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.

scholarly journals Natural Genetic Transformation in Monoculture Acinetobacter sp. Strain BD413 Biofilms

2003 ◽  
Vol 69 (3) ◽  
pp. 1721-1727 ◽  
Author(s):  
Larissa Hendrickx ◽  
Martina Hausner ◽  
Stefan Wuertz
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Genetic Transformation ◽  
Exposure Time ◽  
Growth Phase ◽  
Natural Transformation ◽  
Optimal Growth ◽  
Continuous Exposure ◽  
Dna Concentration ◽  
Natural Genetic Transformation

ABSTRACT Horizontal gene transfer by natural genetic transformation in Acinetobacter sp. strain BD413 was investigated by using gfp carried by the autonomously replicating plasmid pGAR1 in a model monoculture biofilm. Biofilm age, DNA concentration, and biofilm mode of growth were evaluated to determine their effects on natural genetic transformation. The highest transfer frequencies were obtained in young and actively growing biofilms when high DNA concentrations were used and when the biofilm developed during continuous exposure to fresh medium without the presence of a significant amount of cells in the suspended fraction. Biofilms were highly amenable to natural transformation. They did not need to advance to an optimal growth phase which ensured the presence of optimally competent biofilm cells. An exposure time of only 15 min was adequate for transformation, and the addition of minute amounts of DNA (2.4 fg of pGAR1 per h) was enough to obtain detectable transfer frequencies. The transformability of biofilms lacking competent cells due to growth in the presence of cells in the bulk phase could be reestablished by starving the noncompetent biofilm prior to DNA exposure. Overall, the evidence suggests that biofilms offer no barrier against effective natural genetic transformation of Acinetobacter sp. strain BD413.

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 Exploring lowering the optimal growth temperature of Escherichia coli in biotechnology applications

2019 ◽  
Author(s):  
Wenfa Ng
Keyword(s):  
Gene Expression ◽  
Escherichia Coli ◽  
Growth Temperature ◽  
Optimal Growth ◽  
The Other ◽  
Optimal Growth Temperature ◽  
Laboratory Evolution ◽  
E Coli ◽  
Number Of Genes ◽  
Specific Temperature

Different microbes grow at different optimal growth temperature. But, what defines this metabolic adaptation at the molecular and genetic level? And, more importantly, how different metabolic and signalling networks interact to yield a cellular system able to achieve maximal growth rate at a specific temperature? Molecular knowledge of such interacting components could provide a template on which modifications could be made to help adapt a microbe to another optimal growth temperature. However, given the large number of genes, proteins and pathways involved, efforts to re-adapt a microbe to another optimal growth temperature is likely difficult through a rational design approach. On the other hand, laboratory evolution approach might do the trick, but significant efforts are needed to understand the biochemical and physiological logic of the re-adaption. Using the genetically tractable Escherichia coli as model organism, this work aims to explore the possibility of using a rational approach at lowering the optimal growth temperature of the bacterium from 37 oC to 25 oC to help reduce energy costs and carbon emissions of fermentation. To this end, population level RNA-seq would be used to understand the global transcriptome of E. coli cultivated at 25, 30 and 37 oC in LB medium. Highly transcribed genes at 37 oC would represent those that need to be activated during growth at 25 oC. On the other hand, genes transcribed at a low level at 37 oC should remain poorly expressed at 25 oC. While modern genetic engineering tools such as use of promoters and terminators with differentiated strength would allow the targeted tuning of expression of specific genes, potential need for re-engineering the expression of large number of genes might present difficulties. Thus, answers to what tune a microbe to operate optimally at a specific temperature might come from the signalling and gene regulation level where genes and proteins occupying particular nodes in the biochemical network hold sway on the expression of large number of downstream genes. Knowledge such as these could accrue from the feeding of transcriptome data into genome-scale metabolic models able to help identify critical nodes in metabolic pathways whose modulation would change cellular physiology. Given the importance of regulons governed by specific sigma factors, their modulation through altering sigma factor expression might be critical to gaining more widespread control of global gene expression at particular temperature. Collectively, developing rational approaches for tuning the optimal growth temperature of E. coli present critical challenges compared to laboratory evolution methods. As gene expression is regulated at multiple levels using a variety of mechanisms, transposing expression levels of highly transcribed genes at 37 oC to 25 oC would require the simultaneous modulation of different regulatory nodes belonging to both metabolic and signalling pathways.

scholarly journals Exploring lowering the optimal growth temperature of Escherichia coli in biotechnology applications

2019 ◽  
Author(s):  
Wenfa Ng
Keyword(s):  
Gene Expression ◽  
Escherichia Coli ◽  
Growth Temperature ◽  
Optimal Growth ◽  
The Other ◽  
Optimal Growth Temperature ◽  
Laboratory Evolution ◽  
E Coli ◽  
Number Of Genes ◽  
Specific Temperature

Different microbes grow at different optimal growth temperature. But, what defines this metabolic adaptation at the molecular and genetic level? And, more importantly, how different metabolic and signalling networks interact to yield a cellular system able to achieve maximal growth rate at a specific temperature? Molecular knowledge of such interacting components could provide a template on which modifications could be made to help adapt a microbe to another optimal growth temperature. However, given the large number of genes, proteins and pathways involved, efforts to re-adapt a microbe to another optimal growth temperature is likely difficult through a rational design approach. On the other hand, laboratory evolution approach might do the trick, but significant efforts are needed to understand the biochemical and physiological logic of the re-adaption. Using the genetically tractable Escherichia coli as model organism, this work aims to explore the possibility of using a rational approach at lowering the optimal growth temperature of the bacterium from 37 oC to 25 oC to help reduce energy costs and carbon emissions of fermentation. To this end, population level RNA-seq would be used to understand the global transcriptome of E. coli cultivated at 25, 30 and 37 oC in LB medium. Highly transcribed genes at 37 oC would represent those that need to be activated during growth at 25 oC. On the other hand, genes transcribed at a low level at 37 oC should remain poorly expressed at 25 oC. While modern genetic engineering tools such as use of promoters and terminators with differentiated strength would allow the targeted tuning of expression of specific genes, potential need for re-engineering the expression of large number of genes might present difficulties. Thus, answers to what tune a microbe to operate optimally at a specific temperature might come from the signalling and gene regulation level where genes and proteins occupying particular nodes in the biochemical network hold sway on the expression of large number of downstream genes. Knowledge such as these could accrue from the feeding of transcriptome data into genome-scale metabolic models able to help identify critical nodes in metabolic pathways whose modulation would change cellular physiology. Given the importance of regulons governed by specific sigma factors, their modulation through altering sigma factor expression might be critical to gaining more widespread control of global gene expression at particular temperature. Collectively, developing rational approaches for tuning the optimal growth temperature of E. coli present critical challenges compared to laboratory evolution methods. As gene expression is regulated at multiple levels using a variety of mechanisms, transposing expression levels of highly transcribed genes at 37 oC to 25 oC would require the simultaneous modulation of different regulatory nodes belonging to both metabolic and signalling pathways.

scholarly journals Adaptation through horizontal gene transfer in the cryptoendolithic red alga Galdieria phlegrea

2013 ◽  
Vol 23 (19) ◽  
pp. R865-R866 ◽  
Author(s):  
Huan Qiu ◽  
Dana C. Price ◽  
Andreas P.M. Weber ◽  
Valérie Reeb ◽  
Eun Chan Yang ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Red Alga

scholarly journals Transcriptome analysis of Xanthomonas oryzae pv. oryzicola exposed to H2O2 reveals horizontal gene transfer contributes to its oxidative stress response

2019 ◽  
Author(s):  
Yuan Fang ◽  
Haoye Wang ◽  
Xia Liu ◽  
Yuchun Rao ◽  
Xin Dedong ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Gene Expression ◽  
Time Series ◽  
Stress Response ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Oxidative Stress Response ◽  
Xanthomonas Oryzae ◽  
Gene Location ◽  
Rna Seq

AbstractXanthomonas oryzae pv. oryzicola (Xoc) is the causal agent of bacterial leaf streak in rice. It is known as one of the most severe seed-born bacterial diseases of rice, molecular role governing its interaction with rice is mostly still unexplored. To successfully invade rice, the survival of the Xoc is mandotarory following generating a specific response to its host’s oxidative stress condition. However, the response network of Xoc is still unknown. To address this question, we performed a time-series RNA-seq analysis on the Xoc response to H2O2. Overall, our RNA sequence analysis of Xoc revealed a significant global gene expression profile when it exposed to H2O2. The response of key genes was also noted that soxR triggers and regulates the Xoc oxidative stress response in the early stage of infection, gene expression kinetics among the time-series samples, namely for TonB-dependent receptors and the suf and pst operons. Moreover, a hypothetical protein (XOC_2868) showed significant differential expression following its mutant endorsed RNA-seq findings by clearly displaying a greater H2O2 sensitivity and decreased pathogenicity than the wild-type. Gene location and phylogeny analysis strongly suggests that this gene may have been horizontally transferred from a Burkholderiaceae ancestor. Our study not only provides a first glance of Xoc’s global response against oxidative stress, but it also reveals the impact of horizontal gene transfer in the evolutionary history of Xoc.

scholarly journals Phylogenomic analyses of non-Dikarya fungi supports horizontal gene transfer driving diversification of secondary metabolism in the amphibian gastrointestinal symbiont, Basidiobolus

2020 ◽  
Author(s):  
Javier Felipe Tabima ◽  
Ian A. Trautman ◽  
Ying Chang ◽  
Yan Wang ◽  
Stephen J. 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

Research into secondary metabolism (SM) production by fungi has resulted in the discovery of diverse, biologically active compounds with significant medicinal applications. However, the fungi rich in SM production are taxonomically restricted to Dikarya, two phyla of Kingdom Fungi, 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 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.

Conserved patterns of alternative splicing in response to cold acclimation in fish

2018 ◽  
Author(s):  
Timothy M. Healy ◽  
Patricia M. Schulte
Keyword(s):  
Gene Expression ◽  
Alternative Splicing ◽  
Phenotypic Plasticity ◽  
Cold Acclimation ◽  
Gasterosteus Aculeatus ◽  
Expression Patterns ◽  
Functional Enrichment ◽  
Cold Temperatures ◽  
Qualitative Changes

AbstractPhenotypic plasticity is an important aspect of an organism’s response to environmental change that often requires the modulation of gene expression. These changes in gene expression can be quantitative as a result of increases or decreases in the amounts of specific transcripts, or qualitative as a result of the expression of alternative transcripts from the same gene (e.g., via alternative splicing of pre-mRNAs). Although the role of quantitative changes in gene expression in phenotypic plasticity is well known, relatively few studies have examined the role of qualitative changes. Here, we use skeletal muscle RNA-seq data from Atlantic killifish (Fundulus heteroclitus), threespine stickleback (Gasterosteus aculeatus) and zebrafish (Danio rerio) to investigate the extent of qualitative changes in gene expression in response to cold. Fewer genes demonstrated alternative splicing than differential expression as a result of cold acclimation; however, differences in splicing were detected for between 426 and 866 genes depending on species, indicating that large numbers of qualitative changes in gene expression are associated with cold acclimation. Many of these alternatively spliced genes were also differentially expressed, and there was functional enrichment for involvement in muscle contraction among the genes demonstrating qualitative changes in response to cold acclimation. Additionally, there was a common group of 29 genes with cold-acclimation-mediated changes in splicing in all three species, suggesting that there may be a conserved set of genes with expression patterns that respond qualitatively to prolonged cold temperatures across fishes.Summary statementQualitative changes in gene expression, such as those mediated by alternative splicing of mRNAs, are involved in phenotypic plasticity in response to prolonged cold acclimation in ectothermic animals

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