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1.  Crystal Structures of Beryllium Fluoride-Free and Beryllium Fluoride-Bound CheY in Complex with the Conserved C-Terminal Peptide of CheZ Reveal Dual Binding Modes Specific to CheY Conformation 
Journal of molecular biology  2006;359(3):624-645.
Summary
Chemotaxis, the environment-specific swimming behavior of a bacterial cell is controlled by flagellar rotation. The steady-state level of the phosphorylated or activated form of the response regulator CheY dictates the direction of flagellar rotation. CheY phosphorylation is regulated by a fine equilibrium of three phosphotransfer activities: phosphorylation by the kinase CheA, its auto-dephosphorylation and dephosphorylation by its phosphatase CheZ. Efficient dephosphorylation of CheY by CheZ requires two spatially distinct protein-protein contacts: tethering of the two proteins to each other and formation of an active site for dephosphorylation. The latter involves interaction of phosphorylated CheY with the small highly conserved C-terminal helix of CheZ (CheZC), an indispensable structural component of the functional CheZ protein. To understand how the CheZC helix, representing less than 1% of the full-length protein, ascertains molecular specificity of binding to CheY, we have determined crystal structures of CheY in complex with a synthetic peptide corresponding to 15 C-terminal residues of CheZ (CheZ200-214) at resolutions ranging from 2.0 Å to 2.3 Å. These structures provide a detailed view of the CheZC peptide interaction both in the presence and absence of the phosphoryl analog, BeF3−. Our studies reveal that two different modes of binding the CheZ200-214 peptide are dictated by the conformational state of CheY in the complex. Our structures suggest that the CheZC helix binds to a “meta-active” conformation of inactive CheY and it does so in an orientation that is distinct from the one in which it binds activated CheY. Our dual binding mode hypothesis provides implications for reverse information flow in CheY and extends previous observations on inherent resilience in CheY-like signaling domains.
doi:10.1016/j.jmb.2006.03.050
PMCID: PMC3666561  PMID: 16674976
CheY; CheZ peptide; crystal structure; beryllium fluoride; dual binding mode
2.  Loss of the Urothelial Differentiation Marker FOXA1 Is Associated with High Grade, Late Stage Bladder Cancer and Increased Tumor Proliferation 
PLoS ONE  2012;7(5):e36669.
Approximately 50% of patients with muscle-invasive bladder cancer (MIBC) develop metastatic disease, which is almost invariably lethal. However, our understanding of pathways that drive aggressive behavior of MIBC is incomplete. Members of the FOXA subfamily of transcription factors are implicated in normal urogenital development and urologic malignancies. FOXA proteins are implicated in normal urothelial differentiation, but their role in bladder cancer is unknown. We examined FOXA expression in commonly used in vitro models of bladder cancer and in human bladder cancer specimens, and used a novel in vivo tissue recombination system to determine the functional significance of FOXA1 expression in bladder cancer. Logistic regression analysis showed decreased FOXA1 expression is associated with increasing tumor stage (p<0.001), and loss of FOXA1 is associated with high histologic grade (p<0.001). Also, we found that bladder urothelium that has undergone keratinizing squamous metaplasia, a precursor to the development of squamous cell carcinoma (SCC) exhibited loss of FOXA1 expression. Furthermore, 81% of cases of SCC of the bladder were negative for FOXA1 staining compared to only 40% of urothelial cell carcinomas. In addition, we showed that a subpopulation of FOXA1 negative urothelial tumor cells are highly proliferative. Knockdown of FOXA1 in RT4 bladder cancer cells resulted in increased expression of UPK1B, UPK2, UPK3A, and UPK3B, decreased E-cadherin expression and significantly increased cell proliferation, while overexpression of FOXA1 in T24 cells increased E-cadherin expression and significantly decreased cell growth and invasion. In vivo recombination of bladder cancer cells engineered to exhibit reduced FOXA1 expression with embryonic rat bladder mesenchyme and subsequent renal capsule engraftment resulted in enhanced tumor proliferation. These findings provide the first evidence linking loss of FOXA1 expression with histological subtypes of MIBC and urothelial cell proliferation, and suggest an important role for FOXA1 in the malignant phenotype of MIBC.
doi:10.1371/journal.pone.0036669
PMCID: PMC3349679  PMID: 22590586
3.  Regulation of Response Regulator Autophosphorylation through Interdomain Contacts*♦ 
The Journal of Biological Chemistry  2010;285(42):32325-32335.
DNA-binding response regulators (RRs) of the OmpR/PhoB subfamily alternate between inactive and active conformational states, with the latter having enhanced DNA-binding affinity. Phosphorylation of an aspartate residue in the receiver domain, usually via phosphotransfer from a cognate histidine kinase, stabilizes the active conformation. Many of the available structures of inactive OmpR/PhoB family proteins exhibit extensive interfaces between the N-terminal receiver and C-terminal DNA-binding domains. These interfaces invariably involve the α4-β5-α5 face of the receiver domain, the locus of the largest differences between inactive and active conformations and the surface that mediates dimerization of receiver domains in the active state. Structures of receiver domain dimers of DrrB, DrrD, and MtrA have been determined, and phosphorylation kinetics were analyzed. Analysis of phosphotransfer from small molecule phosphodonors has revealed large differences in autophosphorylation rates among OmpR/PhoB RRs. RRs with substantial domain interfaces exhibit slow rates of phosphorylation. Rates are greatly increased in isolated receiver domain constructs. Such differences are not observed between autophosphorylation rates of full-length and isolated receiver domains of a RR that lacks interdomain interfaces, and they are not observed in histidine kinase-mediated phosphotransfer. These findings suggest that domain interfaces restrict receiver domain conformational dynamics, stabilizing an inactive conformation that is catalytically incompetent for phosphotransfer from small molecule phosphodonors. Inhibition of phosphotransfer by domain interfaces provides an explanation for the observation that some RRs cannot be phosphorylated by small molecule phosphodonors in vitro and provides a potential mechanism for insulating some RRs from small molecule-mediated phosphorylation in vivo.
doi:10.1074/jbc.M110.157164
PMCID: PMC2952233  PMID: 20702407
Allosteric Regulation; Bacterial Signal Transduction; Bioenergetics; Crystal Structure; Enzyme Kinetics; Histidine Kinases; Kinetics; Acetyl Phosphate; Bacterial Response Regulators; Bacterial Two-component Systems
4.  FYN is overexpressed in human prostate cancer 
BJU international  2008;103(2):171-177.
Objective
FYN is a member of the SRC family of kinases (SFKs), functionally distinct from other SFKs. It interacts with FAK and paxillin (PXN)- regulators of cell morphology and motility. We hypothesized that FYN is upregulated in prostate cancer (CaP).
Patients and Methods
Through datamining in Oncomine; cell line profiling with immunoblotting and quantitative RT-PCR; and immunohistochemical analysis, we describe FYN expression in CaP. This analysis included 32 cases of CaP, 9 prostatic intraepithelial neoplasia (PIN), and 19 normal. Samples were scored for the percentage of stained glands and intensity of staining (from 0-3). Each sample was assigned a composite score generated by multiplying percentage and intensity.
Results
Datamining showed an 8-fold increase in FYN expression in CaP compared to normal tissue. This was specific to FYN and not present for other SFKs. Expression of FYN in CaP cell lines (LNCaP, 22Rv1, PC3, DuPro) was detected using quantitative RT-PCR and immunoblot. Expression of FYN and its signaling partners FAK and PXN was demonstrated in human tissue. Comparing normal to cancer, there was a 2.1-fold increase in median composite score for FYN (p<0.001) 1.7-fold increase in FAK (p<0.001), and a 2-fold increase in PXN (p<0.05). There was a 1.7-fold increase in FYN (p<0.05), a 1.6-fold increase in FAK (p<0.01) in CaP as compared to PIN.
Conclusions
These studies support the hypothesis that the FYN and its related signaling partners are upregulated in CaP and supports further investigation into the role of the FYN as a therapeutic target.
doi:10.1111/j.1464-410X.2008.08009.x
PMCID: PMC2741693  PMID: 18990162
FYN; SRC; prostate cancer; paxillin; FAK
5.  Knockdown of the Drosophila GTPase Nucleostemin 1 Impairs Large Ribosomal Subunit Biogenesis, Cell Growth, and Midgut Precursor Cell Maintenance 
Molecular Biology of the Cell  2009;20(20):4424-4434.
Mammalian nucleostemin (NS) is a nucleolar guanosine triphosphate-binding protein implicated in cell cycle progression, stem cell proliferation, and ribosome assembly. Drosophila melanogaster contains a four-member nucleostemin family (NS1–4). NS1 is the closest orthologue to human NS; it shares 33% identity and 67% similarity with human NS. We show that NS1 has intrinsic GTPase and ATPase activity and that it is present within nucleoli of most larval and adult cells. Endogenous NS1 and lightly expressed green fluorescent protein (GFP)-NS1 enrich within the nucleolar granular regions as expected, whereas overexpressed GFP-NS1 localized throughout the nucleolus and nucleoplasm, and to several transcriptionally active interbands of polytene chromosomes. Severe overexpression correlated with the appearance of melanotic tumors and larval/pupal lethality. Depletion of 60% of NS1 transcripts also lead to larval and pupal lethality. NS1 protein depletion>95 correlated with the loss of imaginal island (precursor) cells in the larval midgut and to an apparent block in the nucleolar release of large ribosomal subunits in terminally differentiated larval midgut polyploid cells. Ultrastructural examination of larval Malpighian tubule cells depleted for NS1 showed a loss of cytoplasmic ribosomes and a concomitant appearance of cytoplasmic preautophagosomes and lysosomes. We interpret the appearance of these structures as indicators of cell stress response.
doi:10.1091/mbc.E08-06-0592
PMCID: PMC2762133  PMID: 19710426
6.  Mitogen-Activated Protein Kinase Kinase 4/c-Jun NH2-Terminal Kinase Kinase 1 Protein Expression Is Subject to Translational Regulation in Prostate Cancer Cell Lines 
Molecular cancer research : MCR  2008;6(3):501-508.
Mitogen-activated protein kinase kinase 4/c-Jun NH2-terminal kinase kinase 1 (MKK4/JNKK1; hereafter referred to as MKK4) is a dual-specificity kinase with a critical role in regulating the activity of c-Jun NH2-terminal kinase and p38 kinases. We identified a novel biological function for MKK4 in the regulation of growth of ovarian and prostate cancer metastases. Clinical correlative studies showed that MKK4 protein levels were reduced in high-grade prostate cancer and prostate and ovarian cancer metastases compared with normal tissue, which prompted investigation into the mechanism(s) responsible for down-regulation of MKK4 in a panel of cancer cell lines. Initial studies found that low levels of MKK4 protein did not correlate with either exon deletion or decreased levels of MKK4 mRNA, suggesting that MKK4 protein levels were regulated posttranscriptionally by either reduced translation or reduced protein stability. Endogenous MKK4 was highly stable and not subject to altered proteolysis. Instead, MKK4 biosynthesis seemed to be regulated by altered translation. In support of this assertion, we found that cytosolic MKK4 mRNA was shifted toward active polysomes in cells with higher levels of MKK4 protein, suggesting that MKK4 mRNA was translated more efficiently in these cells. This study supports a novel mechanism for the regulation of MKK4 protein levels. Further, these findings have potential therapeutic implications for modulating the expression of a signaling kinase involved in the regulation of metastatic growth.
doi:10.1158/1541-7786.MCR-07-2075
PMCID: PMC2435180  PMID: 18337456
7.  Salmonella enterica Serovar Typhimurium BipA Exhibits Two Distinct Ribosome Binding Modes▿  
Journal of Bacteriology  2008;190(17):5944-5952.
BipA is a highly conserved prokaryotic GTPase that functions to influence numerous cellular processes in bacteria. In Escherichia coli and Salmonella enterica serovar Typhimurium, BipA has been implicated in controlling bacterial motility, modulating attachment and effacement processes, and upregulating the expression of virulence genes and is also responsible for avoidance of host defense mechanisms. In addition, BipA is thought to be involved in bacterial stress responses, such as those associated with virulence, temperature, and symbiosis. Thus, BipA is necessary for securing bacterial survival and successful invasion of the host. Steady-state kinetic analysis and pelleting assays were used to assess the GTPase and ribosome-binding properties of S. enterica BipA. Under normal bacterial growth, BipA associates with the ribosome in the GTP-bound state. However, using sucrose density gradients, we demonstrate that the association of BipA and the ribosome is altered under stress conditions in bacteria similar to those experienced during virulence. The data show that this differential binding is brought about by the presence of ppGpp, an alarmone that signals the onset of stress-related events in bacteria.
doi:10.1128/JB.00763-08
PMCID: PMC2519513  PMID: 18621905
8.  Kinetic Analysis of Yersinia pestis DNA Adenine Methyltransferase Activity Using a Hemimethylated Molecular Break Light Oligonucleotide 
PLoS ONE  2007;2(8):e801.
Background
DNA adenine methylation plays an important role in several critical bacterial processes including mismatch repair, the timing of DNA replication and the transcriptional control of gene expression. The dependence of bacterial virulence on DNA adenine methyltransferase (Dam) has led to the proposal that selective Dam inhibitors might function as broad spectrum antibiotics.
Methodology/Principal Findings
Herein we report the expression and purification of Yersinia pestis Dam and the development of a continuous fluorescence based assay for DNA adenine methyltransferase activity that is suitable for determining the kinetic parameters of the enzyme and for high throughput screening against potential Dam inhibitors. The assay utilised a hemimethylated break light oligonucleotide substrate containing a GATC methylation site. When this substrate was fully methylated by Dam, it became a substrate for the restriction enzyme DpnI, resulting in separation of fluorophore (fluorescein) and quencher (dabcyl) and therefore an increase in fluorescence. The assays were monitored in real time using a fluorescence microplate reader in 96 well format and were used for the kinetic characterisation of Yersinia pestis Dam, its substrates and the known Dam inhibitor, S-adenosylhomocysteine. The assay has been validated for high throughput screening, giving a Z-factor of 0.71±0.07 indicating that it is a sensitive assay for the identification of inhibitors.
Conclusions/Significance
The assay is therefore suitable for high throughput screening for inhibitors of DNA adenine methyltransferases and the kinetic characterisation of the inhibition.
doi:10.1371/journal.pone.0000801
PMCID: PMC1949145  PMID: 17726531
9.  Structural Analysis of the Domain Interface in DrrB, a Response Regulator of the OmpR/PhoB Subfamily 
Journal of Bacteriology  2003;185(14):4186-4194.
The N-terminal regulatory domains of bacterial response regulator proteins catalyze phosphoryl transfer and function as phosphorylation-dependent regulatory switches to control the output activities of C-terminal effector domains. Structures of numerous isolated regulatory and effector domains have been determined. However, a detailed understanding of regulatory interactions among these domains has been limited by the relative paucity of structural data for intact multidomain response regulator proteins. The first multidomain structures determined, those of transcription factor NarL and methylesterase CheB, both revealed extensive interdomain interfaces. The regulatory domains obstruct access to the functional sites of the effector domains, indicating a regulatory mechanism based on inhibition. In contrast, the recently determined structure of the OmpR/PhoB homologue DrrD revealed no significant interdomain interface, suggesting that the domains are tethered by a flexible linker and lack a fixed orientation relative to each other. To address the generality of this feature, we have determined the 1.8-Å resolution crystal structure of Thermotoga maritima DrrB, providing a second structure of a multidomain response regulator of the OmpR/PhoB subfamily. The structure reveals an extensive domain interface of 751 Å2 and therefore differs greatly from that observed in DrrD. Residues that are crucial players in defining the activation state of the regulatory domain contribute to this interface, implying that conformational changes associated with phosphorylation will influence these intramolecular contacts. The DrrB and DrrD structures are suggestive of different signaling mechanisms, with intramolecular communication between N- and C-terminal domains making substantially different contributions to effector domain regulation in individual members of the OmpR/PhoB family.
doi:10.1128/JB.185.14.4186-4194.2003
PMCID: PMC164896  PMID: 12837793

Results 1-9 (9)