4,427 results match your criteria Journal of molecular evolution[Journal]


Frontiers in Molecular Evolutionary Medicine.

J Mol Evol 2019 Apr 9. Epub 2019 Apr 9.

Department of Ecology and Evolutionary Biology, Yale University, PO Box 208106, New Haven, CT, 06520-8106, USA.

This paper surveys some of the important insights that molecular evolution has contributed to evolutionary medicine; they include phage therapy, cancer biology, helminth manipulation of the host immune system, quality control of gametes, and pathogen outbreaks. Molecular evolution has helped to revolutionize our understanding of cancer, of autoimmune disease, and of the origin, spread, and pathogenesis of emerging diseases, where it has suggested new therapies, illuminated mechanisms, and revealed historical processes: all have practical therapeutic implications. While much has been accomplished, much remains to be done. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00239-019-09893-5DOI Listing

More Pieces of Ancient than Recent Theoretical Minimal Proto-tRNA-Like RNA Rings in Genes Coding for tRNA Synthetases.

J Mol Evol 2019 Apr 5. Epub 2019 Apr 5.

The National Natural History Collections, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel.

Theoretical minimal RNA rings were designed to mimick life's primordial RNAs by forming stem-loop hairpins and coding once for each of the 20 amino acids, a start and a stop codon. At most 25 22-nucleotide long RNA rings follow these criteria. These align well with a consensus tRNA sequence, predicting for each RNA ring an anticodon and an associated cognate amino acid. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00239-019-09892-6DOI Listing

Testing Empirical Support for Evolutionary Models that Root the Tree of Life.

J Mol Evol 2019 Apr 18;87(2-3):131-142. Epub 2019 Mar 18.

Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, and Illinois Informatics Institute, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.

Trees of life (ToLs) can only be rooted with direct methods that seek optimization of character state information in ingroup taxa. This involves optimizing phylogenetic tree, model and data in an exercise of reciprocal illumination. Rooted ToLs have been built from a census of protein structural domains in proteomes using two kinds of models. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00239-019-09891-7DOI Listing
April 2019
2 Reads

Visualization of Genetic Drift Processes Using the Conserved Collagen 1α1 GXY Domain.

J Mol Evol 2019 Apr 13;87(2-3):106-130. Epub 2019 Mar 13.

Triskelion, Utrechtseweg 48, 3704 HE, Zeist, The Netherlands.

Speciation proceeds by the accumulation of DNA differences in time. The genetic code changes as a result of genetic drift and by selective pressure. In variable domains, exposure to high selective pressure obscures the view on background mutations. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00239-019-09890-8DOI Listing

Conserved Critical Evolutionary Gene Structures in Orthologs.

J Mol Evol 2019 Apr 28;87(2-3):93-105. Epub 2019 Feb 28.

Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, c/Nicolás Cabrera 1, 28049, Madrid, Spain.

Unravelling gene structure requires the identification and understanding of the constraints that are often associated with the evolutionary history and functional domains of genes. We speculated in this manuscript with the possibility of the existence in orthologs of an emergent highly conserved gene structure that might explain their coordinated evolution during speciation events and their parental function. Here, we will address the following issues: (1) is there any conserved hypothetical structure along ortholog gene sequences? (2) If any, are such conserved structures maintained and conserved during speciation events? The data presented show evidences supporting this hypothesis. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00239-019-09889-1DOI Listing
April 2019
3 Reads

The Chemical Likelihood of Ribonucleotide-α-Amino acid Copolymers as Players for Early Stages of Evolution.

J Mol Evol 2019 Apr 20;87(2-3):83-92. Epub 2019 Feb 20.

IBMM, University of Montpellier, CNRS, ENSCM, Montpellier, France.

How ribosomal translation could have evolved remains an open question in most available scenarios for the early developments of life. Rather than considering RNA and peptides as two independent systems, this work is aimed at assessing the possibility of formation and stability of co-polymers or co-oligomers of α-amino acids and nucleotides from which translation might have evolved. Here we show that the linkages required to build such mixed structures have lifetimes of several weeks to months at neutral pH and 20 °C owing to the mutual protecting effect of both neighboring phosphoramidate and ester functional groups increasing their stability by factors of about 1 and 3 orders of magnitude, respectively. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00239-019-9887-7DOI Listing
April 2019
1 Read

A New Editorial Beginning at Journal of Molecular Evolution.

Authors:
David A Liberles

J Mol Evol 2019 Apr;87(2-3):69-71

Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA, 19122, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00239-019-09888-2DOI Listing

In Vitro Selection of a DNA Aptamer by Cell-SELEX as a Molecular Probe for Cervical Cancer Recognition and Imaging.

J Mol Evol 2019 Apr 19;87(2-3):72-82. Epub 2019 Jan 19.

CAS Key Laboratory of Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215123, China.

Aptamers have become the most promising recognition reagents in terms of early diagnosis and effective treatment of cancers. In this study, using cervical cancer as a model, we have identified a DNA aptamer specifically binding to cervical cancer cells with high affinity using the cell-SELEX (systematic evolution of ligands by exponential enrichment) method, in which a negative selection was carried out using normal epithelial cells as control. The binding abilities of 6 selected truncated aptamers were determined by laser confocal fluorescence microscopy and flow cytometry, while most of them only recognize the target cells and do not bind the control cells, and the aptamer C-9S with 51-mer shows the best binding affinity to Ca Ski cells (target cells) with a dissociation constant value of 19. Read More

View Article

Download full-text PDF

Source
http://link.springer.com/10.1007/s00239-019-9886-8
Publisher Site
http://dx.doi.org/10.1007/s00239-019-9886-8DOI Listing
April 2019
14 Reads
1.680 Impact Factor

An Extension of the Kimura Two-Parameter Model to the Natural Evolutionary Process.

J Mol Evol 2019 Jan 10;87(1):60-67. Epub 2019 Jan 10.

Department of Information Sciences, Tokyo University of Science, Noda, Chiba, 278-8510, Japan.

Accurate estimates of genetic difference are required for research in evolutionary biology. Here we extend the Kimura two-parameter (K2P) model by considering gaps (insertions and/or deletions) and introduce a new measure for estimating genetic difference between two nucleotide sequences in terms of nucleotide changes that have occurred during the evolutionary process. Using the nuclear ribosomal DNA internal transcribed spacer 2 region from the genus Physalis, we demonstrate that species identification and phylogenetic studies strongly depend on evolutionary models. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00239-018-9885-1DOI Listing
January 2019
1 Read

Gene Encoding a Novel Enzyme of LDH2/MDH2 Family is Lost in Plant and Animal Genomes During Transition to Land.

J Mol Evol 2019 Jan 4;87(1):52-59. Epub 2019 Jan 4.

The A.O. Kovalevsky Institute of Marine Biology Research of RAS, Nakhimov av., 2, Sevastopol, Russia, 299011.

L-Lactate/malate dehydrogenases (LDH/MDH) and type 2 L-lactate/malate dehydrogenases (LDH2/MDH2) belong to NADH/NADPH-dependent oxidoreductases (anaerobic dehydrogenases). They form a large protein superfamily with multiple enzyme homologs found in all branches of life: from bacteria and archaea to eukaryotes, and play an essential role in metabolism. Here, we describe the gene encoding a new enzyme of LDH2/MDH2 oxidoreductase family. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00239-018-9884-2DOI Listing
January 2019
1 Read

Understanding the Evolution of Mitochondrial Genomes in Phaeophyceae Inferred from Mitogenomes of Ishige okamurae (Ishigeales) and Dictyopteris divaricata (Dictyotales).

J Mol Evol 2019 Jan 2;87(1):16-26. Epub 2019 Jan 2.

Bantry Marine Research Station, Gearhies, Bantry, Co. Cork, Ireland.

To gain further insight into the evolution of mitochondrial genomes (mtDNAs) in Phaeophyceae, the first recorded characterization of an Ishigeophycidae mtDNA from Ishige okamurae (Yendo), and only the second recorded characterization of a Dictyotophycidae mtDNA from Dictyopteris divaricata (Okamura) Okamura are presented in this study. The 35,485 bp I. okamurae mtDNA contained 36 protein-coding genes (PCGs), 22 tRNAs, three rRNAs, and four open reading frames (orfs), and the 32,021 bp D. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00239-018-9881-5DOI Listing
January 2019
1 Read

Alarmones as Vestiges of a Bygone RNA World.

J Mol Evol 2019 Jan 2;87(1):37-51. Epub 2019 Jan 2.

Facultad de Ciencias, Universidad Nacional Autónoma de México, Cd. Universitaria, 04510, Mexico City, Mexico.

All known alarmones are ribonucleotides or ribonucleotide derivatives that are synthesized when cells are under stress conditions, triggering a stringent response that affects major processes such as replication, gene expression, and metabolism. The ample phylogenetic distribution of alarmones (e.g. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00239-018-9883-3DOI Listing
January 2019
3 Reads

Genetic Code Error Minimization as a Non-Adaptive But Beneficial Trait.

Authors:
Steven E Massey

J Mol Evol 2019 Jan 2;87(1):4-6. Epub 2019 Jan 2.

Biology Department, University of Puerto Rico - Rio Piedras, San Juan, PR, 00931, USA.

In a recent Letter, Di Giulio questions the use of the term 'neutral' when describing the process by which error minimization may have arisen as a side-product of genetic code expansion, resulting from the addition of similar amino acids to similar codons (Di Giulio, in J Mol Evol 86(9):593-597, 2018). However, I point out that in this scenario error minimization is non-adaptive, and so 'neutral' is an appropriate term to describe its imperviousness to direct selection. Error minimization is a form of mutational robustness, and so commonly viewed as beneficial. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00239-018-9880-6DOI Listing
January 2019
1 Read

Amino Acids in Life: A Prebiotic Division of Labor.

J Mol Evol 2019 Jan 2;87(1):1-3. Epub 2019 Jan 2.

Center for Molecular Evolution, California State University, California, USA.

There are more than 20 amino acids used in Biology, and their utilization is enigmatic. Here, I propose that there was a prebiotic division of labor between two subsets of amino acids. The first set is the alpha-L set, which includes all the genetically encoded amino acids. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00239-018-9879-zDOI Listing
January 2019
1 Read

Biophysical Spandrels form a Hot-Spot for Kosmotropic Mutations in Bacteriophage Thermal Adaptation.

J Mol Evol 2019 Jan 18;87(1):27-36. Epub 2018 Dec 18.

Department of Biological Science, Florida State University, 319 Stadium Dr., Tallahassee, FL, 32306, USA.

Temperature plays a dominating role in protein structure and function, and life has evolved myriad strategies to adapt proteins to environmental thermal stress. Cellular systems can utilize kosmotropic osmolytes, the products of complex biochemical pathways, to act as chemical chaperones. These extrinsic molecules, e. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00239-018-9882-4DOI Listing
January 2019
1 Read

Genes Encoding Mammalian Oviductal Proteins Involved in Fertilization are Subjected to Gene Death and Positive Selection.

J Mol Evol 2018 Dec 20;86(9):655-667. Epub 2018 Nov 20.

PRC, INRA, CNRS, IFCE, Université de Tours, 37380, Nouzilly, France.

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. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00239-018-9878-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6267676PMC
December 2018
16 Reads

Genomic Signatures Among Acanthamoeba polyphaga Entoorganisms Unveil Evidence of Coevolution.

J Mol Evol 2019 Jan 20;87(1):7-15. Epub 2018 Nov 20.

Laboratório de Genética Evolutiva Paulo Leminsk, Departamento de Biologia Molecular, Centro de Ciencias Exatas e da Natureza, Universidade Federal da Paraíba, João Pessoa, Brazil.

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. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00239-018-9877-1DOI Listing
January 2019
4 Reads

Folding, Assembly, and Persistence: The Essential Nature and Origins of Biopolymers.

J Mol Evol 2018 Dec 19;86(9):598-610. Epub 2018 Nov 19.

School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA.

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. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00239-018-9876-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6267704PMC
December 2018
11 Reads

Delineation of the Genera Haemoproteus and Plasmodium Using RNA-Seq and Multi-gene Phylogenetics.

J Mol Evol 2018 Dec 13;86(9):646-654. Epub 2018 Nov 13.

Department of Biology, San Francisco State University, 1700 Holloway Ave, San Francisco, CA, 94132, USA.

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. Read More

View Article

Download full-text PDF

Source
http://link.springer.com/10.1007/s00239-018-9875-3
Publisher Site
http://dx.doi.org/10.1007/s00239-018-9875-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6430206PMC
December 2018
15 Reads

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.

J Mol Evol 2018 Dec 3;86(9):613-617. Epub 2018 Nov 3.

Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, 8415 MRB IV, 2213 Garland Ave, 37232-0615, Nashville, TN, USA.

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. Read More

View Article

Download full-text PDF

Source
http://link.springer.com/10.1007/s00239-018-9873-5
Publisher Site
http://dx.doi.org/10.1007/s00239-018-9873-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6309332PMC
December 2018
6 Reads

Why Prokaryotes Genomes Lack Genes with Introns Processed by Spliceosomes?

J Mol Evol 2018 Dec 31;86(9):611-612. Epub 2018 Oct 31.

Laboratorio de Organización y Evolución del Genoma, Unidad Genómica Evolutiva, Facultad de Ciencias, 11400, Montevideo, Uruguay.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00239-018-9874-4DOI Listing
December 2018
1 Read

Positive Selection in the Evolution of Mammalian CRISPs.

J Mol Evol 2018 Dec 28;86(9):635-645. Epub 2018 Oct 28.

Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico.

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. Read More

View Article

Download full-text PDF

Source
http://link.springer.com/10.1007/s00239-018-9872-6
Publisher Site
http://dx.doi.org/10.1007/s00239-018-9872-6DOI Listing
December 2018
19 Reads

A Non-neutral Origin for Error Minimization in the Origin of the Genetic Code.

J Mol Evol 2018 Dec 25;86(9):593-597. Epub 2018 Oct 25.

Early Evolution of Life Laboratory, Institute of Biosciences and Bioresources, CNR, Via P. Castellino, 111, 80131, Naples, Italy.

Massey (J Mol Evol 67:510-516, 2008; J Theor Biol 408:237-242, 2016; Nat Comput. https://doi.org/10. Read More

View Article

Download full-text PDF

Source
http://link.springer.com/10.1007/s00239-018-9871-7
Publisher Site
http://dx.doi.org/10.1007/s00239-018-9871-7DOI Listing
December 2018
12 Reads

Evolutionary Genetics of Hypoxia and Cold Tolerance in Mammals.

J Mol Evol 2018 Dec 16;86(9):618-634. Epub 2018 Oct 16.

Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.

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. Read More

View Article

Download full-text PDF

Source
http://link.springer.com/10.1007/s00239-018-9870-8
Publisher Site
http://dx.doi.org/10.1007/s00239-018-9870-8DOI Listing
December 2018
3 Reads

Circular Permutation Obscures Universality of a Ribosomal Protein.

J Mol Evol 2018 Oct 10;86(8):581-592. Epub 2018 Oct 10.

School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332-0400, USA.

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. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00239-018-9869-1DOI Listing
October 2018
1 Read

Ancestral and Compensatory Mutations that Promote Antiviral Resistance in Influenza N1 Neuraminidase Revealed by a Phylonumerics Approach.

J Mol Evol 2018 Oct 9;86(8):546-553. Epub 2018 Oct 9.

Infectious Disease Responses Laboratory, Prince of Wales Clinical School, University of New South Wales, Sydney, NSW, 2052, Australia.

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. Read More

View Article

Download full-text PDF

Source
http://link.springer.com/10.1007/s00239-018-9866-4
Publisher Site
http://dx.doi.org/10.1007/s00239-018-9866-4DOI Listing
October 2018
2 Reads

An Analysis of IS630/Tc1/mariner Transposons in the Genome of a Pacific Oyster, Crassostrea gigas.

J Mol Evol 2018 Oct 3;86(8):566-580. Epub 2018 Oct 3.

Department of Medicine, Novosibirsk State University, Pirogova st., 1, Novosibirsk, Russia, 630090.

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. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00239-018-9868-2DOI Listing
October 2018
1 Read

The Ammonium Channel NOD26 is the Evolutionary Innovation that Drives the Emergence, Consolidation, and Dissemination of Nitrogen-Fixing Symbiosis in Angiosperms.

J Mol Evol 2018 Oct 20;86(8):554-565. Epub 2018 Sep 20.

Instituto de Genética Ewald A. Favret (IGEAF), De los Reseros S/N, Castelar C25(1712), Buenos Aires, Argentina.

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. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00239-018-9867-3DOI Listing
October 2018
1 Read

Computational Models of Polymer Synthesis Driven by Dehydration/Rehydration Cycles: Repurination in Simulated Hydrothermal Fields.

J Mol Evol 2018 Oct 15;86(8):501-510. Epub 2018 Sep 15.

University of California Santa Cruz , 1156 High Street, Santa Cruz, CA, 95064, USA.

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. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00239-018-9865-5DOI Listing
October 2018
1 Read

Three-Finger Toxin Diversification in the Venoms of Cat-Eye Snakes (Colubridae: Boiga).

J Mol Evol 2018 Oct 12;86(8):531-545. Epub 2018 Sep 12.

Venom Evolution Lab, School of Biological Sciences, University of Queensland, St Lucia, QLD, 4072, Australia.

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. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00239-018-9864-6DOI Listing
October 2018
2 Reads

Identification and Analysis of OVATE Family Members from Genome of the Early Land Plants Provide Insights into Evolutionary History of OFP Family and Function.

J Mol Evol 2018 Oct 11;86(8):511-530. Epub 2018 Sep 11.

Department of Botany, University of Delhi, Delhi, 110007, India.

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. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00239-018-9863-7DOI Listing
October 2018
1 Read

Oligomerization of a Bimolecular Ribozyme Modestly Rescues its Structural Defects that Disturb Interdomain Assembly to Form the Catalytic Site.

J Mol Evol 2018 Aug 14;86(7):431-442. Epub 2018 Aug 14.

Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, Toyama, 930-8555, Japan.

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. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00239-018-9862-8DOI Listing
August 2018
1 Read
1.680 Impact Factor

Cotranscriptional 3'-End Processing of T7 RNA Polymerase Transcripts by a Smaller HDV Ribozyme.

J Mol Evol 2018 Aug 11;86(7):425-430. Epub 2018 Aug 11.

Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA.

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. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00239-018-9861-9DOI Listing
August 2018
1 Read

Scratching the Surface of an Itch: Molecular Evolution of Aculeata Venom Allergens.

J Mol Evol 2018 Aug 31;86(7):484-500. Epub 2018 Jul 31.

Venom Evolution Lab, School of Biological Sciences, University of Queensland, St Lucia, QLD, 4072, Australia.

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 A, phospholipase A, acid phosphatase, hyaluronidase, serine protease and antigen 5. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00239-018-9860-xDOI Listing
August 2018
18 Reads

Investigation on the Evolutionary Relation of Diverse Polyhydroxyalkanoate Gene Clusters in Betaproteobacteria.

J Mol Evol 2018 Aug 31;86(7):470-483. Epub 2018 Jul 31.

Department of Biotechnology and Bioengineering, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Av. IPN 2508, Zacatenco Gustavo A. Madero, Mexico, DF, Mexico.

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. Read More

View Article

Download full-text PDF

Source
https://www.researchgate.net/publication/225501674_Isolation
Web Search
http://link.springer.com/10.1007/s00239-018-9859-3
Publisher Site
http://dx.doi.org/10.1007/s00239-018-9859-3DOI Listing
August 2018
9 Reads

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.

J Mol Evol 2018 Aug 28;86(7):457-469. Epub 2018 Jul 28.

Department of Biological Science, Graduate School of Science, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan.

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. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00239-018-9858-4DOI Listing
August 2018
1 Read

Evolutionary Perspectives of Genotype-Phenotype Factors in Leishmania Metabolism.

J Mol Evol 2018 Aug 19;86(7):443-456. Epub 2018 Jul 19.

Chemical Engineering and Process Development, CSIR-National Chemical Laboratory, Pune, Maharashtra, India.

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. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00239-018-9857-5DOI Listing
August 2018
1 Read

Retroelements and DNA Methylation Could Contribute to Diversity of 5S rDNA in Agave L.

J Mol Evol 2018 Jul 10;86(6):404-423. Epub 2018 Jul 10.

Unidad de Biotecnología, Centro de Investigación Científica de Yucatán A.C., Calle 43 No. 130, Colonia Chuburná de Hidalgo, C.P. 97200, Mérida, Yucatán, Mexico.

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. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00239-018-9856-6DOI Listing
July 2018
1 Read

Haplogroup Context is Less Important in the Penetrance of Mitochondrial DNA Complex I Mutations Compared to mt-tRNA Mutations.

J Mol Evol 2018 Jul 9;86(6):395-403. Epub 2018 Jul 9.

Institute of Genetic Medicine, Newcastle University, Newcastle-upon-Tyne, NE1 3BZ, UK.

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. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00239-018-9855-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6061473PMC
July 2018
5 Reads

Evolution of the Biosynthetic Pathway for Cyanogenic Glucosides in Lepidoptera.

J Mol Evol 2018 Jul 4;86(6):379-394. Epub 2018 Jul 4.

Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark.

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. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00239-018-9854-8DOI Listing
July 2018
1 Read

The Standard Genetic Code Facilitates Exploration of the Space of Functional Nucleotide Sequences.

J Mol Evol 2018 Jul 29;86(6):325-339. Epub 2018 Jun 29.

PhD Program in Systems, Synthetic, and Physical Biology, Rice University, Houston, TX, 77005, USA.

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. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00239-018-9852-xDOI Listing
July 2018
3 Reads

Correlated Selection on Amino Acid Deletion and Replacement in Mammalian Protein Sequences.

J Mol Evol 2018 Jul 28;86(6):365-378. Epub 2018 Jun 28.

Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204-5001, USA.

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. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00239-018-9853-9DOI Listing
July 2018
1 Read

Evolutionary Dynamics of Copy Number and Meiotic Recombination in Murine 5S rDNA: Possible Involvement of Natural Selection.

J Mol Evol 2018 Jun 12;86(5):312-323. Epub 2018 Jun 12.

Graduate School of Earth Science, Hokkaido University, North 10, West 5, Sapporo, 060-0810, Japan.

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. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00239-018-9848-6DOI Listing
June 2018
12 Reads

Correction to: Transposable Elements Activity is Positively Related to Rate of Speciation in Mammals.

J Mol Evol 2018 Jun;86(5):311

Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy.

The original version of the article unfortunately contained tagging error in Given and Surname of all the authors. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00239-018-9850-zDOI Listing
June 2018
1 Read

Concurrent Duplication of Drosophila Cid and Cenp-C Genes Resulted in Accelerated Evolution and Male Germline-Biased Expression of the New Copies.

J Mol Evol 2018 Jul 23;86(6):353-364. Epub 2018 Jun 23.

Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil.

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. Read More

View Article

Download full-text PDF

Source
http://link.springer.com/10.1007/s00239-018-9851-y
Publisher Site
http://dx.doi.org/10.1007/s00239-018-9851-yDOI Listing
July 2018
4 Reads

Genes Relocated Between Drosophila Chromosome Arms Evolve Under Relaxed Selective Constraints Relative to Non-Relocated Genes.

J Mol Evol 2018 Jul 21;86(6):340-352. Epub 2018 Jun 21.

Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204, USA.

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. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00239-018-9849-5DOI Listing
July 2018
2 Reads

Transposable Elements Activity is Positively Related to Rate of Speciation in Mammals.

J Mol Evol 2018 Jun 31;86(5):303-310. Epub 2018 May 31.

Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy.

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). Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00239-018-9847-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6028844PMC
June 2018
1 Read

Exploration of RNA Sequence Space in the Absence of a Replicase.

J Mol Evol 2018 Jun 11;86(5):264-276. Epub 2018 May 11.

Department Biology & Biochemistry, University of Houston, 3455 Cullen Blvd, Suite #342, Houston, TX, 77204-5001, USA.

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. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00239-018-9846-8DOI Listing
June 2018
4 Reads

Chiral Monomers Ensure Orientational Specificity of Monomer Binding During Polymer Self-Replication.

J Mol Evol 2018 Jun 3;86(5):255-263. Epub 2018 May 3.

Integrated Mathematical Oncology Department and Cancer Biology and Evolution Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA.

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. Read More

View Article

Download full-text PDF

Source
http://link.springer.com/10.1007/s00239-018-9845-9
Publisher Site
http://dx.doi.org/10.1007/s00239-018-9845-9DOI Listing
June 2018
4 Reads

Domain-Specific Proteogenomic Analysis of Collagens to Evaluate De Novo Sequencing Results and Database Information.

J Mol Evol 2018 Jun 2;86(5):293-302. Epub 2018 May 2.

Triskelion, Utrechtseweg 48, 3704 HE, Zeist, The Netherlands.

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. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00239-018-9844-xDOI Listing
June 2018
5 Reads