the monosaccharides glucose and ribose, as well as those of the nucleobases adenine, guanine, cytosine, uracil, and thymine...
November 30, 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29177973/phylogenetic-profiling-of-mitochondrial-proteins-and-integration-analysis-of-bacterial-transcription-units-suggest-evolution-of-f1fo-atp-synthase-from-multiple-modules
#3
Yulong Niu, Shayan Moghimyfiroozabad, Sepehr Safaie, Yi Yang, Elizabeth A Jonas, Kambiz N Alavian
ATP synthase is a complex universal enzyme responsible for ATP synthesis across all kingdoms of life. The F-type ATP synthase has been suggested to have evolved from two functionally independent, catalytic (F1) and membrane bound (Fo), ancestral modules. While the modular evolution of the synthase is supported by studies indicating independent assembly of the two subunits, the presence of intermediate assembly products suggests a more complex evolutionary process. We analyzed the phylogenetic profiles of the human mitochondrial proteins and bacterial transcription units to gain additional insight into the evolution of the F-type ATP synthase complex...
November 24, 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29177972/conservation-of-the-enzyme-coenzyme-interfaces-in-fad-and-nadp-binding-adrenodoxin-reductase-a-ubiquitous-enzyme
#4
Israel Hanukoglu
FAD and NAD(P) together represent an ideal pair for coupled redox reactions in their capacity to accept two electrons and their redox potentials. Enzymes that bind both NAD(P) and FAD represent large superfamilies that fulfill essential roles in numerous metabolic pathways. Adrenodoxin reductase (AdxR) shares Rossmann fold features with some of these superfamilies but remains in a group of its own in the absence of sequence homology. This article documents the phylogenetic distribution of AdxR by examining whole genome databases for Metazoa, Plantae, Fungi, and Protista, and determines the conserved structural features of AdxR...
November 24, 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29143083/the-polyphyletic-origins-of-primase-helicase-bifunctional-proteins
#5
Ankita Gupta, Supriya Patil, Ramya Vijayakumar, Kiran Kondabagil
We studied the evolutionary relationships of different primase-helicase bifunctional proteins, found mostly in viruses, virophages, plasmids, and organellar genomes, by phylogeny and correlation analysis. Our study suggests independent origins of primase-helicase bifunctional proteins resulting from multiple fusion events between genes encoding primase and helicase domains of different families. The correlation analysis further indicated strong functional dependencies of domains in the bifunctional proteins that are part of smaller genomes and plasmids...
November 15, 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29127445/negative-epistasis-in-experimental-rna-fitness-landscapes
#6
REVIEW
Devin P Bendixsen, Bjørn Østman, Eric J Hayden
Mutations and their effects on fitness are a fundamental component of evolution. The effects of some mutations change in the presence of other mutations, and this is referred to as epistasis. Epistasis can occur between mutations in different genes or within the same gene. A systematic study of epistasis requires the analysis of numerous mutations and their combinations, which has recently become feasible with advancements in DNA synthesis and sequencing. Here we review the mutational effects and epistatic interactions within RNA molecules revealed by several recent high-throughput mutational studies involving two ribozymes studied in vitro, as well as a tRNA and a snoRNA studied in yeast...
November 10, 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29110026/pirnas-and-evolutionary-trajectories-in-genome-size-and-content
#7
LETTER
Rachel Lockridge Mueller
No abstract text is available yet for this article.
November 6, 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29094190/evolution-of-single-domain-globins-in-hydrothermal-vent-scale-worms
#8
J Projecto-Garcia, A-S Le Port, T Govindji, D Jollivet, S W Schaeffer, S Hourdez
Hypoxia at deep-sea hydrothermal vents represents one of the most basic challenges for metazoans, which then requires specific adaptations to acquire oxygen to meet their metabolic needs. Hydrothermal vent scale-worms (Polychaeta; Polynoidae) express large amounts of extracellular single- and multi-domain hemoglobins, in contrast with their shallow-water relatives that only possess intracellular globins in their nervous system (neuroglobins). We sequenced the gene encoding the single-domain (SD) globin from nine species of polynoids found in various vent and deep-sea reduced microhabitats (and associated constraints) to determine if the Polynoidae SD globins have been the targets of diversifying selection...
November 1, 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29075833/transcriptome-profiling-of-neurosensory-perception-genes-in-wing-tissue-of-two-evolutionary-distant-insect-orders-diptera-drosophila-melanogaster-and-hemiptera-acyrthosiphon-pisum
#9
Sandra Agnel, Martine da Rocha, Alain Robichon
The neurogenesis and neuronal functions in insect wing have been understudied mainly due to technical hindrances that have prevented electrophysiology studies for decades. The reason is that the nano-architecture of the wing chemosensory bristles hampers the receptors accessibility of odorants/tastants to receptors in fixed setup, whereas in nature, the wing flapping mixes these molecules in bristle lymph. In this report, we analyzed the transcriptome of the wing tissue of two species phylogenetically strongly divergent: Drosophila melanogaster a generic model for diptera order (complete metamorphosis) and the aphid acyrthosiphon pisum, representative of hemiptera order (incomplete metamorphosis) for which a conditional winged/wingless polyphenism is under control of population density and resources...
October 26, 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29103173/a-role-for-the-mutagenic-dna-self-catalyzed-depurination-mechanism-in-the-evolution-of-7sl-derived-rnas
#10
Maxwell P Gold, Jacques R Fresco
The Alu element, the most prevalent SINE (short interspersed element) in the human genome, is one of the many RNA-encoding genes that evolved from the 7SL RNA gene. During analysis of the evolution of 7SL-derived RNAs, two distinct evolutionary intermediates capable of self-catalyzed DNA depurination (SDP) were identified. These SDP sequences spontaneously create apurinic sites that can result in increased mutagenesis due to their error-prone repair. This DNA self-depurination mechanism has been shown both in vitro and in vivo to lead to substitution and short frameshift mutations at a frequency that far exceeds their occurrence due to random errors in DNA replication...
October 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29085968/evolution-of-the-aux-iaa-gene-family-in-hexaploid-wheat
#11
Linyi Qiao, Li Zhang, Xiaojun Zhang, Lei Zhang, Xin Li, Jianzhong Chang, Haixian Zhan, Huijuan Guo, Jun Zheng, Zhijian Chang
The Aux/IAA (IAA) gene family, involved in the auxin signalling pathway, acts as an important regulator in plant growth and development. In this study, we explored the evolutionary trajectory of the IAA family in common wheat. The results showed ten pairs of paralogs among 34 TaIAA family members. Seven of the pairs might have undergone segmental duplication, and the other three pairs appear to have experienced tandem duplication. Except for TaIAA15-16, these duplication events occurred in the ancestral genomes before the divergence of Triticeae...
October 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29071358/tracing-the-evolutionary-history-of-the-cap-superfamily-of-proteins-using-amino-acid-sequence-homology-and-conservation-of-splice-sites
#12
Anup Abraham, Douglas E Chandler
Proteins of the CAP superfamily play numerous roles in reproduction, innate immune responses, cancer biology, and venom toxicology. Here we document the breadth of the CAP (Cysteine-RIch Secretory Protein (CRISP), Antigen 5, and Pathogenesis-Related) protein superfamily and trace the major events in its evolution using amino acid sequence homology and the positions of exon/intron borders within their genes. Seldom acknowledged in the literature, we find that many of the CAP subfamilies present in mammals, where they were originally characterized, have distinct homologues in the invertebrate phyla...
October 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29071357/evolutionary-analysis-of-pectin-lyases-of-the-genus-colletotrichum
#13
Alicia Lara-Márquez, Ken Oyama, María G Zavala-Páramo, Maria G Villa-Rivera, Ulises Conejo-Saucedo, Horacio Cano-Camacho
Pectin lyases (PNLs) are important enzymes that are involved in plant cell wall degradation during the infection process. Colletotrichum is a diverse genus of fungi, which allows the study of the evolution of PNLs and their possible role in pathogen-host interactions and lifestyle adaptations. The phylogenetic reconstruction of PNLs from Colletotrichum and analysis of selection pressures showed the formation of protein lineages by groups of species with different selection pressures and specific patterns. The analysis of positive selection at individual sites using different methods allowed for the identification of three codons with evidence of positive selection in the oligosaccharide-binding region and two codons on the antiparallel sheet, which may influence the interaction with the substrate...
October 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/28916841/some-liked-it-hot-a-hypothesis-regarding-establishment-of-the-proto-mitochondrial-endosymbiont-during-eukaryogenesis
#14
Cory D Dunn
Eukaryotic cells are characterized by a considerable increase in subcellular compartmentalization when compared to prokaryotes. Most evidence suggests that the earliest eukaryotes consisted of mitochondria derived from an α-proteobacterial ancestor enclosed within an archaeal host cell. However, what benefits the archaeal host and the proto-mitochondrial endosymbiont might have obtained at the beginning of this endosymbiotic relationship remains unclear. In this work, I argue that heat generated by the proto-mitochondrion initially permitted an archaeon living at high temperatures to colonize a cooler environment, thereby removing apparent limitations on cellular complexity...
October 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/28828631/microevolution-rather-than-large-genome-divergence-determines-the-effectiveness-of-legume-rhizobia-symbiotic-interaction-under-field-conditions
#15
LETTER
Cintia Jozefkowicz, Silvina Brambilla, Romina Frare, Margarita Stritzler, Mariana Puente, Carlos Piccinetti, Gabriela Soto, Nicolás Ayub
Despite the vast screening for natural nitrogen-fixing isolates by public and private consortia, no significant progresses in the production of improved nitrogen-fixing inoculants for alfalfa production have been made in the last years. Here, we present a comprehensive characterization of the nitrogen-fixing strain Ensifer meliloti B399 (originally named Rhizobium meliloti 102F34), probably the inoculant most widely used in alfalfa production since the 1960s. Complete nucleotide sequence and genome analysis of strain B399 showed that the three replicons present in this commercial strain and the model bacterium Ensifer meliloti 1021 are extremely similar to each other in terms of nucleotide identity and synteny conservation...
October 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/28835989/idxl-species-tree-inference-using-internode-distance-and-excess-gene-leaf-count
#16
Sourya Bhattacharyya, Jayanta Mukherjee
We propose an extension of the distance matrix methods NJst and ASTRID to infer species trees from incongruent gene trees having Incomplete Lineage Sorting. Both approaches consider the average internode distance (ID) between individual taxa pairs as the distance measure. The measure ID does not use the root of a tree, and thus may not always infer the relative position of a taxon with respect to the root. We define a novel distance measure excess gene leaf count (XL) between individual couplets. The XL measure is computed using the root of a tree...
August 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/28795237/the-adaptive-evolution-database-taed-a-new-release-of-a-database-of-phylogenetically-indexed-gene-families-from-chordates
#17
Russell A Hermansen, Benjamin P Oswald, Stormy Knight, Stephen D Shank, David Northover, Katharine L Korunes, Stephen N Michel, David A Liberles
With the large collections of gene and genome sequences, there is a need to generate curated comparative genomic databases that enable interpretation of results in an evolutionary context. Such resources can facilitate an understanding of the co-evolution of genes in the context of a genome mapped onto a phylogeny, of a protein structure, and of interactions within a pathway. A phylogenetically indexed gene family database, the adaptive evolution database (TAED), is presented that organizes gene families and their evolutionary histories in a species tree context...
August 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/28785970/the-central-symbiosis-of-molecular-biology-molecules-in-mutualism
#18
Kathryn A Lanier, Anton S Petrov, Loren Dean Williams
As illustrated by the mitochondrion and the eukaryotic cell, little in biology makes sense except in light of mutualism. Mutualisms are persistent, intimate, and reciprocal exchanges; an organism proficient in obtaining certain benefits confers those on a partner, which reciprocates by conferring different benefits. Mutualisms (i) increase fitness, (ii) inspire robustness, (iii) are resilient and resistant to change, (iv) sponsor co-evolution, (v) foster innovation, and (vi) involve partners that are distantly related with contrasting yet complementary proficiencies...
August 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/28765990/the-origin-of-life-reactor-and-reduction-of-co2-by-h2-in-inorganic-precipitates
#19
LETTER
J Baz Jackson
It has been suggested that inorganic membranes were forerunners of organic membranes at the origin of life. Such membranes, interposed between alkaline fluid in submarine vents and the more acidic Hadean ocean, were thought to house inorganic molecular machines. H(+) flowed down the pH gradient (ΔpH) from ocean to vent through the molecular machines to drive metabolic reactions for early life. A set of experiments was performed by Herschy et al. (J Mol Evol 79:213-227, 2014) who followed earlier work to construct inorganic precipitate membranes which, they argued, would be transected by a ΔpH...
August 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/28744787/on-the-possibility-of-an-early-evolutionary-origin-for-the-spliced-leader-trans-splicing
#20
Zuzana Krchňáková, Juraj Krajčovič, Matej Vesteg
Trans-splicing is a process by which 5'- and 3'-ends of two pre-RNA molecules transcribed from different sites of the genome can be joined together to form a single RNA molecule. The spliced leader (SL) trans-splicing is mediated by the spliceosome and it allows the replacement of 5'-end of pre-mRNA by 5'(SL)-end of SL-RNA. This form of splicing has been observed in many phylogenetically unrelated eukaryotes. Either the SL trans-splicing (SLTS) originated in the last eukaryotic common ancestor (LECA) (or even earlier) and it was lost in most eukaryotic lineages, or this mechanism of RNA processing evolved several times independently in various unrelated eukaryotic taxa...
August 2017: Journal of Molecular Evolution
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