scholarly journals The parallel origins of vertebrate venoms

2021 ◽  
Author(s):  
Agneesh Barua ◽  
Ivan Koludarov ◽  
Alexander S. Mikheyev
Keyword(s):  
Phylogenetic Analysis ◽  
Comparative Genomics ◽  
Gene Cluster ◽  
Serine Proteases ◽  
Evolutionary Biology ◽  
Central Question ◽  
Venomous Snake ◽  
The Core ◽  
Venomous Animals ◽  
Venom Evolution

AbstractEvolution can occur with surprising predictability when faced with similar ecological challenges. How and why this repeatability occurs remains a central question in evolutionary biology, but the complexity of most traits makes it challenging to answer. Reptiles and mammals independently evolved oral venoms that consist of proteinaceous cocktails which allow straightforward mapping between genotype and phenotype. Although biochemically similar toxins can occur as major venom components across many taxa, whether these toxins evolved via convergent or parallel means remains unknown. Most notable among them are kallikrein-like serine proteins, which form the core of most vertebrate venoms, and are employed by all venomous snake families. Here we used a combination of comparative genomics and phylogenetics to investigate whether serine protease recruitment into the venom occurred independently or in parallel across the different tetrapod lineages. Using syntenic relationships between genes flanking known toxins, we traced the origin of kallikreins to a single locus containing one or more nearby paralogous kallikrein-like clusters. Independently, phylogenetic analysis of vertebrate serine proteases revealed that the same gene cluster gave rise to toxins in mammals and reptiles. Given the shared regulatory and genetic machinery underlying venom evolution, these findings suggest a unified model underlying vertebrate venom evolution by exaptation of homologous ancestral kallikreins. Furthermore, the ubiquitous distribution of kallikreins across vertebrates suggests that the evolution of envenomation may be more common than previously recognized, blurring the line between venomous and non-venomous animals.

scholarly journals Co-option of the same ancestral gene family gave rise to mammalian and reptilian toxins

BMC Biology ◽  
2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Agneesh Barua ◽  
Ivan Koludarov ◽  
Alexander S. Mikheyev
Keyword(s):  
Phylogenetic Analysis ◽  
Serine Proteases ◽  
Biochemical Activity ◽  
Ancestral Gene ◽  
The Core ◽  
Venomous Animals ◽  
Regulatory Architecture ◽  
Vasodilatory Activity ◽  
Venom Evolution ◽  
Shared Genetic

Abstract Background Evolution can occur with surprising predictability when organisms face similar ecological challenges. For most traits, it is difficult to ascertain whether this occurs due to constraints imposed by the number of possible phenotypic solutions or because of parallel responses by shared genetic and regulatory architecture. Exceptionally, oral venoms are a tractable model of trait evolution, being largely composed of proteinaceous toxins that have evolved in many tetrapods, ranging from reptiles to mammals. Given the diversity of venomous lineages, they are believed to have evolved convergently, even though biochemically similar toxins occur in all taxa. Results Here, we investigate whether ancestral genes harbouring similar biochemical activity may have primed venom evolution, focusing on the origins of kallikrein-like serine proteases that form the core of most vertebrate oral venoms. Using syntenic relationships between genes flanking known toxins, we traced the origin of kallikreins to a single locus containing one or more nearby paralogous kallikrein-like clusters. Additionally, phylogenetic analysis of vertebrate serine proteases revealed that kallikrein-like toxins in mammals and reptiles are genetically distinct from non-toxin ones. Conclusions Given the shared regulatory and genetic machinery, these findings suggest that tetrapod venoms evolved by co-option of proteins that were likely already present in saliva. We term such genes ‘toxipotent’—in the case of salivary kallikreins they already had potent vasodilatory activity that was weaponized by venomous lineages. Furthermore, the ubiquitous distribution of kallikreins across vertebrates suggests that the evolution of envenomation may be more common than previously recognized, blurring the line between venomous and non-venomous animals.

scholarly journals Distance and Similarity Measures in Comparative Genomics

2020 ◽  
Author(s):  
Diego P. Rubert ◽  
Jens Stoye ◽  
Fábio H. V. Martinez
Keyword(s):  
Comparative Genomics ◽  
Molecular Biology ◽  
Similarity Measures ◽  
Central Question ◽  
Similarities And Differences

Research in comparative genomics supports the investigation of important questions in molecular biology, genetics and biomedicine. A central question in this field is the elucidation of similarities and differences between genomes by means of different measures. This summary, submitted to CTD 2020, briefly describes the main contributions, originality and impact possibilities of the thesis entitled "Distance and Similarity Measures in Comparative Genomics", by Diego P. Rubert.

scholarly journals Diversity of cultivable protease-producing bacteria and their extracellular proteases associated to scleractinian corals

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9055
Author(s):  
Hongfei Su ◽  
Zhenlun Xiao ◽  
Kefu Yu ◽  
Qinyu Huang ◽  
Guanghua Wang ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Serine Proteases ◽  
Organic Nitrogen ◽  
Vital Role ◽  
Scleractinian Corals ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
16S Rrna Gene Sequences ◽  
Extracellular Proteases ◽  
Aspartic Proteases

Protease-producing bacteria play a vital role in degrading organic nitrogen in marine environments. However, the diversity of the bacteria and extracellular proteases has seldom been addressed, especially in communities of coral reefs. In this study, 136 extracellular protease-producing bacterial strains were isolated from seven genera of scleractinian corals from Luhuitou fringing reef, and their protease types were characterized. The massive coral had more cultivable protease-producing bacteria than branching or foliose corals. The abundance of cultivable protease-producing bacteria reached 106 CFU g−1 of coral. Phylogenetic analysis of 16S rRNA gene sequences revealed that the isolates were assigned to 24 genera, from which 20 corresponded to the phyla Firmicutes and Proteobacteria. Bacillus and Fictibacillus were retrieved from all coral samples. Moreover, Vibrio and Pseudovibrio were most prevalent in massive or foliose coral Platygyra and Montipora. In contrast, 11 genera were each identified in only one isolate. Nearly all the extracellular proteases from the bacteria were serine proteases or metalloproteases; 45.83% of isolates also released cysteine or aspartic proteases. These proteases had different hydrolytic ability against different substrates. This study represents a novel insight on the diversity of cultivable protease-producing bacteria and their extracellular proteases in scleractinian corals.

Molecular evolution of the actin family

2002 ◽  
Vol 115 (13) ◽  
pp. 2619-2622 ◽  
Author(s):  
Holly V. Goodson ◽  
William F. Hawse
Keyword(s):  
Phylogenetic Analysis ◽  
Molecular Evolution ◽  
Chromatin Remodeling ◽  
The Core ◽  
Nuclear Process ◽  
Core Set ◽  
Eukaryotic Proteins ◽  
Related Proteins

Members of the actin family have well-characterized cytoskeletal functions,but actin and actin-related proteins (ARPs) have also been implicated in nuclear activities. Previous analyses of the actin family have identified four conserved subfamilies, but many actin-related proteins (ARPs) do not fall into these groups. A new systematic phylogenetic analysis reveals that at least eight ARP subfamilies are conserved from humans to yeast, indicating that these ARPs are part of the core set of eukaryotic proteins. Members of at least three subfamilies appear to be involved in chromatin remodeling,suggesting that ARPs play ancient, fundamental roles in this nuclear process.

Introduction

2021 ◽  
pp. 1-6
Author(s):  
Matthew D. Lundberg
Keyword(s):  
Central Question ◽  
Extreme Situation ◽  
Christian Life ◽  
The Core

The introduction briefly explores Christianity’s fascination with its martyrs. It develops a series of optical metaphors—spotlight, lens, prism, mirror—to show that the core theological function of naming martyrs is to make an argument about what the faithful Christian life looks like. The martyr, from her extreme situation, illuminates and brings into clearer focus the contours of discipleship as they are supposed to be lived out in more ordinary situations. Hence the book’s central question: if martyrdom’s argument about the Christian life points to the call to suffer violence, then what are we to think about the mainstream church’s historic sanctioning of the inflicting of violence in certain circumstances?

scholarly journals Heterologous Expression of the Core Genes in the Complex Fusarubin Gene Cluster of Fusarium Solani

2020 ◽  
Vol 21 (20) ◽  
pp. 7601
Author(s):  
Tobias Bruun Pedersen ◽  
Mikkel Rank Nielsen ◽  
Sebastian Birkedal Kristensen ◽  
Eva Mie Lang Spedtsberg ◽  
Wafaa Yasmine ◽  
...  
Keyword(s):  
Heterologous Expression ◽  
Gene Cluster ◽  
Fusarium Solani ◽  
Biosynthetic Gene Cluster ◽  
Vector System ◽  
Biosynthetic Gene ◽  
The Core ◽  
Maximum Titer ◽  
Sequential Transformation ◽  
Core Genes

Through stepwise recreation of the biosynthetic gene cluster containing PKS3 from Fusarium solani, it was possible to produce the core scaffold compound of bostrycoidin, a red aza-anthraquinone pigment in Saccharomyces cerevisiae. This was achieved through sequential transformation associated recombination (TAR) cloning of FvPPT, fsr1, fsr2, and fsr3 into the pESC-vector system, utilizing the inducible bidirectional galactose promoter for heterologous expression in S. cerevisiae. The production of the core metabolite bostrycoidin was investigated through triplicate growth cultures for 1–4 days, where the maximum titer of bostrycoidin was achieved after 2 days of induction, yielding 2.2 mg/L.

scholarly journals Phylogenetic Comparative Methods and the Evolution of Multivariate Phenotypes

2019 ◽  
Vol 50 (1) ◽  
pp. 405-425 ◽  
Author(s):  
Dean C. Adams ◽  
Michael L. Collyer
Keyword(s):  
Phylogenetic Analysis ◽  
Evolutionary Biology ◽  
Generalized Least Squares ◽  
Comparative Methods ◽  
High Dimensional ◽  
Phenotypic Integration ◽  
Phylogenetic Comparative Methods ◽  
Evolutionary Trends ◽  
Phenotype Space ◽  
Multivariate Phenotypes

Evolutionary biology is multivariate, and advances in phylogenetic comparative methods for multivariate phenotypes have surged to accommodate this fact. Evolutionary trends in multivariate phenotypes are derived from distances and directions between species in a multivariate phenotype space. For these patterns to be interpretable, phenotypes should be characterized by traits in commensurate units and scale. Visualizing such trends, as is achieved with phylomorphospaces, should continue to play a prominent role in macroevolutionary analyses. Evaluating phylogenetic generalized least squares (PGLS) models (e.g., phylogenetic analysis of variance and regression) is valuable, but using parametric procedures is limited to only a few phenotypic variables. In contrast, nonparametric, permutation-based PGLS methods provide a flexible alternative and are thus preferred for high-dimensional multivariate phenotypes. Permutation-based methods for evaluating covariation within multivariate phenotypes are also well established and can test evolutionary trends in phenotypic integration. However, comparing evolutionary rates and modes in multivariate phenotypes remains an important area of future development.

scholarly journals The Rice Genome Knowledgebase (RGKbase): an annotation database for rice comparative genomics and evolutionary biology

2012 ◽  
Vol 41 (D1) ◽  
pp. D1199-D1205 ◽  
Author(s):  
Dapeng Wang ◽  
Yan Xia ◽  
Xinna Li ◽  
Lixia Hou ◽  
Jun Yu
Keyword(s):  
Comparative Genomics ◽  
Evolutionary Biology ◽  
Rice Genome ◽  
Annotation Database

scholarly journals Magnetosome Gene Duplication as an Important Driver in the Evolution of Magnetotaxis in the Alphaproteobacteria

mSystems ◽  
2019 ◽  
Vol 4 (5) ◽  
Author(s):  
Haijian Du ◽  
Wenyan Zhang ◽  
Wensi Zhang ◽  
Weijia Zhang ◽  
Hongmiao Pan ◽  
...  
Keyword(s):  
Gene Duplication ◽  
Gene Cluster ◽  
Geomagnetic Field ◽  
Evolutionary Biology ◽  
Genomic Analysis ◽  
Magnetotactic Bacteria ◽  
Duplication Event ◽  
Comparative Genomic ◽  
Content Type ◽  
Evolutionary Trajectories

ABSTRACT The evolution of microbial magnetoreception (or magnetotaxis) is of great interest in the fields of microbiology, evolutionary biology, biophysics, geomicrobiology, and geochemistry. Current genomic data from magnetotactic bacteria (MTB), the only prokaryotes known to be capable of sensing the Earth’s geomagnetic field, suggests an ancient origin of magnetotaxis in the domain Bacteria. Vertical inheritance, followed by multiple independent magnetosome gene cluster loss, is considered to be one of the major forces that drove the evolution of magnetotaxis at or above the class or phylum level, although the evolutionary trajectories at lower taxonomic ranks (e.g., within the class level) remain largely unstudied. Here we report the isolation, cultivation, and sequencing of a novel magnetotactic spirillum belonging to the genus Terasakiella (Terasakiella sp. strain SH-1) within the class Alphaproteobacteria. The complete genome sequence of Terasakiella sp. strain SH-1 revealed an unexpected duplication event of magnetosome genes within the mamAB operon, a group of genes essential for magnetosome biomineralization and magnetotaxis. Intriguingly, further comparative genomic analysis suggests that the duplication of mamAB genes is a common feature in the genomes of alphaproteobacterial MTB. Taken together, with the additional finding that gene duplication appears to have also occurred in some magnetotactic members of the Deltaproteobacteria, our results indicate that gene duplication plays an important role in the evolution of magnetotaxis in the Alphaproteobacteria and perhaps the domain Bacteria. IMPORTANCE A diversity of organisms can sense the geomagnetic field for the purpose of navigation. Magnetotactic bacteria are the most primitive magnetism-sensing organisms known thus far and represent an excellent model system for the study of the origin, evolution, and mechanism of microbial magnetoreception (or magnetotaxis). The present study is the first report focused on magnetosome gene cluster duplication in the Alphaproteobacteria, which suggests the important role of gene duplication in the evolution of magnetotaxis in the Alphaproteobacteria and perhaps the domain Bacteria. A novel scenario for the evolution of magnetotaxis in the Alphaproteobacteria is proposed and may provide new insights into evolution of magnetoreception of higher species.

Ecological approaches to perceptual learning: learning to perceive and perceiving as learning

2019 ◽  
Vol 27 (6) ◽  
pp. 363-388 ◽  
Author(s):  
Agnes Szokolszky ◽  
Catherine Read ◽  
Zsolt Palatinus ◽  
Kinga Palatinus
Keyword(s):  
Language Development ◽  
Perceptual Learning ◽  
Tool Use ◽  
Evolutionary Biology ◽  
Ecological Psychology ◽  
Current Theory ◽  
Review Article ◽  
The Core ◽  
Core Concepts ◽  
Development And Evolution

In this theoretical review article, our primary goal is to contribute to the post-cognitivist understanding of learning to perceive and perceiving as learning, by discussing a framework for perception and perceptual learning initiated by James J Gibson, and extended by Eleanor J Gibson and others. This Ecological Psychology has a coherent set of assumptions based on the concept of mutualism between the perceiving organism and its surroundings, and the idea of affordances as action possibilities of the surround that are perceptible by the organism. At the same time, Ecological Psychology, broadly construed, consists of different perspectives that take different routes to address questions related to the core concepts of perceptual learning. In this article, we focus on three theoretical stances within Ecological Psychology on the issue of perceptual learning: that of Eleanor J Gibson, the current theory of direct learning by Jacobs and Michaels, and the “organicist” approach based on ideas of organicist biology and developments in evolutionary biology. We consider perceptual learning as embedded in development and evolution, and we explore perceptual learning in more depth in the context of tool use and language development. We also discuss the relation between Ecological Psychology and Enactivism on the nature of perception. In conclusion, we summarize the benefits of Ecological Psychology, as a robust but still developing post-cognitivist framework, for the study of perceptual learning and cognitive science in general.

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