Fragile X mental retardation protein interactions with the microtubule associated protein 1B RNA

Fragile X mental retardation syndrome, the most common form of inherited mental retardation, is caused by the absence of the fragile X mental retardation protein (FMRP). FMRP has been shown to use its arginine-glycine-glycine (RGG) box to bind to a subset of RNA targets that form a G quadruplex structure. We performed a detailed analysis of the interactions between the FMRP RGG box and the microtubule associated protein 1B (MAP1B) mRNA, a relevant in vivo FMRP target. We show that MAP1B RNA forms an intramolecular G quadruplex structure, which is bound with high affinity and specificity by the FMRP RGG box. We determined that hydrophobic interactions are important in the FMRP RGG box-MAP1B RNA association, with minor contributions from electrostatic interactions. Our findings that at low protein:RNA ratios the RNA G quadruplex structure is slightly stabilized, whereas at high ratios is unfolded, suggest a mechanism by which the FMRP concentration variation in response to a neurotransmitter stimulation event could act as a regulatory switch for the protein function, from translation repressor to translation activator.     

SeMoP: a new computational strategy for the unrestricted search for modified peptides using LC-MS/MS data

A novel computational approach, termed Search for Modified Peptides (SeMoP), for the unrestricted discovery and verification of peptide modifications in shotgun proteomic experiments using low resolution ion trap MS/MS spectra is presented. Various peptide modifications, including post-translational modifications, sequence polymorphisms, as well as sample handling-induced changes, can be identified using this approach. SeMoP utilizes a three-step strategy: (1) a standard database search to identify proteins in a sample; (2) an unrestricted search for modifications using a newly developed algorithm; and (3) a second standard database search targeted to specific modifications found using the unrestricted search. This targeted approach provides verification of discovered modifications and, due to increased sensitivity, a general increase in the number of peptides with the specific modification. The feasibility of the overall strategy has been first demonstrated in the analysis of 65 plasma proteins. Various sample handling induced modifications, such as beta-elimination of disulfide bridges and pyrocarbamidomethylation, as well as biologically induced modifications, such as phosphorylation and methylation, have been detected. A subsequent targeted Sequest search has been used to verify selected modifications, and a 4-fold increase in the number of modified peptides was obtained. In a second application, 1367 proteins of a cervical cancer cell line were processed, leading to detection of several novel amino acid substitutions. By conducting the search against a database of peptides derived from proteins with decoy sequences, a false discovery rate of less than 5% for the unrestricted search resulted. SeMoP is shown to be an effective and easily implemented approach for the discovery and verification of peptide modifications.     

Assignment-free solution NMR method reveals CesT as an unswapped homodimer

The X-ray structure of the homodimeric chaperone CesT is the only structure among the type three secretion system (TTSS) chaperones that shows a domain swap. This swap has potential importance for the mechanism of effector translocation through a TTSS. Here we present two nuclear magnetic resonance strategies exploiting pre-existing structural models and residual dipolar couplings (RDCs), which reveal the unswapped 35.4-kDa dimer to be present in solution. Particularly efficient is the discrimination of a swapped and unswapped structural state performed simultaneously to automatic backbone assignment using only HN-RDCs and carbonyl backbone chemical shifts. This direct approach may prove to be generally useful to rapidly differentiate two structural models.     

A comparative molecular field and comparative molecular similarity indices analyses (CoMFA and CoMSIA) of N-phenyl-N'-(2-chloroethyl)ureas targeting the colchicine-binding site as anticancer agents

To decipher the mechanism underlying the covalent binding of N-phenyl-N'-(2-chloroethyl)ureas (CEU) to the colchicine-binding site on beta(II)-tubulin and to design new and selective antimitotic drugs, we developed 3D quantitative structure-activity relationships (3D-QSAR) models using CoMFA and CoMSIA analyses. The present study correlates the cell growth inhibition activities of 56 structurally related CEU derivatives to several physicochemical parameters representing steric, electrostatic, and hydrophobic fields. Both CoMFA and CoMSIA models using two different optimum numbers of components (ONC) 10 and 4, respectively, gave good internal predictions and their cross-validated r2 values were between 0.639 and 0.743. These comprehensive CoMFA and CoMSIA models are useful in understanding the structure-activity relationships of CEU. The two models were compared to the X-ray crystal structure of the complex of tubulin-colchicine and analyzed for similarities between the two modes of analysis. These models will inspire the design of new CEU derivatives with enhanced inhibition of tumor cell growth and targeting specificity of beta(II)-tubulin and the cytoskeleton.     

Characterization of resistance mechanism in transgenic Nicotiana benthamiana containing Turnip crinkle virus coat protein

Two transgenic lines, of Nicotiana benthamiana expressing Turnip crinkle virus (TCV)-coat protein (CP) gene with contrasting phenotype, the highest (#3) and the lowest (#18) CP expressers, were selected and challenged with the homologous TCV. The former, the highest expresser, showed nearly five times more CP expression than the latter. Progenies of #3 and #18 lines showed 30 and 100% infection rates, respectively. The infected progenies of #3 line showed mild and delayed symptom with TCV. This is a coat protein-mediated resistance (CP-MR), and its resistance level is directly proportional to CP transgene expression. However, CP-MR of the transgenic plants was specific only for TCV but not for heterologous viruses. Newly growing leaves of those infected progenies of #3 line did not show any visible symptoms at 4-week post-inoculation (wpi) with TCV, suggesting a reversal from infection. This was confirmed by RT-PCR analysis with the disappearance of the target at 4 wpi. This is a case of RNA-mediated resistance, and a threshold level of transgene expression may be needed to achieve the silent state. To confirm the RNA silencing, we infiltrated Agrobacterium carrying TCV-CP into leaves of progenies of #3 and performed RT-PCR analysis. The results indicate that TCV-CP’s suppressor activity against RNA silencing itself can be silenced by the homologous expression of TCV-CP in the transgenic plants. The transgenic plants containing TCV-CP seem to be a model system to study viral protection mediated by a combination of protein and RNA silencing. Ayyappan Vasudevan and Tae-Kyun Oh have contributed equally in this study.     

The Cell Surface Receptor Tartan Is a Potential In Vivo Substrate for the Receptor Tyrosine Phosphatase Ptp52F

Receptor-linked protein-tyrosine phosphatases (RPTPs) are essential regulators of axon guidance and synaptogenesis in Drosophila, but the signaling pathways in which they function are poorly defined. We identified the cell surface receptor Tartan (Trn) as a candidate substrate for the neuronal RPTP Ptp52F by using a modified two-hybrid screen with a substrate-trapping mutant of Ptp52F as “bait.” Trn can bind to the Ptp52F substrate-trapping mutant in transfected Drosophila S2 cells if v-Src kinase, which phosphorylates Trn, is also expressed. Coexpression of wild-type Ptp52F causes dephosphorylation of v-Src-phosphorylated Trn. To examine the specificity of the interaction in vitro, we incubated Ptp52F-glutathione S-transferase (GST) fusion proteins with pervanadate-treated S2 cell lysates. Wild-type Ptp52F dephosphorylated Trn, as well as most other bands in the lysate. GST “pulldown” experiments demonstrated that the Ptp52F substrate-trapping mutant binds exclusively to phospho-Trn. Wild-type Ptp52F pulled down dephosphorylated Trn, suggesting that it forms a stable Ptp52F-Trn complex that persists after substrate dephosphorylation. To evaluate whether Trn and Ptp52F are part of the same pathway in vivo, we examined motor axon guidance in mutant embryos. trn and Ptp52F mutations produce identical phenotypes affecting the SNa motor nerve. The genes also display dosage-dependent interactions, suggesting that Ptp52F regulates Trn signaling in SNa motor neurons.Receptor-linked protein-tyrosine phosphatases (RPTPs) are enzymes with extracellular (XC) domains, a single transmembrane domain, and one or two cytoplasmic protein tyrosine phosphatase (PTP) homology domains. Many RPTPs have XC sequences that resemble those of cell adhesion molecules (for a review, see reference 33). This sequence organization suggests that RPTPs can couple cell-cell recognition events to dephosphorylation of cytoplasmic substrates. Interestingly, while phosphotyrosine (PY) pathways involved in cell growth and differentiation typically involve receptor tyrosine kinases that bind to growth factors and are regulated by nontransmembrane PTPs, those that control axon guidance often use RPTPs and nontransmembrane TKs. This implies that the cues that affect PY signaling in axonal growth cones may interact with RPTPs rather than with receptor tyrosine kinases (reviewed in reference 14).There are 17 active RPTPs encoded in the human genome, while Drosophila has six. Most of the mammalian RPTPs are expressed in nonneural tissues, but four of the six fly RPTPs are expressed only by central nervous system (CNS) neurons in late embryos. All published zygotic phenotypes produced by Rptp mutations are alterations in axon guidance or synaptogenesis. These results suggest that the major functions of the Drosophila RPTPs are in neural development (for a review, see reference 16). Analysis of axon guidance phenotypes in embryos bearing single or multiple Rptp mutations is consistent with the idea that RPTP interactions with ligands at growth cone choice points convey “information,” in the form of changes in substrate phosphorylation within growth cones, that is used to determine pathway decisions.In the Drosophila neuromuscular system, 36 motor axons grow out within six nerve bundles in each abdominal hemisegment, and each axonal growth cone makes a series of genetically determined guidance decisions that direct it to the appropriate muscle fiber (for a review, see reference 27). Our work on Rptp mutant combinations suggests that each pathway decision uses a specific subset of the six RPTPs. RPTPs can exhibit functional redundancy, so that the loss of one does not produce a defect unless another RPTP is also absent, or competition, in which loss of one RPTP suppresses the phenotype produced by loss of another (5, 6, 31). Examination of RPTP expression patterns suggests that the RPTPs are expressed by most (or possibly all) CNS neurons, including motor neurons. If so, the requirements for individual RPTPs for execution of particular guidance decisions cannot be due to selective expression of these RPTPs on specific motor axons. These requirements might instead be determined by the expression patterns of RPTP ligands, so that only RPTPs whose ligands were localized to the vicinity of a growth cone choice point would participate in that pathway decision. Alternatively (or in addition), the necessity of a particular RPTP for a pathway decision might arise from selective expression of RPTP substrates, so that an RPTP would be important for guidance decisions made by a growth cone of a specific motor neuron only if that neuron expressed the relevant substrate(s).Evaluation of such models requires identification of specific XC ligands and intracellular substrates for the Drosophila RPTPs. Only one set of ligands has been identified thus far. These are the heparan sulfate proteoglycans Syndecan (Sdc) and Dallylike (Dlp), which bind to the Lar RPTP with nanomolar affinity and contribute to its functions in axon guidance and synapse growth (9, 15). Similarly, little is known about substrate specificity in vivo. Lar can dephosphorylate the Enabled (Ena) protein, which regulates the growth cone cytoskeleton, and genetic interaction studies suggest that Ena may be an in vivo substrate for Lar (35). The transmembrane protein gp150 can be dephosphorylated by Ptp10D in cell culture and intact fly larvae, but genetics has not provided evidence that Ptp10D and gp150 are in the same signaling pathway in vivo (7).The identification of in vivo substrates for RPTPs has been hampered by the fact that purified RPTP cytoplasmic domains often do not exhibit high selectivity in vitro when tested for dephosphorylation activity on peptides or proteins. The most fruitful method for finding substrates for both RPTPs and cytoplasmic PTPs has been the use of “substrate-trapping” mutants. The most effective substrate traps were devised by Tonks and coworkers, and are created by changing an invariant Asp (D) residue within the PTP active site to Ala (A) (8). The D residue has an abnormal pK and is thus able to donate a proton to the phosphorus-oxygen bond, facilitating displacement of the tyrosine (Y) OH by the invariant Cys (C) nucleophile of the enzyme. This creates a phosphoenzyme intermediate. The dephosphorylated substrate then dissociates, and water attacks the Cys-phosphate bond, releasing the phosphate and reconstituting the enzyme. In D→A mutants, the polarization of the phosphorus-oxygen bond by protonation cannot take place, and the PY substrate remains bound to the enzyme. Substrate-trapping mutants expressed in cells often bind to only a few phosphoproteins, suggesting that PTPs exhibit high specificity in vivo (see, for example, reference 11).We conducted a modified yeast two-hybrid screen to find Drosophila phosphoproteins that bind selectively to RPTP substrate-trapping mutants. We identified the cell surface receptor Tartan (Trn) in this screen and showed that it is a substrate for the Ptp52F RPTP in Drosophila Schneider 2 (S2) cells. Axon guidance phenotypes in trn mutants are identical to those seen in Ptp52F mutants, and trn and Ptp52F exhibit dosage-dependent genetic interactions. These results suggest that Ptp52F is a regulator of Trn signaling in motor neurons in vivo.     

A new monorchiid trematode, <Emphasis Type="Italic">Paramonorcheides selaris</Emphasis> n. sp., from the carangid fish <Emphasis Type="Italic">Selar crumenophthalmus</Emphasis> in the Bay of Bengal off the Visakhapatnam coast of India

Paramonorcheides selaris n. sp. is described from the intestine of the carangid fish Selar crumenophthalmus (Bloch) off the Visakhapatnam coast, Bay of Bengal. It is closest to the Australian species P. pseudocaranxi Dove & Cribb, 1998, but differs in its shorter cirrus-sac extending only to the level of the ovary rather than to the level of the testes, in lacking eye-spot pigment and in details of the armature of the terminal genitalia. P. pseudocaranxi of Machida (2005) is regarded as identical to the new species. The validity of Allobacciger Hafeezullah & Siddiqi, 1970, as distinct from Monorcheides Odhner, 1905, is discussed. A key to the six species of Paramonorcheides Yamaguti, 1938 is presented.     

Threonine phosphorylation prevents promoter DNA binding of the Group B Streptococcus response regulator CovR

All living organisms communicate with the external environment for their survival and existence. In prokaryotes, communication is achieved by two-component systems (TCS) comprising histidine kinases and response regulators. In eukaryotes, signalling is accomplished by serine/threonine and tyrosine kinases. Although TCS and serine/threonine kinases coexist in prokaryotes, direct cross-talk between these families was first described in Group B Streptococcus (GBS). A serine/threonine kinase (Stk1) and a TCS (CovR/CovS) co-regulate toxin expression in GBS. Typically, promoter binding of regulators like CovR is controlled by phosphorylation of the conserved active site aspartate (D53). In this study, we show that Stk1 phosphorylates CovR at threonine 65. The functional consequence of threonine phosphorylation of CovR in GBS was evaluated using phosphomimetic and silencing substitutions. GBS encoding the phosphomimetic T65E allele are deficient for CovR regulation unlike strains encoding the non-phosphorylated T65A allele. Further, compared with wild-type or T65A CovR, the T65E CovR is unable to bind promoter DNA and is decreased for phosphorylation at D53, similar to Stk1-phosphorylated CovR. Collectively, we provide evidence for a novel mechanism of response regulator control that enables GBS (and possibly other prokaryotes) to fine-tune gene expression for environmental adaptation.     

Comparative activity against pathogenic bacteria of the root,stem, and leaf of <Emphasis Type="Italic">Raphanus sativus</Emphasis> grown in India

Aqueous, methanol, ethyl acetate, and chloroform extracts of the root, stem, and leaf of Raphanus sativus were studied for antibacterial activity against food-borne and resistant pathogens. All extracts except the aqueous extracts had significant broad-spectrum inhibitory activity. The ethyl acetate extract of the root had the potent antibacterial activity, with a minimum inhibitory concentration (MIC) of 0.016–0.064 mg/ml and a minimum bactericidal concentration (MBC) of 0.016–0.512 mg/ml against health-damaging bacteria. This was followed by the ethyl acetate extracts of the leaf and stem with MICs of 0.064–0.256 and 0.128–0.256 mg/ml, respectively and MBCs of 0.128–2.05 and 0.256–2.05 mg/ml, respectively. The ethyl acetate extracts of the different parts of R. sativus retained their antibacterial activity after heat treatment at 100°C for 30 min, and their antibacterial activity was enhanced when pH was maintained in the acidic range. Hence this study, for the first time, demonstrated that the root, stem, and leaf of R. sativus had significant bactericidal effects against human pathogenic bacteria, justifying their traditional use as anti-infective agents in herbal medicines.     

Use of Saccharum spontaneum (wild sugarcane) as biomaterial for cell immobilization and modulated ethanol production by thermotolerant Saccharomyces cerevisiae VS3

Saccharum spontaneum is a wasteland weed consists of 45.10 ± 0.35% cellulose and 22.75 ± 0.28% of hemicellulose on dry solid (DS) basis. Aqueous ammonia delignified S. spontaneum yielded total reducing sugars, 53.91 ± 0.44 g/L (539.10 ± 0.55 mg/g of substrate) with a hydrolytic efficiency of 77.85 ± 0.45%. The enzymes required for hydrolysis were prepared from culture supernatants of Aspergillus oryzae MTCC 1846. A maximum of 0.85 ± 0.07 IU/mL of filter paperase (FPase), 1.25 ± 0.04 IU/mL of carboxy methyl cellulase (CMCase) and 55.56 ± 0.52 IU/mL of xylanase activity was obtained after 7 days of incubation at 28 ± 0.5 °C using delignified S. spontaneum as carbon source under submerged fermentation conditions. Enzymatic hydrolysate of S. spontaneum was then tested for ethanol production under batch and repeated batch production system using “in-situ” entrapped Saccharomyces cerevisiae VS₃ cells in S. spontaneum stalks (1 cm × 1 cm) size. Immobilization was confirmed by the scanning electron microscopy (SEM). Batch fermentation of VS₃ free cells and immobilized cells showed ethanol production, 19.45 ± 0.55 g/L (yield, 0.410 ± 0.010 g/g) and 21.66 ± 0.62 g/L (yield, 0.434 ± 0.021 g/g), respectively. Immobilized VS₃ cells showed maximum ethanol production (22.85 ± 0.44 g/L, yield, 0.45 ± 0.04 g/g) up to 8th cycle during repeated batch fermentation followed by a gradual reduction in subsequent cycles of fermentation.