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Article: Proteomic Interactome of C. elegans Mediator Complex Subunit 28 (MDT-28) Reveals Predominant Association with a Restricted Set of Core Mediator Subunits and an Affinity to Additional Structural and Enzymatic Proteins.

Yilma, P / Kostrouchová, M / Talacko, P / Kostrouchová, V / Kostrouch, D / Novák, P

2020 Volume 65, Issue 5-6, Page(s) 203–211

Abstract: Transcription factors exert their regulatory potential on RNA polymerase II machinery through a multiprotein complex called Mediator complex or Mediator. The Mediator complex integrates regulatory signals from cell regulatory cascades with the regulation ...

Abstract	Transcription factors exert their regulatory potential on RNA polymerase II machinery through a multiprotein complex called Mediator complex or Mediator. The Mediator complex integrates regulatory signals from cell regulatory cascades with the regulation by transcription factors. The Mediator complex consists of 25 subunits in Saccharomyces cerevisiae and 30 or more subunits in multicellular eukaryotes. Mediator subunit 28 (MED28), along with MED30, MED23, MED25 and MED26, belong to presumably evolutionarily new subunits that seem to be absent in unicellular eukaryotes and are likely to have evolved together with multicellularity and cell differentiation. Previously, we have shown that an originally uncharacterized predicted gene, F28F8.5, is the true MED28 orthologue in Caenorhabditis elegans (mdt-28) and showed that it is involved in a spectrum of developmental processes. Here, we studied the proteomic interactome of MDT-28 edited as GFP::MDT-28 using Crispr/Cas9 technology or MDT-28::GFP expressed from extrachromosomal arrays in transgenic C. elegans exploiting the GFPTRAP system and mass spectrometry. The results show that MDT-28 associates with the Head module subunits MDT-6, MDT-8, MDT-11, MDT-17, MDT- 20, MDT-22, and MDT-30 and the Middle module subunit MDT-14. The analyses also identified additional proteins as preferential MDT-28 interactants, including chromatin-organizing proteins, structural proteins and enzymes. The results provide evidence for MDT-28 engagement in the Mediator Head module and support the possibility of physical (direct or indirect) interaction of MDT-28 with additional proteins, reflecting the transcription-regulating potential of primarily structural and enzymatic proteins at the level of the Mediator complex.
MeSH term(s)	Alleles ; Animals ; Caenorhabditis elegans/metabolism ; Caenorhabditis elegans Proteins/metabolism ; Mediator Complex/metabolism ; Nuclear Proteins/metabolism ; Protein Binding ; Protein Subunits/metabolism ; Proteomics
Chemical Substances	Caenorhabditis elegans Proteins ; MDT-28 protein, C elegans ; Mediator Complex ; Nuclear Proteins ; Protein Subunits
Language	English
Publishing date	2020-04-07
Publishing country	Czech Republic
Document type	Journal Article
ZDB-ID	419223-0
ISSN	0015-5500
ISSN	0015-5500
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Kolorektální karcinom u seniorů - děláme to dobře?

Kostrouch, D / Martínek, L / Hoch, J

Rozhledy v chirurgii : mesicnik Ceskoslovenske chirurgicke spolecnosti

2017 Volume 96, Issue 5, Page(s) 197–201

Abstract: Introduction: Geriatric patients form a significant part of patients with colorectal cancer and their numbers will probably continue to increase. Analysis of the quality of care provided to seniors and the results from their treatment are currently ... ...

Title translation	Colorectal cancer in senior patients - are we doing it well?
Abstract	Introduction: Geriatric patients form a significant part of patients with colorectal cancer and their numbers will probably continue to increase. Analysis of the quality of care provided to seniors and the results from their treatment are currently gaining more attention. The aim of this study was to compare how often standard oncological therapy is administered to seniors with colorectal cancer and to compare their results with younger patients along with complications of the therapy. Method: A retrospective analysis of data from 170 patients with the diagnosis of colorectal cancer undergoing an elective curative surgical procedure in 2014 and 2015 was performed. Patients were divided into three groups according to their age (<60 years old, 6079 years old, 80 years old). We compared their ASA score, tumor stage (IIV), tumor localization (colon, rectum), incidence of serious complications grade 35 on the Clavien-Dindo scale and adherence to standard oncological treatment in the individual age groups. Results: Patients 80 years and older had significantly higher ASA scores (p=0.0001) and significantly higher stages of tumors according to TNM-7 classification (p=0.0413) in comparison to younger patients. Differences in numbers of serious complications (<60 years - 14%, 6079 years - 13%, 80 years 30%, p=0.1499) did not reach statistical significance. Seniors underwent modified oncological treatment (<60 years - 6%, 6079 years - 9%, 80 years 30%, p = 0.0095) significantly more frequently in comparison to younger age groups. Conclusion: The application of standard multimodal oncological treatment is possible even in selected patients that are 80 years and older. Implementation of more reliable methods to objectively predict postoperative complications can become a tool to modify the treatment and improve the results of surgical care in elderly patients.Key words: geriatric patients - oncosurgery complex geriatric assessment colorectal cancer.
MeSH term(s)	Aged ; Aged, 80 and over ; Colorectal Neoplasms/surgery ; Humans ; Middle Aged ; Postoperative Complications ; Retrospective Studies
Language	Czech
Publishing date	2017-07-27
Publishing country	Czech Republic
Document type	Journal Article
ZDB-ID	414059-x
ISSN	1805-4579 ; 0035-9351
ISSN (online)	1805-4579
ISSN	0035-9351
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Cholecystostomie--obsoletní, nebo aktuální řešení?

Martínek, L / Kostrouch, D / Hoch, J

Rozhledy v chirurgii : mesicnik Ceskoslovenske chirurgicke spolecnosti

2015 Volume 94, Issue 9, Page(s) 367–371

Abstract: Introduction: Percutaneous cholecystostomy is considered to be an emergency treatment option when conservative treatment of acute cholecystitis fails in elderly and critically ill patients. The question is: to what extent is this technique still up-to- ... ...

Title translation	Cholecystostomy--an obsolete or relevant treatment?.
Abstract	Introduction: Percutaneous cholecystostomy is considered to be an emergency treatment option when conservative treatment of acute cholecystitis fails in elderly and critically ill patients. The question is: to what extent is this technique still up-to-date or obsolete. Methods: We retrospectively reviewed data of patients who underwent a computer tomography (CT) guided percutaneous cholecystostomy between 1/20101/2015. We analyzed the patient data, the success rate, complications of the procedure, short- and long-term outcomes. Results: 30 patients undergoing CT-guided percutaneous cholecystostomy at the Department of Surgery, 2nd Faculty of Medicine, Charles University in Prague and Motol University Hospital during the study period were enrolled. The study group included 21 females (70%) and 9 males (30%) with mean age of 78 years (SD±12.3), median 82 years (range 3493 years). Percutaneous cholecystostomy was indicated for patients with severe cholecystitis/empyema of the gallbladder not responding to conservative therapy who were poor candidates for operative cholecystectomy. Of these, 23 patients (77%) were successfully treated with initial percutaneous cholecystostomy whereas 7 patients (23%) experienced treatment failure - one was subsequently successfully treated with repeated percutaneous cholecystostomy and six underwent emergency cholecystectomy. The mean length of stay was 16.5 days (SD±8.2), median 15 days (7-49 days). The total 30-day mortality was 17%, and indication-related mortality was 10%. Three patients (10%) had a recurrence. One patient required repeated percutaneous drainage, the second recovered on conservative treatment and the third patient underwent acute cholecystectomy. Only one patient (3%) underwent delayed laparoscopic cholecystectomy without complications. Conclusion: CT guided percutaneous cholecystostomy is a safe and effective therapeutic modality in patients unfit for surgery.
MeSH term(s)	Adult ; Aged ; Aged, 80 and over ; Cholecystectomy ; Cholecystitis/surgery ; Cholecystography ; Cholecystostomy ; Contraindications ; Female ; Humans ; Male ; Middle Aged ; Patient Selection ; Radiography, Interventional ; Retrospective Studies
Language	Czech
Publishing date	2015-09
Publishing country	Czech Republic
Document type	Journal Article
ZDB-ID	414059-x
ISSN	1805-4579 ; 0035-9351
ISSN (online)	1805-4579
ISSN	0035-9351
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

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Article: The nematode homologue of Mediator complex subunit 28, F28F8.5, is a critical regulator of

Kostrouchová, Markéta / Kostrouch, David / Chughtai, Ahmed A / Kaššák, Filip / Novotný, Jan P / Kostrouchová, Veronika / Benda, Aleš / Krause, Michael W / Saudek, Vladimír / Kostrouchová, Marta / Kostrouch, Zdeněk

PeerJ

2017 Volume 5, Page(s) e3390

Abstract: The evolutionarily conserved Mediator complex is a critical player in regulating transcription. Comprised of approximately two dozen proteins, the Mediator integrates diverse regulatory signals through direct protein-protein interactions that, in turn, ... ...

Abstract	The evolutionarily conserved Mediator complex is a critical player in regulating transcription. Comprised of approximately two dozen proteins, the Mediator integrates diverse regulatory signals through direct protein-protein interactions that, in turn, modulate the influence of Mediator on RNA Polymerase II activity. One Mediator subunit, MED28, is known to interact with cytoplasmic structural proteins, providing a potential direct link between cytoplasmic dynamics and the control of gene transcription. Although identified in many animals and plants, MED28 is not present in yeast; no bona fide MED28 has been described previously in
Language	English
Publishing date	2017-06-06
Publishing country	United States
Document type	Journal Article
ZDB-ID	2703241-3
ISSN	2167-8359
ISSN	2167-8359
DOI	10.7717/peerj.3390
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Trichoplax adhaerens

Novotný, Jan Philipp / Chughtai, Ahmed Ali / Kostrouchová, Markéta / Kostrouchová, Veronika / Kostrouch, David / Kaššák, Filip / Kaňa, Radek / Schierwater, Bernd / Kostrouchová, Marta / Kostrouch, Zdenek

PeerJ

2017 Volume 5, Page(s) e3789

Abstract: Trichoplax ... ...

Abstract	Trichoplax adhaerens
Language	English
Publishing date	2017-09-29
Publishing country	United States
Document type	Journal Article
ZDB-ID	2703241-3
ISSN	2167-8359
ISSN	2167-8359
DOI	10.7717/peerj.3789
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: SKIP and BIR-1/Survivin have potential to integrate proteome status with gene expression.

Kostrouch, David / Kostrouchová, Markéta / Yilma, Petr / Chughtai, Ahmed Ali / Novotný, Jan Philipp / Novák, Petr / Kostrouchová, Veronika / Kostrouchová, Marta / Kostrouch, Zdeněk

Journal of proteomics

2014 Volume 110, Page(s) 93–106

Abstract: SKIP and BIR are evolutionarily conserved proteins; SKIP (SKP-1) is a known transcription and splicing cofactor while BIR-1/Survivin regulates cell division, gene expression and development. Their loss of function induces overlapping developmental ... ...

Abstract	SKIP and BIR are evolutionarily conserved proteins; SKIP (SKP-1) is a known transcription and splicing cofactor while BIR-1/Survivin regulates cell division, gene expression and development. Their loss of function induces overlapping developmental phenotypes. We searched for SKP-1 and BIR-1 interaction on protein level using yeast two-hybrid screens and identified partially overlapping categories of proteins as SKIP-1 and BIR-1 interactors. The interacting proteins included ribosomal proteins, transcription factors, translation factors and cytoskeletal and motor proteins suggesting involvement in multiple protein complexes. To visualize the effect of BIR-1 on the proteome in Caenorhabditis elegans we induced a short time pulse BIR-1 overexpression in synchronized L1 larvae. This led to a dramatic alteration of the whole proteome pattern indicating that BIR-1 alone has the capacity to alter the chromatographic profile of many target proteins including proteins found to be interactors in yeast two hybrid screens. The results were validated for ribosomal proteins RPS3 and RPL5, non-muscle myosin and TAC-1, a transcription cofactor and a centrosome associated protein. Together, these results suggest that SKP-1 and BIR-1 are multifunctional proteins that form multiple protein complexes in both shared and distinct pathways and have the potential to connect proteome signals with the regulation of gene expression. Biological significance: The genomic organization of the genes encoding BIR-1 and SKIP (SKP-1) in C. elegans have suggested that these two factors, each evolutionarily conserved, have related functions. However, these functional connections have remained elusive and underappreciated in light of limited information from C. elegans and other biological systems. Our results provide further evidence for a functional link between these two factors and suggest they may transmit proteome signals towards the regulation of gene expression.
MeSH term(s)	Animals ; Caenorhabditis elegans/metabolism ; Caenorhabditis elegans Proteins/metabolism ; Gene Expression Regulation/physiology ; Nuclear Proteins/metabolism ; Proteome/metabolism ; Signal Transduction/physiology ; Survivors ; Ubiquitin-Protein Ligase Complexes
Chemical Substances	Caenorhabditis elegans Proteins ; Nuclear Proteins ; Proteome ; bir-1 protein, C elegans ; Ubiquitin-Protein Ligase Complexes (EC 2.3.2.23) ; skp-1 protein, C elegans (EC 2.3.2.23)
Language	English
Publishing date	2014-08-01
Publishing country	Netherlands
Document type	Journal Article ; Research Support, N.I.H., Intramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2400835-7
ISSN	1876-7737 ; 1874-3919
ISSN (online)	1876-7737
ISSN	1874-3919
DOI	10.1016/j.jprot.2014.07.023
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: BIR-1, the homologue of human Survivin, regulates expression of developmentally active collagen genes in C. elegans.

Libý, P / Pohludka, M / Vohánka, J / Kostrouchová, M / Kostrouch, D / Rall, J E / Kostrouch, Z

Folia biologica

2006 Volume 52, Issue 4, Page(s) 101–108

Abstract: BIR-1 and Survivin are highly conserved members of the inhibitor of apoptosis protein family that regulate cell division in nematodes and mammals and inhibit apoptosis in mammals. In the C. elegans genome, bir-1 is organized in an operon together with ... ...

Abstract	BIR-1 and Survivin are highly conserved members of the inhibitor of apoptosis protein family that regulate cell division in nematodes and mammals and inhibit apoptosis in mammals. In the C. elegans genome, bir-1 is organized in an operon together with transcription and splicing cofactor CeSKIP (skp-1) and is highly expressed during embryogenesis as well as in non-dividing cells during larval development. Previously we have shown that BIR-1 regulates transcription and development and its loss-of-function phenotype overlaps with loss of function of CeSKIP and nuclear hormone receptor CHR3 (NHR-23). Here we searched for genes whose expression is affected by BIR-1 loss of function using whole-genome microarray experiments and identified several collagen genes as candidate targets of bir-1 inhibition in L1 larval stage. The decreased expression of selected collagen genes in bir-l-inhibited larvae was confirmed by quantitative RT-PCR. Next, we generated transgenic lines expressing bir-1 mRNA under a heat shock-regulated promoter and tested whether bir-1 overexpression has the potential to augment the expression of genes that showed decreased expression in worms treated with bir-1 RNAi. Overexpression of bir-1 resulted in a pronounced increase (2 to 5 times) of the expression of these genes. Our findings support the concept that BIR-1, a protein generally regarded as a mitotic factor, is involved in the regulation of transcription during normal development of C. elegans and has a strong ability to affect transcription of developmentally active genes if overexpressed.
MeSH term(s)	Animals ; Caenorhabditis elegans/genetics ; Caenorhabditis elegans/growth & development ; Caenorhabditis elegans Proteins/metabolism ; Collagen/genetics ; Gene Expression Profiling ; Gene Expression Regulation, Developmental ; Genes, Helminth/genetics ; Humans ; Inhibitor of Apoptosis Proteins ; Larva/metabolism ; Microarray Analysis ; Microtubule-Associated Proteins/metabolism ; Neoplasm Proteins/metabolism ; RNA Interference ; Reproducibility of Results ; Sequence Homology ; Survivin ; Transcription, Genetic
Chemical Substances	BIRC5 protein, human ; Caenorhabditis elegans Proteins ; Inhibitor of Apoptosis Proteins ; Microtubule-Associated Proteins ; Neoplasm Proteins ; Survivin ; bir-1 protein, C elegans ; Collagen (9007-34-5)
Language	English
Publishing date	2006
Publishing country	Czech Republic
Document type	Journal Article
ZDB-ID	419223-0
ISSN	0015-5500
ISSN	0015-5500
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

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Article: SKIP and BIR-1/Survivin have potential to integrate proteome status with gene expression

Kostrouch, David / Ahmed Ali Chughtai / Jan Philipp NovotnÃ½ / MarkÃ©ta KostrouchovÃ¡ / Marta KostrouchovÃ¡ / Petr NovÃ¡k / Petr Yilma / Veronika KostrouchovÃ¡ / ZdenÄk Kostrouch

Journal of proteomics. 2014 Oct. 14, v. 110

2014

Abstract	SKIP and BIR are evolutionarily conserved proteins; SKIP (SKP-1) is a known transcription and splicing cofactor while BIR-1/Survivin regulates cell division, gene expression and development. Their loss of function induces overlapping developmental phenotypes. We searched for SKP-1 and BIR-1 interaction on protein level using yeast two-hybrid screens and identified partially overlapping categories of proteins as SKIP-1 and BIR-1 interactors. The interacting proteins included ribosomal proteins, transcription factors, translation factors and cytoskeletal and motor proteins suggesting involvement in multiple protein complexes. To visualize the effect of BIR-1 on the proteome in Caenorhabditis elegans we induced a short time pulse BIR-1 overexpression in synchronized L1 larvae. This led to a dramatic alteration of the whole proteome pattern indicating that BIR-1 alone has the capacity to alter the chromatographic profile of many target proteins including proteins found to be interactors in yeast two hybrid screens. The results were validated for ribosomal proteins RPS3 and RPL5, non-muscle myosin and TAC-1, a transcription cofactor and a centrosome associated protein. Together, these results suggest that SKP-1 and BIR-1 are multifunctional proteins that form multiple protein complexes in both shared and distinct pathways and have the potential to connect proteome signals with the regulation of gene expression.The genomic organization of the genes encoding BIR-1 and SKIP (SKP-1) in C. elegans have suggested that these two factors, each evolutionarily conserved, have related functions. However, these functional connections have remained elusive and underappreciated in light of limited information from C. elegans and other biological systems. Our results provide further evidence for a functional link between these two factors and suggest they may transmit proteome signals towards the regulation of gene expression.
Keywords	Caenorhabditis elegans ; cell division ; centrosomes ; chromatography ; cytoskeleton ; gene expression regulation ; gene overexpression ; genes ; hybrids ; larvae ; myosin ; nucleotide sequences ; phenotype ; proteome ; ribosomal proteins ; transcription (genetics) ; transcription factors ; translation (genetics) ; two hybrid system techniques ; yeasts
Language	English
Dates of publication	2014-1014
Size	p. 93-106.
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	2400835-7
ISSN	1876-7737 ; 1874-3919
ISSN (online)	1876-7737
ISSN	1874-3919
DOI	10.1016/j.jprot.2014.07.023
Database	NAL-Catalogue (AGRICOLA)

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Article: Proteomic Interactome of C. elegans Mediator Complex Subunit 28 (MDT-28) Reveals Predominant Association with a Restricted Set of Core Mediator Subunits and an Affinity to Additional Structural and Enzymatic Proteins.

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Article: Kolorektální karcinom u seniorů - děláme to dobře?

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Article: Cholecystostomie--obsoletní, nebo aktuální řešení?

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Article: The nematode homologue of Mediator complex subunit 28, F28F8.5, is a critical regulator of

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Article: Trichoplax adhaerens

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Article ; Online: SKIP and BIR-1/Survivin have potential to integrate proteome status with gene expression.

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Article: BIR-1, the homologue of human Survivin, regulates expression of developmentally active collagen genes in C. elegans.

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Article: SKIP and BIR-1/Survivin have potential to integrate proteome status with gene expression

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