Physiological and Dual Transcriptional Analysis of Microalga Graesiella emersonii–Amoeboaphelidium protococcarum Pathosystem Uncovers Conserved Defense Response and Robust Pathogenicity

The underlying mechanisms of microalgal host–pathogen interactions remain largely unknown. In this study, we applied physiological and simultaneous dual transcriptomic analysis to characterize the microalga Graesiella emersonii–Amoeboaphelidium protococcarum interaction. Three infection stages were determined according to infection rate and physiological features. Dual RNA-seq results showed that the genes expression of G. emersonii and A. protococcarum were strongly dynamically regulated during the infection. For microalgal hosts, similar to plant defense response, the expression of defense genes involved in the pattern recognition receptors, large heat shock proteins, and reactive oxygen scavenging enzymes (glutathione, ferritin, and catalase) were significantly upregulated during infection. However, some genes encoding resistance proteins (R proteins) with a leucine-rich repeat domain exhibited no significant changes during infection. For endoparasite A. protococcarum, genes for carbohydrate-active enzymes, pathogen–host interactions, and putative effectors were significantly upregulated during infection. Furthermore, the genes in cluster II were significantly enriched in pathways associated with the modulation of vacuole transport, including endocytosis, phagosome, ubiquitin-mediated proteolysis, and SNARE interactions in vesicular transport pathways. These results suggest that G. emersonii has a conserved defense system against pathogen and that endoparasite A. protococcarum possesses a robust pathogenicity to infect the host. Our study characterizes the first transcriptomic profile of microalgae–endoparasite interaction, providing a new promising basis for complete understanding of the algal host defense strategies and parasite pathogenicity.

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Physiological and Dual Transcriptional Analysis of Microalga Graesiella Emersonii–Amoeboaphelidium Protococcarum Pathosystem Uncovers Conserved Defense Response and Robust Pathogenicity

10.21203/rs.3.rs-844765/v1 ◽

2021 ◽

Author(s):

Yi Ding ◽

Zhongjie Wang ◽

Yali Wang ◽

Yahong Geng ◽

Xiaobin Wen ◽

...

Keyword(s):

Control Strategies ◽

Lipid Production ◽

Transcriptional Analysis ◽

Transport Pathways ◽

Defense Strategies ◽

Genes Encoding ◽

Algal Host ◽

Underlying Mechanisms ◽

Scavenging Enzymes ◽

Shock Proteins

Abstract Background: The oleaginous microalga Graesiella emersonii, a potential industrial strain for lipid production, is frequently infected by the endoparasite Amoeboaphelidium protococcarum. It is essential to investigate the microalgae–endoparasite interaction to prevent and control microalgal diseases. However, the underlying mechanisms of microalgal host-pathogen interactions remain largely unknown. In this study, we applied physiological and simultaneous dual transcriptomic analysis to characterize the G. emersonii–A. protococcarum interaction for the first time. Results: Three infection stages were determined according to infection rate and physiological features. Dual RNA-seq results showed that the genes expression of G. emersonii and A. protococcarum were strongly dynamically regulated during the infection. For microalgal hosts, the expression of defense genes involved in the pattern recognition receptors, large heat shock proteins, and reactive oxygen scavenging enzymes (glutathione, ferritin, and catalase) were significantly upregulated during infection. However, some genes encoding resistance proteins (R proteins) with a leucine-rich repeat domain exhibited no significant changes during infection. Furthermore, ubiquitin-mediated proteolysis and endocytosis were strongly affected by A. protococcarum infection. For endoparasite A. protococcarum, genes for carbohydrate-active enzymes, pathogen-host interactions, and putative effectors were significantly upregulated during infection. Furthermore, the genes in cluster II were significantly enriched in pathways associated with the modulation of vacuole transport, including endocytosis, phagosome, ubiquitin-mediated proteolysis, and SNARE interactions in vesicular transport pathways.Conclusions: Our data provide a new promising basis for complete understanding of the algal host defense strategies and parasite pathogenicity. This is beneficial for the screening of resistant microalgal strains and developing control strategies for microalgal diseases.

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Global Transcriptome Analysis of the Cold Shock Response of Shewanellaoneidensis MR-1 and Mutational Analysis of Its ClassicalCold ShockProteins

Journal of Bacteriology ◽

10.1128/jb.01908-05 ◽

2006 ◽

Vol 188 (12) ◽

pp. 4560-4569 ◽

Cited By ~ 82

Author(s):

Haichun Gao ◽

Zamin K. Yang ◽

Liyou Wu ◽

Dorothea K. Thompson ◽

Jizhong Zhou

Keyword(s):

Cold Shock ◽

Mutational Analysis ◽

Expression Patterns ◽

Shewanella Oneidensis ◽

Transcriptional Analysis ◽

Cold Shock Response ◽

Shock Response ◽

Genes Encoding ◽

Temperature Downshift ◽

Shock Proteins

ABSTRACT This study presents a global transcriptional analysis of the cold shock response of Shewanella oneidensis MR-1 after a temperature downshift from 30°C to 8 or 15°C based on time series microarray experiments. More than 700 genes were found to be significantly affected (P ≤ 0.05) upon cold shock challenge, especially at 8°C. The temporal gene expression patterns of the classical cold shock genes varied, and only some of them, most notably so1648 and so2787, were differentially regulated in response to a temperature downshift. The global response of S. oneidensis to cold shock was also characterized by the up-regulation of genes encoding membrane proteins, DNA metabolism and translation apparatus components, metabolic proteins, regulatory proteins, and hypothetical proteins. Most of the metabolic proteins affected are involved in catalytic processes that generate NADH or NADPH. Mutational analyses confirmed that the small cold shock proteins, So1648 and So2787, are involved in the cold shock response of S. oneidensis. The analyses also indicated that So1648 may function only at very low temperatures.

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Genome-Wide Transcriptional Analysis of the Cold Shock Response in Wild-Type and Cold-Sensitive, Quadruple-csp-Deletion Strains of Escherichia coli

Journal of Bacteriology ◽

10.1128/jb.186.20.7007-7014.2004 ◽

2004 ◽

Vol 186 (20) ◽

pp. 7007-7014 ◽

Cited By ~ 130

Author(s):

Sangita Phadtare ◽

Masayori Inouye

Keyword(s):

Escherichia Coli ◽

Cold Shock ◽

Sugar Transport ◽

Sugar Metabolism ◽

Transcriptional Analysis ◽

Cold Shock Response ◽

New Genes ◽

Genes Encoding ◽

Cold Sensitive ◽

Shock Proteins

ABSTRACT A DNA microarray-based global transcript profiling of Escherichia coli in response to cold shock showed that in addition to the known cold shock-inducible genes, new genes such as the flagellar operon, those encoding proteins involved in sugar transport and metabolism, and remarkably, genes encoding certain heat shock proteins are induced by cold shock. In the light of strong reduction in metabolic activity of the cell after temperature downshift, the induction of sugar metabolism machinery is unexpected. The deletion of four csps (cspA, cspB, cspG, and cspE) affected cold shock induction of mostly those genes that are transiently induced in the acclimation phase, emphasizing that CspA homologues are essential in the acclimation phase. Relevance of these findings with respect to the known RNA chaperone function of CspA homologues is discussed.

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Release mechanisms of major DAMPs

APOPTOSIS ◽

10.1007/s10495-021-01663-3 ◽

2021 ◽

Vol 26 (3-4) ◽

pp. 152-162

Author(s):

Atsushi Murao ◽

Monowar Aziz ◽

Haichao Wang ◽

Max Brenner ◽

Ping Wang

Keyword(s):

Rna Binding ◽

High Mobility ◽

Live Cells ◽

Membrane Channel ◽

Membrane Rupture ◽

Underlying Mechanisms ◽

Shock Proteins ◽

Molecular Patterns ◽

Damage Associated Molecular Patterns ◽

Secretory Lysosomes

AbstractDamage-associated molecular patterns (DAMPs) are endogenous molecules which foment inflammation and are associated with disorders in sepsis and cancer. Thus, therapeutically targeting DAMPs has potential to provide novel and effective treatments. When establishing anti-DAMP strategies, it is important not only to focus on the DAMPs as inflammatory mediators but also to take into account the underlying mechanisms of their release from cells and tissues. DAMPs can be released passively by membrane rupture due to necrosis/necroptosis, although the mechanisms of release appear to differ between the DAMPs. Other types of cell death, such as apoptosis, pyroptosis, ferroptosis and NETosis, can also contribute to DAMP release. In addition, some DAMPs can be exported actively from live cells by exocytosis of secretory lysosomes or exosomes, ectosomes, and activation of cell membrane channel pores. Here we review the shared and DAMP-specific mechanisms reported in the literature for high mobility group box 1, ATP, extracellular cold-inducible RNA-binding protein, histones, heat shock proteins, extracellular RNAs and cell-free DNA.

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Lupeol Accumulation Correlates with Auxin in the Epidermis of Castor

Molecules ◽

10.3390/molecules26102978 ◽

2021 ◽

Vol 26 (10) ◽

pp. 2978

Author(s):

Donghai Li ◽

Cheng Pan ◽

Jianjun Lu ◽

Wajid Zaman ◽

Huayan Zhao ◽

...

Keyword(s):

Auxin Transport ◽

Biosynthesis Pathway ◽

Comparative Transcriptome ◽

Hormone Activity ◽

Promoter Regions ◽

Pentacyclic Triterpene ◽

Large Numbers ◽

Genes Encoding ◽

Low Levels ◽

Underlying Mechanisms

Lupeol, a natural lupane-type pentacyclic triterpene, possesses various pharmacological properties, and its production attracts attention. Significant quantities of lupeol are deposited on the castor aerial organ surface and are easily extractable as a predominant wax constituent. Thus, castor might be considered as a potential bioreactor for the production of lupeol. The lupeol biosynthesis pathway is well known, but how it is regulated remains largely unknown. Among large numbers of castor cultivars, we targeted one accession line (337) with high levels of lupeol on its stem surface and low levels thereof on its hypocotyl surface, implicating that lupeol synthesis is differentially regulated in the two organs. To explore the underlying mechanisms, we did comparative transcriptome analysis of the first internode of 337 stem and the upper hypocotyl. Our results show that large amounts of auxin-related genes are differentially expressed in both parts, implying some possible interactions between auxin and lupeol production. We also found that several auxin-responsive cis-elements are present in promoter regions of HMGR and LUS genes encoding two key enzymes involved in lupeol production. Furthermore, auxin treatments apparently induced the expression levels of RcHMGR and RcLUS. Furthermore, we observed that auxin treatment significantly increased lupeol contents, whereas inhibiting auxin transport led to an opposite phenotype. Our study reveals some relationships between hormone activity and lupeol synthesis and might provide a promising way for improving lupeol yields in castor.

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Environmental Regulation and Virulence Attributes of the Ysa Type III Secretion System of Yersinia enterocolitica Biovar 1B

Infection and Immunity ◽

10.1128/iai.73.9.5961-5977.2005 ◽

2005 ◽

Vol 73 (9) ◽

pp. 5961-5977 ◽

Cited By ~ 47

Author(s):

Krista Venecia ◽

Glenn M. Young

Keyword(s):

Yersinia Enterocolitica ◽

Type Iii Secretion ◽

Chromosomal Locus ◽

Host Interactions ◽

Type Iii ◽

Genes Encoding ◽

Transposon Mutants ◽

Phase Temperature ◽

Mouse Model Of Infection ◽

Definitive Role

ABSTRACT Pathogenic biovars of Yersinia enterocolitica maintain the well-studied plasmid-encoded Ysc type III secretion (TTS) system, which has a definitive role in virulence. Y. enterocolitica biovar 1B additionally has a distinct chromosomal locus, the Yersinia secretion apparatus pathogenicity island (YSA PI) that encodes the Ysa TTS system. The signals to which the Ysa TTS system responds and its role in virulence remain obscure. This exploratory study was conducted to define environmental cues that promote the expression of Ysa TTS genes and to define how the Ysa TTS system influences bacterium-host interactions. Using a genetic approach, a collection of Y. enterocolitica Ysa TTS mutants was generated by mutagenesis with a transposon carrying promoterless lacZYA. This approach identified genes both within and outside of the YSA PI that contribute to Ysa TTS. Expression of these genes was regulated in response to growth phase, temperature, NaCl, and pH. Additional genetic analysis demonstrated that two regulatory genes encoding components of the YsrR-YsrS (ysrS) and RcsC-YojN-RcsB (rcsB) phosphorelay systems affect the expression of YSA PI genes and each other. The collection of Ysa TTS-defective transposon mutants, along with other strains carrying defined mutations that block Ysa and Ysc TTS, was examined for changes in virulence properties by using the BALB/c mouse model of infection. This analysis revealed that the Ysa TTS system impacts the ability of Y. enterocolitica to colonize gastrointestinal tissues. These results reveal facets of how Y. enterocolitica controls the function of the Ysa TTS system and uncovers a role for the Ysa TTS during the gastrointestinal phase of infection.

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Acidophilic green algal genome provides insights into adaptation to an acidic environment

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1707072114 ◽

2017 ◽

Vol 114 (39) ◽

pp. E8304-E8313 ◽

Cited By ~ 33

Author(s):

Shunsuke Hirooka ◽

Yuu Hirose ◽

Yu Kanesaki ◽

Sumio Higuchi ◽

Takayuki Fujiwara ◽

...

Keyword(s):

Plasma Membrane ◽

Draft Genome ◽

Acidic Environment ◽

Green Algal ◽

Genes Encoding ◽

Acidic Environments ◽

Arsenic Detoxification ◽

Shock Proteins ◽

Acidophilic Algae ◽

Algal Genome

Some microalgae are adapted to extremely acidic environments in which toxic metals are present at high levels. However, little is known about how acidophilic algae evolved from their respective neutrophilic ancestors by adapting to particular acidic environments. To gain insights into this issue, we determined the draft genome sequence of the acidophilic green alga Chlamydomonas eustigma and performed comparative genome and transcriptome analyses between C. eustigma and its neutrophilic relative Chlamydomonas reinhardtii. The results revealed the following features in C. eustigma that probably contributed to the adaptation to an acidic environment. Genes encoding heat-shock proteins and plasma membrane H+-ATPase are highly expressed in C. eustigma. This species has also lost fermentation pathways that acidify the cytosol and has acquired an energy shuttle and buffering system and arsenic detoxification genes through horizontal gene transfer. Moreover, the arsenic detoxification genes have been multiplied in the genome. These features have also been found in other acidophilic green and red algae, suggesting the existence of common mechanisms in the adaptation to acidic environments.

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Transcriptional analysis of genes encoding proteins significantly increased in Kitasatospora setae KM-6054T under submerged culture

The Journal of General and Applied Microbiology ◽

10.2323/jgam.60.276 ◽

2014 ◽

Vol 60 (6) ◽

pp. 276-280

Author(s):

Hiromi Miura ◽

Yasufumi Yagisawa ◽

Yasuki Kato ◽

Kenji Hayashi ◽

Nobuyuki Fujita ◽

...

Keyword(s):

Submerged Culture ◽

Transcriptional Analysis ◽

Genes Encoding

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Characterization and Analyses of Hydrophobic Clusters, Acetylation and Myristoylation Sites in Plant Glutathione Peroxidase Sequences

International Letters of Natural Sciences ◽

10.18052/www.scipress.com/ilns.28.27 ◽

2014 ◽

Vol 28 ◽

pp. 27-33

Author(s):

Sayak Ganguli ◽

Anisha Polley ◽

Abhijit Datta

Keyword(s):

Glutathione Peroxidase ◽

Alternative Pathway ◽

Vascular Plant ◽

Radical Scavenging ◽

Primary Source ◽

Land Plant ◽

Defense Strategies ◽

Glutathione Peroxidases ◽

Plant Groups ◽

Scavenging Enzymes

Incomplete reduction of oxygen molecules is the primary source for the formation of reactive oxygen species (ROS) during cytosolic metabolism or mitochondrial respiration. These phenomenons may be as a result of biotic or abiotic stress. Exposure to exogenous stimuli such as radiation might be an alternative pathway of ROS production. Thus plants require counter defense strategies to combat the increase of this toxic molecular build up in its cell cytoplasm. As a result they have devised an army of free radical scavenging enzymes which enable them to dissipate the oxidative stress imposed by the accumulation of these toxic moieties. Glutathione Peroxidase forms an important part of this arms race along with several catalases and organelle specific enzymes such as superoxide dismutase. Plant glutathione peroxidases (GPXs) have been studied exclusively for their evolutionary lineages since they represent a hybrid class of molecules in context of the presence and absence of selenocysteine at their catalytic centres, the former situation predominant in non vascular plant groups while the later a predominant feature of vascular plants. This analysis focuses on three important aspects of protein structure analyses – hydrophobic cluster analyses for identification of homologues, and acetylation and myristoylation sites which provide us with information regarding the post translational modifications of a particular protein group. Specific patterns of clusters along with acetylation and myristoylation site frequencies were obtained which indicate that GPXs of non vascular plant members possess less chances of getting myristoylated while acetylation was predominant in most land plant lineages but absent in aquatic members.

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Transcriptomic Responses in the Bloom-Forming Cyanobacterium Microcystis Induced during Exposure to Zooplankton

Applied and Environmental Microbiology ◽

10.1128/aem.02832-16 ◽

2016 ◽

Vol 83 (5) ◽

Cited By ~ 16

Author(s):

Matthew J. Harke ◽

Jennifer G. Jankowiak ◽

Brooke K. Morrell ◽

Christopher J. Gobler

Keyword(s):

Secondary Metabolites ◽

Daphnia Pulex ◽

Transcriptional Response ◽

Extracellular Polysaccharides ◽

Gas Vesicles ◽

Transcriptomic Response ◽

Content Type ◽

Genes Encoding ◽

Transcriptomic Responses ◽

Shock Proteins

ABSTRACT The bloom-forming, toxic cyanobacterium Microcystis synthesizes multiple secondary metabolites and has been shown to deter zooplankton grazing. However, the biochemical and/or molecular basis by which Microcystis deters zooplankton remains unclear. This global transcriptomic study explored the response of Microcystis to direct and indirect exposures to multiple densities of two cladoceran grazers, Daphnia pulex and D. magna. Higher densities of both daphnids significantly reduced Microcystis cell densities and elicited a stronger transcriptional response in Microcystis. While many putative grazer deterrence genes (encoding microcystin, aeruginosin, cyanopeptolin, and microviridin) were largely unaffected by zooplankton, transcripts for heat shock proteins (hsp) increased in abundance. Beyond metabolites and hsp, large increases in the abundances of transcripts from photosynthetic processes were observed, evidencing energy acquisition pathways were stimulated by grazing. In addition, transcripts of genes associated with the production of extracellular polysaccharides and gas vesicles significantly increased in abundance. These genes have been associated with colony formation and may have been invoked to deter grazers. Collectively, this study demonstrates that daphnid grazers induce a significant transcriptomic response in Microcystis, suggesting this cyanobacterium upregulates specific biochemical pathways to adapt to predation. IMPORTANCE This work explores the transcriptomic responses of Microcystis aeruginosa following exposure to grazing by two cladocerans, Daphnia magna and D. pulex. Contrary to previous hypotheses, Microcystis did not employ putative grazing deterrent secondary metabolites in response to the cladocerans, suggesting they may have other roles within the cell, such as oxidative stress protection. The transcriptional metabolic signature during intense grazing was largely reflective of a growth and stress response, although increasing abundances of transcripts encoding extracellular polysaccharides and gas vesicles were potentially related to predator avoidance.

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