The Phaeodactylum genome reveals the evolutionary history of diatom genomes

Diatoms are photosynthetic secondary endosymbionts found throughout marine and freshwater environments, and are believed to be responsible for around one-fifth of the primary productivity on Earth. The genome sequence of the marine centric diatom Thalassiosira pseudonana was recently reported, revealing a wealth of information about diatom biology. Here we report the complete genome sequence of the pennate diatom Phaeodactylum tricornutum and compare it with that of T. pseudonana to clarify evolutionary origins, functional significance and ubiquity of these features throughout diatoms. In spite of the fact that the pennate and centric lineages have only been diverging for 90 million years, their genome structures are dramatically different and a substantial fraction of genes ( approximately 40%) are not shared by these representatives of the two lineages. Analysis of molecular divergence compared with yeasts and metazoans reveals rapid rates of gene diversification in diatoms. Contributing factors include selective gene family expansions, differential losses and gains of genes and introns, and differential mobilization of transposable elements. Most significantly, we document the presence of hundreds of genes from bacteria. More than 300 of these gene transfers are found in both diatoms, attesting to their ancient origins, and many are likely to provide novel possibilities for metabolite management and for perception of environmental signals. These findings go a long way towards explaining the incredible diversity and success of the diatoms in contemporary oceans.     

Correlation of structural elements and infectivity of the HET-s prion

Prions are believed to be infectious, self-propagating polymers of otherwise soluble, host-encoded proteins. This concept is now strongly supported by the recent findings that amyloid fibrils of recombinant prion proteins from yeast, Podospora anserina and mammals can induce prion phenotypes in the corresponding hosts. However, the structural basis of prion infectivity remains largely elusive because acquisition of atomic resolution structural properties of amyloid fibrils represents a largely unsolved technical challenge. HET-s, the prion protein of P. anserina, contains a carboxy-terminal prion domain comprising residues 218-289. Amyloid fibrils of HET-s(218-289) are necessary and sufficient for the induction and propagation of prion infectivity. Here, we have used fluorescence studies, quenched hydrogen exchange NMR and solid-state NMR to determine the sequence-specific positions of amyloid fibril secondary structure elements of HET-s(218-289). This approach revealed four beta-strands constituted by two pseudo-repeat sequences, each forming a beta-strand-turn-beta-strand motif. By using a structure-based mutagenesis approach, we show that this conformation is the functional and infectious entity of the HET-s prion. These results correlate distinct structural elements with prion infectivity.     

Proteomic and molecular investigations revealed that Acidithiobacillus caldus adopts multiple strategies for adaptation to NaCl stress

Acidithiobacillus caldus plays an important role in commercial bioleaching.To understand how NaCl stress adaptation occurs in A.caldus,we grew A.caldus strain SM-1 in media containing high NaCl concentrations.SM-1 grew at concentrations of up to 1.0-mol L~(-1)NaCl,but growth was severely inhibited at higher concentrations.Proteomic analysis showed that SM-1 used multiple strategies to respond to NaCl stress.In addition to several heatshock proteins,enzymes involved in proline biosynthesis increased under NaCl stress.In addition,two DNA-binding proteins and a third protein of unknown function(Atc_(1291)),which was subsequently identified as a putative single-stranded DNA-binding protein,were up-regulated in the presence of NaCl stress.These DNA-binding proteins might play a role in response to osmotic stress.Atc_(1291)was cloned and expressed in Escherichia coli.Surprisingly,we found that E.coli BL21/pET28a-atc_(1291)grew to higher cell densities than E.coli BL21/pET28a,regardless of NaCI stress.Homologs to Atc_(1291)were identified in several groups of Proleohacleria.The role of Atc_(1291)in enhancing cell growth needs further investigation.