HIPK2: a multitalented partner for transcription factors in DNA damage response and developmentThis paper is one of a selection of papers published in this Special Issue, entitled 28th International West Coast Chromatin and Chromosome Conference, and has undergone the Journal's usual peer review process.

2007 ◽  
Vol 85 (4) ◽  
pp. 411-418 ◽  
Author(s):  
Cinzia Rinaldo ◽  
Andrea Prodosmo ◽  
Francesca Siepi ◽  
Silvia Soddu
Keyword(s):  
Transcription Factors ◽  
Gene Transcription ◽  
Review Process ◽  
Peer Review Process ◽  
Post Translational Modification ◽  
Interacting Protein ◽  
Cellular Processes ◽  
New Family ◽  
Damage Response ◽  
Selection Of

Protein phosphorylation is a widely diffuse and versatile post-translational modification that controls many cellular processes, from signal transduction to gene transcription. The homeodomain-interacting protein kinases (HIPKs) belong to a new family of serine–threonine kinases first identified as corepressors for homeodomain transcription factors. Different screenings for the identification of new partners of transcription factors have indicated that HIPK2, the best characterized member of the HIPK family, is a multitalented coregulator of an increasing number of transcription factors and cofactors. The aim of this review is to describe the different mechanisms through which HIPK2 regulates gene transcription.

Recent developments in mass spectrometry-based quantitative phosphoproteomicsThis paper is one of a selection of papers published in this Special Issue, entitled CSBMCB — Systems and Chemical Biology, and has undergone the Journal's usual peer review process.

2008 ◽  
Vol 86 (2) ◽  
pp. 137-148 ◽  
Author(s):  
Jeffrey C. Smith ◽  
Daniel Figeys
Keyword(s):  
Mass Spectrometry ◽  
Protein Phosphorylation ◽  
Review Process ◽  
Peer Review Process ◽  
Cellular Systems ◽  
Post Translational Modification ◽  
Dynamic Nature ◽  
Cellular Processes ◽  
Recent Developments ◽  
Selection Of

Protein phosphorylation is a reversible post-translational modification that is involved in virtually all eukaryotic cellular processes and has been studied in great detail in recent years. Many developments in mass spectrometry (MS)-based proteomics have been successfully applied to study protein phosphorylation in highly complicated samples. Furthermore, the emergence of a variety of enrichment strategies has allowed some of the challenges associated with low phosphorylation stoichiometry and phosphopeptide copy number to be overcome. The dynamic nature of protein phosphorylation complicates its analysis; however, a number of methods have been developed to successfully quantitate phosphorylation changes in a variety of cellular systems. The following review details some of the most recent breakthroughs in the study of protein phosphorylation, or phosphoproteomics, using MS-based approaches. The majority of the focus is placed on detailing strategies that are currently used to conduct MS-based quantitative phosphoproteomics.

Structural and functional implications of phosphorylation and acetylation in the regulation of the AAA+ protein p97This paper is one of a selection of papers published in this special issue entitled 8th International Conference on AAA Proteins and has undergone the Journal's usual peer review process.

2010 ◽  
Vol 88 (1) ◽  
pp. 41-48 ◽  
Author(s):  
Caroline A. Ewens ◽  
Patrik Kloppsteck ◽  
Andreas Förster ◽  
Xiaodong Zhang ◽  
Paul S. Freemont
Keyword(s):  
Review Process ◽  
Peer Review Process ◽  
Adaptor Proteins ◽  
Post Translational Modifications ◽  
Aaa Atpase ◽  
Cellular Processes ◽  
Transcription Factor Activation ◽  
Functional Implications ◽  
Aaa Protein ◽  
Selection Of

p97, also known as VCP (valosin-containing protein), is a hexameric AAA+ ATPase that participates in a variety of cellular processes. It is believed that p97 mediates these processes through the binding of various adaptor proteins. Many factors govern adaptor binding and the regulatory mechanisms are not yet well understood. Sites of phosphorylation and acetylation on p97 have been identified and such post-translational modifications may be involved in regulating p97 function. Phosphorylation and, to a lesser extent, acetylation of p97 have been shown to modify its properties — for example, by modulating adaptor binding and directing subcellular localization. These modifications have been implicated in a number of p97-mediated processes, including misfolded protein degradation, membrane fusion, and transcription factor activation. This review describes the known phosphorylation and acetylation sites on p97 and discusses their possible structural and functional implications.

The nucleosome: a little variation goes a long wayThis paper is one of a selection of papers published in this Special Issue, entitled 27th International West Coast Chromatin and Chromosome Conference, and has undergone the Journal's usual peer review process.

2006 ◽  
Vol 84 (4) ◽  
pp. 505-507 ◽  
Author(s):  
Emily Bernstein ◽  
Sandra B. Hake
Keyword(s):  
Peer Review Process ◽  
Gene Activation ◽  
Epigenetic Inheritance ◽  
Histone Variants ◽  
Post Translational Modifications ◽  
Chromatin Compaction ◽  
Cellular Processes ◽  
Chromatin Template ◽  
Mitosis And Meiosis ◽  
Selection Of

Changes in the overall structure of chromatin are essential for the proper regulation of cellular processes, including gene activation and silencing, DNA repair, chromosome segregation during mitosis and meiosis, X chromosome inactivation in female mammals, and chromatin compaction during apoptosis. Such alterations of the chromatin template occur through at least 3 interrelated mechanisms: post-translational modifications of histones, ATP-dependent chromatin remodeling, and the incorporation (or replacement) of specialized histone variants into chromatin. Of these mechanisms, the exchange of variants into and out of chromatin is the least well understood. However, the exchange of conventional histones for variant histones has distinct and profound consequences within the cell. This review focuses on the growing number of mammalian histone variants, their particular biological functions and unique features, and how they may affect the structure of the nucleosome. We propose that a given nucleosome might not consist of heterotypic variants, but rather, that only specific histone variants come together to form a homotypic nucleosome, a hypothesis that we refer to as the nucleosome code. Such nucleosomes might in turn participate in marking specific chromatin domains that may contribute to epigenetic inheritance.

Expression and bioactivity of recombinant segments of human perforinThis paper is one of a selection of papers in this Special Issue, entitled International Symposium on Recent Advances in Molecular, Clinical, and Social Medicine, and has undergone the Journal's usual peer-review process.

2007 ◽  
Vol 85 (2) ◽  
pp. 203-208 ◽  
Author(s):  
Hongmei Dong ◽  
Xiaohu Xu ◽  
Mohong Deng ◽  
Xiaojun Yu ◽  
Hu Zhao ◽  
...  
Keyword(s):  
Recombinant Proteins ◽  
Fusion Proteins ◽  
Target Genes ◽  
Review Process ◽  
Peer Review Process ◽  
Nitrilotriacetic Acid ◽  
E Coli ◽  
Recombinant Plasmids ◽  
Expression Plasmids ◽  
Selection Of

The aim of the study was to prepare an active recombinant human perforin by comparing 5 candidate segments of human perforin. Full-length perforin, MAC1 (28–349 aa), MAC2 (166–369 aa), C-100, and N-60 of human perforin were selected as candidate active segments and designated, respectively, HP1, HP2, HP3, HP4, and HP5. The target genes were amplified by PCR and the products were individually subcloned into pGEM-T. The genes for HP1, HP2, HP3, and HP5 were subcloned into pET-DsbA, whereas pET-41a (+) was used as the expression vector of HP4. The fusion proteins were expressed in Escherichia coli BL21pLysS(DE3) and purified using nickel nitrilotriacetic acid (NTA) agarose affinity chromatography. The hemolysis microassay was used as an activity assay of fusion protein. From this study, we obtained the recombinant plasmids pGEM-T-HP1, -HP2, -HP3, -HP4 and -HP5, consisting of 1600, 960, 600, 300bp, and 180, respectively. From these recombinant plasmids, expression plasmids were successfully constructed and expressed in E. coli BL21pLysS(DE3). The resultant fusion proteins, affinity purified using Ni–NTA, were ~80, 58, 45, 44, and 30 kDa, respectively. The recombinant proteins were assayed for activity on hemolysis. HP2 and HP5 were the only recombinant proteins that were active in hemolysis, and the hemolytic function was concentration dependent. These results demonstrate that active recombinant forms of perforin can be synthesized in a prokaryote model. The recombinant N-60 and MAC1 (28–349 aa) of human perforin have the function of forming pores. Our study provides the experimental basis for further investigation on the application of perforin.

Interactions of lactoferrin with cells involved in immune functionThis paper is one of a selection of papers published in this Special Issue, entitled 7th International Conference on Lactoferrin: Structure, Function, and Applications, and has undergone the Journal's usual peer review process.

2006 ◽  
Vol 84 (3) ◽  
pp. 282-290 ◽  
Author(s):  
Dominique Legrand ◽  
Elisabeth Elass ◽  
Mathieu Carpentier ◽  
Joël Mazurier
Keyword(s):  
Immune Cells ◽  
Host Response ◽  
Review Process ◽  
Peer Review Process ◽  
Direct Interaction ◽  
Antimicrobial Activities ◽  
Nuclear Targeting ◽  
Cellular Targets ◽  
Anti Inflammatory ◽  
Selection Of

The antimicrobial activities of lactoferrin (Lf) depend on its capacity to bind iron and on its direct interaction with the surface of microorganisms. Its protective effect also extends to the regulation of the host response to infections. Depending on the immune status of an individual, Lf can have anti-inflammatory properties that downregulate the immune response and prevent septic shock and damage to tissues. It also acts as a promoter of the activation, differentiation, and (or) proliferation of immune cells. Although most of the anti-inflammatory activities are correlated with the neutralization of proinflammatory molecules by Lf, the promoting activity seems to be related to a direct effect of Lf on immune cells. Although the mechanisms that govern these activities are not clearly defined, and probably differ from cell to cell, several cellular targets and possible mechanisms of action are highlighted. The majority of the molecular targets at the surface of cells are multiligand receptors but, interestingly, most of them have been reported as signaling, endocytosis, and nuclear-targeting molecules. This review focuses on the known and putative mechanisms that allow the immunoregulating effect of Lf in its interactions with immune cells.

scholarly journals Genetically Encoded Fluorescent Sensor for Poly-ADP-Ribose

2020 ◽  
Vol 21 (14) ◽  
pp. 5004
Author(s):  
Ekaterina O. Serebrovskaya ◽  
Nadezda M. Podvalnaya ◽  
Varvara V. Dudenkova ◽  
Anna S. Efremova ◽  
Nadya G. Gurskaya ◽  
...  
Keyword(s):  
Ubiquitin Ligase ◽  
Mammalian Cells ◽  
Fluorescent Proteins ◽  
Fluorescent Sensor ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Post Translational Modification ◽  
Cellular Processes ◽  
Hydrogen Peroxide Treatment ◽  
Damage Response

Poly-(ADP-ribosyl)-ation (PARylation) is a reversible post-translational modification of proteins and DNA that plays an important role in various cellular processes such as DNA damage response, replication, transcription, and cell death. Here we designed a fully genetically encoded fluorescent sensor for poly-(ADP-ribose) (PAR) based on Förster resonance energy transfer (FRET). The WWE domain, which recognizes iso-ADP-ribose internal PAR-specific structural unit, was used as a PAR-targeting module. The sensor consisted of cyan Turquoise2 and yellow Venus fluorescent proteins, each in fusion with the WWE domain of RNF146 E3 ubiquitin ligase protein. This bipartite sensor named sPARroW (sensor for PAR relying on WWE) enabled monitoring of PAR accumulation and depletion in live mammalian cells in response to different stimuli, namely hydrogen peroxide treatment, UV irradiation and hyperthermia.

scholarly journals Structure of the H1 C-terminal domain and function in chromatin condensationThis paper is one of a selection of papers published in a Special Issue entitled 31st Annual International Asilomar Chromatin and Chromosomes Conference, and has undergone the Journal’s usual peer review process.

2011 ◽  
Vol 89 (1) ◽  
pp. 35-44 ◽  
Author(s):  
Tamara L. Caterino ◽  
Jeffrey J. Hayes
Keyword(s):  
Review Process ◽  
Peer Review Process ◽  
Special Issue ◽  
Direct Role ◽  
Linker Histones ◽  
Terminal Domain ◽  
Chromatin Folding ◽  
And Function ◽  
Positively Charged ◽  
Selection Of

Linker histones are multifunctional proteins that are involved in a myriad of processes ranging from stabilizing the folding and condensation of chromatin to playing a direct role in regulating gene expression. However, how this class of enigmatic proteins binds in chromatin and accomplishes these functions remains unclear. Here we review data regarding the H1 structure and function in chromatin, with special emphasis on the C-terminal domain (CTD), which typically encompasses approximately half of the mass of the linker histone and includes a large excess of positively charged residues. Owing to its amino acid composition, the CTD was previously proposed to function in chromatin as an unstructured polycation. However, structural studies have shown that the CTD adopts detectable secondary structure when interacting with DNA and macromolecular crowding agents. We describe classic and recent experiments defining the function of this domain in chromatin folding and emerging data indicating that the function of this protein may be linked to intrinsic disorder.

Towards a unifying mechanism for ClpB/Hsp104-mediated protein disaggregation and prion propagationThis paper is one of a selection of papers published in this special issue entitled 8th International Conference on AAA Proteins and has undergone the Journal's usual peer review process.

2010 ◽  
Vol 88 (1) ◽  
pp. 63-75 ◽  
Author(s):  
Tobias Haslberger ◽  
Bernd Bukau ◽  
Axel Mogk
Keyword(s):  
Review Process ◽  
Peer Review Process ◽  
Special Issue ◽  
Yeast Prions ◽  
Substrate Interaction ◽  
Initial Substrate ◽  
Hsp70 Chaperone ◽  
Prion Propagation ◽  
Precise Role ◽  
Selection Of

The oligomeric AAA+ chaperones ClpB/Hsp104 mediate the reactivation of aggregated proteins, an activity that is crucial for the survival of cells during severe stress. Hsp104 is also essential for the propagation of yeast prions by severing prion fibres. Protein disaggregation depends on the cooperation of ClpB/Hsp104 with a cognate Hsp70 chaperone system. While Hsp70 chaperones are also involved in prion propagation, their precise role is much less well defined compared with its function in aggregate solubilization. Therefore, it remained unclear whether both ClpB/Hsp104 activities are based on common or different mechanisms. Novel data show that ClpB/Hsp104 uses a motor threading activity to remodel both protein aggregates and prion fibrils. Moreover, transfer of both types of substrates to the ClpB/Hsp104 processing pore site requires initial substrate interaction of Hsp70. Together these data emphasize the similarity of thermotolerance and prion propagation pathways and point to a shared mechanistic principle of Hsp70–ClpB/Hsp104-mediated solubilization of amorphous and ordered aggregates.

Glycogen: an overview of possible regulatory roles of the proteins associated with the granuleThis paper is one of a selection of papers published in this Special Issue, entitled 14th International Biochemistry of Exercise Conference – Muscles as Molecular and Metabolic Machines, and has undergone the Journal’s usual peer review process.

2009 ◽  
Vol 34 (3) ◽  
pp. 488-492 ◽  
Author(s):  
Terry E. Graham
Keyword(s):  
Peer Review ◽  
Muscle Glycogen ◽  
Review Process ◽  
Peer Review Process ◽  
Glycogen Granule ◽  
Special Issue ◽  
Dynamic Regulation ◽  
Considerable Evidence ◽  
The Past ◽  
Selection Of

While scientists have routinely measured muscle glycogen in many metabolic situations for over 4 decades, there is surprisingly little known regarding its regulation. In the past decade, considerable evidence has illustrated that the carbohydrate stores in muscle are not homogeneous, and it is very likely that metabolic pools exist or that each granule has independent regulation. The fundamental aspects appear to be associated with a complex set of proteins that associate with both the granule and each other in a dynamic fashion. Some of the proteins are enzymes and others play scaffolding roles. A number of the proteins can translocate, depending on the metabolic stimulus. These various processes appear to be the mechanisms that give the glycogen granule precise yet dynamic regulation. This may also allow the stores to serve as an important metabolic regulator of other metabolic events.

scholarly journals No evidence of any systematic bias against manuscripts by women in the peer review process of 145 scholarly journals

2020 ◽  
Author(s):  
Flaminio Squazzoni ◽  
Giangiacomo Bravo ◽  
Pierpaolo Dondio ◽  
Mike Farjam ◽  
Ana Marusic ◽  
...  
Keyword(s):  
Peer Review ◽  
Review Process ◽  
Peer Review Process ◽  
Gender Diversity ◽  
Systematic Bias ◽  
Scholarly Journals ◽  
Female Authors ◽  
Social Nature ◽  
Editorial Decisions ◽  
Selection Of

This article examines gender bias in peer review with complete data on 145 journals in various fields of research, including about 1.7 million authors and 740,000 referees. We reconstructed three possible sources of bias, i.e., the editorial selection of referees, referee recommendations, and editorial decisions, and examined all their possible relationships. In line with previous research, we found that editors were sensitive to gender homophily in that they tended to match authors and referee by gender systematically. Results showed that in general manuscripts written by women as solo authors or co-authored by women are treated even more favorably by referees and editors. This is especially so in biomedicine and health journals, whereas women were treated relatively less favorably in social science & humanities journals, i.e., the field in which the ratio of female authors was the highest in our sample. Although with some caveat, our findings suggest that peer review and editorial processes in scholarly journals do not penalize manuscripts by women. However, considering the complex social nature of gender prejudices, journals should increase gender diversity among reviewers and editors as a means of correcting signals potentially biasing the perceptions of authors and referees.

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