Identifying Modules of Coexpressed Transcript Units and Their Organization of Saccharopolyspora erythraea from Time Series Gene Expression Profiles

BACKGROUND: The Saccharopolyspora erythraea genome sequence was released in 2007. In order to look at the gene regulations at whole transcriptome level, an expression microarray was specifically designed on the S. erythraea strain NRRL 2338 genome sequence. Based on these data, we set out to investigate the potential transcriptional regulatory networks and their organization. METHODOLOGY/PRINCIPAL FINDINGS: In view of the hierarchical structure of bacterial transcriptional regulation, we constructed a hierarchical coexpression network at whole transcriptome level. A total of 27 modules were identified from 1255 differentially expressed transcript units (TUs) across time course, which were further classified in to four groups. Functional enrichment analysis indicated the biological significance of our hierarchical network. It was indicated that primary metabolism is activated in the first rapid growth phase (phase A), and secondary metabolism is induced when the growth is slowed down (phase B). Among the 27 modules, two are highly correlated to erythromycin production. One contains all genes in the erythromycin-biosynthetic (ery) gene cluster and the other seems to be associated with erythromycin production by sharing common intermediate metabolites. Non-concomitant correlation between production and expression regulation was observed. Especially, by calculating the partial correlation coefficients and building the network based on Gaussian graphical model, intrinsic associations between modules were found, and the association between those two erythromycin production-correlated modules was included as expected. CONCLUSIONS: This work created a hierarchical model clustering transcriptome data into coordinated modules, and modules into groups across the time course, giving insight into the concerted transcriptional regulations especially the regulation corresponding to erythromycin production of S. erythraea. This strategy may be extendable to studies on other prokaryotic microorganisms

The silicalite(MFI)/p-nitroaniline system. I. Location of the sorbed molecules at medium and high pore-fillings. A study by X-ray powder diffraction,

Structural investigation of the silicalite(MFI)/np-nitroaniline system by X-ray powder diffraction, establishes the existence of two single phased host/guest complexes corresponding to n=4 and 8 at medium and high pore-fillings respectively. Predictive studies by molecular mechanics simulations indicate that the pNAN molecules are located at the channel-intersections (for n=4) or in the elliptic channel-sections of the MFI topology (for n=8). 29Si solid-state mas NMR measurements show that the actual MFI framework symmetry of the silicalite.4pNAN complex is acentric Pn21a. Interpretation of the XRD pattern corresponding to the saturated silicalite. 8pNAN complex by Rietveld type structure refinements shows that two independent pNAN molecules are located on sites II (zig-zag channel sections) and sites III (straight channel sections). The van der Waals type interactions between the sorbed molecules take place at the channel-intersections (sites I). These sites are not occupied by extra-framework species. This is in agreement with the commensurability criterion already observed in several MFI/sorbate systems

Crystallographic Determination of the Positions of the Copper Cations in Zeolite MFI

International audienceCopper-exchanged Cu-MFI (Cu-ZSM-5) materials have been prepared by reacting H-MFI samples with 0.1 M Cu(II) acetate solutions. Interpretation (Rietveld method) of X-ray powder diffraction (XRPD) profiles corresponding to two fully dehydrated Cu-MFI phases, reveals the presence of several independent extra framework Cu centers. In H1.04Cu(I)1.19Cu(II)0.51MFI and H1.99Cu(I)2.37Cu(II)0.00MFI, four and five Cu cations are located, respectively. In these two phases, the Cu1/Cu2/Cu2'/Cu3/Cu3' populations are 0.0/1.07/0.02/0.17/0.45 and 0.18/1.12/0.44/0.20/0.50 per unit cell (uc), respectively. Cu2 is the most populated one. The shortest distances between copper sites and framework oxygen atoms involve the Cu1, Cu2, and Cu2' sites (Cu-O in the 1.99-2.32 Å range). The Cu1, Cu3, and Cu3' sites are trapped in secondary five and six ring channel sections of the MFI framework. Cu2 and Cu2' are very close to the 10-membered rings of the straight channel sections. One or both of these cations, which are immediately accessible to guest molecules, appear to be the prime candidates for the catalytically active sites in copper-exchanged MFI

Hydrated Cs+-Exchanged MFI Zeolites: Location of Extraframework Species in CsxHyMFI·zH2O Phases from X-ray Powder Diffraction and Differential Molar Adsorption Calorimetry

International audienceThe locations and populations of extraframework species in zeolitic Cs-exchanged H-MFI materials have recently been reported both in several fully dehydrated phases (J. Phys. Chem. B 2006, 110, 97-106) and in hydrated Cs6.6H0.3MFI·zH2O (1.5 < z < 28) samples (J. Phys. Chem. B 2006, 110, 13741-13752). The present paper extends our study to more general compositions, i.e., CsxHyMFI·zH2O phases spanning the range 0.7 < x < 7.7, 0.3 < y < 5.3 and 4 < z < 32. Structural information is obtained from Rietveld refinements of laboratory X-ray powder diffraction data collected at room temperature (RT, 22 or 26 C). We discovered that flushing fully hydrated CsxHyMFI·zH2O samples with a stream of dinitrogen (N2) gas corresponds to a rather strong isothermal water desorption effect. This effect is intimately correlated with the origin (synthesis method, postsynthesis treatments, and defect concentration) of the Cs-exchanged sample. Special attention is focused on the Cs2.3H1.1MFI·24H2O sample, for which high precision differential molar adsorption calorimetry data corresponding to its complete hydration process exist. In order to be able to interpret the observed water adsorption heats, we had to take several correlations into account: those existing between the Si/Al ratio and the (H,Li,Na,Cs)/uc cationic contents versus water loadings, in addition to the specific interactions between the cations or protons with aromatics as benzene or p-xylene. It is shown that in the 0-4.5 Al/uc range the maximum water/uc content, in all of the investigated H-MFI samples, is strictly proportional to the Al/uc values (about 8.5 water molecules per Al/uc). In most cation exchanged samples, this value is significantly different: it is either lower (e.g., Na and Cs) or higher (e.g., Li). In the case of p-xylene sorbed in fully dehydrated H-MFI materials (0 < H/uc < 4.5), all samples adsorb about eight molecules/uc, whereas the presence of extraframework cations lowers dramatically this sorption capacity. It is shown that the crystallinity of a ZSM-5 zeolite might be conveniently estimated by simply inspecting the XRPD profile corresponding to the p-xylene saturated parent H-MFI phase. In this work, it is shown how calorimetric data can be exploited to complement crystal structure results and detect subtle sorbent/sorbate interactions on the molecular level, which cannot be revealed by Rietveld-type powder diffraction profile structure refinements alone. The influence of structural defects (essentially -OH silanol groups attached to Si/Al framework atoms) on the observed adsorption heats is particularly pronounced. The host/guest interactions, observed at very low water loadings for the Cs2.3H1.1MFI/water system, are estimated by computer simulations (molecular mechanics (MM) calculations)