Katia Duquesne

Bacterial immobilization and oxidation of arsenic in acid mine drainage (Carnoulès creek, France).

The acid waters (pH=2.73-3.37) originating from the Carnoulès mine tailings contain high dissolved concentrations of arsenic (1-3.5 mmol l(-1)) and iron (20-40 mmol l(-1)). At the outlet, arsenite predominates. During the first 30 m of downflow, 20-60% is removed by coprecipitation with Fe(III). This process results from bacterially mediated As- and Fe-oxidation. The precipitation rates in the creek depend on the oxygen concentration in spring water and are lower during the dry summer period when the anoxic character of the spring water inhibits the activity of oxidizing bacteria. Ex situ experiments show that the presence of bacteria-rich precipitates increases the As- and Fe-removal rates. Three strains of bacteria promoting the oxidation of As have been isolated, and two of them have the characteristics of Thiomonas ynys1. The third strain, which is not identified yet, also catalyzes the oxidation of Fe.

Rusticyanin gene expression of Acidithiobacillus ferrooxidans ATCC 33020 in sulfur- and in ferrous iron media

Among the bioleaching microorganisms, Acidithiobacillus ferrooxidans is one of the most studied. The bioleaching and bioremediation properties of this obligate chemolithoautotroph originate from its energetic metabolism. Even though several electron-transfer proteins have been identified, there is no convincing argument to tell in which respiratory chain these proteins are involved. Rusticyanin is the A. ferrooxidans redox protein which has been the most extensively studied. This periplasmic blue copper protein is widely considered to play an important role in ferrous oxidation mainly because of its higher concentration in iron-grown cells compared to sulfur-grown cells. To gain more insight on which conditions rusticyanin is synthesized, we have studied the rus gene expression all along the growth in iron- and sulfur-supplemented media at the translational level by immunodetection and at the transcriptional level by Northern blot analyses and quantitative RT-PCR experiments. In the A. ferrooxidans ATCC 33020 strain, rusticyanin was present in ferrous iron-grown cells throughout all the growth phases. In sulfur-grown cells, rusticyanin was present only during the exponential phase, but to a lower level than in iron conditions, and disappeared at the stationary phase. In cultures switched from sulfur- to iron-medium, there was a correlation between iron oxidation and the rusticyanin level. Strikingly, the de novo synthesis of rusticyanin was observed in sulfur-grown cells. All these data agree with a control on rusticyanin level in the cells depending on the electron donor present in the medium and on the growth phase in sulfur-grown cells. Furthermore, they are consistent with the involvement of rusticyanin in iron oxidation.

Forces guiding assembly of light-harvesting complex 2 in native membranes

Interaction forces of membrane protein subunits are of importance in their structure, assembly, membrane insertion, and function. In biological membranes, and in the photosynthetic apparatus as a paradigm, membrane proteins fulfill their function by ensemble actions integrating a tight assembly of several proteins. In the bacterial photosynthetic apparatus light-harvesting complexes 2 (LH2) transfer light energy to neighboring tightly associated core complexes, constituted of light-harvesting complexes 1 (LH1) and reaction centers (RC). While the architecture of the photosynthetic unit has been described, the forces and energies assuring the structural and functional integrity of LH2, the assembly of LH2 complexes, and how LH2 interact with the other proteins in the supramolecular architecture are still unknown. Here we investigate the molecular forces of the bacterial LH2 within the native photosynthetic membrane using atomic force microscopy single-molecule imaging and force measurement in combination. The binding between LH2 subunits is fairly weak, of the order of kBT, indicating the importance of LH2 ring architecture. In contrast LH2 subunits are solid with a free energy difference of 90 kBT between folded and unfolded states. Subunit α-helices unfold either in one-step, α- and β-polypeptides unfold together, or sequentially. The unfolding force of transmembrane helices is approximately 150 pN. In the two-step unfolding process, the β-polypeptide is stabilized by the molecular environment in the membrane. Hence, intermolecular forces influence the structural and functional integrity of LH2.

High‐resolution architecture of the outer membrane of the Gram‐negative bacteria Roseobacter denitrificans

The outer membrane of Gram‐negative bacteria protects the cell against bactericidal substances. Passage of nutrients and waste is assured by outer membrane porins, beta‐barrel transmembrane channels. While atomic structures of several porins have been solved, so far little is known on the supramolecular structure of the outer membrane. Here we present the first high‐resolution view of a bacterial outer membrane gently purified maintaining remnants of peptidoglycan on the perisplasmic surface. Atomic force microscope images of outer membrane fragments of the size of ∼50% of the bacterial envelope revealed that outer membrane porins are by far more densely packed than previously assumed. Indeed the outer membrane is a molecular sieve rather than a membrane. Porins cover ∼70% of the membrane surface and form locally regular lattices. The potential role of exposed aromatic residues in the formation of the supramolecular assembly is discussed. Finally, we present first structural data of the outer membrane porin from the marine Gram‐negative bacteria Roseobacter denitrificans, and we perform a sequence alignment with porins of known structure.

Membrane Protein Solubilization

A critical step in any in vitro analysis of membrane proteins is the solubilization of the membrane to extract the protein of interest in an active form to obtain an aqueous solution containing the membrane protein complexed with detergents and lipids in a form suitable for purification and further analysis. This process is particularly delicate as the aim is to maximally disrupt the lipid components of the membrane while putting the protein components in an un-natural detergent environment without perturbing them. Looked at this way, it is remarkable that it ever works. Although the process is difficult and hard to master, an increasing number of membrane proteins have been successfully solubilized in active forms, allowing some general principles to be established that we illustrate in the method developed in this chapter.

Antenna mixing in photosynthetic membranes from Phaeospirillum molischianum

We have investigated the adaptation of the light-harvesting system of the photosynthetic bacterium Phaeospirillum molischianum (DSM120) to very low light conditions. This strain is able to respond to changing light conditions by differentially modulating the expression of a family of puc operons that encode for peripheral light-harvesting complex (LH2) polypeptides. This modulation can result in a complete shift between the production of LH2 complexes absorbing maximally near 850 nm to those absorbing near 820 nm. In contradiction to prevailing wisdom, analysis of the LH2 rings found in the photosynthetic membranes during light adaptation are shown to have intermediate spectral and electrostatic properties. By chemical cross-linking and mass-spectrometry we show that individual LH2 rings and subunits can contain a mixture of polypeptides derived from the different operons. These observations show that polypeptide synthesis and insertion into the membrane are not strongly coupled to LH2 assembly. We show that the light-harvesting complexes resulting from this mixing could be important in maintaining photosynthetic efficiency during adaptation.

Quinone Pathways in Entire Photosynthetic Chromatophores of Rhodospirillum photometricum

In photosynthetic organisms, membrane pigment-protein complexes [light-harvesting complex 1 (LH1) and light-harvesting complex 2 (LH2)] harvest solar energy and convert sunlight into an electrical and redox potential gradient (reaction center) with high efficiency. Recent atomic force microscopy studies have described their organization in native membranes. However, the cytochrome (cyt) bc(1) complex remains unseen, and the important question of how reduction energy can efficiently pass from core complexes (reaction center and LH1) to distant cyt bc(1) via membrane-soluble quinones needs to be addressed. Here, we report atomic force microscopy images of entire chromatophores of Rhodospirillum photometricum. We found that core complexes influence their molecular environment within a critical radius of approximately 250 A. Due to the size mismatch with LH2, lipid membrane spaces favorable for quinone diffusion are found within this critical radius around cores. We show that core complexes form a network throughout entire chromatophores, providing potential quinone diffusion pathways that will considerably speed the redox energy transfer to distant cyt bc(1). These long-range quinone pathway networks result from cooperative short-range interactions of cores with their immediate environment.

Draft Genome Sequence of the Purple Photosynthetic Bacterium Phaeospirillum molischianum DSM120, a Particularly Versatile Bacterium

Here we present the draft genome sequence of the versatile and adaptable purple photosynthetic bacterium Phaeospirillum molischianum DSM120. This study advances the understanding of the adaptability of this bacterium, as well as the differences between the Phaeospirillum and Rhodospirillum genera.

Shotgun Genome Sequence of the Large Purple Photosynthetic Bacterium Rhodospirillum photometricum DSM122

Here, we present the shotgun genome sequence of the purple photosynthetic bacterium Rhodospirillum photometricum DSM122. The photosynthetic apparatus of this bacterium has been particularly well studied by microscopy. The knowledge of the genome of this oversize bacterium will allow us to compare it with the other purple bacterial organisms to follow the evolution of the photosynthetic apparatus.

Molecular Origins and Consequences of High-800 LH2 in Roseobacter denitrificans

Roseobacter denitrificans is a marine bacterium capable of using a wide variety of different metabolic schemes and in particular is an anoxygenic aerobic photosynthetic bacterium. In the work reported here we use a deletion mutant that we have constructed to investigate the structural origin of the unusual High-800 light-harvesting complex absorption in this bacterium. We suggest that the structure is essentially unaltered when compared to the usual nonameric complexes but that a change in the environment of the C(13:1) carbonyl group is responsible for the change in spectrum. We tentatively relate this change to the presence of a serine residue in the α-polypeptide. Surprisingly, the low spectral overlap between the peripheral and core light-harvesting systems appears not to compromise energy collection efficiency too severely. We suggest that this may be at the expense of maintaining a low antenna size.