Towards Exploring Toxin-Antitoxin Systems in Geobacillus: A Screen for Type II Toxin-Antitoxin System Families in a Thermophilic Genus

The toxin-antitoxin (TA) systems have been attracting attention due to their role in regulating stress responses in prokaryotes and their biotechnological potential. Much recognition has been given to type II TA system of mesophiles, while thermophiles have received merely limited attention. Here, we are presenting the putative type II TA families encoded on the genomes of four Geobacillus strains. We employed the TA finder tool to mine for TA-coding genes and manually curated the results using protein domain analysis tools. We also used the NCBI BLAST, Operon Mapper, ProOpDB, and sequence alignment tools to reveal the geobacilli TA features. We identified 28 putative TA pairs, distributed over eight TA families. Among the identified TAs, 15 represent putative novel toxins and antitoxins, belonging to the MazEF, MNT-HEPN, ParDE, RelBE, and XRE-COG2856 TA families. We also identified a potentially new TA composite, AbrB-ParE. Furthermore, we are suggesting the Geobacillus acetyltransferase TA (GacTA) family, which potentially represents one of the unique TA families with a reverse gene order. Moreover, we are proposing a hypothesis on the xre-cog2856 gene expression regulation, which seems to involve the c-di-AMP. This study aims for highlighting the significance of studying TAs in Geobacillus and facilitating future experimental research.

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Towards Exploring Toxin-Antitoxin Systems in Geobacillus: A Screen for Type II Toxin-Antitoxin System Families in A Thermophilic Genus

10.20944/preprints201910.0325.v1 ◽

2019 ◽

Author(s):

Rawana N. Alkhalili ◽

Joel Wallenius ◽

Björn Canbäck

Keyword(s):

Gene Expression ◽

Experimental Research ◽

Gene Order ◽

Limited Attention ◽

Type Ii ◽

Hypothetical Proteins ◽

Biotechnological Potential ◽

Prokaryotic Cell ◽

Cell Responses

The toxin-antitoxin (TA) systems have been attracting attention due to their role in regulating prokaryotic cell responses to stress and their biotechnological potential. Much recognition has been given to type II TA system of mesophiles, but so far, limited attention has been given to thermophiles. Here, we are presenting the putative type II TA families encoded on the genomes of four Geobacillus strains. We employed the TA finder tool to mine for TA-coding genes and manually curated the results using various tools. We identified 28 putative TA pairs, distributed over 8 TA families. Among the identified TAs, 15 represent putative novel toxins and antitoxins that have been overlooked or annotated as hypothetical proteins in their genome records. We also identified a potentially new TA composite, AbrB-ParE. Furthermore, we are suggesting the Geobacillus acetyltransferase toxin-antitoxin (GacTA) family which potentially represents one of the unique TA families that has a reverse gene order. Moreover, we are proposing a hypothesis on the regulation of the xre-cog2856 gene expression, which seems to involve c-di-AMP. This study aims for highlighting the significance of studying TAs in Geobacillus, since they have special features. It also aims for facilitating future experimental research.

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Adaptation of plasticity to predicted climates in Australian rainbowfishes (Melanotaenia) across climatically defined bioregions

10.1101/859769 ◽

2019 ◽

Author(s):

Jonathan Sandoval-Castillo ◽

Katie Gates ◽

Chris J. Brauer ◽

Steve Smith ◽

Louis Bernatchez ◽

...

Keyword(s):

Gene Expression ◽

Stress Responses ◽

Gene Expression Regulation ◽

Thermal Response ◽

Thermal Conditions ◽

Common Garden ◽

Model Framework ◽

Network Analyses ◽

Biogeographic History ◽

Adaptive Resilience

AbstractResilience to environmental stressors due to climate warming is influenced by local adaptations, including the capacity for plastic responses. The recent literature has focussed on genomic signatures of climatic adaptation, however little work has been done to address how plastic capacity may be influenced by biogeographic history and evolutionary processes. Here, we investigate phenotypic plasticity as a target of climatic selection, hypothesising that lineages that evolved under warmer climate will exhibit greater plastic adaptive resilience to thermal stress. This was tested using common garden experiments to compare gene expression regulation within and among a temperate, a subtropical and a desert ecotype of Australian rainbowfish. Individuals from each ecotype were subjected to contemporary and projected summer thermal conditions for 2070, and their global patterns of gene expression were characterized using liver transcriptomes. Critical thermal maximums were also determined for each ecotype to assess thermal tolerance. A comparative phylogenetic expression variance and evolution model framework was used to assess plastic and evolved changes in gene expression. Similar changes in both the direction and the magnitude of expressed genes were found within ecotypes. Although most expressed genes were identified in all ecotypes, 532 genes were identified as candidates subject to ecotype-specific directional selection. Twenty-three of those genes showed signal of adaptive (i.e. genetic-based) plastic response to future increases in temperature. Network analyses demonstrated centrality of these genes in thermal response pathways, along with several highly conserved hub genes thought to be integral for heat stress responses. The greatest adaptive resilience to warming was shown by the subtropical ecotype, followed by the desert and temperate ecotypes. Our findings indicate that vulnerability to climate change will be highly influenced by biogeographic factors, and we stress the need for integrative assessments of climatic adaptive traits for accurate estimations of population and ecosystem responses.

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A minimal model for gene expression dynamics of bacterial type II toxin–antitoxin systems

Scientific Reports ◽

10.1038/s41598-021-98570-z ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Kosmas Kosmidis ◽

Marc-Thorsten Hütt

Keyword(s):

Gene Expression ◽

Mathematical Modelling ◽

Kinetic Parameters ◽

Stress Responses ◽

Minimal Model ◽

Time Course ◽

Mechanistic Model ◽

Quantitative Description ◽

Type Ii ◽

Computational Systems Biology

AbstractToxin–antitoxin (TA) modules are part of most bacteria’s regulatory machinery for stress responses and general aspects of their physiology. Due to the interplay of a long-lived toxin with a short-lived antitoxin, TA modules have also become systems of interest for mathematical modelling. Here we resort to previous modelling efforts and extract from these a minimal model of type II TA system dynamics on a timescale of hours, which can be used to describe time courses derived from gene expression data of TA pairs. We show that this model provides a good quantitative description of TA dynamics for the 11 TA pairs under investigation here, while simpler models do not. Our study brings together aspects of Biophysics with its focus on mathematical modelling and Computational Systems Biology with its focus on the quantitative interpretation of ’omics’ data. This mechanistic model serves as a generic transformation of time course information into kinetic parameters. The resulting parameter vector can, in turn, be mechanistically interpreted. We expect that TA pairs with similar mechanisms are characterized by similar vectors of kinetic parameters, allowing us to hypothesize on the mode of action for TA pairs still under discussion.

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Candida auris gene expression: modulation upon caspofungin treatment

Access Microbiology ◽

10.1099/acmi.cc2021.po0096 ◽

2021 ◽

Vol 3 (12) ◽

Author(s):

Lysangela Alves ◽

Rafaela Amatuzzi ◽

Daniel Zamith-Miranda ◽

Sharon Martins ◽

Joshua Nosanchuk

Keyword(s):

Gene Expression ◽

Stress Responses ◽

Ribosomal Proteins ◽

Gene Expression Regulation ◽

Extracellular Vesicle ◽

Health Warnings ◽

Candida Auris ◽

Fungal Biology ◽

Invasive Infections ◽

Survival Mechanisms

Candida auris has emerged as a serious worldwide threat by causing invasive infections in humans that are frequently resistant to one or more conventional antifungal medications, resulting in high mortality rates. Against this backdrop, health warnings around the world have focused efforts on understanding C. auris fungal biology and effective treatment approaches to combat this fungus. To date, there is little information about C. auris gene expression regulation in response to antifungal treatment. Our integrated analyses focused on the comparative transcriptomics of C. auris in the presence and absence of caspofungin as well as a detailed analysis of the yeast's extracellular vesicle (EV)-RNA composition. The results showed that genes coding oxidative stress response, ribosomal proteins, cell wall, and cell cycle were significantly up-regulated in the presence of caspofungin, whereas transcriptional regulators and proteins related to nucleus were down-regulated. The mRNAs in the EVswere associated with the stress responses induced by caspofungin and the ncRNA content of the EVs shifted during caspofungin treatment. Altogether, the results provide further insights into the fungal response to caspofungin and demonstrate that analyses of C. auris growth under antifungal stress can elucidate resistance and survival mechanisms of this fungus in response to medical therapy.

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Regulation of Gene Expression of Methionine Sulfoxide Reductases and Their New Putative Roles in Plants

International Journal of Molecular Sciences ◽

10.3390/ijms20061309 ◽

2019 ◽

Vol 20 (6) ◽

pp. 1309 ◽

Cited By ~ 2

Author(s):

Ewa Kalemba ◽

Ewelina Stolarska

Keyword(s):

Gene Expression ◽

Transcription Factors ◽

Stress Responses ◽

Gene Expression Regulation ◽

Developmental Process ◽

Regulation Of Gene Expression ◽

Methionine Sulfoxide ◽

Stimulus Term ◽

Ontology Term ◽

Methionine Sulfoxide Reductases

Oxidation of methionine to methionine sulfoxide is a type of posttranslational modification reversed by methionine sulfoxide reductases (Msrs), which present an exceptionally high number of gene copies in plants. The side-form general antioxidant function-specific role of each Msr isoform has not been fully studied. Thirty homologous genes of Msr type A (MsrA) and type B (MsrB) that originate from the genomes of Arabidopsis thaliana, Populus trichocarpa, and Oryza sativa were analyzed in silico. From 109 to 201 transcription factors and responsive elements were predicted for each gene. Among the species, 220 and 190 common transcription factors and responsive elements were detected for the MsrA and MsrB isoforms, respectively. In a comparison of 14 MsrA and 16 MsrB genes, 424 transcription factors and responsive elements were reported in both types of genes, with almost ten times fewer unique elements. The transcription factors mainly comprised plant growth and development regulators, transcription factors important in stress responses with significant overrepresentation of the myeloblastosis viral oncogene homolog (MYB) and no apical meristem, Arabidopsis transcription activation factor and cup-shaped cotyledon (NAC) families and responsive elements sensitive to ethylene, jasmonate, sugar, and prolamine. Gene Ontology term-based functional classification revealed that cellular, metabolic, and developmental process terms and the response to stimulus term dominated in the biological process category. Available experimental transcriptomic and proteomic data, in combination with a set of predictions, gave coherent results validating this research. Thus, new manners Msr gene expression regulation, as well as new putative roles of Msrs, are proposed.

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Novel insights into the cold resistance of Hevea brasiliensis through coexpression networks

10.1101/2021.11.02.466997 ◽

2021 ◽

Author(s):

Carla Cristina Silva ◽

Stephanie Karenina Bajay ◽

Alexandre Hild Aono ◽

Felipe Roberto Francisco ◽

Ramir Bavaresco Junior ◽

...

Keyword(s):

Gene Expression ◽

Cold Stress ◽

Cold Exposure ◽

Stress Responses ◽

Hevea Brasiliensis ◽

Large Scale ◽

Gene Expression Regulation ◽

Rubber Tree ◽

Early Years ◽

Cold Response

Hevea brasiliensis, a tropical tree species from the Amazon rainforest, is the main source of natural rubber worldwide. Due to the high pressure of fungal diseases in hot, humid regions, rubber plantations have been moved to escape areas, which are dryer and have lower temperatures during the winter. Here, we combined gene expression data of a primary (GT1) and a secondary (RRIM600) young rubber tree clones, which present different cold tolerance strategies, to analyze rubber tree gene expression regulation during 24 h of cold exposure (10 degrees Celsius). Together with traditional differential expression approaches, a RNA sequencing (RNA-seq) gene coexpression network (GCN) comprising 27,220 genes was established in which the genes were grouped into 832 clusters. In the GCN, most of the rubber tree molecular responses to cold stress were grouped in 26 clusters, which were divided into three GCN modules: a downregulated group comprising 12 clusters and two upregulated groups comprising eleven and three clusters. Considering the three modules identified, the general Hevea response to short-term cold exposure involved downregulation of gibberellin (GA) signaling, complex regulation of jasmonic acid (JA) stress responses and programmed cell death (PCD) and upregulation of ethylene responsive genes. The hub genes of the cold-responsive modules were subsequently identified and analyzed. As a result of the GCN strategy applied in this study, we could not only access individual DEGs related to the Hevea cold response, but also provide insights into a deeper cascade of associated mechanisms involved in the response to cold stress in young rubber trees. Our results may represent the genetic stress responses of the species, developed during its evolution, since the varieties chosen for this work are genotypes that were selected during the early years of rubber tree domestication. The understanding of H. brasiliensis cold response mechanisms can greatly improve the breeding strategies for this crop, which has a narrow genetic base, is impacted by climate change and is the only source for large-scale rubber production.

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