scholarly journals Rapid functional activation of a horizontally transferred eukaryotic gene in a bacterial genome in the absence of selection

2019 ◽  
Vol 47 (12) ◽  
pp. 6351-6359 ◽  
Author(s):  
Zhichao Li ◽  
Ralph Bock
Keyword(s):  
Bacterial Genome ◽  
Marker Gene ◽  
Gene Activation ◽  
Gene Cassette ◽  
Selective Advantage ◽  
Porphyridium Purpureum ◽  
Eukaryotic Genes ◽  
Eukaryotic Gene ◽  
Domains Of Life ◽  
Bacterial Genes

Abstract Horizontal gene transfer has occurred between organisms of all domains of life and contributed substantially to genome evolution in both prokaryotes and eukaryotes. Phylogenetic evidence suggests that eukaryotic genes horizontally transferred to bacteria provided useful new gene functions that improved metabolic plasticity and facilitated adaptation to new environments. How these eukaryotic genes evolved into functional bacterial genes is not known. Here, we have conducted a genetic screen to identify the mechanisms involved in functional activation of a eukaryotic gene after its transfer into a bacterial genome. We integrated a eukaryotic selectable marker gene cassette driven by expression elements from the red alga Porphyridium purpureum into the genome of Escherichia coli. Following growth under non-selective conditions, gene activation events were indentified by antibiotic selection. We show that gene activation in the bacterial recipient occurs at high frequency and involves two major types of spontaneous mutations: deletion and gene amplification. We further show that both mechanisms result in promoter capture and are frequently triggered by microhomology-mediated recombination. Our data suggest that horizontally transferred genes have a high probability of acquiring functionality, resulting in their maintenance if they confer a selective advantage.

scholarly journals Unexpected Specificity within Dynamic Transcriptional Protein-Protein Complexes

2020 ◽  
Author(s):  
Matthew J. Henley ◽  
Brian M. Linhares ◽  
Brittany S. Morgan ◽  
Tomasz Cierpicki ◽  
Carol A. Fierke ◽  
...  
Keyword(s):  
Molecular Recognition ◽  
Electrostatic Interactions ◽  
Protein Complexes ◽  
Critical Role ◽  
Gene Activation ◽  
Disordered Proteins ◽  
Conformational Ensemble ◽  
Regulation Of Transcription ◽  
Protein Protein Interaction ◽  
Eukaryotic Gene

AbstractA key functional event in eukaryotic gene activation is the formation of dynamic protein-protein interaction networks between transcriptional activators and transcriptional coactivators. Seemingly incongruent with the tight regulation of transcription, many biochemical and biophysical studies suggest that activators use nonspecific hydrophobic and/or electrostatic interactions to bind to coactivators, with few if any specific contacts. Here a mechanistic dissection of a set of representative dynamic activator•coactivator complexes, comprised of the ETV/PEA3 family of activators and the coactivator Med25, reveals a different molecular recognition model. The data demonstrate that small sequence variations within an activator family significantly redistribute the conformational ensemble of the complex while not affecting overall affinity, and distal residues within the activator—not often considered as contributing to binding—play a key role in mediating conformational redistribution. The ETV/PEA3•Med25 ensembles are directed by specific contacts between the disordered activator and the Med25 interface, which is facilitated by structural shifts of the coactivator binding surface. Taken together, these data highlight the critical role coactivator plasticity plays in recognition of disordered activators, and indicates that molecular recognition models of disordered proteins must consider the ability of the binding partners to mediate specificity.

scholarly journals The Dual Origin of the Yeast Mitochondrial Proteome

Yeast ◽  
2000 ◽  
Vol 1 (3) ◽  
pp. 170-187 ◽  
Author(s):  
Olof Karlberg ◽  
Björn Canbäck ◽  
Charles G. Kurland ◽  
Siv G. E. Andersson
Keyword(s):  
Nuclear Genome ◽  
Mitochondrial Proteins ◽  
Mitochondrial Proteome ◽  
Phylogenetic Reconstructions ◽  
Eukaryotic Genes ◽  
Genes Encoding ◽  
Parallel Mode ◽  
Bacterial Genes ◽  
Dual Origin ◽  
Regulatory Functions

We propose a scheme for the origin of mitochondria based on phylogenetic reconstructions with more than 400 yeast nuclear genes that encode mitochondrial proteins. Half of the yeast mitochondrial proteins have no discernable bacterial homologues, while one-tenth are unequivocally of α-proteobacterial origin. These data suggest that the majority of genes encoding yeast mitochondrial proteins are descendants of two different genomic lineages that have evolved in different modes. First, the ancestral free-living α-proteobacterium evolved into an endosymbiont of an anaerobic host. Most of the ancestral bacterial genes were lost, but a small fraction of genes supporting bioenergetic and translational processes were retained and eventually transferred to what became the host nuclear genome. In a second, parallel mode, a larger number of novel mitochondrial genes were recruited from the nuclear genome to complement the remaining genes from the bacterial ancestor. These eukaryotic genes, which are primarily involved in transport and regulatory functions, transformed the endosymbiont into an ATP-exporting organelle.

Bacterial and eukaryotic systems collide in the three Rs of Methanococcus

2011 ◽  
Vol 39 (1) ◽  
pp. 111-115
Author(s):  
Richard P. Parker ◽  
Alison D. Walters ◽  
James P.J. Chong
Keyword(s):  
Protein A ◽  
Genetic System ◽  
Replication Proteins ◽  
Minichromosome Maintenance ◽  
Methanococcus Maripaludis ◽  
Eukaryotic Genes ◽  
Domains Of Life ◽  
Specific Proteins ◽  
Novel Interactions ◽  
The Three Rs

Methanococcus maripaludis S2 is a methanogenic archaeon with a well-developed genetic system. Its mesophilic nature offers a simple system in which to perform complementation using bacterial and eukaryotic genes. Although information-processing systems in archaea are generally more similar to those in eukaryotes than those in bacteria, the order Methanococcales has a unique complement of DNA replication proteins, with multiple MCM (minichromosome maintenance) proteins and no obvious originbinding protein. A search for homologues of recombination and repair proteins in M. maripaludis has revealed a mixture of bacterial, eukaryotic and some archaeal-specific homologues. Some repair pathways appear to be completely absent, but it is possible that archaeal-specific proteins could carry out these functions. The replication, recombination and repair systems in M. maripaludis are an interesting mixture of eukaryotic and bacterial homologues and could provide a system for uncovering novel interactions between proteins from different domains of life.

scholarly journals Protective Effect of Icariin on the Development of Preimplantation Mouse Embryos against Hydrogen Peroxide-Induced Oxidative Injury

2017 ◽  
Vol 2017 ◽  
pp. 1-11 ◽  
Author(s):  
Rong Ye ◽  
Songhua Xu ◽  
Yue Liu ◽  
Lili Pang ◽  
Xiuli Lian ◽  
...  
Keyword(s):  
Marker Gene ◽  
Gene Activation ◽  
Developmental Rate ◽  
Preimplantation Embryos ◽  
Control Group ◽  
In Vitro Cultivation ◽  
Preimplantation Embryo Development ◽  
Zygotic Gene ◽  
Underlying Mechanisms

During in vitro cultivation of preimplantation embryos, the balance between ROS production and clearance is disturbed and may lead to incompetent embryos, which might be a main reason of IVF-ET failure. Icariin (ICA) is reported to be active in clearing ROS. The present study aimed to investigate whether ICA could reverse H2O2pretreatment-induced mouse preimplantation embryo development arrest and, furthermore, to study the underlying mechanisms by detecting ROS levels, mitochondrial membrane potential (ΔΨm), and zygotic gene expression. The results showed that, after pretreating mouse 1-cell embryos with 40 μM or 60 μM H2O2for 30 min, the developmental rate of each stage embryos decreased obviously. And by adding 40 μM ICA, the developmental arrest of 60 μM H2O2pretreated preimplantation embryos was significantly reversed. Immunostaining results showed that, comparing with the control group, ROS levels of H2O2pretreated 1-cell embryos were elevated and ΔΨm levels decreased. By adding ICA, the ROS levels of H2O2pretreated 1-cell embryos were decreased and ΔΨm levels were elevated. Furthermore, RT-qPCR results showed that the addition of ICA reversed the H2O2-induced downregulation of eIF-1A mRNA expression levels. These results indicate that ICA, when used in appropriate concentration, could decrease ROS levels, increase ΔΨm levels, and modulate the expression of zygotic gene activation (ZGA) marker gene eIF-1A, and thus promote the development of H2O2-pretreated mouse preimplantation embryos.

scholarly journals Eukaryotic transcription: The core of eukaryotic gene activation

2001 ◽  
Vol 11 (13) ◽  
pp. R510-R513 ◽  
Author(s):  
Kristina M Johnson ◽  
Katherine Mitsouras ◽  
Michael Carey
Keyword(s):  
Gene Activation ◽  
Eukaryotic Transcription ◽  
The Core ◽  
Eukaryotic Gene

scholarly journals Induction of Plant Defense Gene Expression by Plant Activators and Pseudomonas syringae pv. tomato in Greenhouse-Grown Tomatoes

2008 ◽  
Vol 98 (11) ◽  
pp. 1226-1232 ◽  
Author(s):  
M. A. B. Herman ◽  
J. K. Davidson ◽  
C. D. Smart
Keyword(s):  
Gene Expression ◽  
Plant Defense ◽  
Pseudomonas Syringae ◽  
Systemic Acquired Resistance ◽  
Marker Gene ◽  
Gene Activation ◽  
Systemic Resistance ◽  
Defense Gene Expression ◽  
Defense Gene ◽  
Bacterial Speck

Plant activators provide an appealing management option for bacterial diseases of greenhouse-grown tomatoes. Two types of plant activators, one that induces systemic acquired resistance (SAR) and a second that activates induced systemic resistance (ISR), were evaluated for control of Pseudomonas syringae pv. tomato and effect on plant defense gene activation. Benzothiadiazole (BTH, SAR-inducing compound) effectively reduced bacterial speck incidence and severity, both alone and in combination with the ISR-inducing product. Application of BTH also led to elevated activation of salicylic acid and ethylene-mediated responses, based on real-time polymerase chain reaction analysis of marker gene expression levels. In contrast, the ISR-inducing product (made up of plant growth-promoting rhizobacteria) inconsistently modified defense gene expression and did not provide disease control to the same level as did BTH. No antagonism was observed by combining the two activators as control of bacterial speck was similar to or better than BTH alone.

scholarly journals Reduction of bacterial genome size and expansion resulting from obligate intracellular lifestyle and adaptation to soil habitat.

2001 ◽  
Vol 48 (2) ◽  
pp. 367-381 ◽  
Author(s):  
T Stepkowski ◽  
A B Legocki
Keyword(s):  
Genome Size ◽  
Soil Bacteria ◽  
Bacterial Genome ◽  
Housekeeping Genes ◽  
Eukaryotic Cell ◽  
Genome Reduction ◽  
Mutational Bias ◽  
Effective Population ◽  
Obligate Intracellular ◽  
Bacterial Genes

Prokaryotic organisms are exposed in the course of evolution to various impacts, resulting often in drastic changes of their genome size. Depending on circumstances, the same lineage may diverge into species having substantially reduced genomes, or such whose genomes have undergone considerable enlargement. Genome reduction is a consequence of obligate intracellular lifestyle rendering numerous genes expendable. Another consequence of intracellular lifestyle is reduction of effective population size and limited possibility of gene acquirement via lateral transfer. This causes a state of relaxed selection resulting in accumulation of mildly deleterious mutations that can not be corrected by recombination with the wild type copy. Thus, gene loss is usually irreversible. Additionally, constant environment of the eukaryotic cell renders that some bacterial genes involved in DNA repair are expandable. The loss of these genes is a probable cause of mutational bias resulting in a high A+T content. While causes of genome reduction are rather indisputable, those resulting in genome expansion seem to be less obvious. Presumably, the genome enlargement is an indirect consequence of adaptation to changing environmental conditions and requires the acquisition and integration of numerous genes. It seems that the need for a great number of capabilities is common among soil bacteria irrespective of their phylogenetic relationship. However, this would not be possible if soil bacteria lacked indigenous abilities to exchange and accumulate genetic information. The latter are considerably facilitated when housekeeping genes are physically separated from adaptive loci which are useful only in certain circumstances.

scholarly journals Eukaryotic Association Module in Phage WO Genomes from Wolbachia

2016 ◽  
Author(s):  
Sarah R. Bordenstein ◽  
Seth R. Bordenstein
Keyword(s):  
Genetic Manipulation ◽  
Cleavage Sites ◽  
Obligate Intracellular ◽  
Domain Specific ◽  
Protease Cleavage ◽  
Eukaryotic Genes ◽  
Attachment Sites ◽  
Protease Cleavage Sites ◽  
Obligate Intracellular Bacteria ◽  
Bacterial Genes

AbstractViruses are trifurcated into eukaryotic, archaeal and bacterial categories. This domain-specific ecology underscores why eukaryotic viruses typically co-opt eukaryotic genes and bacteriophages commonly harbor bacterial genes. However, the presence of bacteriophages in obligate intracellular bacteria of eukaryotes may promote DNA transfers between eukaryotes and bacteriophages. Here we report the metagenomic analysis of purified bacteriophage WO particles of Wolbachia and uncover a eukaryotic association module. It encodes domains, such as the black widow latrotoxin C-terminal domain, that are uninterrupted in bacteriophage genomes, enriched with eukaryotic protease cleavage sites, and combined with additional domains to forge one of the largest bacteriophage genes to date (14,256 bp). These domains have never before been reported in packaged bacteriophages, to our knowledge, and their phylogeny, distribution and sequence diversity imply lateral transfers between animal and bacteriophage genomes. Finally, the WO genome sequences and identification of attachment sites will potentially advance genetic manipulation of Wolbachia.

The induction of anterior and posterior neural genes in Xenopus laevis

Development ◽  
1990 ◽  
Vol 109 (4) ◽  
pp. 765-774 ◽  
Author(s):  
C.R. Sharpe ◽  
J.B. Gurdon
Keyword(s):  
Gene Expression ◽  
Marker Gene ◽  
Gene Activation ◽  
Neural Induction ◽  
Marker Genes ◽  
Neural Genes ◽  
Marker Gene Expression ◽  
Induction Process ◽  
Neural Marker ◽  
Neurula Stage

We have investigated the interactions between mesoderm and ectoderm that result in the formation of a regionally differentiated nervous system in Xenopus embryos. We have used genes expressed at different positions along the neural tube as regional markers of neural induction in both whole, and in experimentally manipulated embryos. By comparing transcription from the anterior marker, XIF3, with that from the posterior marker, X1Hbox6, and the general neural marker XIF6, we have shown that the normal induction process requires interactions between ectoderm and mesoderm that persist through gastrulation into the late neurula stages. We have found that competence of the ectoderm to respond to induction is lost at the same early neurula stage for all three marker genes. Using rhodamine dextran-labelled mesoderm, we have established that the duration of contact between ectoderm and mesoderm required for gene activation in conjugates is the same for each of the markers. We have, however, identified regions of the mesoderm that can induce different combinations of neural marker gene expression. The anterior mesoderm induces expression of the anterior marker, XIF3, and the later migrating posterior mesoderm induces the ectoderm overlying it to express the posterior marker X1Hbox6. It has been proposed that neural inducing signals reach the ectoderm by two different routes: from mesoderm lying directly beneath the ectoderm or along the plane of the ectoderm. We have assessed the contribution of each route in respect of our three neural markers and find that a signal passing directly from mesoderm to ectoderm fully accounts for neural gene expression. We were unable to detect an inducing signal that passes along the plane of the ectoderm.

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