scholarly journals An evolutionary perspective on protein moonlighting

2014 ◽  
Vol 42 (6) ◽  
pp. 1684-1691 ◽  
Author(s):  
Shelley D. Copley
Keyword(s):  
Point Mutations ◽  
Optimal Solution ◽  
Gene Encoding ◽  
Genetic Changes ◽  
Moonlighting Protein ◽  
History Of ◽  
Moonlighting Proteins ◽  
Ultimate Outcome ◽  
Moonlighting Functions ◽  
Population Effects

Moonlighting proteins serve one or more novel functions in addition to their canonical roles. Moonlighting functions arise when an adventitious interaction between a protein and a new partner improves fitness of the organism. Selective pressure for improvement in the new function can result in two alternative outcomes. The gene encoding the newly bifunctional protein may duplicate and diverge so as to encode two proteins, each of which serves only one function. Alternatively, genetic changes that minimize adaptive conflict between the two functions and/or improve control over the time and place at which each function is served can lead to a moonlighting protein. Importantly, genetic changes that enhance a moonlighting function can occur in the gene encoding the moonlighting protein itself, in a gene that affects the structure of its new partner or in a gene encoding a transcription factor that controls expression of either partner. The evolutionary history of each moonlighting protein is complex, depending on the stochastic occurrence of genetic changes such as gene duplication and point mutations, and the effects of those changes on fitness. Population effects, particularly loss of promising individuals due to random genetic drift, also play a role in the emergence of a moonlighting protein. The ultimate outcome is not necessarily the ‘optimal’ solution to the problem of serving two functions, but may be ‘good enough’ so that fitness becomes limited by some other function.

Medical and Veterinary Importance of the Moonlighting Functions of Triosephosphate Isomerase

2019 ◽  
Vol 20 (4) ◽  
pp. 304-315 ◽  
Author(s):  
Mónica Rodríguez-Bolaños ◽  
Ruy Perez-Montfort
Keyword(s):  
Cell Cycle ◽  
Immune Response ◽  
Triosephosphate Isomerase ◽  
Dihydroxyacetone Phosphate ◽  
Canonical Function ◽  
Moonlighting Protein ◽  
Veterinary Importance ◽  
Moonlighting Functions

Triosephosphate isomerase is the fifth enzyme in glycolysis and its canonical function is the reversible isomerization of glyceraldehyde-3-phosphate and dihydroxyacetone phosphate. Within the last decade multiple other functions, that may not necessarily always involve catalysis, have been described. These include variations in the degree of its expression in many types of cancer and participation in the regulation of the cell cycle. Triosephosphate isomerase may function as an auto-antigen and in the evasion of the immune response, as a factor of virulence of some organisms, and also as an important allergen, mainly in a variety of seafoods. It is an important factor to consider in the cryopreservation of semen and seems to play a major role in some aspects of the development of Alzheimer's disease. It also seems to be responsible for neurodegenerative alterations in a few cases of human triosephosphate isomerase deficiency. Thus, triosephosphate isomerase is an excellent example of a moonlighting protein.

scholarly journals Real-time SARS-CoV-2 diagnostic and variants tracking over multiple candidates using nanopore DNA sequencing

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
François Stüder ◽  
Jean-Louis Petit ◽  
Stefan Engelen ◽  
Marco Antonio Mendoza-Parra
Keyword(s):  
Real Time ◽  
Optimal Solution ◽  
Proof Of Concept ◽  
Gene Encoding ◽  
Spike Gene ◽  
Long Period ◽  
The World ◽  
Receptor Recognition ◽  
Nanopore Dna Sequencing ◽  
Novel Coronavirus

AbstractSince December 2019, a novel coronavirus responsible for a severe acute respiratory syndrome (SARS-CoV-2) is accountable for a major pandemic situation. The emergence of the B.1.1.7 strain, as a highly transmissible variant has accelerated the world-wide interest in tracking SARS-CoV-2 variants’ occurrence. Similarly, other extremely infectious variants, were described and further others are expected to be discovered due to the long period of time on which the pandemic situation is lasting. All described SARS-CoV-2 variants present several mutations within the gene encoding the Spike protein, involved in host receptor recognition and entry into the cell. Hence, instead of sequencing the whole viral genome for variants’ tracking, herein we propose to focus on the SPIKE region to increase the number of candidate samples to screen at once; an essential aspect to accelerate diagnostics, but also variants’ emergence/progression surveillance. This proof of concept study accomplishes both at once, population-scale diagnostics and variants' tracking. This strategy relies on (1) the use of the portable MinION DNA sequencer; (2) a DNA barcoding and a SPIKE gene-centered variant’s tracking, increasing the number of candidates per assay; and (3) a real-time diagnostics and variant’s tracking monitoring thanks to our software RETIVAD. This strategy represents an optimal solution for addressing the current needs on SARS-CoV-2 progression surveillance, notably due to its affordable implementation, allowing its implantation even in remote places over the world.

Subfunctionalization of Duplicate mitf Genes Associated With Differential Degeneration of Alternative Exons in Fish

Genetics ◽  
2002 ◽  
Vol 161 (1) ◽  
pp. 259-267 ◽  
Author(s):  
Joachim Altschmied ◽  
Jacqueline Delfgaauw ◽  
Brigitta Wilde ◽  
Jutta Duschl ◽  
Laurence Bouneau ◽  
...  
Keyword(s):  
Danio Rerio ◽  
Evolutionary History ◽  
Single Gene ◽  
Regulatory Elements ◽  
Fugu Rubripes ◽  
Gene Encoding ◽  
Tetraodon Nigroviridis ◽  
Mammalian Lineage ◽  
History Of ◽  
Fish Proteins

Abstract The microphthalmia-associated transcription factor (MITF) exists in at least four isoforms. These are generated in higher vertebrates using alternative 5′ exons and promoters from a single gene. Two separate genes (mitf-m and mitf-b), however, are present in different teleost fish species including the poeciliid Xiphophorus, the pufferfishes Fugu rubripes and Tetraodon nigroviridis, and the zebrafish Danio rerio. Fish proteins MITF-m and MITF-b correspond at both the structural and the expression levels to one particular bird/mammalian MITF isoform. In the teleost lineage subfunctionalization of mitf genes after duplication at least 100 million years ago is associated with the degeneration of alternative exons and, probably, regulatory elements and promoters. For example, a remnant of the first exon specific for MITF-m is detected within the pufferfish gene encoding MITF-b. Retracing the evolutionary history of mitf genes in vertebrates uncovered the differential recruitment of new introns specific for either the teleost or the bird/mammalian lineage.

Sequence variation and evolution of nuclear DNA in man and the primates

1981 ◽  
Vol 292 (1057) ◽  
pp. 133-142 ◽  
Keyword(s):  
Dna Sequence ◽  
Sequence Variation ◽  
Nuclear Dna ◽  
Sequence Divergence ◽  
Gene Arrangement ◽  
Human Populations ◽  
Genetic Changes ◽  
Detailed Structural Analysis ◽  
Dna Sequence Variation ◽  
History Of

Recent advances in nucleic acid technology have facilitated the detection and detailed structural analysis of a wide variety of genes in higher organisms, including those in man. This in turn has opened the way to an examination of the evolution of structural genes and their surrounding and intervening sequences. In a study of the evolution of haemoglobin genes and neighbouring sequences in man and the primates, we have investigated gene arrangement and DNA sequence divergence both within and between species ranging from Old World monkeys to man. This analysis is beginning to reveal the evolutionary constraints that have acted on this region of the genome during primate evolution. Furthermore, DNA sequence variation, both within and between species, provides, in principle, a novel and powerful method for determining inter-specific phylogenetic distances and also for analysing the structure of present-day human populations. Application of this new branch of molecular biology to other areas of the human genome should prove important in unravelling the history of genetic changes that have occurred during the evolution of man.

scholarly journals Moonlighting in Mitosis: Analysis of the Mitotic Functions of Transcription and Splicing Factors

Cells ◽  
2020 ◽  
Vol 9 (6) ◽  
pp. 1554 ◽  
Author(s):  
Maria Patrizia Somma ◽  
Evgeniya N. Andreyeva ◽  
Gera A. Pavlova ◽  
Claudia Pellacani ◽  
Elisabetta Bucciarelli ◽  
...  
Keyword(s):  
Evolutionary Process ◽  
Splicing Factors ◽  
Insufficient Data ◽  
Primary Role ◽  
Interphase Nuclei ◽  
Protein Databases ◽  
Moonlighting Proteins ◽  
Bona Fide ◽  
Cellular Compartments ◽  
Moonlighting Functions

Moonlighting proteins can perform one or more additional functions besides their primary role. It has been posited that a protein can acquire a moonlighting function through a gradual evolutionary process, which is favored when the primary and secondary functions are exerted in different cellular compartments. Transcription factors (TFs) and splicing factors (SFs) control processes that occur in interphase nuclei and are strongly reduced during cell division, and are therefore in a favorable situation to evolve moonlighting mitotic functions. However, recently published moonlighting protein databases, which comprise almost 400 proteins, do not include TFs and SFs with secondary mitotic functions. We searched the literature and found several TFs and SFs with bona fide moonlighting mitotic functions, namely they localize to specific mitotic structure(s), interact with proteins enriched in the same structure(s), and are required for proper morphology and functioning of the structure(s). In addition, we describe TFs and SFs that localize to mitotic structures but cannot be classified as moonlighting proteins due to insufficient data on their biochemical interactions and mitotic roles. Nevertheless, we hypothesize that most TFs and SFs with specific mitotic localizations have either minor or redundant moonlighting functions, or are evolving towards the acquisition of these functions.

scholarly journals Regulated aggregative multicellularity in a close unicellular relative of metazoa

eLife ◽  
2013 ◽  
Vol 2 ◽  
Author(s):  
Arnau Sebé-Pedrós ◽  
Manuel Irimia ◽  
Javier del Campo ◽  
Helena Parra-Acero ◽  
Carsten Russ ◽  
...  
Keyword(s):  
Life Cycle ◽  
Alternative Splicing ◽  
Splicing Regulation ◽  
Tissue Architecture ◽  
Genetic Changes ◽  
Aggregative Behavior ◽  
History Of

The evolution of metazoans from their unicellular ancestors was one of the most important events in the history of life. However, the cellular and genetic changes that ultimately led to the evolution of multicellularity are not known. In this study, we describe an aggregative multicellular stage in the protist Capsaspora owczarzaki, a close unicellular relative of metazoans. Remarkably, transition to the aggregative stage is associated with significant upregulation of orthologs of genes known to establish multicellularity and tissue architecture in metazoans. We further observe transitions in regulated alternative splicing during the C. owczarzaki life cycle, including the deployment of an exon network associated with signaling, a feature of splicing regulation so far only observed in metazoans. Our results reveal the existence of a highly regulated aggregative stage in C. owczarzaki and further suggest that features of aggregative behavior in an ancestral protist may had been co-opted to develop some multicellular properties currently seen in metazoans.

scholarly journals Epidemiological aspects of group B streptococci of bovine and human origin

1996 ◽  
Vol 117 (3) ◽  
pp. 417-422 ◽  
Author(s):  
N. E. Jensen ◽  
F. M. Aarestrup
Keyword(s):  
Streptococcus Agalactiae ◽  
Double Diffusion ◽  
Restriction Enzymes ◽  
Group B Streptococci ◽  
Gene Encoding ◽  
Genetic Changes ◽  
Lactose Fermentation ◽  
Phenotypic Variations ◽  
Group B ◽  
Reference Strains

SummaryRestriction fragment length polymorphism of the gene encoding rRNA (ribotyping) was used in combination with conventional epidemiological markers to study phenotypic variations amongStreptococcus agalactiaeof bovine origin and the possible epidemiological interrelationship between the bovine and human reservoirs ofStreptococcus agalactiae.The bovine material constituted 53 strains (9 antigen combinations) isolated from 11 herds. Herds with a uniform as well as heterogenic antigenic pattern were included. Furthermore, strains isolated in the course of time from the same persistently infected quarters were examined. The human material constituted 16 strains, 4 each of 4 serotypes, isolated from healthy carriers. Finally, nine serotype- and the group reference strains were examined. All strains were serotyped by double diffusion in agarose gel, biotyped (lactose ±), and ribotyped using two restriction enzymes,HindIII andHhaI.All isolates could be typed by ribotyping and seven ribotypes were identified among the reference strains. The restriction enzymes used alone or in combination gave typing results that allowed discrimination between and within serotype. Combined use of serotype,HindIII andHhaI ribotypes produced 11 types among the 16 human strains. Ribotype analysis discriminated between herds infected with the same serotype. Strains of varying antigenic patterns from the same herd had the same ribotype. Phenotypic variations in serotype observed in persistent intramammary infection were not related to genetic changes as monitored by ribotype. Two ribotypes were represented among both bovine and human strains. The discriminating capability of lactose fermentation was of limited value.

scholarly journals Parameter Identification of the Vortex-Induced Vertical Force Model Using a New Adaptive PSO

2018 ◽  
Vol 2018 ◽  
pp. 1-9
Author(s):  
Xiaoxia Tian ◽  
Jingwen Yan ◽  
Chi Xiao
Keyword(s):  
Optimal Solution ◽  
Time History ◽  
Vertical Displacement ◽  
Force Model ◽  
Vertical Force ◽  
Inertia Weight ◽  
Adaptive Pso ◽  
Short Run ◽  
History Of ◽  
Searching Ability

The paper proposes a new adaptive PSO (NAPSO) that adaptively adjust the inertial weight of every particle according to its own current fitness. In NAPSO, the searching ability of each particle is controlled by the inertial weight. In pursuit of the optimal solution, if a particle has a rather small value of normalized fitness, it has a small inertia weight so as to increase local searching ability; on the contrary, it has a large inertia weight to increase global searching ability. Simulation results include three parts: the NAPSO shows fast convergence and good stability compared with other PSOs; the NAPSO shows good fit and short run-time compared with GA and GALMA; according to the identified parameters, the time history of predicted vertical displacement is quite in accordance with the time history of measured displacement. As far as the nonlinear VIVF model is concerned, the NAPSO is a simple and effective identification method.

scholarly journals Ancient origin of the gene encoding involucrin, a precursor of the cross-linked envelope of epidermis and related epithelia

2008 ◽  
Vol 105 (40) ◽  
pp. 15481-15486 ◽  
Author(s):  
Amandine Vanhoutteghem ◽  
Philippe Djian ◽  
Howard Green
Keyword(s):  
Terminal Differentiation ◽  
Ancient History ◽  
Gene Encoding ◽  
Cornified Envelope ◽  
Good Substrate ◽  
History Of ◽  
The Cross ◽  
Characteristic Product

The cross-linked (cornified) envelope is a characteristic product of terminal differentiation in the keratinocyte of the epidermis and related epithelia. This envelope contains many proteins of which involucrin was the first to be discovered and shown to become cross-linked by a cellular transglutaminase. Involucrin has evolved greatly in placental mammals, but retains the glutamine repeats that make it a good substrate for the transglutaminase. Until recently, it has been impossible to detect involucrin outside the placental mammals, but analysis of the GenBank and Ensembl databases that have become available since 2006 reveals the existence of involucrin in marsupials and birds. We describe here the properties of these involucrins and the ancient history of their evolution.

scholarly journals The genetic basis of evolutionary change in gene expression levels

2010 ◽  
Vol 365 (1552) ◽  
pp. 2581-2590 ◽  
Author(s):  
J. J. Emerson ◽  
Wen-Hsiung Li
Keyword(s):  
Gene Expression ◽  
Genetic Basis ◽  
Regulation Of Gene Expression ◽  
Specific Expression ◽  
Genetic Changes ◽  
Expression Variation ◽  
Regulatory Variation ◽  
Global Mapping ◽  
History Of ◽  
Trait Locus

The regulation of gene expression is an important determinant of organismal phenotype and evolution. However, the widespread recognition of this fact occurred long after the synthesis of evolution and genetics. Here, we give a brief sketch of thoughts regarding gene regulation in the history of evolution and genetics. We then review the development of genome-wide studies of gene regulatory variation in the context of the location and mode of action of the causative genetic changes. In particular, we review mapping of the genetic basis of expression variation through expression quantitative trait locus studies and measuring the cis / trans component of expression variation in allele-specific expression studies. We conclude by proposing a systematic integration of ideas that combines global mapping studies, cis / trans tests and modern population genetics methodologies, in order to directly estimate the forces acting on regulatory variation within and between species.

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