Male Fertility Potential Molecular Mechanisms Revealed by iTRAQ-Based Quantitative Proteomic Analysis of the Epididymis from Wip1−/− Mice

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 a genetically induced prostate inflammation mouse model via custom 4-plex DiLeu isobaric labeling

AJP Renal Physiology ◽

10.1152/ajprenal.00387.2018 ◽

2019 ◽

Vol 316 (6) ◽

pp. F1236-F1243 ◽

Cited By ~ 3

Author(s):

Ling Hao ◽

Samuel Thomas ◽

Tyler Greer ◽

Chad M. Vezina ◽

Sagar Bajpai ◽

...

Keyword(s):

Mass Spectrometry ◽

Proteomic Analysis ◽

Molecular Mechanisms ◽

Biomarker Discovery ◽

Urinary Proteins ◽

Quantitative Proteomic Analysis ◽

Prostate Inflammation ◽

Ultrahigh Performance Liquid Chromatography ◽

Isobaric Tags ◽

Accurate Quantification

Inflammation is involved in many prostate pathologies including infection, benign prostatic hyperplasia, and prostate cancer. Preclinical models are critical to our understanding of disease mechanisms, yet few models are genetically tractable. Here, we present a comparative quantitative proteomic analysis of urine from mice with and without prostate-specific inflammation induced by conditional prostate epithelial IL-1β expression. Relative quantification and sample multiplexing was achieved using custom 4-plex N, N-dimethyl leucine (DiLeu) isobaric tags and nanoflow ultrahigh-performance liquid chromatography coupled to high-resolution tandem mass spectrometry. Each set of 4-plex DiLeu reagents allows four urine samples to be analyzed simultaneously, providing high-throughput and accurate quantification of urinary proteins. Proteins involved in the acute phase response, including haptoglobin, inter-α-trypsin inhibitor, and α1-antitrypsin 1-1, were differentially represented in the urine of mice with prostate inflammation. Mass spectrometry-based quantitative urinary proteomics represents a promising bioanalytical strategy for biomarker discovery and the elucidation of molecular mechanisms in urological research.

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iTRAQ-Based Quantitative Proteomic Analysis of Heat Stress-Induced Mechanisms in Pepper Seedlings

10.21203/rs.3.rs-46970/v1 ◽

2020 ◽

Author(s):

Jing Wang ◽

Chengliang Liang ◽

Sha Yang ◽

Jingshuang Song ◽

Xuefeng Li ◽

...

Keyword(s):

Heat Stress ◽

Stress Response ◽

Heat Tolerance ◽

Proteomic Analysis ◽

Molecular Mechanisms ◽

Negative Impact ◽

Growth And Yield ◽

Vegetable Crops ◽

Heat Stress Response ◽

Quantitative Proteomic Analysis

Abstract Background: As one of the most important vegetable crops, pepper has rich nutritional value and high economic value. Increasing heat stress due to the global warming has a negative impact on the growth and yield of pepper. Result: In the present study, we investigated the changes of phenotype, physiology, and proteome in heat-tolerant (17CL30) and heat-sensitive (05S180) pepper seedlings in response to heat stress. Phenotypic and physiological changes showed that 17CL30 had a stronger ability to resist heat stress compared with 05S180. In proteomic analysis, a total of 3,874 proteins were identified, and 1,591 proteins were considered to participate in the process of heat stress response. According to bioinformatic analysis of heat-responsive proteins, the heat tolerance of 17CL30 might be related to a higher photosynthesis, signal transduction, carbohydrate metabolism, and stress defense, compared with 05S180. Conclusion: To understand the heat stress response mechanism of pepper, an iTRAQ-based quantitative proteomic analysis was employed to identify possible heat-responsive proteins and metabolic pathways in 17CL30 and 05S180 pepper seedlings under heat stress. This study provided new insights into the molecular mechanisms involved in heat tolerance of pepper and might offer supportive reference for the breeding of new pepper variety with heat resistance.

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iTRAQ-based quantitative proteomic analysis of dark-germinated soybeans in response to salt stress

RSC Advances ◽

10.1039/c8ra02996b ◽

2018 ◽

Vol 8 (32) ◽

pp. 17905-17913 ◽

Cited By ~ 6

Author(s):

Yongqi Yin ◽

Fei Qi ◽

Lu Gao ◽

Shengqi Rao ◽

Zhenquan Yang ◽

...

Keyword(s):

Salt Stress ◽

Proteomic Analysis ◽

Molecular Mechanisms ◽

Quantitative Proteomic Analysis

iTRAQ-based quantitative proteomic analysis reveals the molecular mechanisms of dark-germinated soybeans in response to salt stress.

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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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Comparative Proteome Research in a Zebrafish Model for Vanishing White Matter Disease

International Journal of Molecular Sciences ◽

10.3390/ijms22052707 ◽

2021 ◽

Vol 22 (5) ◽

pp. 2707

Author(s):

Doeun Kim ◽

Yu-Ri Lee ◽

Tae-Ik Choi ◽

Se-Hee Kim ◽

Hoon-Chul Kang ◽

...

Keyword(s):

White Matter ◽

Proteomic Analysis ◽

Molecular Mechanisms ◽

Early Death ◽

Mrna Levels ◽

Zebrafish Model ◽

Quantitative Proteomic Analysis ◽

Eukaryotic Translation ◽

Vanishing White Matter Disease ◽

Vanishing White Matter

Vanishing white matter (VWM) disease is a genetic leukodystrophy leading to severe neurological disease and early death. VWM is caused by bi-allelic mutations in any of the five genes encoding the subunits of the eukaryotic translation factor 2B (EIF2B). Previous studies have attempted to investigate the molecular mechanism of VWN by constructing models for each subunit of EIF2B that causes VWM disease. The underlying molecular mechanisms of the way in which mutations in EIF2B3 result in VWM are largely unknown. Based on our recent results, we generated an eif2b3 knockout (eif2b3−/−) zebrafish model and performed quantitative proteomic analysis between the wild-type (WT) and eif2b3−/− zebrafish, and identified 25 differentially expressed proteins. Four proteins were significantly upregulated, and 21 proteins were significantly downregulated in eif2b3−/− zebrafish compared to WT. Lon protease and the neutral amino acid transporter SLC1A4 were significantly increased in eif2b3−/− zebrafish, and crystallin proteins were significantly decreased. The differential expression of proteins was confirmed by the evaluation of mRNA levels in eif2b3−/− zebrafish, using whole-mount in situ hybridization analysis. This study identified proteins which candidates as key regulators of the progression of VWN disease, using quantitative proteomic analysis in the first EIF2B3 animal model of VWN disease.

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