Label-Free Quantitative Proteomic Analysis of the Global Response to Indole-3-Acetic Acid in Newly Isolated Pseudomonas sp. Strain LY1

Indole-3-acetic acid (IAA), known as a common plant hormone, is one of the most distributed indole derivatives in the environment, but the degradation mechanism and cellular response network to IAA degradation are still not very clear. The objective of this study was to elucidate the molecular mechanisms of IAA degradation at the protein level by a newly isolated strain Pseudomonas sp. LY1. Label-free quantitative proteomic analysis of strain LY1 cultivated with IAA or citrate/NH4Cl was applied. A total of 2,604 proteins were identified, and 227 proteins have differential abundances in the presence of IAA, including 97 highly abundant proteins and 130 less abundant proteins. Based on the proteomic analysis an IAA degrading (iad) gene cluster in strain LY1 containing IAA transformation genes (organized as iadHABICDEFG), genes of the β-ketoadipate pathway for catechol and protocatechuate degradation (catBCA and pcaABCDEF) were identified. The iadA, iadB, and iadE-disrupted mutants lost the ability to grow on IAA, which confirmed the role of the iad cluster in IAA degradation. Degradation intermediates were analyzed by HPLC, LC-MS, and GC-MS analysis. Proteomic analysis and identified products suggested that multiple degradation pathways existed in strain LY1. IAA was initially transformed to dioxindole-3-acetic acid, which was further transformed to isatin. Isatin was then transformed to isatinic acid or catechol. An in-depth data analysis suggested oxidative stress in strain LY1 during IAA degradation, and the abundance of a series of proteins was upregulated to respond to the stress, including reaction oxygen species (ROS) scavenging, protein repair, fatty acid synthesis, RNA protection, signal transduction, chemotaxis, and several membrane transporters. The findings firstly explained the adaptation mechanism of bacteria to IAA degradation.

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Quantitative Proteomic Analysis of the Response to Cold Stress in Jojoba, a Tropical Woody Crop

International Journal of Molecular Sciences ◽

10.3390/ijms20020243 ◽

2019 ◽

Vol 20 (2) ◽

pp. 243 ◽

Cited By ~ 3

Author(s):

Fei Gao ◽

Pengju Ma ◽

Yingxin Wu ◽

Yijun Zhou ◽

Genfa Zhang

Keyword(s):

Superoxide Dismutase ◽

Stress Response ◽

Cold Stress ◽

Proteomic Analysis ◽

Molecular Mechanisms ◽

Soluble Sugars ◽

Pcr Analysis ◽

Ros Scavenging ◽

Quantitative Proteomic Analysis ◽

Woody Crop

Jojoba (Simmondsia chinensis) is a semi-arid, oil-producing industrial crop that have been widely cultivated in tropical arid region. Low temperature is one of the major environmental stress that impair jojoba’s growth, development and yield and limit introduction of jojoba in the vast temperate arid areas. To get insight into the molecular mechanisms of the cold stress response of jojoba, a combined physiological and quantitative proteomic analysis was conducted. Under cold stress, the photosynthesis was repressed, the level of malondialdehyde (MDA), relative electrolyte leakage (REL), soluble sugars, superoxide dismutase (SOD) and phenylalanine ammonia-lyase (PAL) were increased in jojoba leaves. Of the 2821 proteins whose abundance were determined, a total of 109 differentially accumulated proteins (DAPs) were found and quantitative real time PCR (qRT-PCR) analysis of the coding genes for 7 randomly selected DAPs were performed for validation. The identified DAPs were involved in various physiological processes. Functional classification analysis revealed that photosynthesis, adjustment of cytoskeleton and cell wall, lipid metabolism and transport, reactive oxygen species (ROS) scavenging and carbohydrate metabolism were closely associated with the cold stress response. Some cold-induced proteins, such as cold-regulated 47 (COR47), staurosporin and temperature sensitive 3-like a (STT3a), phytyl ester synthase 1 (PES1) and copper/zinc superoxide dismutase 1, might play important roles in cold acclimation in jojoba seedlings. Our work provided important data to understand the plant response to the cold stress in tropical woody crops.

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Label-free quantitative proteomic analysis of the inhibition effect of Lactobacillus rhamnosus GG on Escherichia coli biofilm formation in co-culture

Proteome Science ◽

10.1186/s12953-021-00172-0 ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

Huiyi Song ◽

Ni Lou ◽

Jianjun Liu ◽

Hong Xiang ◽

Dong Shang

Keyword(s):

Escherichia Coli ◽

Proteomic Analysis ◽

Biofilm Formation ◽

Lactobacillus Rhamnosus ◽

Differentially Expressed ◽

Differentially Expressed Proteins ◽

Label Free ◽

Quantitative Proteomic Analysis ◽

E Coli ◽

Protein Ubiquitination

Abstract Background Escherichia coli (E. coli) is the principal pathogen that causes biofilm formation. Biofilms are associated with infectious diseases and antibiotic resistance. This study employed proteomic analysis to identify differentially expressed proteins after coculture of E. coli with Lactobacillus rhamnosus GG (LGG) microcapsules. Methods To explore the relevant protein abundance changes after E. coli and LGG coculture, label-free quantitative proteomic analysis and qRT-PCR were applied to E. coli and LGG microcapsule groups before and after coculture, respectively. Results The proteomic analysis characterised a total of 1655 proteins in E. coli K12MG1655 and 1431 proteins in the LGG. After coculture treatment, there were 262 differentially expressed proteins in E. coli and 291 in LGG. Gene ontology analysis showed that the differentially expressed proteins were mainly related to cellular metabolism, the stress response, transcription and the cell membrane. A protein interaction network and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analysis indicated that the differentiated proteins were mainly involved in the protein ubiquitination pathway and mitochondrial dysfunction. Conclusions These findings indicated that LGG microcapsules may inhibit E. coli biofilm formation by disrupting metabolic processes, particularly in relation to energy metabolism and stimulus responses, both of which are critical for the growth of LGG. Together, these findings increase our understanding of the interactions between bacteria under coculture conditions.

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Chromatin-Associated Proteins Revealed by SILAC-Proteomic Analysis Exhibit a High Likelihood of Requirement for Growth Fitness under DNA Damage Stress

International Journal of Proteomics ◽

10.1155/2012/630409 ◽

2012 ◽

Vol 2012 ◽

pp. 1-12

Author(s):

Han Wang ◽

Pornpimol Tipthara ◽

Lei Zhu ◽

Suk Yean Poon ◽

Kai Tang ◽

...

Keyword(s):

Dna Damage ◽

Proteomic Analysis ◽

Ribosomal Proteins ◽

Cell Extract ◽

Label Free ◽

High Likelihood ◽

Nonhistone Proteins ◽

Quantitative Proteomic Analysis ◽

Proteomic Approach ◽

Associated Functions

Chromatin-associated nonhistone proteins (CHRAPs) are readily collected from the DNaseI digested crude chromatin preparation. In this study, we show that the absolute abundance-based label-free quantitative proteomic analysis fail to identify potential CHRAPs from the CHRAP-prep. This is because that the most-highly abundant cytoplasmic proteins such as ribosomal proteins are not effectively depleted in the CHRAP-prep. Ribosomal proteins remain the top-ranked abundant proteins in the CHRAP-prep. On the other hand, we show that relative abundance-based SILAC-mediated quantitative proteomic analysis is capable of discovering the potential CHRAPs in the CHRAP-prep when compared to the whole-cell-extract. Ribosomal proteins are depleted from the top SILAC ratio-ranked proteins. In contrast, nucleus-localized proteins or potential CHRAPs are enriched in the top SILAC-ranked proteins. Consistent with this, gene-ontology analysis indicates that CHRAP-associated functions such as transcription, regulation of chromatin structures, and DNA replication and repair are significantly overrepresented in the top SILAC-ranked proteins. Some of the novel CHRAPs are confirmed using the traditional method. Notably, phenotypic assessment reveals that the top SILAC-ranked proteins exhibit the high likelihood of requirement for growth fitness under DNA damage stress. Taken together, our results indicate that the SILAC-mediated proteomic approach is capable of determining CHRAPs without prior knowledge.

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Highly Reproducible Label Free Quantitative Proteomic Analysis of RNA Polymerase Complexes

Molecular & Cellular Proteomics ◽

10.1074/mcp.m110.000687 ◽

2010 ◽

Vol 10 (2) ◽

pp. M110.000687 ◽

Cited By ~ 50

Author(s):

Amber L. Mosley ◽

Mihaela E. Sardiu ◽

Samantha G. Pattenden ◽

Jerry L. Workman ◽

Laurence Florens ◽

...

Keyword(s):

Rna Polymerase ◽

Proteomic Analysis ◽

Label Free ◽

Quantitative Proteomic Analysis

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Label-free Quantitative Proteomic Analysis of Drought-Responsive Proteins in Panax ginseng Meyer

Korean Journal of Medicinal Crop Science ◽

10.7783/kjmcs.2021.29.6.369 ◽

2021 ◽

Vol 29 (6) ◽

pp. 369-379

Author(s):

Ju Young Jung ◽

Cheol Woo Min ◽

Hye Won Shin ◽

Truong Van Nguyen ◽

Ji hyun Kim ◽

...

Keyword(s):

Panax Ginseng ◽

Proteomic Analysis ◽

Label Free ◽

Quantitative Proteomic Analysis

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Simplified ARCHITECT microfluidic chip through a dual-flip strategy enables stable and versatile tumoroid formation combined with label-free quantitative proteomic analysis

Biofabrication ◽

10.1088/1758-5090/abe5b5 ◽

2021 ◽

Author(s):

Danni Feng ◽

Junwei Lv ◽

Aynur Abdulla ◽

Jianwei Xu ◽

Xiao Sang ◽

...

Keyword(s):

Microfluidic Chip ◽

Proteomic Analysis ◽

Label Free ◽

Quantitative Proteomic Analysis

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Sphingolipid biosynthesis upregulation by TOR complex 2–Ypk1 signaling during yeast adaptive response to acetic acid stress

Biochemical Journal ◽

10.1042/bcj20160565 ◽

2016 ◽

Vol 473 (23) ◽

pp. 4311-4325 ◽

Cited By ~ 27

Author(s):

Joana F. Guerreiro ◽

Alexander Muir ◽

Subramaniam Ramachandran ◽

Jeremy Thorner ◽

Isabel Sá-Correia

Keyword(s):

Acetic Acid ◽

Protein Kinase ◽

Cellular Response ◽

Molecular Mechanisms ◽

Acid Stress ◽

Acid Tolerance ◽

Industrial Biotechnology ◽

Acetic Acid Tolerance ◽

Spoilage Yeasts ◽

Sphingolipid Biosynthesis

Acetic acid-induced inhibition of yeast growth and metabolism limits the productivity of industrial fermentation processes, especially when lignocellulosic hydrolysates are used as feedstock in industrial biotechnology. Tolerance to acetic acid of food spoilage yeasts is also a problem in the preservation of acidic foods and beverages. Thus understanding the molecular mechanisms underlying adaptation and tolerance to acetic acid stress is increasingly important in industrial biotechnology and the food industry. Prior genetic screens for Saccharomyces cerevisiae mutants with increased sensitivity to acetic acid identified loss-of-function mutations in the YPK1 gene, which encodes a protein kinase activated by the target of rapamycin (TOR) complex 2 (TORC2). We show in the present study by several independent criteria that TORC2–Ypk1 signaling is stimulated in response to acetic acid stress. Moreover, we demonstrate that TORC2-mediated Ypk1 phosphorylation and activation is necessary for acetic acid tolerance, and occurs independently of Hrk1, a protein kinase previously implicated in the cellular response to acetic acid. In addition, we show that TORC2–Ypk1-mediated activation of l-serine:palmitoyl-CoA acyltransferase, the enzyme complex that catalyzes the first committed step of sphingolipid biosynthesis, is required for acetic acid tolerance. Furthermore, analysis of the sphingolipid pathway using inhibitors and mutants indicates that it is production of certain complex sphingolipids that contributes to conferring acetic acid tolerance. Consistent with that conclusion, promoting sphingolipid synthesis by adding exogenous long-chain base precursor phytosphingosine to the growth medium enhanced acetic acid tolerance. Thus appropriate modulation of the TORC2–Ypk1–sphingolipid axis in industrial yeast strains may have utility in improving fermentations of acetic acid-containing feedstocks.

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