Role of a ribosomal RNA phosphate oxygen during the EF-G-triggered hydrolysis

Elongation factor-catalyzed GTP hydrolysis is a key reaction during the ribosomal elongation cycle. Recent crystal structures of G proteins, such as elongation factor G (EF-G) bound to the ribosome, as well as many biochemical studies, provide evidence that the direct interaction of translational GTPases (trGTPases) with the sarcin-ricin loop (SRL) of ribosomal RNA (rRNA) is pivotal for hydrolysis. However, the precise mechanism remains elusive and is intensively debated. Based on the close proximity of the phosphate oxygen of A2662 of the SRL to the supposedly catalytic histidine of EF-G (His87), we probed this interaction by an atomic mutagenesis approach. We individually replaced either of the two nonbridging phosphate oxygens at A2662 with a methyl group by the introduction of a methylphosphonate instead of the natural phosphate in fully functional, reconstituted bacterial ribosomes. Our major finding was that only one of the two resulting diastereomers, the SP methylphosphonate, was compatible with efficient GTPase activation on EF-G. The same trend was observed for a second trGTPase, namely EF4 (LepA). In addition, we provide evidence that the negative charge of the A2662 phosphate group must be retained for uncompromised activity in GTP hydrolysis. (1) In summary, our data strongly corroborate that the nonbridging proSP phosphate oxygen at the A2662 of the SRL is critically involved in the activation of GTP hydrolysis. A mechanistic scenario is supported in which positioning of the catalytically active, protonated His87 through electrostatic interactions with the A2662 phosphate group and H-bond networks are key features of ribosome-triggered activation of trGTPases.

Role of a ribosomal RNA phosphate oxygen during the EF-G-triggered hydrolysis

Elongation factor-catalyzed GTP hydrolysis is a key reaction during the ribosomal elongation cycle. Recent crystal structures of G proteins, such as elongation factor G (EF-G) bound to the ribosome, as well as many biochemical studies, provide evidence that the direct interaction of translational GTPases (trGTPases) with the sarcin-ricin loop (SRL) of ribosomal RNA (rRNA) is pivotal for hydrolysis. However, the precise mechanism remains elusive and is intensively debated. Based on the close proximity of the phosphate oxygen of A2662 of the SRL to the supposedly catalytic histidine of EF-G (His87), we probed this interaction by an atomic mutagenesis approach. We individually replaced either of the two nonbridging phosphate oxygens at A2662 with a methyl group by the introduction of a methylphosphonate instead of the natural phosphate in fully functional, reconstituted bacterial ribosomes. Our major finding was that only one of the two resulting diastereomers, the SP methylphosphonate, was compatible with efficient GTPase activation on EF-G. The same trend was observed for a second trGTPase, namely EF4 (LepA). In addition, we provide evidence that the negative charge of the A2662 phosphate group must be retained for uncompromised activity in GTP hydrolysis. (1) In summary, our data strongly corroborate that the nonbridging proSP phosphate oxygen at the A2662 of the SRL is critically involved in the activation of GTP hydrolysis. A mechanistic scenario is supported in which positioning of the catalytically active, protonated His87 through electrostatic interactions with the A2662 phosphate group and H-bond networks are key features of ribosome-triggered activation of trGTPases.

Kinetics and Mechanism of Oxygen Delignification

Considerable research has been conducted into the kinetics and selectivity of the oxygen delignification process to overcome limitation in its use. However most studies were performed in a batch reactor whereby the hydroxide and dissolved oxygen concentrations are changing during the reaction time in an effort to simulate tower performance in pulp mills. This makes it difficult to determine the reaction order of the different reactants in the rate expressions. Also the lignin content and cellulose degradation of the pulp are only established at the end of the experiment when the sample is removed from the batch reactor. To overcome these deficiencies, we have adopted a differential reactor system used frequently for fluid-solid rate studies (so-called Berty reactor) for measurement of oxygen delignification kinetics. In this reactor, the dissolved oxygen concentration and the alkali concentration in the feed are kept constant, and the rate of lignin removal is determined from the dissolved lignin content in the outflow stream measured by UV absorption. The mass of lignin removed is verified by analyzing the pulp at several time intervals. Experiments were performed at different temperatures, oxygen pressures and caustic concentrations. The delignification rate was found to be first order in HexA-free residual lignin content. The delignification rate reaction order in caustic concentration and oxygen pressure were determined to be 0.42 and 0.44 respectively. The activation energy was found to be 53kJ/mol. The carbohydrate degradation during oxygen delignification can be described by two contributions: one due to radicals produced by phenolic delignification, and a much smaller contribution due to alkaline hydrolysis. From the first order of the reaction and the pKa of the active lignin site, a new oxygen delignification mechanism is proposed. The number 3 carbon atom in the aromatic ring with the attached methoxyl group forms the lignin active site for oxygen adsorption and subsequent electrophic reaction to form a hydroperoxide with a pKa value similar to that of the present delignification kinetics. The uniform presence of the aromatic methoxyl groups in residual lignin further support the first order in lignin kinetics.

VERIFICATION OF DNA PREDICTED PROTEIN SEQUENCES BY ENZYME HYDROLYSIS AND MASS SPECTROMETRIC ANALYSIS

The focus of this thesis lies in the development of a sensitive method for the analysis of protein primary structure which can be easily used to confirm the DNA sequence of a protein's gene and determine the modifications which are made after translation. This technique involves the use of dipeptidyl aminopeptidase (DAP) and dipeptidyl carboxypeptidase (DCP) to hydrolyze the protein and the mass spectrometric analysis of the dipeptide products.^ Dipeptidyl carboxypeptidase was purified from human lung tissue and characterized with respect to its proteolytic activity. The results showed that the enzyme has a relatively unrestricted specificity, making it useful for the analysis of the C-terminal of proteins. Most of the dipeptide products were identified using gas chromatography/mass spectrometry (GC/MS). In order to analyze the peptides not hydrolyzed by DCP and DAP, as well as the dipeptides not identified by GC/MS, a FAB ion source was installed on a quadrupole mass spectrometer and its performance evaluated with a variety of compounds.^ Using these techniques, the sequences of the N-terminal and C-terminal regions and seven fragments of bacteriophage P22 tail protein have been verified. All of the dipeptides identified in these analysis were in the same DNA reading frame, thus ruling out the possibility of a single base being inserted or deleted from the DNA sequence. The verification of small sequences throughout the protein sequence also indicates that no large portions of the protein have been removed after translation. ^

Genetic and functional analyses of cell division proteins FtsZ and FtsA in Escherichia coli

In the current model for bacterial cell division, the FtsZ protein forms a ring that marks the division plane, creating a cytoskeletal framework for the subsequent action of other essential division proteins such as FtsA and ZipA. The putative protein complex ultimately generates the division septum. The essential cell division protein FtsZ is a functional and structural homolog of eukaryotic tubulin, and like tubulin, FtsZ hydrolyzes GTP and self-assembles into protein filaments in a strictly GTP-dependent manner. FtsA shares sequence similarity with members of the ATPase superfamily that include actin, but its actual function remains unknown. To test the division model and elucidate functions of the division proteins, this dissertation primarily focuses on the analysis of FtsZ and FtsA in Escherichia coli. ^ By tagging with green fluorescent protein, we first demonstrated that FtsA also exhibits a ring-like structure at the potential division site. The localization of FtsA was dependent on functional FtsZ, suggesting that FtsA is recruited to the septum by the FtsZ ring. In support of this idea, we showed that FtsA and FtsZ directly interact. Using a novel E. coli in situ assay, we found that the FtsA-FtsZ interaction appears to be species-specific, although an interspecies interaction could occur between FtsA and FtsZ proteins from two closely related organisms. In addition, mutagenesis of FtsA revealed that no single domain is solely responsible for its septal localization or interaction with FtsZ. To explore the function of FtsA, we purified FtsA protein and demonstrated that it has ATPase activity. Furthermore, purified FtsA stimulates disassembly of FtsZ polymers in a sedimentation assay but does not affect GTP hydrolysis of FtsZ. This result suggests that in the cell, FtsA may function similarly in regulating dynamic instability of the FtsZ ring during the cell division process. ^ To elucidate the structure-function relationship of FtsZ, we carried out thorough genetic and functional analyses of the mutagenized FtsZ derivatives. Our results indicate that the conserved N-terminal domain of FtsZ is necessary and sufficient for FtsZ self-assembly and localization. Moreover, we discovered a critical role for an extreme C-terminal domain of FtsZ that consists of only 12 residues. Truncated FtsZ derivatives lacking this domain, though able to polymerize and localize, are defective in ring formation in vivo as well as interaction with FtsA and ZipA. Alanine scanning mutagenesis of this region pinpointed at least five residues necessary for the function of FtsZ. Studies of protein levels and protein-protein interactions suggested that these residues may be involved in regulating protein stability and/or FtsZ-FtsA interactions. Interestingly, two of the point mutants exhibited dominant-negative phenotypes. ^ In summary, results from this thesis work have provided additional support for the division machinery model and will contribute to a better understanding of the coordinate functions of FtsA and FtsZ in the cell division process. ^

RNA polymerase II large subunit degradation induced by ecteinascidin 743: Molecular characterization and subsequent rational investigation of antitumor mechanisms in cancers with clinical response

Ecteinascidin 743 (Et-743), which is a novel DNA minor groove alkylator with a unique spectrum of antitumor activity, is currently being evaluated in phase II/III clinical trials. Although the precise molecular mechanisms responsible for the observed antitumor activity are poorly understood, recent data suggests that post-translational modifications of RNA polymerase II Large Subunit (RNAPII LS) may play a central role in the cellular response to this promising anticancer agent. The stalling of an actively transcribing RNAPII LS at Et-743-DNA adducts is the initial cellular signal for transcription-coupled nucleotide excision repair (TC-NER). In this manner, Et-743 poisons TC-NER and produces DNA single strand breaks. Et-743 also inhibits the transcription and RNAPII LS-mediated expression of selected genes. Because the poisoning of TC-NER and transcription inhibition are critical components of the molecular response to Et-743 treatment, we have investigated if changes in RNAPII LS contribute to the disruption of these two cellular pathways. In addition, we have studied changes in RNAPII LS in two tumors for which clinical responses were reported in phase I/II clinical trials: renal cell carcinoma and Ewing's sarcoma. Our results demonstrate that Et-743 induces degradation of the RNAPII LS that is dependent on active transcription, a functional 26S proteasome, and requires functional TC-NER, but not global genome repair. Additionally, we have provided the first experimental data indicating that degradation of RNAPII LS might lead to the inhibition of activated gene transcription. A set of studies performed in isogenic renal carcinoma cells deficient in von Hippel-Lindau protein, which is a ubiquitin-E3-ligase for RNAPII LS, confirmed the central role of RNAPII LS degradation in the sensitivity to Et-743. Finally, we have shown that RNAPII LS is also degraded in Ewing's sarcoma tumors following Et-743 treatment and provide data to suggest that this event plays a role in decreased expression of the Ewing's sarcoma oncoprotein, EWS-Fli1. Altogether, these data implicate degradation of RNAPII LS as a critical event following Et-743 exposure and suggest that the clinical activity observed in renal carcinoma and Ewing's sarcoma may be mediated by disruption of molecular pathways requiring a fully functional RNAPII LS. ^

The association of previous induced abortion with the subsequent pregnancy complication of placenta previa

Placenta previa is alleged to be more common among women with a history of prior induced abortion. To investigate further whether there is a relationship between previous induced abortion and subsequent pregnancy complication of placenta previa, a matched case-comparison study was conducted comparing the reproductive histories of 256 women with placenta previa matched on age, date of delivery, and hospital with those of 256 women having normal deliveries and cesarean section deliveries without placental complications.^ Women with placenta previa had a twofold increase in the odds of having had one previous induced abortion (odds ratio 2.25) over women with no placental complications. Women with placenta previa and two or more previous induced abortions had a sevenfold increase in odds.^ The significant association of placenta previa and previous induced abortion remained after including gravida status, previous dilatation and curettage (D&C) status, previous spontaneous abortion, and race in a conditional logistic regression model. There is interaction between high gravidity and previous spontaneous abortion. Dilatation and curettage is associated with placenta previa primarily because women with abortion histories have also had a dilatation and curettage.^ Women who are seeking abortion and wish to have children later should be informed that there may be a longterm effect of developing placental complications in subsequent pregnancies. Women who have had at least one induced abortion or any dilatation and curettage procedure should be monitored carefully during any subsequent pregnancy for the risk of the complication of placenta previa. This knowledge should alert the physician or nurse-midwife to treat those women with a history of previous induced abortions as potential high risk pregnancies and could perhaps reduce maternal and fetal morbidity rates. ^

Low birthweight and the risk of developing subsequent high blood pressure and/or dyslipidemia in childhood

The association between birthweight and blood pressure (BP), and birthweight and serum lipid concentrations at age 7 through 11 years was examined in 1446 black and white children. The prevalence ratio (with 95% confidence interval) for being in the race-, sex- and age-specific upper decile of diastolic BP in children born with low birthweight (LBW, $<$2500 grams) versus children with birthweight $\geq$2500 grams was for black boys, 2.66 (1.24-5.70). In the other race-sex groups for diastolic BP, and in all race-sex groups for systolic BP this ratio did not differ from one. Among white boys with LBW, but not in the other race-sex groups, higher than expected percentages of subjects were in the highest decile group of triglyceride concentrations (0.01 $<$ p $<$ 0.05). The prevalence ratio was 2.42 (1.19-4.91). When prematures were excluded only more than expected white girls with LBW were in the highest decile group of triglyceride concentrations. The prevalence ratio was 3.23 (1.16-9.00). Prevalence ratios for triglyceride concentrations in black boys and girls, and for LDL/HDL-C ratio, cholesterol and VLDL-C concentrations in all race-sex groups were not different from one in analyses including and in those excluding prematures. Mean triglyceride concentrations stratified by tertiles of Quetelet Index, race and sex showed a strongly positive association between triglyceride concentrations and Quetelet Index, and in the upper tertile of the Quetelet Index an association between LBW and raised triglyceride concentrations. Multiple linear regression analyses showed that after adjusting for sex, race and age present Quetelet Index (p $<$ 0.001) is a much stronger predictor of systolic and diastolic BP, and also of LDL-C/HDL-C ratio and triglyceride concentrations in this age group than birthweight (p $>$ 0.05). Thus, an association between LBW and subsequent risk for elevated BP was confirmed for diastolic BP in black boys, but not for the other race-sex groups, and not for systolic BP in any group. This is the first study finding an association between LBW and elevated triglyceride concentrations in boys (white and black) and girls (white). A follow-up study to assess whether the findings can be confirmed at adult age is recommended. ^

Count data of germinated Gonyostomum semen cells and subsequent cell divisions

Colonization of new habitats through dispersal of phytoplankton cysts might be limited, if resident populations outcompete invaders during germination. We reciprocally transferred Gonyostomum semen (Raphidophyceae) cysts from three lakes into native and foreign waters originating from the respective habitats. Germination rate and germling growth were impacted by water origin, but there was no preference for native water. Gonyostomum semen's ability to germinate in different conditions might explain its expansion in northern Europe.

Hydrolysis of lignocellulosic material to sugars as feedstock for growing microorganisms

Los materiales lignocelulósicos son potenciales precursores de recursos bioenergéticos, por lo que sería interesante desarrollar tecnologías capaces de capturar su energía y utilizarla en el sector del transporte como combustibles. El azúcar contenido en los materiales lignocelulósicos puede ser liberado por medio de la hidrólisis y usado después por microorganismos. El objetivo del proyecto es encontrar un método de separación de la celulosa y la biomasa de chopo en monómeros de glucosa por medio de la hidrólisis. Para ello se han estudiado tres métodos de hidrólisis: la mecano-catálisis, utilizando diferentes tipos de molinos y caolinita como catalizador, la hidrólisis con líquidos iónicos, estudiando la viabilidad de los reactivos [C4mim+][I-] y [C4mim+][PF6-], y la hidrólisis ácida, usando HCl en concentraciones y temperaturas distintas para optimizar el proceso. En todos los casos se ha llevado a cabo un pretratamiento y se ha aplicado el método de TLC como verificación del proceso. Los tres métodos se han comparado y se ha desarrollado un método de correlación entre la mancha de TLC y la concentración del producto.

Influence of body weight of the pullets at hatch on egg production at the onset of the subsequent laying period

We studied the influence of pre-incubation weight of eggs (EW) laid by 24 wk-old brown laying breeders on egg production from 18 (start of egg production) to 22 wk of age (average egg production across EW treatments of 87.8%). The experiment consisted in 7 treatments based on the initial EW (47 to 53 g with 1 g difference between groups) Average BW of the extreme groups varied at hatching from 32.5 to 35.4 g, respectively. Feed intake, egg production, and egg weight were recorded weekly by replicate as well as for the entire experiment (18 to 22 wk of age). Hens were weighed by replicate at the beginning and at the end of the experiment. From these data, ADFI, egg production, egg weight, egg mass, feed conversion ratio per kilogram of eggs and per dozen of eggs, and BW gain were calculated by week and for the entire experiment. Also, the number of dirty, broken, and shell-less eggs was recorded daily by replicate in all eggs produced. Data were analyzed as a completely randomized design with 7 treatments differing in the initial pre-hatching EW. Effects of EW on the variables studied were partitioned into linear and quadratic components. EW did not affect the age at which pullets reached 50% egg production, cumulative egg production, or BW gain of the hens from 18 to 22 wk of age. Egg weight and the proportion of dirty, broken, and shell-less eggs were not affected by the BW of the pullets at hatching. In summary, small eggs (>47 g) laid by young, healthy laying breeders, can be used successfully to produce high quality pullets

Non-enzymatic and enzymatic hydrolysis of alkyl halides: A haloalkane dehalogenation enzyme evolved to stabilize the gas-phase transition state of an SN2 displacement reaction

The semiempirical PM3 method, calibrated against ab initio HF/6–31+G(d) theory, has been used to elucidate the reaction of 1,2-dichloroethane (DCE) with the carboxylate of Asp-124 at the active site of haloalkane dehalogenase of Xanthobacter autothropicus. Asp-124 and 13 other amino acid side chains that make up the active site cavity (Glu-56, Trp-125, Phe-128, Phe-172, Trp-175, Leu-179, Val-219, Phe-222, Pro-223, Val-226, Leu-262, Leu-263, and His-289) were included in the calculations. The three most significant observations of the present study are that: (i) the DCE substrate and Asp-124 carboxylate, in the reactive ES complex, are present as an ion-molecule complex with a structure similar to that seen in the gas-phase reaction of AcO− with DCE; (ii) the structures of the transition states in the gas-phase and enzymatic reaction are much the same where the structure formed at the active site is somewhat exploded; and (iii) the enthalpies in going from ground states to transition states in the enzymatic and gas-phase reactions differ by only a couple kcal/mol. The dehalogenase derives its catalytic power from: (i) bringing the electrophile and nucleophile together in a low-dielectric environment in an orientation that allows the reaction to occur without much structural reorganization; (ii) desolvation; and (iii) stabilizing the leaving chloride anion by Trp-125 and Trp-175 through hydrogen bonding.