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Keratinases are exciting proteolytic enzymes that display the capability to degrade the insoluble protein keratin. These enzymes are produced by diverse microorganisms belonging to the Eucarya, Bacteria, and Archea domains. Keratinases display a great diversity in their biochemical and biophysical properties. Most keratinases are optimally active at neutral to alkaline pH and 40-60°C, but examples of microbial keratinolysis at alkalophilic and thermophilic conditions have been well documented. Several keratinases have been associated to the subtilisin family of serine-type proteases by analysis of their protein sequences. Studies with specific substrates and inhibitors indicated that keratinases are often serine or metalloproteases with preference for hydrophobic and aromatic residues at the P1 position. Keratinolytic enzymes have several current and potential applications in agroindustrial, pharmaceutical, and biomedical fields. Their use in biomass conversion into biofuels may address the increasing concern on energy conservation and recycling.

The recent discovery of diverse very large viruses, such as the mimivirus, has fostered a profusion of hypotheses positing that these viruses define a new domain of life together with the three cellular ones (Archaea, Bacteria and Eucarya). It has also been speculated that they have played a key role in the origin of eukaryotes as donors of important genes or even as the structures at the origin of the nucleus. Thanks to the increasing availability of genome sequences for these giant viruses, those hypotheses are amenable to testing via comparative genomic and phylogenetic analyses. This task is made very difficult by the high evolutionary rate of viruses, which induces phylogenetic artefacts, such as long branch attraction, when inadequate methods are applied. It can be demonstrated that phylogenetic trees supporting viruses as a fourth domain of life are artefactual. In most cases, the presence of homologues of cellular genes in viruses is best explained by recurrent horizontal gene transfer from cellular hosts to their infecting viruses and not the opposite. Today, there is no solid evidence for the existence of a viral domain of life or for a significant implication of viruses in the origin of the cellular domains.

The acquisitions of mitochondria and plastids were important events in the evolution of the eukaryotic cell, supplying it with compartmentalized bioenergetic and biosynthetic factories. Ancient invasions by eubacteria through symbiosis more than a billion years ago initiated these processes. Advances in geochemistry, molecular phylogeny, and cell biology have offered insight into complex molecular events that drove the evolution of endosymbionts into contemporary organelles. In losing their autonomy, endosymbionts lost the bulk of their genomes, necessitating the evolution of elaborate mechanisms for organelle biogenesis and metabolite exchange. In the process, symbionts acquired many host-derived properties, lost much of their eubacterial identity, and were transformed into extraordinarily diverse organelles that reveal complex histories that we are only beginning to decipher.

Most cultivated and characterized eukaryotes can be confidently assigned to one of eight major groups. After a few false starts, we are beginning to resolve relationships among these major groups as well. However, recent developments are radically revising this picture again, particularly (i) the discovery of the likely antiquity and taxonomic diversity of ultrasmall eukaryotes, and (ii) a fundamental rethinking of the position of the root. Together these data suggest major gaps in our understanding simply of what eukaryotes are or, when it comes to the tree, even which end is up.

Key Points Despite early assumptions, gene order in eukaryotes is not random. In all well-studied genomes, genes of similar and/or coordinated expression tend to be linked. Understanding the clustering of related genes is crucial to our understanding of chromosome function and evolution. Clusters are not only found for co-expressed genes, but are also found for genes with products that are involved in the same metabolic pathway or that are associated in protein–protein complexes. There seems to be a correlation between the physical size of co-expression clusters and organism complexity, ranging from a few kilobases in yeast to several megabases in mammals. Many small clusters might be the result of shared regulatory elements. Co-expression (or co-suppression) of genes in many larger clusters can result from histone modifications, which spread down a chromosome until they meet a boundary element. Positioning of genes within the three-dimensional chromatin structure might promote or repress expression. In addition, some clusters might promote the association of genes with nuclear structures (for example, the nucleolus or SC-35 domains). The initial formation of clusters might be unrelated to expression regulation; for example, genetic linkage might be favoured for interacting loci. A theory of the evolution of genome organization is needed. This must incorporate mechanisms of genome rearrangement, mechanisms of gene-expression control and the evolutionary forces that result from different interactions between loci. In eukaryotes, unlike in bacteria, gene order has typically been assumed to be random. However, the first statistically rigorous analyses of complete genomes, together with the availability of abundant gene-expression data, have forced a paradigm shift: in every complete eukaryotic genome that has been analysed so far, gene order is not random. It seems that genes that have similar and/or coordinated expression are often clustered. Here, we review this evidence and ask how such clusters evolve and how this relates to mechanisms that control gene expression.

Gene expression in eukaryotes requires several multi-component cellular machines. Each machine carries out a separate step in the gene expression pathway, which includes transcription, several pre-messenger RNA processing steps and the export of mature mRNA to the cytoplasm. Recent studies lead to the view that, in contrast to a simple linear assembly line, a complex and extensively coupled network has evolved to coordinate the activities of the gene expression machines. The extensive coupling is consistent with a model in which the machines are tethered to each other to form 'gene expression factories' that maximize the efficiency and specificity of each step in gene expression.

We report a ribosomal tag pyrosequencing study of the phylogenetic diversity of Archaea , Bacteria and Eucarya over a depth profile at the Hawaii Ocean Time-Series Station, ALOHA. The V9 region of the SSU rRNA gene was amplified from samples representing the epi- (10 m), meso- (800 m) and bathy- (4400 m) pelagia. The primers used are expected to amplify representatives of ∼80% of known phylogenetic diversity across all three domains. Comparisons of unique sequences revealed a remarkably low degree of overlap between communities at each depth. The 444 147 sequence tags analyzed represented 62 975 unique sequences. Of these, 3707 (5.9%) occurred at two depths, and only 298 (0.5%) were observed at all three depths. At this level of phylogenetic resolution, Bacteria diversity decreased with depth but was still equivalent to that reported elsewhere for different soil types. Archaea diversity was highest in the two deeper samples. Eucarya observations and richness estimates are almost one order of magnitude higher than any previous marine microbial Eucarya richness estimates. The associations of many Eucarya sequences with putative parasitic organisms may have significant impacts on our understanding of the mechanisms controlling host population density and diversity, and point to a more significant role for microbial Eucarya in carbon flux through the microbial loop. We posit that the majority of sequences detected from the deep sea that have closest matches to sequences from non-pelagic sources are indeed native to the marine environment, and are possibly responsible for key metabolic processes in global biogeochemical cycles.

Patterns in the spatial distribution of organisms provide important information about mechanisms that regulate the diversity of life and the complexity of ecosystems 1 , 2 . Although microorganisms may comprise much of the Earth's biodiversity 3 , 4 and have critical roles in biogeochemistry and ecosystem functioning 5 , 6 , 7 , little is known about their spatial diversification. Here we present quantitative estimates of microbial community turnover at local and regional scales using the largest spatially explicit microbial diversity data set available (> 10 6 sample pairs). Turnover rates were small across large geographical distances, of similar magnitude when measured within distinct habitats, and did not increase going from one vegetation type to another. The taxa–area relationship of these terrestrial microbial eukaryotes was relatively flat (slope z = 0.074) and consistent with those reported in aquatic habitats 8 , 9 . This suggests that despite high local diversity, microorganisms may have only moderate regional diversity. We show how turnover patterns can be used to project taxa–area relationships up to whole continents. Taxa dissimilarities across continents and between them would strengthen these projections. Such data do not yet exist, but would be feasible to collect.

Key Points The analysis of unstable kernel phenotypes in maize led to the discovery and characterization of active class 2 DNA transposable elements (TEs). These active elements are a very small fraction of the TEs found in plant genomes. Access to all or part of the genomic sequence of an organism has led to the development of new techniques to analyse the life cycle of TEs and their interactions with the 'host' genome. Two types of element — miniature inverted-repeat transposable elements (MITEs) and long terminal repeat (LTR) retrotransposons — predominate in plant genomes. MITEs are non-autonomous class 2 elements, but most can now be connected with two superfamilies of transposases: Tc1/ mariner and PIF/ harbinger . LTR retrotransposons are the single largest component of plant genomes and are responsible for the recent genome expansion in some plants. Despite evidence of recent activity, TEs that are present in high copy numbers in plant genomes are almost universally found to be defective and/or epigenetically silenced. Some LTR retrotransposons are transcriptionally activated by various biotic and abiotic stresses. Availability of mutant backgrounds that are deficient in epigenetic regulation offers the promise of activating previously silenced TEs and revealing new facets of their biology. Transposable elements are the single largest component of the genetic material of most eukaryotes. The recent availability of large quantities of genomic sequence has led to a shift from the genetic characterization of single elements to genome-wide analysis of enormous transposable-element populations. Nowhere is this shift more evident than in plants, in which transposable elements were first discovered and where they are still actively reshaping genomes.

Based on (i) an analysis of the regularities in the standard genetic code and (ii) comparative genomics of the anticodon modification machinery in the three branches of life, we derive the tRNA set and its anticodon modifications as it was present in LUCA. Previously we proposed that an early ancestor of LUCA contained a set of 23 tRNAs with unmodified anticodons that was capable of translating all 20 amino acids while reading 55 of the 61 sense codons of the standard genetic code (SGC). Here we use biochemical and genomic evidence to derive that LUCA contained a set of 44 or 45 tRNAs containing 2 or 3 modifications while reading 59 or 60 of the 61 sense codons. Subsequent tRNA modifications occurred independently in the Bacteria and Eucarya, while the Archaea have remained quite close to the tRNA set as it was present in LUCA.