scholarly journals Comparative Proteomics Analysis Reveals Unique Early Signaling Response of Saccharomyces cerevisiae to Oxidants with Different Mechanism of Action

2020 ◽  
Vol 22 (1) ◽  
pp. 167
Author(s):  
Prajita Pandey ◽  
Khadiza Zaman ◽  
Laszlo Prokai ◽  
Vladimir Shulaev
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Signaling Pathways ◽  
Mechanism Of Action ◽  
Mapk Signaling ◽  
Comparative Proteomics ◽  
Mass Analyzer ◽  
Label Free ◽  
Proteomics Analysis ◽  
Yeast Saccharomyces Cerevisiae ◽  
Signaling Mechanism

The early signaling events involved in oxidant recognition and triggering of oxidant-specific defense mechanisms to counteract oxidative stress still remain largely elusive. Our discovery driven comparative proteomics analysis revealed unique early signaling response of the yeast Saccharomyces cerevisiae on the proteome level to oxidants with a different mechanism of action as early as 3 min after treatment with four oxidants, namely H2O2, cumene hydroperoxide (CHP), and menadione and diamide, when protein abundances were compared using label-free quantification relying on a high-resolution mass analyzer (Orbitrap). We identified significant regulation of 196 proteins in response to H2O2, 569 proteins in response to CHP, 369 proteins in response to menadione and 207 proteins in response to diamide. Only 17 proteins were common across all treatments, but several more proteins were shared between two or three oxidants. Pathway analyses revealed that each oxidant triggered a unique signaling mechanism associated with cell survival and repair. Signaling pathways mostly regulated by oxidants were Ran, TOR, Rho, and eIF2. Furthermore, each oxidant regulated these pathways in a unique way indicating specificity of response to oxidants having different modes of action. We hypothesize that interplay of these signaling pathways may be important in recognizing different oxidants to trigger different downstream MAPK signaling cascades and to induce specific responses.

scholarly journals Comparative Proteomics Analysis Reveals New Features of the Oxidative Stress Response in the Polyextremophilic Bacterium Deinococcus radiodurans

2020 ◽  
Vol 8 (3) ◽  
pp. 451 ◽  
Author(s):  
Lihua Gao ◽  
Zhengfu Zhou ◽  
Xiaonan Chen ◽  
Wei Zhang ◽  
Min Lin ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Dna Repair ◽  
Ribosomal Proteins ◽  
Deinococcus Radiodurans ◽  
Resistance Mechanisms ◽  
Comparative Proteomics ◽  
Label Free ◽  
Proteomics Analysis ◽  
Dna Damaging Agents ◽  
Oxidative Resistance

Deinococcus radiodurans is known for its extreme resistance to ionizing radiation, oxidative stress, and other DNA-damaging agents. The robustness of this bacterium primarily originates from its strong oxidative resistance mechanisms. Hundreds of genes have been demonstrated to contribute to oxidative resistance in D. radiodurans; however, the antioxidant mechanisms have not been fully characterized. In this study, comparative proteomics analysis of D. radiodurans grown under normal and oxidative stress conditions was conducted using label-free quantitative proteomics. The abundances of 852 of 1700 proteins were found to significantly differ between the two groups. These differential proteins are mainly associated with translation, DNA repair and recombination, response to stresses, transcription, and cell wall organization. Highly upregulated expression was observed for ribosomal proteins such as RplB, Rpsl, RpsR, DNA damage response proteins (DdrA, DdrB), DNA repair proteins (RecN, RecA), and transcriptional regulators (members of TetR, AsnC, and GntR families, DdrI). The functional analysis of proteins in response to oxidative stress is discussed in detail. This study reveals the global protein expression profile of D. radiodurans in response to oxidative stress and provides new insights into the regulatory mechanism of oxidative resistance in D. radiodurans.

scholarly journals Nystose regulates the response of rice roots to cold stress via multiple signaling pathways: A comparative proteomics analysis

PLoS ONE ◽  
2020 ◽  
Vol 15 (9) ◽  
pp. e0238381
Author(s):  
Zijie Zhang ◽  
Wenfei Xiao ◽  
Jieren Qiu ◽  
Ya Xin ◽  
Qinpo Liu ◽  
...  
Keyword(s):  
Cold Stress ◽  
Signaling Pathways ◽  
Comparative Proteomics ◽  
Proteomics Analysis ◽  
Rice Roots ◽  
Multiple Signaling

scholarly journals D-Xylose Sensing in Saccharomyces cerevisiae: Insights from D-Glucose Signaling and Native D-Xylose Utilizers

2021 ◽  
Vol 22 (22) ◽  
pp. 12410
Author(s):  
Daniel P. Brink ◽  
Celina Borgström ◽  
Viktor C. Persson ◽  
Karen Ofuji Osiro ◽  
Marie F. Gorwa-Grauslund
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Signaling Pathways ◽  
Raw Materials ◽  
Current Status ◽  
Chemical Production ◽  
Edible Plant ◽  
Yeast Saccharomyces Cerevisiae ◽  
Glucose Signaling ◽  
Glucose Depletion ◽  
Wide Range

Extension of the substrate range is among one of the metabolic engineering goals for microorganisms used in biotechnological processes because it enables the use of a wide range of raw materials as substrates. One of the most prominent examples is the engineering of baker’s yeast Saccharomyces cerevisiae for the utilization of d-xylose, a five-carbon sugar found in high abundance in lignocellulosic biomass and a key substrate to achieve good process economy in chemical production from renewable and non-edible plant feedstocks. Despite many excellent engineering strategies that have allowed recombinant S. cerevisiae to ferment d-xylose to ethanol at high yields, the consumption rate of d-xylose is still significantly lower than that of its preferred sugar d-glucose. In mixed d-glucose/d-xylose cultivations, d-xylose is only utilized after d-glucose depletion, which leads to prolonged process times and added costs. Due to this limitation, the response on d-xylose in the native sugar signaling pathways has emerged as a promising next-level engineering target. Here we review the current status of the knowledge of the response of S. cerevisiae signaling pathways to d-xylose. To do this, we first summarize the response of the native sensing and signaling pathways in S. cerevisiae to d-glucose (the preferred sugar of the yeast). Using the d-glucose case as a point of reference, we then proceed to discuss the known signaling response to d-xylose in S. cerevisiae and current attempts of improving the response by signaling engineering using native targets and synthetic (non-native) regulatory circuits.

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