scholarly journals Elucidation of Zymomonas mobilis physiology and stress responses by quantitative proteomics and transcriptomics

2014 ◽  
Vol 5 ◽  
Author(s):  
Shihui Yang ◽  
Chongle Pan ◽  
Gregory B. Hurst ◽  
Lezlee Dice ◽  
Brian H. Davison ◽  
...  
Keyword(s):  
Stress Responses ◽  
Quantitative Proteomics ◽  
Zymomonas Mobilis

Comparative Quantitative Proteomics Reveals the Desiccation Stress Responses of the Intertidal Seaweed NEOPORPHYRA haitanensis

2020 ◽  
Vol 56 (6) ◽  
pp. 1664-1675
Author(s):  
Dongmei Wang ◽  
Wuxin You ◽  
Nianci Chen ◽  
Min Cao ◽  
Xianghai Tang ◽  
...  
Keyword(s):  
Stress Responses ◽  
Quantitative Proteomics ◽  
Desiccation Stress ◽  
Intertidal Seaweed

scholarly journals Systems Biology Analysis of Zymomonas mobilis ZM4 Ethanol Stress Responses

PLoS ONE ◽  
2013 ◽  
Vol 8 (7) ◽  
pp. e68886 ◽  
Author(s):  
Shihui Yang ◽  
Chongle Pan ◽  
Timothy J. Tschaplinski ◽  
Gregory B. Hurst ◽  
Nancy L. Engle ◽  
...  
Keyword(s):  
Systems Biology ◽  
Stress Responses ◽  
Zymomonas Mobilis ◽  
Ethanol Stress

Quantitative Proteomics for the Comprehensive Analysis of Stress Responses ofLactobacillus paracaseisubsp.paracaseiF19

2017 ◽  
Vol 16 (10) ◽  
pp. 3816-3829 ◽  
Author(s):  
Ann-Sophie Schott ◽  
Jürgen Behr ◽  
Andreas J. Geißler ◽  
Bernhard Kuster ◽  
Hannes Hahne ◽  
...  
Keyword(s):  
Stress Responses ◽  
Quantitative Proteomics ◽  
Comprehensive Analysis

scholarly journals ITRAQ-based quantitative proteomic analysis of japonica rice seedling during cold stress

2021 ◽  
Author(s):  
Dongjin Qing ◽  
Yinghua Pan ◽  
Gaoxing Dai ◽  
Lijun Gao ◽  
Haifu Liang ◽  
...  
Keyword(s):  
Cold Stress ◽  
Stress Responses ◽  
Protein Level ◽  
Quantitative Proteomics ◽  
Rice Variety ◽  
Mrna Level ◽  
Growth And Yield ◽  
Pcr Analysis ◽  
Control Group ◽  
Japonica Rice

Low temperature is one of the important environmental factors that affect rice growth and yield. To better understand the japonica rice responses to cold stress, isobaric tags for relative and absolute quantification (iTRAQ) labeling based quantitative proteomics approach was used to detected changes in protein level. Two-week-old seedlings of the cold tolerance rice variety Kongyu131 were treated at 8? for 24, 48 and 72 h, then the total proteins were extracted from tissues and used for quantitative proteomics analysis. A total of 5082 proteins were detected for quantitative analysis, of which 289 proteins were significantly regulated, consisting of 169 uniquely up-regulated proteins and 125 uniquely down-regulated proteins in cold stress groups relative to control group. Functional analysis revealed most of regulation proteins involved in photosynthesis, metabolic pathway, biosynthesis of secondary metabolites and carbon metabolism. Western blot analysis showed that protein regulation was consistent with the iTRAQ data. The corresponding genes of 25 regulation proteins were used for quantitative real time PCR analysis, and the results showed that the mRNA level was not always parallel to the corresponding protein level. The importance of our study is providing new insights into cold stress responses in rice on proteomic aspect.

scholarly journals Discovery of Ethanol-Responsive Small RNAs in Zymomonas mobilis

2014 ◽  
Vol 80 (14) ◽  
pp. 4189-4198 ◽  
Author(s):  
Seung Hee Cho ◽  
Roy Lei ◽  
Trey D. Henninger ◽  
Lydia M. Contreras
Keyword(s):  
Stress Responses ◽  
Small Rnas ◽  
Zymomonas Mobilis ◽  
Computational Prediction ◽  
Ethanol Stress ◽  
Content Type ◽  
Energy Applications ◽  
Metabolic Functions ◽  
Experimental Approaches ◽  
Cellular Stresses

ABSTRACTZymomonas mobilisis a bacterium that can produce ethanol by fermentation. Due to its unique metabolism and efficient ethanol production,Z. mobilishas attracted special interest for biofuel energy applications; an important area of study is the regulation of those specific metabolic pathways. Small RNAs (sRNAs) have been studied as molecules that function as transcriptional regulators in response to cellular stresses. While sRNAs have been discovered in various organisms by computational prediction and experimental approaches, their discovery inZ. mobilishas not yet been reported. In this study, we have applied transcriptome analysis and computational predictions to facilitate identification and validation of 15 novel sRNAs inZ. mobilis. We furthermore characterized their expression in the context of high and low levels of intracellular ethanol. Here, we report that 3 of the sRNAs (Zms2, Zms4, and Zms6) are differentially expressed under aerobic and anaerobic conditions, when low and high ethanol productions are observed, respectively. Importantly, when we tested the effect of ethanol stress on the expression of sRNAs inZ. mobilis, Zms2, Zms6, and Zms18 showed differential expression under 5% ethanol stress conditions. These data suggest that in this organism regulatory RNAs can be associated with metabolic functions involved in ethanol stress responses.

scholarly journals A High-efficacy CRISPRi System for Gene Function Discovery in Zymomonas mobilis

2020 ◽  
Author(s):  
Amy B. Banta ◽  
Amy L. Enright ◽  
Cheta Siletti ◽  
Jason M. Peters
Keyword(s):  
Gene Function ◽  
Stress Responses ◽  
Zymomonas Mobilis ◽  
Rational Design ◽  
Strain Engineering ◽  
Essential Genes ◽  
Biofuel Production ◽  
Alcohol Tolerance ◽  
High Efficacy ◽  
Function Discovery

ABSTRACTZymomonas mobilis is a promising biofuel producer due to its high alcohol tolerance and streamlined metabolism that efficiently converts sugar to ethanol. Z. mobilis genes are poorly characterized relative to model bacteria, hampering our ability to rationally engineer the genome with pathways capable of converting sugars from plant hydrolysates into valuable biofuels and bioproducts. Many of the unique properties that make Z. mobilis an attractive biofuel producer are controlled by essential genes; however, these genes cannot be manipulated using traditional genetic approaches (e.g., deletion or transposon insertion) because they are required for viability. CRISPR interference (CRISPRi) is a programmable gene knockdown system that can precisely control the timing and extent of gene repression, thus enabling targeting of essential genes. Here, we establish a stable, high-efficacy CRISPRi system in Z. mobilis that is capable of perturbing all genes—including essentials. We show that Z. mobilis CRISPRi causes either strong knockdowns (>100-fold) using single guide RNA (sgRNA) spacers that perfectly match target genes, or partial knockdowns using spacers with mismatches. We demonstrate the efficacy of Z. mobilis CRISPRi by targeting essential genes that are universally conserved in bacteria, key to the efficient metabolism of Z. mobilis, or underlie alcohol tolerance. Our Z. mobilis CRISPRi system will enable comprehensive gene function discovery, opening a path to rational design of biofuel production strains with improved yields.IMPORTANCEBiofuels produced by microbial fermentation of plant feedstocks provide renewable and sustainable energy sources that have the potential to mitigate climate change and improve energy security. Engineered strains of the bacterium Z. mobilis can convert sugars extracted from plant feedstocks into next generation biofuels such as isobutanol; however, conversion by these strains remains inefficient due to key gaps in our knowledge about genes involved in metabolism and stress responses such as alcohol tolerance. Here, we develop CRISPRi as a tool to characterize gene function in Z. mobilis. We identify genes that are essential for growth, required to ferment sugar to ethanol, and involved in resistance to alcohol. Our Z. mobilis CRISPRi system makes it straightforward to define gene function and can be applied to improve strain engineering and increase biofuel yields.

Quantitative proteomics of heavy metal stress responses in Sydney rock oysters

PROTEOMICS ◽  
2012 ◽  
Vol 12 (6) ◽  
pp. 906-921 ◽  
Author(s):  
Sridevi Muralidharan ◽  
Emma Thompson ◽  
David Raftos ◽  
Gavin Birch ◽  
Paul A. Haynes
Keyword(s):  
Heavy Metal ◽  
Stress Responses ◽  
Quantitative Proteomics ◽  
Heavy Metal Stress ◽  
Metal Stress
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