scholarly journals Ancient Origin of the Tryptophan Operon and the Dynamics of Evolutionary Change

2003 ◽  
Vol 67 (3) ◽  
pp. 303-342 ◽  
Author(s):  
Gary Xie ◽  
Nemat O. Keyhani ◽  
Carol A. Bonner ◽  
Roy A. Jensen
Keyword(s):  
Gene Fusion ◽  
Fusion Gene ◽  
Dynamic State ◽  
Specific Gene ◽  
Flux Analysis ◽  
Ancestral Gene ◽  
History Of ◽  
Tryptophan Operon ◽  
Operon Organization ◽  
Genome Representation

SUMMARY The seven conserved enzymatic domains required for tryptophan (Trp) biosynthesis are encoded in seven genetic regions that are organized differently (whole-pathway operons, multiple partial-pathway operons, and dispersed genes) in prokaryotes. A comparative bioinformatics evaluation of the conservation and organization of the genes of Trp biosynthesis in prokaryotic operons should serve as an excellent model for assessing the feasibility of predicting the evolutionary histories of genes and operons associated with other biochemical pathways. These comparisons should provide a better understanding of possible explanations for differences in operon organization in different organisms at a genomics level. These analyses may also permit identification of some of the prevailing forces that dictated specific gene rearrangements during the course of evolution. Operons concerned with Trp biosynthesis in prokaryotes have been in a dynamic state of flux. Analysis of closely related organisms among the Bacteria at various phylogenetic nodes reveals many examples of operon scission, gene dispersal, gene fusion, gene scrambling, and gene loss from which the direction of evolutionary events can be deduced. Two milestone evolutionary events have been mapped to the 16S rRNA tree of Bacteria, one splitting the operon in two, and the other rejoining it by gene fusion. The Archaea, though less resolved due to a lesser genome representation, appear to exhibit more gene scrambling than the Bacteria. The trp operon appears to have been an ancient innovation; it was already present in the common ancestor of Bacteria and Archaea. Although the operon has been subjected, even in recent times, to dynamic changes in gene rearrangement, the ancestral gene order can be deduced with confidence. The evolutionary history of the genes of the pathway is discernible in rough outline as a vertical line of descent, with events of lateral gene transfer or paralogy enriching the analysis as interesting features that can be distinguished. As additional genomes are thoroughly analyzed, an increasingly refined resolution of the sequential evolutionary steps is clearly possible. These comparisons suggest that present-day trp operons that possess finely tuned regulatory features are under strong positive selection and are able to resist the disruptive evolutionary events that may be experienced by simpler, poorly regulated operons.

scholarly journals FOXO1 gene involvement in a non-rhabdomyosarcomatous neoplasm

2021 ◽  
Author(s):  
Simon Haefliger ◽  
Muriel Genevay ◽  
Michel Bihl ◽  
Romina Marone ◽  
Daniel Baumhoer ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Soft Tissue ◽  
Genetic Heterogeneity ◽  
Gene Fusion ◽  
Fusion Gene ◽  
Soft Tissue Tumors ◽  
Gene Fusions ◽  
Mesenchymal Tumors ◽  
Myoepithelial Differentiation ◽  
Foxo1 Gene

AbstractMyoepithelial neoplasms of soft tissue are rare tumors with clinical, morphological, immunohistochemical, and genetic heterogeneity. The morphological spectrum of these tumors is broad, and the diagnosis often requires immunostaining to confirm myoepithelial differentiation. Rarely, tumors show a morphology that is typical for myoepithelial neoplasms, while the immunophenotype fails to confirm myoepithelial differentiation. For such lesions, the term “myoepithelioma-like” tumor was introduced. Recently, two cases of myoepithelioma-like tumors of the hands and one case of the foot were described with previously never reported OGT-FOXO gene fusions. Here, we report a 50-year-old woman, with a myoepithelial-like tumor localized in the soft tissue of the forearm and carrying a OGT-FOXO1 fusion gene. Our findings extend the spectrum of mesenchymal tumors involving members of the FOXO family of transcription factors and point to the existence of a family of soft tissue tumors that carry the gene fusion of the OGT-FOXO family.

Ancestral gene fusion in cellobiose dehydrogenases reflects a specific evolution of GMC oxidoreductases in fungi

Gene ◽  
2004 ◽  
Vol 338 (1) ◽  
pp. 1-14 ◽  
Author(s):  
Marcel Zámocký ◽  
Martin Hallberg ◽  
Roland Ludwig ◽  
Christina Divne ◽  
Dietmar Haltrich
Keyword(s):  
Gene Fusion ◽  
Ancestral Gene

Retroviral and pseudogene insertion sites reveal the lineage of human salivary and pancreatic amylase genes from a single gene during primate evolution

1990 ◽  
Vol 10 (6) ◽  
pp. 2513-2520
Author(s):  
L C Samuelson ◽  
K Wiebauer ◽  
C M Snow ◽  
M H Meisler
Keyword(s):  
Gene Family ◽  
Single Gene ◽  
Primate Evolution ◽  
Endogenous Retrovirus ◽  
Gene Copy ◽  
Nucleotide Sequence Analysis ◽  
Ancestral Gene ◽  
Molecular Events ◽  
Amylase Genes ◽  
History Of

We have analyzed the junction regions of inserted elements within the human amylase gene complex. This complex contains five genes which are expressed at high levels either in the pancreas or in the parotid gland. The proximal 5'-flanking regions of these genes contain two inserted elements. A gamma-actin pseudogene is located at a position 200 base pairs upstream of the first coding exon. All of the amylase genes contain this insert. The subsequent insertion of an endogenous retrovirus interrupted the gamma-actin pseudogene within its 3'-untranslated region. Nucleotide sequence analysis of the inserted elements associated with each of the five human amylase genes has revealed a series of molecular events during the recent history of this gene family. The data indicate that the entire gene family was generated during primate evolution from one ancestral gene copy and that the retroviral insertion activated a cryptic promoter.

scholarly journals Synstable Fusion: A Network-Based Algorithm for Estimating Driver Genes in Fusion Structures

Molecules ◽  
2018 ◽  
Vol 23 (8) ◽  
pp. 2055 ◽  
Author(s):  
Mingzhe Xu ◽  
Zhongmeng Zhao ◽  
Xuanping Zhang ◽  
Aiqing Gao ◽  
Shuyan Wu ◽  
...  
Keyword(s):  
Gene Networks ◽  
Gene Fusion ◽  
Fusion Gene ◽  
Driver Gene ◽  
Clinical Practices ◽  
Driver Genes ◽  
Multiple Networks ◽  
Fusion Data ◽  
Evaluation Algorithm ◽  
Chromosomal Mutations

Gene fusion structure is a class of common somatic mutational events in cancer genomes, which are often formed by chromosomal mutations. Identifying the driver gene(s) in a fusion structure is important for many downstream analyses and it contributes to clinical practices. Existing computational approaches have prioritized the importance of oncogenes by incorporating prior knowledge from gene networks. However, different methods sometimes suffer different weaknesses when handling gene fusion data due to multiple issues such as fusion gene representation, network integration, and the effectiveness of the evaluation algorithms. In this paper, Synstable Fusion (SYN), an algorithm for computationally evaluating the fusion genes, is proposed. This algorithm uses network-based strategy by incorporating gene networks as prior information, but estimates the driver genes according to the destructiveness hypothesis. This hypothesis balances the two popular evaluation strategies in the existing studies, thereby providing more comprehensive results. A machine learning framework is introduced to integrate multiple networks and further solve the conflicting results from different networks. In addition, a synchronous stability model is established to reduce the computational complexity of the evaluation algorithm. To evaluate the proposed algorithm, we conduct a series of experiments on both artificial and real datasets. The results demonstrate that the proposed algorithm performs well on different configurations and is robust when altering the internal parameter settings.

Shocks and Operation of the Law of Denial of Negation

2021 ◽  
pp. 100-134
Keyword(s):  
Self Organization ◽  
Dynamic State ◽  
Static System ◽  
Structural Level ◽  
Double Negation ◽  
Structural Hierarchy ◽  
Dynamic Economy ◽  
Self Development ◽  
Technological Base ◽  
History Of

The long history of complication of static economy objectively leads it to exhaustion of self-organization potential and to the point of no return – a leap into dynamic state with self-development mechanism. In the new quality, the dynamic economy is regulated by the dialectical law of negation of negation with new functions of shocks in its operation. As for self-organizing systems, shocks are determined to destroy the structural links that weaken systemic integrity. In order, the static system could jump into a dynamic state, shocks realize the first negation, destroying the vertical hierarchy of structural links, and as for the second negation, shocks destroy basic structural level as well. The epochal task is associated with construction of new dynamic systemic integrity on the modern technological base by forming new structure since the previous structural hierarchy has been completely destroyed by shocks embedded into the dialectical law of double negation.

scholarly journals Retroviral and pseudogene insertion sites reveal the lineage of human salivary and pancreatic amylase genes from a single gene during primate evolution.

1990 ◽  
Vol 10 (6) ◽  
pp. 2513-2520 ◽  
Author(s):  
L C Samuelson ◽  
K Wiebauer ◽  
C M Snow ◽  
M H Meisler
Keyword(s):  
Gene Family ◽  
Single Gene ◽  
Primate Evolution ◽  
Endogenous Retrovirus ◽  
Gene Copy ◽  
Nucleotide Sequence Analysis ◽  
Ancestral Gene ◽  
Molecular Events ◽  
Amylase Genes ◽  
History Of

We have analyzed the junction regions of inserted elements within the human amylase gene complex. This complex contains five genes which are expressed at high levels either in the pancreas or in the parotid gland. The proximal 5'-flanking regions of these genes contain two inserted elements. A gamma-actin pseudogene is located at a position 200 base pairs upstream of the first coding exon. All of the amylase genes contain this insert. The subsequent insertion of an endogenous retrovirus interrupted the gamma-actin pseudogene within its 3'-untranslated region. Nucleotide sequence analysis of the inserted elements associated with each of the five human amylase genes has revealed a series of molecular events during the recent history of this gene family. The data indicate that the entire gene family was generated during primate evolution from one ancestral gene copy and that the retroviral insertion activated a cryptic promoter.

scholarly journals Network-based microsynteny analysis identifies major differences and genomic outliers in mammalian and angiosperm genomes

2019 ◽  
Vol 116 (6) ◽  
pp. 2165-2174 ◽  
Author(s):  
Tao Zhao ◽  
M. Eric Schranz
Keyword(s):  
Gene Families ◽  
Single Copy ◽  
Specific Gene ◽  
Phylogenetic Groups ◽  
History Of ◽  
Mammalian Genomes ◽  
Syntenic Conservation ◽  
Genome Assemblies ◽  
Lineage Specific Gene ◽  
Relative Gene

A comprehensive analysis of relative gene order, or microsynteny, can provide valuable information for understanding the evolutionary history of genes and genomes, and ultimately traits and species, across broad phylogenetic groups and divergence times. We have used our network-based phylogenomic synteny analysis pipeline to first analyze the overall patterns and major differences between 87 mammalian and 107 angiosperm genomes. These two important groups have both evolved and radiated over the last ∼170 MYR. Secondly, we identified the genomic outliers or “rebel genes” within each clade. We theorize that rebel genes potentially have influenced trait and lineage evolution. Microsynteny networks use genes as nodes and syntenic relationships between genes as edges. Networks were decomposed into clusters using the Infomap algorithm, followed by phylogenomic copy-number profiling of each cluster. The differences in syntenic properties of all annotated gene families, including BUSCO genes, between the two clades are striking: most genes are single copy and syntenic across mammalian genomes, whereas most genes are multicopy and/or have lineage-specific distributions for angiosperms. We propose microsynteny scores as an alternative and complementary metric to BUSCO for assessing genome assemblies. We further found that the rebel genes are different between the two groups: lineage-specific gene transpositions are unusual in mammals, whereas single-copy highly syntenic genes are rare for flowering plants. We illustrate several examples of mammalian transpositions, such as brain-development genes in primates, and syntenic conservation across angiosperms, such as single-copy genes related to photosynthesis. Future experimental work can test if these are indeed rebels with a cause.

Phylogenetic evidence for independent origins of GDF1 and GDF3 genes in amphibians and mammals

2018 ◽  
Author(s):  
Juan C. Opazo ◽  
Kattina Zavala
Keyword(s):  
Growth Factor ◽  
Early Development ◽  
Evolutionary History ◽  
Transforming Growth Factor ◽  
Ancestral Gene ◽  
Differentiation Factors ◽  
Duplication Events ◽  
Independent Duplication ◽  
History Of ◽  
Early Developmental

AbstractGrowth differentiation factors 1 (GDF1) and 3 (GDF3) are members of the transforming growth factor superfamily (TGF-β) that is involved in fundamental early-developmental processes that are conserved across vertebrates. The evolutionary history of these genes is still under debate due to ambiguous definitions of homologous relationships among vertebrates. Thus, the goal of this study was to unravel the evolution of the GDF1 and GDF3 genes of vertebrates, emphasizing the understanding of homologous relationships and their evolutionary origin. Surprisingly, our results revealed that the GDF1 and GDF3 genes found in amphibians and mammals are the products of independent duplication events of an ancestral gene in the ancestor of each of these lineages. The main implication of this result is that the GDF1 and GDF3 genes of amphibians and mammals are not 1:1 orthologs. In other words, genes that participate in fundamental processes during early development have been reinvented two independent times during the evolutionary history of tetrapods.

scholarly journals Diversity and evolution of bacterial bioluminescence genes in the global ocean

2020 ◽  
Vol 2 (2) ◽  
Author(s):  
Thomas Vannier ◽  
Pascal Hingamp ◽  
Floriane Turrel ◽  
Lisa Tanet ◽  
Magali Lescot ◽  
...  
Keyword(s):  
Light Emission ◽  
Global Ocean ◽  
Light Emitting ◽  
Planetary Scale ◽  
Bacterial Bioluminescence ◽  
Lux Operon ◽  
History Of ◽  
Operon Evolution ◽  
Operon Organization ◽  
Bacterial Genes

Abstract Although bioluminescent bacteria are the most abundant and widely distributed of all light-emitting organisms, the biological role and evolutionary history of bacterial luminescence are still shrouded in mystery. Bioluminescence has so far been observed in the genomes of three families of Gammaproteobacteria in the form of canonical lux operons that adopt the CDAB(F)E(G) gene order. LuxA and luxB encode the two subunits of bacterial luciferase responsible for light-emission. Our deep exploration of public marine environmental databases considerably expands this view by providing a catalog of new lux homolog sequences, including 401 previously unknown luciferase-related genes. It also reveals a broader diversity of the lux operon organization, which we observed in previously undescribed configurations such as CEDA, CAED and AxxCE. This expanded operon diversity provides clues for deciphering lux operon evolution and propagation within the bacterial domain. Leveraging quantitative tracking of marine bacterial genes afforded by planetary scale metagenomic sampling, our study also reveals that the novel lux genes and operons described herein are more abundant in the global ocean than the canonical CDAB(F)E(G) operon.

Characteristics of a Simple Energy Absorption Transducer

1986 ◽  
Vol 108 (3) ◽  
pp. 676-683 ◽  
Author(s):  
B. T. Beck ◽  
G. L. Wedekind
Keyword(s):  
Experimental Data ◽  
Heat Flux ◽  
Laser Radiation ◽  
Steel Substrate ◽  
Time History ◽  
Radiation Absorption ◽  
Flux Analysis ◽  
Manganese Phosphate ◽  
History Of ◽  
Arbitrary Location

This paper presents the results of an investigation into a simple technique developed primarily for evaluating surface coating effectiveness for the absorption of a nonuniform laser radiation heat flux. Analysis suggests that if the transducer sensor is designed appropriately, and the experimental data analyzed in a particular manner, the temperature–time history of the transducer need be measured at only a single arbitrary location. These conclusions are also supported by experimental measurements of laser radiation absorption at a wavelength of 10.6 μm for polished copper, polished steel, and for a manganese–phosphate coating on a steel substrate. The absorptivities measured for the polished copper and steel agree well with other experimental data in the literature. Limitations of the measurement technique, resulting from the temperature dependence of the transducer material properties, radiation absorptivity, and combined convective and radiative heat flux, are also investigated theoretically and experimentally.

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