scholarly journals Insights into gene expression changes under conditions that facilitate horizontal gene transfer (mating) of a model Archaeon

2020 ◽  
Author(s):  
Andrea M. Makkay ◽  
Artemis S. Louyakis ◽  
Nikhil Ram-Mohan ◽  
Uri Gophna ◽  
J. Peter Gogarten ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Haloferax Volcanii ◽  
Detailed Knowledge ◽  
Expression Of Genes ◽  
Cytoplasmic Bridges ◽  
Mating Conditions ◽  
Differential Expression Of Genes ◽  
Over Time

AbstractHorizontal gene transfer is a means by which bacteria, archaea, and eukaryotes are able to trade DNA within and between species. While there are a variety of mechanisms through which this genetic exchange can take place, one means prevalent in the archaeon Haloferax volcanii involves the transient formation of cytoplasmic bridges between cells and is referred to as mating. This process can result in the exchange of very large fragments of DNA between the participating cells. Genes governing the process of mating, including triggers to initiate mating, mechanisms of cell fusion, and DNA exchange, have yet to be characterized. We used a transcriptomic approach to gain a more detailed knowledge of how mating might transpire. By examining the differential expression of genes expressed in cells harvested from mating conditions on a filter over time and comparing them to those expressed in a shaking culture, we were able to identify genes and pathways potentially associated with mating. These analyses provide new insights into both the mechanisms and barriers of mating in Hfx. volcanii.

scholarly journals Insights into gene expression changes under conditions that facilitate horizontal gene transfer (mating) of a model archaeon

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Andrea M. Makkay ◽  
Artemis S. Louyakis ◽  
Nikhil Ram-Mohan ◽  
Uri Gophna ◽  
J. Peter Gogarten ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Haloferax Volcanii ◽  
Detailed Knowledge ◽  
Expression Of Genes ◽  
Cytoplasmic Bridges ◽  
Mating Conditions ◽  
Differential Expression Of Genes ◽  
Over Time

AbstractHorizontal gene transfer is a means by which bacteria, archaea, and eukaryotes are able to trade DNA within and between species. While there are a variety of mechanisms through which this genetic exchange can take place, one means prevalent in the archaeon Haloferax volcanii involves the transient formation of cytoplasmic bridges between cells and is referred to as mating. This process can result in the exchange of very large fragments of DNA between the participating cells. Genes governing the process of mating, including triggers to initiate mating, mechanisms of cell fusion, and DNA exchange, have yet to be characterized. We used a transcriptomic approach to gain a more detailed knowledge of how mating might transpire. By examining the differential expression of genes expressed in cells harvested from mating conditions on a filter over time and comparing them to those expressed in a shaking culture, we were able to identify genes and pathways potentially associated with mating. These analyses provide new insights into both the mechanisms and barriers of mating in Hfx. volcanii.

scholarly journals Cold Acclimation of the Thermoacidophilic Red Alga Galdieria sulphuraria: Changes in Gene Expression and Involvement of Horizontally Acquired Genes

2018 ◽  
Vol 60 (3) ◽  
pp. 702-712 ◽  
Author(s):  
Alessandro W Rossoni ◽  
Gerald Sch�nknecht ◽  
Hyun Jeong Lee ◽  
Ryan L Rupp ◽  
Samantha Flachbart ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Cold Acclimation ◽  
Growth Temperature ◽  
Toxic Metal ◽  
Optimal Growth ◽  
Red Alga ◽  
Galdieria Sulphuraria ◽  
Cold Temperatures

Abstract Galdieria sulphuraria is a unicellular red alga that lives in hot, acidic, toxic metal-rich, volcanic environments, where few other organisms survive. Its genome harbors up to 5% of genes that were most likely acquired through horizontal gene transfer. These genes probably contributed to G.sulphuraria’s adaptation to its extreme habitats, resulting in today’s polyextremophilic traits. Here, we applied RNA-sequencing to obtain insights into the acclimation of a thermophilic organism towards temperatures below its growth optimum and to study how horizontally acquired genes contribute to cold acclimation. A decrease in growth temperature from 42�C/46�C to 28�C resulted in an upregulation of ribosome biosynthesis, while excreted proteins, probably components of the cell wall, were downregulated. Photosynthesis was suppressed at cold temperatures, and transcript abundances indicated that C-metabolism switched from gluconeogenesis to glycogen degradation. Folate cycle and S-adenosylmethionine cycle (one-carbon metabolism) were transcriptionally upregulated, probably to drive the biosynthesis of betaine. All these cold-induced changes in gene expression were reversible upon return to optimal growth temperature. Numerous genes acquired by horizontal gene transfer displayed temperature-dependent expression changes, indicating that these genes contributed to adaptive evolution in G.sulphuraria.

scholarly journals Phylogenomic Analyses of Non-Dikarya Fungi Supports Horizontal Gene Transfer Driving Diversification of Secondary Metabolism in the Amphibian Gastrointestinal Symbiont, Basidiobolus

2020 ◽  
Vol 10 (9) ◽  
pp. 3417-3433
Author(s):  
Javier F Tabima ◽  
Ian A Trautman ◽  
Ying Chang ◽  
Yan Wang ◽  
Stephen Mondo ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Secondary Metabolism ◽  
Gene Clusters ◽  
Biologically Active ◽  
Constitutive Gene Expression ◽  
Gut Symbionts ◽  
Phylogenomic Analyses ◽  
Siderophore Activity

Abstract Research into secondary metabolism (SM) production by fungi has resulted in the discovery of diverse, biologically active compounds with significant medicinal applications. The fungi rich in SM production are taxonomically concentrated in the subkingdom Dikarya, which comprises the phyla Ascomycota and Basidiomycota. Here, we explore the potential for SM production in Mucoromycota and Zoopagomycota, two phyla of nonflagellated fungi that are not members of Dikarya, by predicting and identifying core genes and gene clusters involved in SM. The majority of non-Dikarya have few genes and gene clusters involved in SM production except for the amphibian gut symbionts in the genus Basidiobolus. Basidiobolus genomes exhibit an enrichment of SM genes involved in siderophore, surfactin-like, and terpene cyclase production, all these with evidence of constitutive gene expression. Gene expression and chemical assays also confirm that Basidiobolus has significant siderophore activity. The expansion of SMs in Basidiobolus are partially due to horizontal gene transfer from bacteria, likely as a consequence of its ecology as an amphibian gut endosymbiont.

Chaperones and protein folding in the archaea

2009 ◽  
Vol 37 (1) ◽  
pp. 46-51 ◽  
Author(s):  
Andrew T. Large ◽  
Martin D. Goldberg ◽  
Peter A. Lund
Keyword(s):  
Protein Folding ◽  
Heat Shock ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Heat Shock Protein ◽  
Haloferax Volcanii ◽  
Functional Specialization ◽  
Type I ◽  
Type Ii ◽  
Shock Proteins

A survey of archaeal genomes for the presence of homologues of bacterial and eukaryotic chaperones reveals several interesting features. All archaea contain chaperonins, also known as Hsp60s (where Hsp is heat-shock protein). These are more similar to the type II chaperonins found in the eukaryotic cytosol than to the type I chaperonins found in bacteria, mitochondria and chloroplasts, although some archaea also contain type I chaperonin homologues, presumably acquired by horizontal gene transfer. Most archaea contain several genes for these proteins. Our studies on the type II chaperonins of the genetically tractable archaeon Haloferax volcanii have shown that only one of the three genes has to be present for the organisms to grow, but that there is some evidence for functional specialization between the different chaperonin proteins. All archaea also possess genes for prefoldin proteins and for small heat-shock proteins, but they generally lack genes for Hsp90 and Hsp100 homologues. Genes for Hsp70 (DnaK) and Hsp40 (DnaJ) homologues are only found in a subset of archaea. Thus chaperone-assisted protein folding in archaea is likely to display some unique features when compared with that in eukaryotes and bacteria, and there may be important differences in the process between euryarchaea and crenarchaea.

scholarly journals Lifestyle and Horizontal Gene Transfer-Mediated Evolution of Mucispirillum schaedleri, a Core Member of the Murine Gut Microbiota

mSystems ◽  
2017 ◽  
Vol 2 (1) ◽  
Author(s):  
Alexander Loy ◽  
Carina Pfann ◽  
Michaela Steinberger ◽  
Buck Hanson ◽  
Simone Herp ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Gut Microbiota ◽  
Intestinal Inflammation ◽  
Effector Proteins ◽  
Secretion Systems ◽  
Associated Bacteria ◽  
Content Type ◽  
Gut Microbiota Composition

ABSTRACT Shifts in gut microbiota composition have been associated with intestinal inflammation, but it remains unclear whether inflammation-associated bacteria are commensal or detrimental to their host. Here, we studied the lifestyle of the gut bacterium Mucispirillum schaedleri, which is associated with inflammation in widely used mouse models. We found that M. schaedleri has specialized systems to handle oxidative stress during inflammation. Additionally, it expresses secretion systems and effector proteins and can modify the mucosal gene expression of its host. This suggests that M. schaedleri undergoes intimate interactions with its host and may play a role in inflammation. The insights presented here aid our understanding of how commensal gut bacteria may be involved in altering susceptibility to disease. Mucispirillum schaedleri is an abundant inhabitant of the intestinal mucus layer of rodents and other animals and has been suggested to be a pathobiont, a commensal that plays a role in disease. In order to gain insights into its lifestyle, we analyzed the genome and transcriptome of M. schaedleri ASF 457 and performed physiological experiments to test traits predicted by its genome. Although described as a mucus inhabitant, M. schaedleri has limited capacity for degrading host-derived mucosal glycans and other complex polysaccharides. Additionally, M. schaedleri reduces nitrate and expresses systems for scavenging oxygen and reactive oxygen species in vivo, which may account for its localization close to the mucosal tissue and expansion during inflammation. Also of note, M. schaedleri harbors a type VI secretion system and putative effector proteins and can modify gene expression in mucosal tissue, suggesting intimate interactions with its host and a possible role in inflammation. The M. schaedleri genome has been shaped by extensive horizontal gene transfer, primarily from intestinal Epsilon- and Deltaproteobacteria, indicating that horizontal gene transfer has played a key role in defining its niche in the gut ecosystem. IMPORTANCE Shifts in gut microbiota composition have been associated with intestinal inflammation, but it remains unclear whether inflammation-associated bacteria are commensal or detrimental to their host. Here, we studied the lifestyle of the gut bacterium Mucispirillum schaedleri, which is associated with inflammation in widely used mouse models. We found that M. schaedleri has specialized systems to handle oxidative stress during inflammation. Additionally, it expresses secretion systems and effector proteins and can modify the mucosal gene expression of its host. This suggests that M. schaedleri undergoes intimate interactions with its host and may play a role in inflammation. The insights presented here aid our understanding of how commensal gut bacteria may be involved in altering susceptibility to disease.

scholarly journals Recombination-driven genome evolution and stability of bacterial species

2016 ◽  
Author(s):  
Purushottam D. Dixit ◽  
Tin Yau Pang ◽  
Sergei Maslov
Keyword(s):  
Population Structure ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Homologous Recombination ◽  
Recombination Frequency ◽  
Bacterial Species ◽  
Structured Populations ◽  
Genome Diversity ◽  
Over Time ◽  
Evolutionary Fate

While bacteria divide clonally, horizontal gene transfer followed by homologous recombination is now recognized as an important and sometimes even dominant contributor to their evolution. However, the details of how the competition between clonal inheritance and recombination shapes genome diversity, population structure, and species stability remains poorly understood. Using a computational model, we find two principal regimes in bacterial evolution and identify two composite parameters that dictate the evolutionary fate of bacterial species. In the divergent regime, characterized by either a low recombination frequency or strict barriers to recombination, cohesion due to recombination is not sufficient to overcome the mutational drift. As a consequence, the divergence between any pair of genomes in the population steadily increases in the course of their evolution. The species as a whole lacks genetic coherence with sexually isolated clonal sub-populations continuously formed and dissolved. In contrast, in the metastable regime, characterized by a high recombination frequency combined with low barriers to recombination, genomes continuously recombine with the rest of the population. The population remains genetically cohesive and stable over time. The transition between these two regimes can be affected by relatively small changes in evolutionary parameters. Using the Multi Locus Sequence Typing (MLST) data we classify a number of well-studied bacterial species to be either the divergent or the metastable type. Generalizations of our framework to include fitness and selection, ecologically structured populations, and horizontal gene transfer of non-homologous regions are discussed.

scholarly journals Assessment of the differential gene expression in anthracnose treated seedlings of yellow lupin

2021 ◽  
Vol 65 (3) ◽  
pp. 330-336
Author(s):  
E. N. Sysoliatin ◽  
V. S. Anokhina ◽  
N. V. Anisimova ◽  
O. G. Babak ◽  
A. V. Kilchevsky
Keyword(s):  
Gene Expression ◽  
Differential Expression ◽  
Differential Gene Expression ◽  
Genetic Determinants ◽  
Yellow Lupin ◽  
Expression Of Genes ◽  
Differential Gene ◽  
Colletotrichum Lupini ◽  
Yellow Lupine ◽  
Differential Expression Of Genes

Seedlings of yellow lupine treated with Colletotrichum lupini isolate were studied by the method of SRAP-analysis with the purpose to assess the differential expression of genes. As a result, the PCR fragment corresponding to tolerant seedlings was found. The genetic determinants found are likely involved in the control of the resistance (tolerance) of lupine plants to anthracnose.

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