A unified framework for unraveling the functional interaction structure of a biomolecular network based on stimulus-response experimental data

Cho, K.H.,Choo, S.M.,Wellstead, P.,Wolkenhauer, O. North-Holland Pub ; Elsevier Science Ltd 2005 FEBS letters Vol.579 No.20

We propose a unified framework for the identification of functional interaction structures of biomolecular networks in a way that leads to a new experimental design procedure. In developing our approach, we have built upon previous work. Thus we begin by pointing out some of the restrictions associated with existing structure identification methods and point out how these restrictions may be eased. In particular, existing methods use specific forms of experimental algebraic equations with which to identify the functional interaction structure of a biomolecular network. In our work, we employ an extended form of these experimental algebraic equations which, while retaining their merits, also overcome some of their disadvantages. Experimental data are required in order to estimate the coefficients of the experimental algebraic equation set associated with the structure identification task. However, experimentalists are rarely provided with guidance on which parameters to perturb, and to what extent, to perturb them. When a model of network dynamics is required then there is also the vexed question of sample rate and sample time selection to be resolved. Supplying some answers to these questions is the main motivation of this paper. The approach is based on stationary and/or temporal data obtained from parameter perturbations, and unifies the previous approaches of Kholodenko et al. (PNAS 99 (2002) 12841-12846) and Sontag et al. (Bioinformatics 20 (2004) 1877-1886). By way of demonstration, we apply our unified approach to a network model which cannot be properly identified by existing methods. Finally, we propose an experiment design methodology, which is not limited by the amount of parameter perturbations, and illustrate its use with an in numero example.

SHORT VEGETATIVE PHASE (SVP) protein negatively regulates miR172 transcription via direct binding to the pri-miR172a promoter in Arabidopsis

Cho, H.J.,Kim, J.J.,Lee, J.H.,Kim, W.,Jung, J.H.,Park, C.M.,Ahn, J.H. North-Holland Pub ; Elsevier Science Ltd 2012 FEBS letters Vol.586 No.16

Plant microRNAs (miRNAs) are non-coding RNAs that negatively regulate expression of their target genes. Although much is known about miRNA biogenesis and repression of target genes by miRNAs, the molecular mechanisms underlying the transcriptional regulation of miRNA itself are poorly understood. Here, we report that SHORT VEGETATIVE PHASE (SVP) protein is a direct transcriptional regulator of miR172. The levels of mature miR172 and pri-miR172a were anti-correlated with SVP activity. miR172a has multiple transcription start sites, among which the transcript starting with cytosine (-671bp, relative to the mature miR172a) was a major species. EMSA and ChIP analysis demonstrated that SVP protein binds to the CArG motifs in the miR172a promoter. These results suggest that SVP protein directly regulates miR172 transcription in Arabidopsis.

A novel zinc-carboxypeptidase SURO-1 regulates cuticle formation and body morphogenesis in Caenorhabditis elegans

Kim, T.H.,Kim, Y.J.,Cho, J.W.,Shim, J. North-Holland Pub ; Elsevier Science Ltd 2011 FEBS letters Vol.585 No.1

Cuticle formation and molting are critical for the development of Caenorhabditis elegans. To understand cuticle formation more clearly, we screened for suppressors in transgenic worms that expressed dominant ROL-6 collagen proteins. The suro-1 mutant, which is mild dumpy, exhibited a different ROL-6::GFP localization pattern compared to other Dpy mutants. We identified mutations in three suro-1 mutants, and found that suro-1 (ORF R11A5.7) encodes a putative zinc-carboxypeptidase homologue. The expression of this enzyme in the hypodermis and the genetic interactions between this enzyme and other collagen-modifying enzyme mutants suggest a regulatory role in collagen processing and cuticle organization for this novel carboxypeptidase. These findings aid our understanding of cuticle formation during worm development.

Establishment of interferon alpha-resistant hepatitis C virus using cell culture system

Tran, H.T.L.,Lim, Y.S.,Hwang, S.B. North-Holland Pub ; Elsevier Science Ltd 2011 FEBS letters Vol.585 No.2

To investigate the molecular mechanisms underlying interferon alpha (IFNα) treatment failure in hepatitis C virus (HCV) patients with chronic hepatitis, we aimed to develop an IFNα-resistant clone of HCV. By treating JFH-1-infected Huh7.5 cells with a prolonged low-dose treatment of IFNα, we selected a clone of HCV that survived against 100U/ml of IFNα. By genetic analysis of this clone, we found four substitution mutations in the C-terminal coding sequence of non-structural 5A (NS5A). By introducing these four mutations into wild-type JFH-1, we established a new HCV clone that acquired IFNα resistant phenotype. These data suggest that four amino acid substitutions in NS5A are involved in IFNα resistance and thus this newly established HCV may be a useful tool for elucidating the molecular mechanisms of IFNα resistance in HCV patients.

HVEM-deficient mice fed a high-fat diet are protected from adipose tissue inflammation and glucose intolerance

Kim, H.J.,Kim, H.M.,Kim, C.S.,Jeong, C.S.,Choi, H.S.,Kawada, T.,Kim, B.S.,Yu, R. North-Holland Pub ; Elsevier Science Ltd 2011 FEBS letters Vol.585 No.14

HVEM is a member of the TNF receptor superfamily that plays a role in the development of various inflammatory diseases. In this study, we show that HVEM deficiency attenuates adipose tissue inflammatory responses and glucose intolerance in diet-induced obesity. Feeding a high-fat diet (HFD) to HVEM-deficient mice elicited a reduction in the number of macrophages and T cells infiltrated into adipose tissue. Proinflammatory cytokine levels in the adipose tissue decreased in HFD-fed HVEM-deficient mice, while levels of the anti-inflammatory cytokine IL-10 increased. Moreover, glucose intolerance and insulin sensitivity were markedly improved in the HFD-fed HVEM-deficient mice. These findings indicate that HVEM may be a useful target for combating obesity-induced inflammatory responses and insulin resistance.

p53 deacetylation by SIRT1 decreases during protein kinase CKII downregulation-mediated cellular senescence

Jang, S.Y.,Kim, S.Y.,Bae, Y.S. North-Holland Pub ; Elsevier Science Ltd 2011 FEBS letters Vol.585 No.21

Cellular senescence is thought to be an important tumor suppression process in vivo. We have previously shown that p53 activation is necessary for CKII inhibition-mediated cellular senescence. Here, CKII inhibition induced acetylation of p53 at K382 in HCT116 and HEK293 cells. This acetylation event was suppressed by SIRT1 activation. CKIIα and CKIIβ were co-immunoprecipitated with SIRT1 in a p53-independent manner. Maltose binding protein pull-down and yeast two-hybrid indicated that SIRT1 bound to CKIIβ, but not to CKIIα. CKII inhibition reduced SIRT1 activity in cells. CKII phosphorylated and activated human SIRT1 in vitro. Finally, SIRT1 overexpression antagonized CKII inhibition-mediated cellular senescence. These results reveal that CKII downregulation induces p53 stabilization by negatively regulating SIRT1 deacetylase activity during senescence. Structured summary of protein interactions: CKII Betabinds to SIRT1 by pull down (View interaction) CKII Betaphysically interacts with SIRT1 by pull down (View interaction) SIRT1physically interacts with CKII Beta and CKII Alpha by anti bait coimmunoprecipitation (View Interaction: 1, 2, 3) CKII Betaphysically interacts with SIRT1 by two hybrid (View interaction)

YrhB is a highly stable small protein with unique chaperone-like activity in Escherichia coli BL21(DE3)

Ahn, K.Y.,Park, J.S.,Han, K.Y.,Song, J.A.,Lee, J. North-Holland Pub ; Elsevier Science Ltd 2012 FEBS letters Vol.586 No.7

Escherichia coli YrhB (10.6kDa) from strain BL21(DE3) that is commonly used for protein overexpression is a stable chaperone-like protein and indispensable for supporting the growth of BL21(DE3) at 48<SUP>o</SUP>C but not defined as conventional heat shock protein (HSP). YrhB effectively prevented heat-induced aggregation of ribonucleotide synthetase (PurK). Without ATP, YrhB alone promoted in vitro refolding of uridine phosphorylase (UDP) and protected thermal denaturation of the refolded UDP. As a cis-acting fusion partner, YrhB also significantly reduced inclusion body formation of nine aggregation-prone heterologous proteins in BL21(DE3). Unlike conventional small HSPs, YrhB remained monomer under heat shock condition.

Crystal structure of Pyrococcus furiosus PF2050, a member of the DUF2666 protein family

Han, B.G.,Jeong, K.C.,Cho, J.W.,Jeong, B.C.,Song, H.K.,Lee, J.Y.,Shin, D.H.,Lee, S.,Lee, B.I. North-Holland Pub ; Elsevier Science Ltd 2012 FEBS letters Vol.586 No.9

Pyrococcus furiosus PF2050 is an uncharacterized putative protein that contains two DUF2666 domains. Functional and structural studies of PF2050 have not previously been performed. In this study, we determined the crystal structure of PF2050. The structure of PF2050 showed that the two DUF2666 domains interact tightly, forming a globular structure. Each DUF2666 domain comprises an antiparallel β-sheet and an α-helical bundle. One side of the PF2050 structure has a positively charged basic cleft, which may have a DNA-binding function. Furthermore, we confirmed that PF2050 interacts with circular and linear dsDNA.

Translation of a histone H3 tail as a model system for studying peptidyl-tRNA drop-off

Kang, T.J.,Suga, H. North-Holland Pub ; Elsevier Science Ltd 2011 FEBS letters Vol.585 No.14

We found that the synthesis of histone H3 N-terminal peptide (tail) in a reconstituted protein synthesis system yielded fragmented peptides along with the full-length product. With the combined use of MALDI-TOF analysis and peptidyl-tRNA hydrolase cleavage of the Flag tagged product species, we concluded that the fragments were generated by peptidyl-tRNA drop-off at specific sites and subsequent translation continuation. Using the histone H3 tail we also found that peptidyl-tRNA drop-off is strongly correlated with the amino acid context. We envision that the system described here would be useful as a model system for studying peptidyl-tRNA drop-off events.

Crystal structure of metagenome-derived LC9-RNase H1 with atypical DEDN active site motif

Nguyen, T.N.,You, D.J.,Kanaya, E.,Koga, Y.,Kanaya, S. North-Holland Pub ; Elsevier Science Ltd 2013 FEBS letters Vol.587 No.9

The crystal structure of metagenome-derived LC9-RNase H1 was determined. The structure-based mutational analyses indicated that the active site motif of LC9-RNase H1 is altered from DEDD to DEDN. In this motif, the location of the second glutamate residue is moved from αA-helix to β1-strand immediately next to the first aspartate residue, as in the active site of RNase H2. However, the structure and enzymatic properties of LC9-RNase H1 highly resemble those of RNase H1, instead of RNase H2. We propose that LC9-RNase H1 represents bacterial RNases H1 with an atypical DEDN active site motif, which are evolutionarily distinct from those with a typical DEDD active site motif.