Structure of Chlorosomes from the Green Filamentous Bacterium Chloroflexus aurantiacus

The green filamentous bacterium Chloroflexus aurantiacus employs chlorosomes as photosynthetic antennae. Chlorosomes contain bacteriochlorophyll aggregates and are attached to the inner side of a plasma membrane via a protein baseplate. The structure of chlorosomes from C. aurantiacus was investigated by using a combination of cryo-electron microscopy and X-ray diffraction and compared with that of Chlorobi species. Cryo-electron tomography revealed thin chlorosomes for which a distinct crystalline baseplate lattice was visualized in high-resolution projections. The baseplate is present only on one side of the chlorosome, and the lattice dimensions suggest that a dimer of the CsmA protein is the building block. The bacteriochlorophyll aggregates inside the chlorosome are arranged in lamellae, but the spacing is much greater than that in Chlorobi species. A comparison of chlorosomes from different species suggested that the lamellar spacing is proportional to the chain length of the esterifying alcohols. C. aurantiacus chlorosomes accumulate larger quantities of carotenoids under high-light conditions, presumably to provide photoprotection. The wider lamellae allow accommodation of the additional carotenoids and lead to increased disorder within the lamellae.Chlorosomes (5, 13) are light-harvesting complexes found in three different phyla of photosynthetic bacteria. Chloroflexus aurantiacus belongs to the filamentous anoxygenic phototrophs (green nonsulfur bacteria) comprising members of the phylum Chloroflexi. All members of the green sulfur bacteria (phylum Chlorobi) contain chlorosomes. Very recently, a phototropic chlorosome-containing organism was found in the phylum Acidobacteria (9).Chlorosomes are oblong bodies attached to the inner side of the cytoplasmic membrane. A unique property of chlorosomes is that their main pigment, bacteriochlorophyll (BChl) c, d, or e, is organized in the form of an aggregate. A similar self-assembled aggregate can form in the absence of proteins and exhibits spectral and excitonic properties similar to those of pigments in the native chlorosomes (for a review, see reference 3). The BChl aggregates were suggested to form lamellar structures in chlorosomes of green sulfur bacteria with lamellar spacing between 2 and 3 nm, depending on the main BChl (BChl c or e) and the prevailing esterifying alcohol (38, 39). In this model, the lamellar layers are maintained by nonspecific hydrophobic interactions of the interdigitated esterifying alcohols, while the in-layer arrangement is mediated through specific interactions between the stacked chlorin rings. In BChl c-containing chlorosomes of Chlorobaculum tepidum (formerly Chlorobium tepidum), the lamellar system (spacing, ∼2 nm) often remains parallel for the whole length of the chlorosome (33, 38). In Chlorobaculum tepidum the lamellae exhibit considerable curvature, which was initially attributed to undulation (38), but recent end-on micrographs revealed a variety of curved lamellar structures, such as lamellar tubules or multilayered wraps, as well as undulations (33). Recently, when chlorosomes from a Chlorobaculum tepidum mutant with well-ordered BChl aggregates were used as a model for electron microscopy (EM) and nuclear magnetic resonance experiments, it was proposed that BChl aggregates form concentric nanotubes with the pigments arranged in helical spirals (14).In contrast, chlorosomes from BChl e-containing bacteria (e.g., Chlorobium phaeovibrioides) contain lamellar pigments that are organized into small domains with random orientations. It has been proposed that this arrangement improves the absorption of photons with different polarizations (39). This, together with aggregation-induced enlargement of the oscillator strength, enables the bacteria to survive under extremely low-light conditions. At this point it is unclear whether these domains also exhibit a multilayer tubular arrangement. The data suggest that while the lamellar nature of BChl aggregates seems to be conserved, the higher-order structure of chlorosomes may be different in different species.Chlorosomes attach to the cytoplasmic membrane via a crystalline baseplate that contains BChl a and carotenoids and acts as an intermediary in energy transfer from the chlorosome to the reaction centers in the membrane. The baseplate consists of multiple CsmA protein subunits (5.7 kDa in C. aurantiacus and 6.2 kDa in Chlorobaculum tepidum [8, 27, 34, 40]). In addition to its role in energy transfer, it has been proposed that the baseplate is essential for the long-range order of lamellar BChl aggregates (2, 19). In addition to CsmA, chlorosomes of C. aurantiacus contain a number of other proteins, all of which are located in the chlorosome envelope (for a review, see reference 13).Recent progress in understanding chlorosome structure has been limited to the Chlorobi, and it is unclear whether there is similar organization in chlorosomes from bacteria belonging to different phyla, such as the Chloroflexi. While Chloroflexi also employ chlorosomes as the main light-harvesting complex, genetically they are only distantly related to the Chlorobi. Chlorobi and Chloroflexi also exhibit substantial differences in the photosynthetic apparatus. The average size of chlorosomes from C. aurantiacus, the model organism of the Chloroflexi, has been reported to be smaller (100 by 30 by 15 nm) than the average size of chlorosomes from the Chlorobi (150 to 200 by 50 by 20 nm) (30, 32). C. aurantiacus chlorosomes contain a single homologue of BChl c (8-ethyl,12-methyl) (16) and several secondary homologues that harbor different esterifying alcohols. The main esterifying alcohol (stearol) and the minor secondary homologues have longer chains than the prevailing alcohol in Chlorobaculum tepidum (farnesol) (11, 16, 22).Carotenoids are thought to play important light-harvesting and protective roles in chlorosomes (10, 13, 26, 36, 37). These hydrophobic molecules were shown to partition into the apolar space between the chlorin planes together with the aliphatic chains of the esterifying alcohols (39), and they also contribute to the hydrophobic driving force during assembly (1, 20). C. aurantiacus exhibits much greater variability of the carotenoid/BChl molar ratio than the Chlorobi. This ratio was observed to increase at most 1.4-fold in the Chlorobi species studied, even if the light intensity was increased more than 2 orders of magnitude (from 0.1 to 50 microeinsteins m⁻² s⁻¹) (6, 7). However, when there was a moderate change in the light intensity (from 400 to 2,000 lx [41] or from 44 to 127 microeinsteins m⁻² s⁻¹ [22]), C. aurantiacus exhibited a robust increase (fivefold) in the carotenoid content. As a result, the carotenoid content can reach levels of approximately one carotenoid molecule per two BChl molecules (41). Thus, a C. aurantiacus chlorosome seems to be able to accumulate significantly more carotenoids than the average Chlorobaculum tepidum chlorosome, which exhibits about one carotenoid molecule per 10 BChl molecules (7, 39).In the present work we examined the overall structure, pigment arrangement, and composition of C. aurantiacus chlorosomes using cryo-electron tomography, X-ray scattering, and quantitative pigment analysis. C. aurantiacus chlorosomes appear to be thin with a distinct two-dimensional baseplate protein array. Our results also demonstrate that BChl c aggregates are lamellar, suggesting that this is a universal feature of chlorosome structure. The greater lamellar spacing is due to the longer esterifying alcohols and allows accommodation of more carotenoids.     

Parvovirus nonstructural protein 2 interacts with chromatin-regulating cellular proteins

Autonomous parvoviruses encode at least two nonstructural proteins, NS1 and NS2. While NS1 is linked to important nuclear processes required for viral replication, much less is known about the role of NS2. Specifically, the function of canine parvovirus (CPV) NS2 has remained undefined. Here we have used proximity-dependent biotin identification (BioID) to screen for nuclear proteins that associate with CPV NS2. Many of these associations were seen both in noninfected and infected cells, however, the major type of interacting proteins shifted from nuclear envelope proteins to chromatin-associated proteins in infected cells. BioID interactions revealed a potential role for NS2 in DNA remodeling and damage response. Studies of mutant viral genomes with truncated forms of the NS2 protein suggested a change in host chromatin accessibility. Moreover, further studies with NS2 mutants indicated that NS2 performs functions that affect the quantity and distribution of proteins linked to DNA damage response. Notably, mutation in the splice donor site of the NS2 led to a preferred formation of small viral replication center foci instead of the large coalescent centers seen in wild-type infection. Collectively, our results provide insights into potential roles of CPV NS2 in controlling chromatin remodeling and DNA damage response during parvoviral replication.     

Patterns of MADS-box gene expression mark flower-type development in Gerbera hybrida (Asteraceae)

Background  

The inflorescence of the cut-flower crop Gerbera hybrida (Asteraceae) consists of two principal flower types, ray and disc, which form a tightly packed head, or capitulum. Despite great interest in plant morphological evolution and the tractability of the gerbera system, very little is known regarding genetic mechanisms involved in flower type specification. Here, we provide comparative staging of ray and disc flower development and microarray screening for differentially expressed genes, accomplished via microdissection of hundreds of coordinately developing flower primordia.     

Endotoxemia is associated with an adverse metabolic profile

Our aim was to analyze whether endotoxemia, i.e. translocation of LPS to circulation, is reflected in the serum metabolic profile in a general population and in participants with cardiometabolic disorders. We investigated three Finnish cohorts separately and in a meta-analysis (n = 7178), namely population-based FINRISK97, FinnTwin16 consisting of young adult twins, and Parogene, a random cohort of cardiac patients. Endotoxemia was determined as serum LPS activity and metabolome by an NMR platform. Potential effects of body mass index (BMI), smoking, metabolic syndrome (MetS), and coronary heart disease (CHD) status were considered. Endotoxemia was directly associated with concentrations of VLDL, IDL, LDL, and small HDL lipoproteins, VLDL particle diameter, total fatty acids (FA), glycoprotein acetyls (GlycA), aromatic and branched-chain amino acids, and Glc, and inversely associated with concentration of large HDL, diameters of LDL and HDL, as well as unsaturation degree of FAs. Some of these disadvantageous associations were significantly stronger in smokers and subjects with high BMI, but did not differ between participants with different CHD status. In participants with MetS, however, the associations of endotoxemia with FA parameters and GlycA were particularly strong. The metabolic profile in endotoxemia appears highly adverse, involving several inflammatory characters and risk factors for cardiometabolic disorders.     

Crystal structures of Streptococcus pyogenes Dpr reveal a dodecameric iron-binding protein with a ferroxidase site

DNA-binding protein from starved cells (Dps)-like proteins are key factors involved in oxidative stress protection in bacteria. They bind and oxidize iron, thus preventing the formation of harmful reactive oxygen species that can damage biomolecules, particularly DNA. Dps-like proteins are composed of 12 identical subunits assembled in a spherical structure with a hollow central cavity. The iron oxidation occurs at 12 intersubunit sites located at dimer interfaces. Streptococcus pyogenes Dps-like peroxide resistance protein (Dpr) has been previously found to protect the catalase-lacking S. pyogenes bacterium from oxidative stress. We have determined the crystal structure of S. pyogenes Dpr, the second Dpr structure from a streptococcal bacterium, in iron-free and iron-bound forms at 2.0- and 1.93-Å resolution, respectively. The iron binds to well-conserved sites at dimer interfaces and is coordinated directly to Asp77 and Glu81 from one monomer, His50 from a twofold symmetry-related monomer, a glycerol molecule, and a water molecule. Upon iron binding, Asp77 and Glu81 change conformation. Site-directed mutagenesis of active-site residues His50, His62, Asp66, Asp77, and Glu81 to Ala revealed a dramatic decrease in iron incorporation. A short helix at the N-terminal was found in a different position compared with other Dps-like proteins. Two types of pores were identified in the dodecamer. Although the N-terminal pore was found to be similar to that of other Dps-like proteins, the C-terminal pore was found to be blocked by bulky Tyr residues instead of small residues present in other Dps-like proteins.     

Modelling spatial patterns in host-associated microbial communities

Microbial communities exhibit spatial structure at different scales, due to constant interactions with their environment and dispersal limitation. While this spatial structure is often considered in studies focusing on free-living environmental communities, it has received less attention in the context of host-associated microbial communities or microbiota. The wider adoption of methods accounting for spatial variation in these communities will help to address open questions in basic microbial ecology as well as realize the full potential of microbiome-aided medicine. Here, we first overview known factors affecting the composition of microbiota across diverse host types and at different scales, with a focus on the human gut as one of the most actively studied microbiota. We outline a number of topical open questions in the field related to spatial variation and patterns. We then review the existing methodology for the spatial modelling of microbiota. We suggest that methodology from related fields, such as systems biology and macro-organismal ecology, could be adapted to obtain more accurate models of spatial structure. We further posit that methodological developments in the spatial modelling and analysis of microbiota could in turn broadly benefit theoretical and applied ecology and contribute to the development of novel industrial and clinical applications.