Comparative Proteomic Analysis within the Developmental Stages of the Mushroom White Hypsizygus marmoreus

(1) Background: The white Hypsizygus marmoreus is a popular edible mushroom in East Asia markets. Research on the systematic investigation of the protein expression changes in the cultivation process of this mushroom are few. (2) Methods: Label-free LC-MS/MS quantitative proteomics analysis technique was adopted to obtain the protein expression profiles of six groups of samples collected in different growth stages. A total of 3468 proteins were identified. The UpSetR plot analysis, Pearson correlation coefficient (PCC) analysis, and principal component (PC) analysis were performed to reveal the correlation among the six groups of samples. The differentially expressed proteins (DEPs) were organised by One-way ANOVA test and divided into four clusters. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were performed to divide the DEPs into different metabolic processes and pathways in each cluster. (3) Results: The DEPs in cluster 1 are of the highest abundance in the mycelium and are mainly involved in protein biosynthesis, biosynthesis of cofactors, lipid metabolism, spliceosome, cell cycle regulation, and MAPK signaling pathway. The DEPs in cluster 2 are enriched in the stem and are mainly associated with protein biosynthesis, biosynthesis of cofactors, carbon, and energy metabolism. The DEPs in cluster 3 are highly expressed in the primordia and unmatured fruiting bodies and are related to amino acids metabolism, carbon and carbohydrate metabolism, protein biosynthesis and processing, biosynthesis of cofactors, cell cycle regulation, MAPK signaling pathway, ubiquitin-mediated proteolysis, and proteasome. The DEPs in cluster 4 are of the highest abundance in the cap and are mainly associated with spliceosome, endocytosis, nucleocytoplasmic transport, protein processing, oxidative phosphorylation, biosynthesis of cofactors, amino acids metabolism, and lipid metabolism. (4) Conclusions: This research reports the proteome analysis of different developmental stages during the cultivation of the commercially relevant edible fungi the white H. marmoreus. In the mycelium stage, most of the DEPs are associated with cell proliferation, signal response, and mycelium growth. In the primordia and unmatured fruiting bodies stage, the DEPs are mainly involved in biomass increase, cell proliferation, signal response, and differentiation. In the mature fruiting body stage, the DEPs in the stem are largely associated with cell elongation and increase in biomass, and most of the DEPs in the cap are mainly related to pileus expansion. Several carbohydrate-active enzymes, transcription factors, heat shock proteins, and some DEPs involved in MAPK and cAMP signaling pathways were determined. These proteins might play vital roles in metabolic processes and activities. This research can add value to the understanding of mechanisms concerning mushroom development during commercial production.

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Cell cycle regulation of thymidine kinase: residues near the carboxyl terminus are essential for the specific degradation of the enzyme at mitosis.

Molecular and Cellular Biology ◽

10.1128/mcb.11.5.2538 ◽

1991 ◽

Vol 11 (5) ◽

pp. 2538-2546 ◽

Cited By ~ 95

Author(s):

M G Kauffman ◽

T J Kelly

Keyword(s):

Cell Cycle ◽

Amino Acids ◽

Thymidine Kinase ◽

Cell Cycle Regulation ◽

Carboxyl Terminus ◽

G1 Phase ◽

Cycle Phase ◽

M Phase ◽

Specific Degradation ◽

Cycle Regulation

The level of human thymidine kinase (TK) polypeptide is subject to cell cycle regulation. The enzyme is barely detectable in G1 phase but increases 10- to 20-fold by M phase. The low level of human TK in G1 phase is due primarily to the specific degradation of the protein during cell division. Substitution of heterologous promoters, removal of the introns, and deletion of all of the 3' untranslated region from the human TK gene do not affect cell cycle regulation of the enzyme. However, deletion of the carboxyl-terminal 40 amino acids or fusion of beta-galactosidase to the carboxyl terminus of human TK completely abolishes cell cycle regulation and stabilizes the protein throughout the cell cycle. These alterations do not significantly alter the specific enzymatic activity of TK. Changing the carboxyl terminus or deletion of the last 10 amino acids does not alter cell cycle regulation. These data demonstrate that residues near the carboxyl terminus of TK are essential for the cell cycle phase-specific degradation of the enzyme.

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Kinomic Profiling of Pediatric Acute Myeloid Leukemia for Detailed Cellular Insights

Blood ◽

10.1182/blood.v124.21.1046.1046 ◽

2014 ◽

Vol 124 (21) ◽

pp. 1046-1046

Author(s):

Hasan Mahmud ◽

Pariya Bezrouzi ◽

Arja ter Elst ◽

Frank J.G. Scherpen ◽

Kim R. Kampen ◽

...

Keyword(s):

Cell Cycle ◽

Acute Myeloid Leukemia ◽

Signaling Pathways ◽

Myeloid Leukemia ◽

Cell Cycle Regulation ◽

Mapk Signaling ◽

Unsupervised Hierarchical Cluster ◽

Cycle Regulation ◽

Cluster 2 ◽

Acute Myeloid

Abstract Acute myeloid leukemia (AML) remains a life threatening malignancy in children. Considerable progress has been made in elucidating the new diagnostic and prognostic markers over the past decades. The precise etiology remains unclear. Therefore, it is essential to evaluate the activation of the components of cellular signaling pathways to understand AML signaling and to design the most successful approach for combinational therapies and new kinase inhibitors. In this study, we used a high-throughput PepChipTMKinomics microarray system containing 976 different kinase substrates and assayed primary leukemic samples of 96 AML patients to produce an exceptionally detailed map of kinome enzymatic activities towards predefined peptide substrates. The generated profiles provide a comprehensive insight in signaling pathways active in AML patients. As expected the activation of proteins belonging to MAPK signaling, PI3K/AKT signaling, cell cycle regulation, apoptosis and insulin signaling pathways along with the signaling receptors and immune system regulators were found. Unsupervised hierarchical cluster analysis separates the AML blast profiles based on 192 peptide activities into two clusters. Cumulative incidence of relapse (CIR) was significantly higher in the patients of cluster-2. Peptide activity patterns were independent of patient characteristics. In addition, with Gaussian network modeling, a total of 540 peptides (55%) showed at least one peptide-peptide association without a prior assumptions whereas 74 peptides (7.5%) had >39 nodes suggesting to be potential interesting signaling hubs. Among these 74 peptides, 10 peptides were identified in cluster-1 and 50 peptides were in cluster-2. Thus, this total analysis defined peptides correlated to low incidence for relapse, for examples AKT1, HGFR, RGS7 and to high incidence for relapse for instance, proteins involve in MAPK pathways (RAF1, RAC1,14-3-3 eta) and cell cycle regulation and cellular growth (c-Myc, FOXO3A, RBL1). In conclusion, our study demonstrates the feasibility of peptide activity profiling to identify two active signaling network clusters in pediatric AML correlated to CIR. Highly correlated peptides belonging to cluster-2 provide stronger leads for selection of novel targets in future therapeutics. Disclosures No relevant conflicts of interest to declare.

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Cell cycle regulation of thymidine kinase: residues near the carboxyl terminus are essential for the specific degradation of the enzyme at mitosis

Molecular and Cellular Biology ◽

10.1128/mcb.11.5.2538-2546.1991 ◽

1991 ◽

Vol 11 (5) ◽

pp. 2538-2546

Author(s):

M G Kauffman ◽

T J Kelly

Keyword(s):

Cell Cycle ◽

Amino Acids ◽

Thymidine Kinase ◽

Cell Cycle Regulation ◽

Carboxyl Terminus ◽

G1 Phase ◽

Cycle Phase ◽

M Phase ◽

Specific Degradation ◽

Cycle Regulation

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The Putative Zinc Finger of the Human Cytomegalovirus IE2 86-Kilodalton Protein Is Dispensable for DNA Binding and Autorepression, Thereby Demarcating a Concise Core Domain in the C Terminus of the Protein

Journal of Virology ◽

10.1128/jvi.78.21.11853-11864.2004 ◽

2004 ◽

Vol 78 (21) ◽

pp. 11853-11864 ◽

Cited By ~ 12

Author(s):

Jasmin Asmar ◽

Lüder Wiebusch ◽

Matthias Truss ◽

Christian Hagemeier

Keyword(s):

Cell Cycle ◽

Amino Acids ◽

Zinc Finger ◽

Human Cytomegalovirus ◽

Cell Cycle Regulation ◽

Core Domain ◽

The Core ◽

Cycle Regulation ◽

Putative Zinc Finger ◽

Zinc Finger Region

ABSTRACT The IE2 86-kDa gene product is an essential regulatory protein of human cytomegalovirus (HCMV) with several functions, including transactivation, negative autoregulation, and cell cycle regulation. In order to understand the physiological significance of each of the IE2 functions, discriminating mutants of IE2 are required that can be tested in a viral background. However, no such mutants of IE2 are available, possibly reflecting structural peculiarities of the large and ill-defined C-terminal domain of IE2. Here, we revisited the C-terminal domain by analyzing IE2 mutants for transactivation, DNA binding, autoregulation, and cell cycle regulation in parallel. We found it to contain an unexpectedly concise core domain (amino acids 450 to 544) that is defined by its absolute sensitivity to any kind of mutation. In contrast, the region adjacent to the core (amino acids 290 to 449) generally tolerates mutations much better. Although it contributes more specific sequence information to distinct IE2 activities, none of the mutations analyzed abolished any particular function. The core is demarcated from the adjacent region by the putative zinc finger region (amino acids 428 to 452). Surprisingly, the deletion of the putative zinc finger region from IE2 revealed that this region is entirely dispensable for any of the IE2 functions tested here in transfection assays. Our work supports the view that the 100 amino acids of the core domain hold the key to most functions of IE2. A systematic, high-density mutational analysis of this region may identify informative mutants discriminating between various IE2 functions that can then be tested in a viral background.

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Multistep phosphorylation systems: tunable components of biological signaling circuits

Molecular Biology of the Cell ◽

10.1091/mbc.e14-02-0774 ◽

2014 ◽

Vol 25 (22) ◽

pp. 3456-3460 ◽

Cited By ~ 20

Author(s):

Evin Valk ◽

Rainis Venta ◽

Mihkel Örd ◽

Ilona Faustova ◽

Mardo Kõivomägi ◽

...

Keyword(s):

Cell Cycle ◽

Cell Cycle Regulation ◽

Phosphorylation Sites ◽

Cyclin Dependent Kinase ◽

Disordered Protein ◽

Phosphorylation Of Proteins ◽

Multisite Phosphorylation ◽

Signal Response ◽

Cycle Regulation ◽

Processing Mechanism

Multisite phosphorylation of proteins is a powerful signal processing mechanism that plays crucial roles in cell division and differentiation as well as in disease. We recently demonstrated a novel phenomenon in cell cycle regulation by showing that cyclin-dependent kinase–dependent multisite phosphorylation of a crucial substrate is performed sequentially in the N-to-C terminal direction along the disordered protein. The process is controlled by key parameters, including the distance between phosphorylation sites, the distribution of serines and threonines in sites, and the position of docking motifs. According to our model, linear patterns of phosphorylation along disordered protein segments determine the signal-response function of a multisite phosphorylation switch. Here we discuss the general advantages and engineering principles of multisite phosphorylation networks as processors of kinase signals. We also address the idea of using the mechanistic logic of linear multisite phosphorylation networks to design circuits for synthetic biology applications.

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