Mycocerosic acid synthase exemplifies the architecture of reducing polyketide synthases

Polyketide synthases (PKSs) are biosynthetic factories that produce natural products with important biological and pharmacological activities1, 2, 3. Their exceptional product diversity is encoded in a modular architecture. Modular PKSs (modPKSs) catalyse reactions colinear to the order of modules in an assembly line3, whereas iterative PKSs (iPKSs) use a single module iteratively as exemplified by fungal iPKSs (fiPKSs)3. However, in some cases non-colinear iterative action is also observed for modPKSs modules and is controlled by the assembly line environment4, 5. PKSs feature a structural and functional separation into a condensing and a modifying region as observed for fatty acid synthases6. Despite the outstanding relevance of PKSs, the detailed organization of PKSs with complete fully reducing modifying regions remains elusive. Here we report a hybrid crystal structure of Mycobacterium smegmatis mycocerosic acid synthase based on structures of its condensing and modifying regions. Mycocerosic acid synthase is a fully reducing iPKS, closely related to modPKSs, and the prototype of mycobacterial mycocerosic acid synthase-like7, 8 PKSs. It is involved in the biosynthesis of C20–C28 branched-chain fatty acids, which are important virulence factors of mycobacteria9. Our structural data reveal a dimeric linker-based organization of the modifying region and visualize dynamics and conformational coupling in PKSs. On the basis of comparative small-angle X-ray scattering, the observed modifying region architecture may be common also in modPKSs. The linker-based organization provides a rationale for the characteristic variability of PKS modules as a main contributor to product diversity. The comprehensive architectural model enables functional dissection and re-engineering of PKSs

The structure of a polyketide synthase bimodule core

Polyketide synthases (PKSs) are predominantly microbial biosynthetic enzymes. They assemble highly potent bioactive natural products from simple carboxylic acid precursors. The most versatile families of PKSs are organized as assembly lines of functional modules. Each module performs one round of precursor extension and optional modification, followed by directed transfer of the intermediate to the next module. While enzymatic domains and even modules of PKSs are well understood, the higher-order modular architecture of PKS assembly lines remains elusive. Here, we visualize a PKS bimodule core using cryo-electron microscopy and resolve a two-dimensional meshwork of the bimodule core formed by homotypic interactions between modules. The sheet-like organization provides the framework for efficient substrate transfer and for sequestration of trans-acting enzymes required for polyketide production

Reflected Light from Sand Grains in the Terrestrial Zone of a Protoplanetary Disk

We show that grains have grown to ~mm size (sand sized) or larger in the terrestrial zone (within ~3 AU) of the protoplanetary disk surrounding the 3 Myr old binary star KH 15D. We also argue that the reflected light in the system reaches us by back scattering off the far side of the same ring whose near side causes the obscuration.Comment: 22 pages, 5 figures. To be published in Nature, March 13, 2008. Contains a Supplemen

Nitrogen hydrides in the cold envelope of IRAS16293-2422

Nitrogen is the fifth most abundant element in the Universe, yet the gas-phase chemistry of N-bearing species remains poorly understood. Nitrogen hydrides are key molecules of nitrogen chemistry. Their abundance ratios place strong constraints on the production pathways and reaction rates of nitrogen-bearing molecules. We observed the class 0 protostar IRAS16293-2422 with the heterodyne instrument HIFI, covering most of the frequency range from 0.48 to 1.78~THz at high spectral resolution. The hyperfine structure of the amidogen radical o-NH2 is resolved and seen in absorption against the continuum of the protostar. Several transitions of ammonia from 1.2 to 1.8~THz are also seen in absorption. These lines trace the low-density envelope of the protostar. Column densities and abundances are estimated for each hydride. We find that NH:NH2:NH3=5:1:300. {Dark clouds chemical models predict steady-state abundances of NH2 and NH3 in reasonable agreement with the present observations, whilst that of NH is underpredicted by more than one order of magnitude, even using updated kinetic rates. Additional modelling of the nitrogen gas-phase chemistry in dark-cloud conditions is necessary before having recourse to heterogen processes

The T Tauri star RY Tau as a case study of the inner regions of circumstellar dust disks

We study the inner region of the circumstellar disk around the TTauri star RY Tau. Our aim is to find a physical description satisfying the available interferometric data, obtained with the mid-infrared interferometric instrument at the Very Large Telescope Interferometer, as well as the spectral energy distribution. We also compare the findings with the results of similar studies, including those of intermediate-mass stars. Our analysis is done within the framework of a passive circumstellar disk, which is optionally supplemented by the effects of accretion and an added envelope. To achieve a more consistent and realistic model, we used our continuum transfer code MC3D. In addition, we studied the shape of the 10um silicate emission feature in terms of the underlying dust population, both for single-dish and for interferometric measurements. We show that a modestly flaring disk model with accretion can explain both the observed spectral energy distribution and the mid-infrared visibilities obtained with the mid-infrared infrared instrument. We found an interesting ambiguity: a circumstellar active disk model with an added envelope, and a lower accretion rate than in the active disk model without envelope, could represent the observations equally as well. This type of model with the envelope should be considered a viable alternative in future models of other TTauri stars. The approach of a disk with a puffed-up inner rim wall and the influence of a stellar companion is also discussed. From the study of the silicate emission feature we see evidence for dust evolution in a TTauri star, with a decreasing fraction of small amorphous and an increasing fraction of crystalline particles closer to the star.Comment: 19 pages, 23 figures; accepted by Astronomy & Astrophysic

First detection of ND in the solar-mass protostar IRAS16293-2422

In the past decade, much progress has been made in characterising the processes leading to the enhanced deuterium fractionation observed in the ISM and in particular in the cold, dense parts of star forming regions such as protostellar envelopes. Very high molecular D/H ratios have been found for saturated molecules and ions. However, little is known about the deuterium fractionation in radicals, even though simple radicals often represent an intermediate stage in the formation of more complex, saturated molecules. The imidogen radical NH is such an intermediate species for the ammonia synthesis in the gas phase. Herschel/HIFI represents a unique opportunity to study the deuteration and formation mechanisms of such species, which are not observable from the ground. We searched here for the deuterated radical ND in order to determine the deuterium fractionation of imidogen and constrain the deuteration mechanism of this species. We observed the solar-mass Class 0 protostar IRAS16293-2422 with the heterodyne instrument HIFI as part of the Herschel key programme CHESS (Chemical HErschel Surveys of Star forming regions). The deuterated form of the imidogen radical ND was detected and securely identified with 2 hyperfine component groups of its fundamental transition in absorption against the continuum background emitted from the nascent protostar. The 3 groups of hyperfine components of its hydrogenated counterpart NH were also detected in absorption. We derive a very high deuterium fractionation with an [ND]/[NH] ratio of between 30 and 100%. The deuterium fractionation of imidogen is of the same order of magnitude as that in other molecules, which suggests that an efficient deuterium fractionation mechanism is at play. We discuss two possible formation pathways for ND, by means of either the reaction of N+ with HD, or deuteron/proton exchange with NH.Comment: Accepted; To appear in A&A Herschel/HIFI Special Issu

Ortho-to-para ratio of interstellar heavy water

Despite the low elemental deuterium abundance in the Galaxy, enhanced molecular D/H ratios have been found in the environments of low-mass star forming regions, and in particular the Class 0 protostar IRAS 16293-2422. The CHESS (Chemical HErschel Surveys of Star forming regions) Key Program aims at studying the molecular complexity of the interstellar medium. The high sensitivity and spectral resolution of the HIFI instrument provide a unique opportunity to observe the fundamental 1,1,1 - 0,0,0 transition of the ortho-D2O molecule, inaccessible from the ground, and to determine the ortho-to-para D2O ratio. We have detected the fundamental transition of the ortho-D2O molecule at 607.35 GHz towards IRAS 16293-2422. The line is seen in absorption with a line opacity of 0.62 +/- 0.11 (1 sigma). From the previous ground-based observations of the fundamental 1,1,0 - 1,0,1 transition of para-D2O seen in absorption at 316.80 GHz we estimate a line opacity of 0.26 +/- 0.05 (1 sigma). We show that the observed absorption is caused by the cold gas in the envelope of the protostar. Using these new observations, we estimate for the first time the ortho to para D2O ratio to be lower than 2.6 at a 3 sigma level of uncertainty, to be compared with the thermal equilibrium value of 2:1.Comment: 5 pages, 5 figures, accepted the A&A HIFI Special Issue as a lette

The distribution of water in the high-mass star-forming region NGC 6334I

We present observations of twelve rotational transitions of H2O-16, H2O-18, and H2O-17 toward the massive star-forming region NGC 6334 I, carried out with Herschel/HIFI as part of the guaranteed time key program Chemical HErschel Surveys of Star forming regions (CHESS). We analyze these observations to obtain insights into physical processes in this region. We identify three main gas components (hot core, cold foreground, and outflow) in NGC 6334 I and derive the physical conditions in these components. The hot core, identified by the emission in highly excited lines, shows a high excitation temperature of 200 K, whereas water in the foreground component is predominantly in the ortho- and para- ground states. The abundance of water varies between 4 10^-5 (outflow) and 10^-8 (cold foreground gas). This variation is most likely due to the freeze-out of water molecules onto dust grains. The H2O-18/H2O-17 abundance ratio is 3.2, which is consistent with the O-18/O-17 ratio determined from CO isotopologues. The ortho/para ratio in water appears to be relatively low 1.6(1) in the cold, quiescent gas, but close to the equilibrium value of three in the warmer outflow material (2.5(0.8)).Comment: 7 pages, 3 figures, accepted by A&

Herschel/HIFI observations of spectrally resolved methylidyne signatures toward the high-mass star-forming core NGC6334I

In contrast to extensively studied dense star-forming cores, little is known about diffuse gas surrounding star-forming regions. We study molecular gas in the high-mass star-forming region NGC6334I, which contains diffuse, quiescent components that are inconspicuous in widely used molecular tracers such as CO. We present Herschel/HIFI observations of CH toward NGC6334I observed as part of the CHESS key program. HIFI resolves the hyperfine components of its J=3/2-1/2 transition, observed in both emission and absorption. The CH emission appears close to the systemic velocity of NGC6334I, while its measured linewidth of 3 km/s is smaller than previously observed in dense gas tracers such as NH3 and SiO. The CH abundance in the hot core is 7 10^-11, two to three orders of magnitude lower than in diffuse clouds. While other studies find distinct outflows in, e.g., CO and H2O toward NGC6334I, we do not detect outflow signatures in CH. To explain the absorption signatures, at least two absorbing components are needed at -3.0 and +6.5 km/s with N(CH)=7 10^13 and 3 10^13 cm^-2. Two additional absorbing clouds are found at +8.0 and 0.0 km/s, both with N(CH)=2 10^13 cm^-2. Turbulent linewidths for the four absorption components vary between 1.5 and 5.0 km/s in FWHM. We constrain physical properties of our CH clouds by matching our CH absorbers with other absorption signatures. In the hot core, molecules such as H2O and CO trace gas that is heated and dynamically influenced by outflow activity, whereas CH traces more quiescent material. The four CH absorbers have column densities and turbulent properties consistent with diffuse clouds: two are located near NGC6334, and two are unrelated foreground clouds. Local density and dynamical effects influence the chemical composition of physical components of NGC6334, causing some components to be seen in CH but not in other tracers, and vice versa.Comment: Accepted by A&A Letters; 5 pages, 1 figure; v2: minor textual and typographical change

The CHESS chemical Herschel surveys of star forming regions: Peering into the protostellar shock L1157-B1. I. Shock chemical complexity

We present the first results of the unbiased survey of the L1157-B1 bow shock, obtained with HIFI in the framework of the key program Chemical Herschel surveys of star forming regions (CHESS). The L1157 outflow is driven by a low-mass Class 0 protostar and is considered the prototype of the so-called chemically active outflows. The bright blue-shifted bow shock B1 is the ideal laboratory for studying the link between the hot (around 1000-2000 K) component traced by H2 IR-emission and the cold (around 10-20 K) swept-up material. The main aim is to trace the warm gas chemically enriched by the passage of a shock and to infer the excitation conditions in L1157-B1. A total of 27 lines are identified in the 555-636 GHz region, down to an average 3 sigma level of 30 mK. The emission is dominated by CO(5-4) and H2O(110-101) transitions, as discussed by Lefloch et al. (2010). Here we report on the identification of lines from NH3, H2CO, CH3OH, CS, HCN, and HCO+. The comparison between the profiles produced by molecules released from dust mantles (NH3, H2CO, CH3OH) and that of H2O is consistent with a scenario in which water is also formed in the gas-phase in high-temperature regions where sputtering or grain-grain collisions are not efficient. The high excitation range of the observed tracers allows us to infer, for the first time for these species, the existence of a warm (> 200 K) gas component coexisting in the B1 bow structure with the cold and hot gas detected from ground