Changes in iTRAQ-Based Proteomic Profiling of the Cladoceran <i>Daphnia magna</i> Exposed to Microcystin-Producing and Microcystin-Free <i>Microcystis aeruginosa</i>

Lyu, Kai; Meng, Qingguo; Zhu, Xiaoyong; Dai, Daoxin; Zhang, Lu; Huang, Yuan; Yang, Zhou

doi:10.1021/acs.est.6b00101

Cited by 74 publications

(23 citation statements)

References 69 publications

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“…These enzymes play an essential role in the homeostatic maintenance of stress response and protein folding, which are crucial when the number of unfolded proteins increases (Walter and Ron ). As reported previously (Asselman et al ; Lyu et al ), exposure to toxic Microcystis inhibited STPK‐PDIK1L and TPK expression in the sensitive clone TH09 and interfered with normal protein folding and repair. In addition, since HSP70B serves as a molecular chaperone, minimizes protein aggregation, and repairs and protects cellular proteins from stress damage (Mayer and Bukau ), it was to be expected that increased HSP70B expression was induced by an abundance of unfolded proteins.…”

Section: Discussionsupporting

confidence: 79%

Transcriptomic analysis dissects the mechanistic insight into the Daphnia clonal variation in tolerance to toxic Microcystis

Lyu

Wang

et al. 2018

Limnology & Oceanography

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Cyanobacteria have become more prevalent than other phytoplankton in freshwater assemblages during summer. In such conditions, cyanobacterial traits may reduce zooplankton fitness and the energy flow efficiency from primary producers to aquatic herbivores. Cladocerans, as the dominant zooplankton grazers in freshwater ecosystems, exhibit clonal variation in their tolerance to cyanobacteria with an increasing gradient in eutrophication history. Hitherto, research on the full modes of action (MoAs) of Daphnia clonal differences in tolerance to toxic Microcystis still remains in its infancy. We conducted fitness and transcriptome analyses on two Daphnia clones, clone TH09 and TH14. A significant decline in body growth rate was detected in the sensitive clone TH09 compared with the tolerant clone TH14 at the presence of toxic Microcystis. Furthermore, transcriptional analysis indicated that major MoAs such as glutathione metabolism, protein processing in endoplasmic reticulum, amino sugar/nucleotide sugar metabolism, and arachidonic acid metabolism were linked to the tolerance fitness in Daphnia similoides. These results provided mechanistic insights into the pathways of genetic and biological processes involved in cyanobacteria tolerance in the Daphnia clonal variation, and propose that the genetic architecture of this fitness‐related trait would be helpful to clarify how zooplankton clones adapt to harmful algal blooms.

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Section: Discussionsupporting

confidence: 79%

Transcriptomic analysis dissects the mechanistic insight into the Daphnia clonal variation in tolerance to toxic Microcystis

Lyu

Wang

et al. 2018

Limnology & Oceanography

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“…Up-and downregulated proteins were stipulated based on many previous studies. 19,39,40 The typical criterion for differentially expressed proteins was a ratio >1.2 or <0.83 coupled with a P value <0.05. A custom SEARCH_DB_UniProt.2017.1.7.fasta database was created to match concerned proteins based on 16S rRNA gene sequences and a few previous reports, 41 All original data and the ProteinPilot output tables were uploaded to iProX (http://www.iprox.org) under the accession number IPX0001034001.…”

Section: ■ Materials and Methodsmentioning

confidence: 99%

Linking Exoproteome Function and Structure to Anammox Biofilm Development

Chen

Meng

Sheng

et al. 2019

Environ. Sci. Technol.

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Extracellular proteins are of paramount importance in the cell−cell interactions of anammox biofilms. However, the inherent aggregation mechanisms of anammox have largely remained elusive. Herein, using a quartz sand extraction protocol and follow-up iTRAQ-based quantitative proteomics, we identified 367 extracellular proteins from initial colonizers, mature biofilm, and detached biofilm. The extracellular proteins were mainly membrane-associated. Most of the recovered proteins (226, 72.5%) originated from the phylum Planctomycetes. In summary, 215 and 190 of the 367 proteins recovered were up-and/ or downregulated at least 1.2-fold during the biofilm formation and detachment periods, respectively. These differentially expressed proteins were dominantly involved in metal ion binding, which was regarded as strong evidence for their abilities to enhance ionic bridges in extracellular polymeric substances (EPS). Scanning electron microscopy−energy-dispersive X-ray spectroscopy (SEM-EDX) analysis of the biofilms further showed substantial levels of calcium and iron minerals. Critically, representative Sec-dependent secretory proteins affiliated with coccoid Planctomycetes, rod-shaped Proteobacteria, and filamentous Chloroflexi (11, 4, and 2 with differential expression, respectively) were found to have typical and abundant inner βsheet structures, wherein hydrophobic moieties can promote anammox aggregation. Overall, these findings highlight links between differentially expressed protein functions and morphologic traits of anammox consortia during biofilm development.

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“…Proteins directly participate in the biological processes and functions; thus, the quantitative proteomic analysis can provide direct evidences for the regulation mechanisms of physiology and metabolism at global level [53]. Because the correlation between transcriptome (mRNA) and proteome is often low, quantitative proteomic analysis becomes especially important to reveal the regulation mechanism of biological processes [54].…”

Section: Resultsmentioning

confidence: 99%

“…The differentially expressed proteins were defined according to previous studies (fold change of ≤ 0.83 for down-regulated proteins, ≥ 1.2 for up-regulated proteins) and manually annotated through NCBI non-redundant protein sequences database (https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastp&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome) and UniProt protein database (https://www.uniprot.org/blast/) with local BLAST programs ( E -value ≤ 1.0E−5) [53, 58]. The heatmap was generated using the pheatmap package of version 3.2.3 on the R statistical platform (https://CRAN.R-project.org/package=pheatmap) KEGG database and KOBAS 3.0 (http://kobas.cbi.pku.edu.cn/) were used to carried out the pathway enrichment of the differentially expressed proteins; pathways with P value of ≤ 0.05 were considered significantly enriched [59].…”

Section: Methodsmentioning

confidence: 99%

Quantitative proteomic analysis reveals the ethanologenic metabolism regulation of Ethanoligenens harbinense by exogenous ethanol addition

Mei

Liu

et al. 2019

Biotechnol Biofuels

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Background H 2 –ethanol-coproducing bacteria, as primary fermenters, play important roles in the microbiome of bioreactors for bioenergy production from organic wastewater or solid wastes. Ethanoligenens harbinense YUAN-3 is an anaerobic ethanol–H 2 -fermenting bacterium. Ethanol is one of the main end-products of strain YUAN-3 that influence its fermentative process. Until recently, the molecular mechanism of metabolic regulation in strain YUAN-3 during ethanol accumulation has still been unclear. This study aims to elucidate the metabolic regulation mechanisms in strain YUAN-3, which contributes to effectively shape the microbiome for biofuel and bioenergy production from waste stream. Results This study reports that ethanol stress altered the distribution of end-product yields in the H 2 –ethanol-coproducing Ethanoligenens harbinense strain YUAN-3. Decreasing trends of hydrogen yield from 1888.6 ± 45.8 to 837 ± 64.7 mL L −1 and acetic acid yield from 1767.7 ± 45 to 160.6 ± 44.7 mg L −1 were observed in strain YUAN-3 with increasing exogenous ethanol (0 mM–200 mM). However, the ethanol yield of strain YUAN-3 increased by 15.1%, 30.1%, and 27.4% in 50 mM, 100 mM, and 200 mM ethanol stress, respectively. The endogenous ethanol accounted for 96.1% (w/w) in liquid end-products when exogenous ethanol of 200 mM was added. The molar ratio of ethanol to acetic acid increased 14 times (exogenous ethanol of 200 mM) compared to the control. iTRAQ-based quantitative proteomic analysis indicated that 263 proteins of strain YUAN-3 were differentially expressed in 50 mM, 100 mM, and 200 mM of exogenous ethanol. These proteins are mainly involved in amino acid transport and metabolism, central carbon metabolism, and oxidative stress response. Conclusion These differentially expressed proteins play important roles in metabolic changes necessary for growth and survival of strain YUAN-3 during ethanol stress. The up-regulation of bifunctional acetaldehyde-CoA/alcohol dehydrogenase (ADHE) was the main reason why ethanol production was enhanced, while hydrogen gas and acetic acid yields declined in strain YUAN-3 during ethanol stress. This study also provides a new approach for the enhancement of ethanologenesis by H 2 –ethanol-coproducing bacteria through exogenous ethanol addition. Electronic supplementary material The online version of this article (10.1186/s13068-019-1511-y) contains supplementary material, which is available to authorized users.

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Changes in iTRAQ-Based Proteomic Profiling of the Cladoceran Daphnia magna Exposed to Microcystin-Producing and Microcystin-Free Microcystis aeruginosa

Cited by 74 publications

References 69 publications

Transcriptomic analysis dissects the mechanistic insight into the Daphnia clonal variation in tolerance to toxic Microcystis

Transcriptomic analysis dissects the mechanistic insight into the Daphnia clonal variation in tolerance to toxic Microcystis

Linking Exoproteome Function and Structure to Anammox Biofilm Development

Quantitative proteomic analysis reveals the ethanologenic metabolism regulation of Ethanoligenens harbinense by exogenous ethanol addition

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