scholarly journals Processed pseudogenes: A substrate for evolutionary innovation

BioEssays ◽  
2021 ◽  
pp. 2100186
Author(s):  
Robin‐Lee Troskie ◽  
Geoffrey J. Faulkner ◽  
Seth W. Cheetham
Keyword(s):  
Evolutionary Innovation ◽  
Processed Pseudogenes

Homology, Genes, and Evolutionary Innovation

2014 ◽  
Author(s):  
Günter P. Wagner
Keyword(s):  
Evolutionary Biology ◽  
Regulatory Networks ◽  
Biological Diversity ◽  
Cell Types ◽  
Origin And Evolution ◽  
Major Transitions ◽  
Form And Function ◽  
Historical Continuity ◽  
Evolutionary Innovation ◽  
Character Identity

Homology—a similar trait shared by different species and derived from common ancestry, such as a seal's fin and a bird's wing—is one of the most fundamental yet challenging concepts in evolutionary biology. This book provides the first mechanistically based theory of what homology is and how it arises in evolution. The book argues that homology, or character identity, can be explained through the historical continuity of character identity networks—that is, the gene regulatory networks that enable differential gene expression. It shows how character identity is independent of the form and function of the character itself because the same network can activate different effector genes and thus control the development of different shapes, sizes, and qualities of the character. Demonstrating how this theoretical model can provide a foundation for understanding the evolutionary origin of novel characters, the book applies it to the origin and evolution of specific systems, such as cell types; skin, hair, and feathers; limbs and digits; and flowers. The first major synthesis of homology to be published in decades, this book reveals how a mechanistically based theory can serve as a unifying concept for any branch of science concerned with the structure and development of organisms, and how it can help explain major transitions in evolution and broad patterns of biological diversity.

scholarly journals From immune to olfactory expression: neofunctionalization of formyl peptide receptors

2021 ◽  
Vol 383 (1) ◽  
pp. 387-393
Author(s):  
Madlaina Boillat ◽  
Alan Carleton ◽  
Ivan Rodriguez
Keyword(s):  
Expression Patterns ◽  
Vomeronasal Organ ◽  
Formyl Peptide Receptor ◽  
Regulatory Sequence ◽  
Powerful Source ◽  
Peptide Receptor ◽  
Gene Shuffling ◽  
Evolutionary Innovation ◽  
Vomeronasal Receptor ◽  
Formyl Peptide

Abstract Variations in gene expression patterns represent a powerful source of evolutionary innovation. In a rodent living about 70 million years ago, a genomic accident led an immune formyl peptide receptor (FPR) gene to hijack a vomeronasal receptor regulatory sequence. This gene shuffling event forced an immune pathogen sensor to transition into an olfactory chemoreceptor, which thus moved from sensing the internal world to probing the outside world. We here discuss the evolution of the FPR gene family, the events that led to their neofunctionalization in the vomeronasal organ and the functions of immune and vomeronasal FPRs.

scholarly journals Evolutionary direction of processed pseudogenes

2016 ◽  
Vol 59 (8) ◽  
pp. 839-849 ◽  
Author(s):  
Guoqing Liu ◽  
Xiangjun Cui ◽  
Hong Li ◽  
Lu Cai
Keyword(s):  
Processed Pseudogenes

scholarly journals A strategy to detect and isolate an intron-containing gene in the presence of multiple processed pseudogenes

1989 ◽  
Vol 86 (17) ◽  
pp. 6691-6695 ◽  
Author(s):  
B Davies ◽  
S Feo ◽  
E Heard ◽  
M Fried
Keyword(s):  
Ribosomal Protein ◽  
Recombinant Dna ◽  
Single Gene ◽  
Ribosomal Protein Gene ◽  
Pcr Primers ◽  
Pcr Product ◽  
Dna Libraries ◽  
Processed Pseudogenes ◽  
Polymerase Chain ◽  
Genomic Dna Sequence

We have devised a strategy that utilizes the polymerase chain reaction (PCR) for the detection and isolation of intron-containing genes in the presence of an abundance of processed pseudogenes. The method depends on the genomic DNA sequence between the PCR primers spanning at least one intron in the gene of interest, resulting in the generation of a larger intron-containing PCR product in addition to the smaller PCR product amplified from the intronless pseudogenes. A unique intron probe isolated from the larger PCR product is used for the detection of intron-containing clones from recombinant DNA libraries that also contain pseudogene clones. This method has been used successfully for the selective isolation of an intron-containing rat L19 ribosomal protein gene in the presence of multiple pseudogenes. Analysis of a number of mammalian ribosomal protein multigene families by PCR indicates that they all contain only a single gene with introns.

scholarly journals One of the tightly clustered genes of the mouse surfeit locus is a highly expressed member of a multigene family whose other members are predominantly processed pseudogenes.

1988 ◽  
Vol 8 (9) ◽  
pp. 3898-3905 ◽  
Author(s):  
C Huxley ◽  
T Williams ◽  
M Fried
Keyword(s):  
Multigene Family ◽  
Open Reading Frame ◽  
The Other ◽  
Base Pairs ◽  
Regulation Of Expression ◽  
Reading Frame ◽  
Processed Pseudogenes ◽  
Dna Fragment ◽  
Basic Polypeptide

The mouse surfeit locus is unusual in that it contains a number of closely clustered genes (Surf-1, -2, and -4) that alternate in their direction of transcription (T. Williams, J. Yon, C. Huxley, and M. Fried, Proc. Natl. Acad. Sci. USA 85:3527-3530, 1988). The heterogeneous 5' ends of Surf-1 and Surf-2 are separated by 15 to 73 base pairs (bp), and the 3' ends of Surf-2 and Surf-4 overlap by 133 bp (T. Williams and M. Fried, Mol. Cell. Biol. 6:4558-4569, 1986; T. Williams and M. Fried, Nature (London) 322:275-279, 1986). A fourth gene in this locus, Surf-3, which is a member of a multigene family, has been identified. The poly(A) addition site of Surf-3 lies only 70 bp from the poly(A) addition site of Surf-1. Transcription of Surf-3 has been studied in the absence of the other members of its multigene family after transfection of a cloned genomic mouse DNA fragment, containing the Surf-3 gene, into heterologous monkey cells. Surf-3 specifies a highly expressed 1.0-kilobase mRNA that contains a long open reading frame of 266 amino acids, which would encode a highly basic polypeptide (23% Arg plus Lys). The other members of the Surf-3 multigene family are predominantly, if not entirely, intronless pseudogenes with the hallmarks of being generated by reverse transcription. The role of the very tight clustering on regulation of expression of the genes in the surfeit locus is discussed.

Environmental–biomechanical reciprocity and the evolution of plant material properties

2021 ◽  
Author(s):  
Karl J Niklas ◽  
Frank W Telewski
Keyword(s):  
Physical Environment ◽  
Structural Changes ◽  
Abiotic Factors ◽  
Biotic Interactions ◽  
Cellular Solids ◽  
Form And Function ◽  
Evolutionary Innovation ◽  
Plant Form ◽  
And Function ◽  
Abiotic Environmental Factors

Abstract Abiotic–biotic interactions have shaped organic evolution since life first began. Abiotic factors influence growth, survival, and reproductive success, whereas biotic responses to abiotic factors have changed the physical environment (and indeed created new environments). This reciprocity is well illustrated by land plants who begin and end their existence in the same location while growing in size over the course of years or even millennia, during which environment factors change over many orders of magnitude. A biomechanical, ecological, and evolutionary perspective reveals that plants are (i) composed of materials (cells and tissues) that function as cellular solids (i.e. materials composed of one or more solid and fluid phases); (ii) that have evolved greater rigidity (as a consequence of chemical and structural changes in their solid phases); (iii) allowing for increases in body size and (iv) permitting acclimation to more physiologically and ecologically diverse and challenging habitats; which (v) have profoundly altered biotic as well as abiotic environmental factors (e.g. the creation of soils, carbon sequestration, and water cycles). A critical component of this evolutionary innovation is the extent to which mechanical perturbations have shaped plant form and function and how form and function have shaped ecological dynamics over the course of evolution.

Bistability of somatic pattern memories: stochastic outcomes in bioelectric circuits underlying regeneration

2021 ◽  
Vol 376 (1821) ◽  
pp. 20190765 ◽  
Author(s):  
Giovanni Pezzulo ◽  
Joshua LaPalme ◽  
Fallon Durant ◽  
Michael Levin
Keyword(s):  
Large Scale ◽  
Computational Models ◽  
State Of The Art ◽  
Memory Representation ◽  
Theme Issue ◽  
Evolutionary Innovation ◽  
New Interpretation ◽  
The Brain

Nervous systems’ computational abilities are an evolutionary innovation, specializing and speed-optimizing ancient biophysical dynamics. Bioelectric signalling originated in cells' communication with the outside world and with each other, enabling cooperation towards adaptive construction and repair of multicellular bodies. Here, we review the emerging field of developmental bioelectricity, which links the field of basal cognition to state-of-the-art questions in regenerative medicine, synthetic bioengineering and even artificial intelligence. One of the predictions of this view is that regeneration and regulative development can restore correct large-scale anatomies from diverse starting states because, like the brain, they exploit bioelectric encoding of distributed goal states—in this case, pattern memories. We propose a new interpretation of recent stochastic regenerative phenotypes in planaria, by appealing to computational models of memory representation and processing in the brain. Moreover, we discuss novel findings showing that bioelectric changes induced in planaria can be stored in tissue for over a week, thus revealing that somatic bioelectric circuits in vivo can implement a long-term, re-writable memory medium. A consideration of the mechanisms, evolution and functionality of basal cognition makes novel predictions and provides an integrative perspective on the evolution, physiology and biomedicine of information processing in vivo . This article is part of the theme issue ‘Basal cognition: multicellularity, neurons and the cognitive lens’.

How cells tell up from down and stick together to construct multicellular tissues – interplay between apicobasal polarity and cell–cell adhesion

2021 ◽  
Vol 134 (21) ◽  
Author(s):  
Claudia G. Vasquez ◽  
Eva L. de la Serna ◽  
Alexander R. Dunn
Keyword(s):  
Cell Adhesion ◽  
Protein Complexes ◽  
Basic Function ◽  
Cell Junction ◽  
Evolutionary Innovation ◽  
Apicobasal Polarity ◽  
Complex Architectures ◽  
Main Components ◽  
Definition Of ◽  
Cell Cell

ABSTRACT Polarized epithelia define a topological inside and outside, and hence constitute a key evolutionary innovation that enabled the construction of complex multicellular animal life. Over time, this basic function has been elaborated upon to yield the complex architectures of many of the organs that make up the human body. The two processes necessary to yield a polarized epithelium, namely regulated adhesion between cells and the definition of the apicobasal (top–bottom) axis, have likewise undergone extensive evolutionary elaboration, resulting in multiple sophisticated protein complexes that contribute to both functions. Understanding how these components function in combination to yield the basic architecture of a polarized cell–cell junction remains a major challenge. In this Review, we introduce the main components of apicobasal polarity and cell–cell adhesion complexes, and outline what is known about their regulation and assembly in epithelia. In addition, we highlight studies that investigate the interdependence between these two networks. We conclude with an overview of strategies to address the largest and arguably most fundamental unresolved question in the field, namely how a polarized junction arises as the sum of its molecular parts.

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