Global warming and planetary health: An open letter to the WHO from scientific and indigenous people urging for paleo-microbiology studies.

This article, written by a collective of international researchers and worldwide representatives of indigenous populations, is an open letter to the WHO, based on the latest elements from the scientific literature, and the latest climatological data. It takes stock of the health consequences of global warming, and urges research organizations to take an interest in infectious agents formerly stored in the layers of ground (frozen or not) and now mobilized, then released from a distance.

Distribution patterns of microbial communities in ultramafic landscape: a metagenetic approach highlights the strong relationships between diversity and environmental traits.

Microbial species richness and assemblages across ultramafic ecosystems were investigated to assess the relationship between their distributional patterns and environmental traits. The structure of microorganism communities in the Koniambo massif, New Caledonia, was investigated using a metagenetic approach correlated with edaphic and floristic factors. Vegetation cover and soil properties significantly shaped the large phylogenetic distribution of operational taxonomic unit within microbial populations, with a mean per habitat of 3.477 (±317) for bacteria and 712 (±43) for fungi. Using variance partitioning, we showed that the effect of aboveground vegetation was the most significant descriptor for both bacterial and fungal communities. The floristic significant predictors explained 43% of the variation for both the bacterial and fungal community structures, while the edaphic significant predictors explained only 32% and 31% of these variations, respectively. These results confirm the previous hypothesis that the distribution of microorganisms was more structured by the vegetation cover rather than the edaphic characteristics and that microbial diversity is not limited in ultramafic ecosystems.

Mimivirus.

Acanthamoeba polyphaga Mimivirus, the first representative and prototype member of the Mimiviridae, is the latest addition to the menagerie of lesser-known big DNA viruses. Due to the size of its particle--a fiber-covered icosahedral protein capsid with a diameter of 0.7 microm--Mimivirus was initially mistaken for an intracellular parasitic bacteria. Its 1.2-Mb genome sequence was then found to encode more than 900 proteins, many of them associated with functions never before encountered in a virus, such as four aminoacyl-tRNA synthetases. The finding of Mimivirus-encoded central components of the protein translation apparatus thought to be the signature of cellular organisms revived the debate about the origin of DNA viruses and their possible role in the emergence of the eukaryotic cell. Despite the many features making it unique in the viral world, Mimivirus is nevertheless phylogenetically close to other large DNA viruses, such as phycodnaviruses and iridoviruses, and most likely share a common ancestry with all nucleocytoplasmic large DNA viruses. Postgenomic studies have now started in various laboratories, slowly shedding some light on the physiology of the largest and most complex virus isolated to date. This chapter summarizes our present knowledge on Mimivirus.

Phylogeny.fr: robust phylogenetic analysis for the non-specialist.

Phylogenetic analyses are central to many research areas in biology and typically involve the identification of homologous sequences, their multiple alignment, the phylogenetic reconstruction and the graphical representation of the inferred tree. The Phylogeny.fr platform transparently chains programs to automatically perform these tasks. It is primarily designed for biologists with no experience in phylogeny, but can also meet the needs of specialists; the first ones will find up-to-date tools chained in a phylogeny pipeline to analyze their data in a simple and robust way, while the specialists will be able to easily build and run sophisticated analyses. Phylogeny.fr offers three main modes. The 'One Click' mode targets non-specialists and provides a ready-to-use pipeline chaining programs with recognized accuracy and speed: MUSCLE for multiple alignment, PhyML for tree building, and TreeDyn for tree rendering. All parameters are set up to suit most studies, and users only have to provide their input sequences to obtain a ready-to-print tree. The 'Advanced' mode uses the same pipeline but allows the parameters of each program to be customized by users. The 'A la Carte' mode offers more flexibility and sophistication, as users can build their own pipeline by selecting and setting up the required steps from a large choice of tools to suit their specific needs. Prior to phylogenetic analysis, users can also collect neighbors of a query sequence by running BLAST on general or specialized databases. A guide tree then helps to select neighbor sequences to be used as input for the phylogeny pipeline. Phylogeny.fr is available at: http://www.phylogeny.fr/

Rickettsia felis, from culture to genome sequencing.

Rickettsia felis has been recently cultured in XTC2 cells. This allows production of enough bacteria to create a genomic bank and to sequence it. The chromosome of R. felis is longer than that of previously sequenced rickettsiae and it possess 2 plasmids. Microscopically, this bacterium exhibits two forms of pili: one resembles a conjugative pilus and another forms hair-like projections that may play a role in pathogenicity. R. felis also exhibits several copies of ankyrin-repeat genes and tetratricopeptide encoding gene that are specifically linked to pathogenic host-associated bacteria. It also contains toxin-antitoxin system encoding genes that are extremely rare in intracellular bacteria and may be linked to plasmid maintenance.

Annotation of bacterial genomes using improved phylogenomic profiles.

MOTIVATION: Phylogenomic profiling is a large-scale comparative genomic method used to infer protein function from evolutionary information first described in a binary form by Pellegrini et al. (1999). Here, we propose improvements of this approach including the use of normalized Blastp bit scores, a normalization of the matrix of profiles to take into account the evolutionary distances between bacteria, the definition of a phylogenomic neighborhood based on continuous pairwise distances between genes and an original annotation procedure including the computation of a p-value for each functional assignment. RESULTS: The method presented here increases the number of Ecocyc enzymes identified as being evolutionarily related by about 25% with respect to the original binary form (absent/present) method. The fraction of 'false' positives is shown to be smaller than 20%. Based on their phylogenomic relationships, genes of unknown function can then be automatically related to annotated genes. Each gene annotation predicted is associated with a p-value, i.e. its probability to be obtained by chance. The validity of this method was extensively tested on a large set of genes of known function using the MultiFun database. We find that 50% of 3122 function attributions that can be made at a p-value level of 10(-11) correspond to the actual gene annotation. The method can be readily applied to any newly sequenced microbial genome. In contrast to earlier work on the same topic, our approach avoids the use of arbitrary cut-off values, and provides a reliability estimate of the functional predictions in form of p-values.

Recent advances in computational genomics.

In the post-genomic era, the new discipline of functional genomics is now facing the challenge of associating a function (as well as estimating its relevance to industrial applications) to about 100,000 microbial, plant or animal genes of known sequence but unknown function. Besides the design of databases, computational methods are increasingly becoming intimately linked with the various experimental approaches. Consequently, bioinformatics is rapidly evolving into independent fields addressing the specific problems of interpreting i) genomic sequences, ii) protein sequences and 3D-structures, as well as iii) transcriptome and macromolecular interaction data. It is thus increasingly difficult for the biologist to choose the computational approaches that perform best in these various areas. This paper attempts to review the most useful developments of the last 2 years.

Mechanisms of evolution in Rickettsia conorii and R. prowazekii.

Rickettsia conorii is an obligate intracellular bacterium that causes Mediterranean spotted fever in humans. We determined the 1,268,755-nucleotide complete genome sequence of R. conorii, containing 1374 open reading frames. This genome exhibits 804 of the 834 genes of the previously determined R. prowazekii genome plus 552 supplementary open reading frames and a 10-fold increase in the number of repetitive elements. Despite these differences, the two genomes exhibit a nearly perfect colinearity that allowed the clear identification of different stages of gene alterations with gene remnants and 37 genes split in 105 fragments, of which 59 are transcribed. A 38-kilobase sequence inversion was dated shortly after the divergence of the genus.

[Transcriptome analysis in cancerology: bioinformatics aspects]. / Analyse du transcriptome en carcérologie: aspects bio-informatiques.

Recent technological advances (e.g. various DNA arrays and chips) allow the measurement of expression level (mRNA abundance) for thousand of genes simultaneously, over multiple conditions or time. Initially developed and tested on model systems such as yeast or in vitro cell line cultures, these techniques have recently begun to be applied to the analysis of human cancers. Initial results are promising, and large-scale gene expression profiling is now expected to become a clinical tool for better tumour identification, prognosis, and optimal treatment design. It is thus important that clinicians become familiar with the theoretical principles underlying the interpretation of gene expression profiles as used in three different contexts: gene discovery, tumour class prediction, and molecular diagnosis. This is the purpose of the present article.

Escherichia coli ykfE ORFan gene encodes a potent inhibitor of C-type lysozyme.

The complete nucleotide sequences of over 37 microbial and three eukaryote genomes are already publicly available, and more sequencing is in progress. Despite this accumulation of data, newly sequenced microbial genomes continue to reveal up to 50% of functionally uncharacterized "anonymous" genes. A majority of these anonymous proteins have homologues in other organisms, whereas the rest exhibit no clear similarity to any other sequence in the data bases. This set of unique, apparently species-specific, sequences are referred to as ORFans. The biochemical and structural analysis of ORFan gene products is of both evolutionary and functional interest. Here we report the cloning and expression of Escherichia coli ORFan ykfE gene and the functional characterization of the encoded protein. Under physiological conditions, the protein is a homodimer with a strong affinity for C-type lysozyme, as revealed by co-purification and co-crystallization. Activity measurements and fluorescence studies demonstrated that the YkfE gene product is a potent C-type lysozyme inhibitor (K(i) approximately 1 nm). To denote this newly assigned function, ykfE has now been registered under the new gene name Ivy (inhibitor of vertebrate lysozyme) at the E. coli genetic stock center.

Identification of odorant receptors from the Alpine marmot (Marmota marmota).

Alpine Marmots (Marmota marmota) are a good model to study intraspecific chemical communication among mammals. This species has been subjected to several behavioural and biochemical studies regarding both their scent-marking behaviour by cheek-rubbing, and the chemical composition of their glandular secretions. However, no molecular study has been undertaken until today on proteins from the olfactory epithelium possibly implicated in chemical perception. In this study, we identified, to our knowledge for the first time, some olfatory receptors from this wild rodent. Starting with olfactory epithelium of an Alpine Marmot, and by mean of reverse transcriptase polymerase chain reaction technique (RT-PCR), we isolated fourteen partial sequences that exhibited a high degree of homology (45-92%) with olfactory receptors from other vertebrates. Conserved identities and structural features clearly defined these Alpine Marmot sequences as members of the seven transmembrane domain olfactory receptors. All sequences were observed as belonging to known olfactory receptor families and were classified into ten subfamilies of the tetrapods OR class. Finally, Northern blot analysis revealed specific expression of these sequences in the Alpine Marmot olfactory epithelium tissue.

Crystallization and preliminary crystallographic study of b0220, an 'ORFan' protein of unknown function from Escherichia coli.

Newly sequenced microbial genomes continue to reveal up to 50% functionally uncharacterized 'anonymous' genes. A significant fraction of these anonymous ORFs does not exhibit any sequence similarity to any protein in the databases and constitutes a set of unique sequences, denoted 'ORFans'. The structure determination of ORFan proteins is both of evolutionary and functional interest. Here, the first crystallization of an Escherichia coli ORFan gene product, the 157 amino-acid b0220 protein, is reported. The crystals belong to the trigonal space group P3 or P3(1), with unit-cell parameters a = b = 47.2, c = 88.4 A. There are two molecules in the asymetric unit. Frozen crystals diffract to 1.6 A resolution using synchrotron radiation. Phasing was performed using multiwavelength anomalous dispersion (MAD) on the selenomethionine-substituted b0220 protein.

Selfish DNA in protein-coding genes of Rickettsia.

Rickettsia conorii, the aetiological agent of Mediterranean spotted fever, is an intracellular bacterium transmitted by ticks. Preliminary analyses of the nearly complete genome sequence of R. conorii have revealed 44 occurrences of a previously undescribed palindromic repeat (150 base pairs long) throughout the genome. Unexpectedly, this repeat was found inserted in-frame within 19 different R. conorii open reading frames likely to encode functional proteins. We found the same repeat in proteins of other Rickettsia species. The finding of a mobile element inserted in many unrelated genes suggests the potential role of selfish DNA in the creation of new protein sequences.

Structural and genomic correlates of hyperthermostability.

While most organisms grow at temperatures ranging between 20 and 50 degrees C, many archaea and a few bacteria have been found capable of withstanding temperatures close to 100 degrees C, or beyond, such as Pyrococcus or Aquifex. Here we report the results of two independent large scale unbiased approaches to identify global protein properties correlating with an extreme thermophile lifestyle. First, we performed a comparative proteome analyses using 30 complete genome sequences from the three kingdoms. A large difference between the proportions of charged versus polar (noncharged) amino acids was found to be a signature of all hyperthermophilic organisms. Second, we analyzed the water accessible surfaces of 189 protein structures belonging to mesophiles or hyperthermophiles. We found that the surfaces of hyperthermophilic proteins exhibited the shift already observed at the genomic level, i.e. a proportion of solvent accessible charged residues strongly increased at the expense of polar residues. The biophysical requirements for the presence of charged residues at the protein surface, allowing protein stabilization through ion bonds, is therefore clearly imprinted and detectable in all genome sequences available to date.

Reverse transcriptase-polymerase chain reaction validation of 25 "orphan" genes from Escherichia coli K-12 MG1655.

Despite the accumulation of sequence information sampling from a broad spectrum of phyla, newly sequenced genomes continue to reveal a high proportion (50%-30%) of "uncharacterized" genes, including a significant number of strictly "orphan" genes, i.e., putative open reading frames (ORFs) without any resemblance to previously determined protein-coding sequences. Most genes found in databases have only been predicted by computer methods and have never been experimentally validated. Although theoretical evolutionary arguments support the reality of genes when homologs are found in a variety of distant species, this is not the case for orphan genes. Here, we report the direct reverse transcriptase-polymerase chain reaction assay of 25 strictly orphan ORFs of Escherichia coli. Two growth conditions, exponential and stationary phases, were tested. Transcripts were identified for a total of 19 orphan genes, with 2 genes found to be expressed in only one of the two growth conditions. Our results suggest that a vast majority of E. coli ORFs presently annotated as "hypothetical" correspond to bona fide genes. By extension, this implies that randomly occurring "junk" ORFs have been actively counter selected during the evolution of the dense E. coli genome.

Patterns of variant polyadenylation signal usage in human genes.

The formation of mature mRNAs in vertebrates involves the cleavage and polyadenylation of the pre-mRNA, 10-30 nt downstream of an AAUAAA or AUUAAA signal sequence. The extensive cDNA data now available shows that these hexamers are not strictly conserved. In order to identify variant polyadenylation signals on a large scale, we compared over 8700 human 3' untranslated sequences to 157,775 polyadenylated expressed sequence tags (ESTs), used as markers of actual mRNA 3' ends. About 5600 EST-supported putative mRNA 3' ends were collected and analyzed for significant hexameric sequences. Known polyadenylation signals were found in only 73% of the 3' fragments. Ten single-base variants of the AAUAAA sequence were identified with a highly significant occurrence rate, potentially representing 14.9% of the actual polyadenylation signals. Of the mRNAs, 28.6% displayed two or more polyadenylation sites. In these mRNAs, the poly(A) sites proximal to the coding sequence tend to use variant signals more often, while the 3'-most site tends to use a canonical signal. The average number of ESTs associated with each signal type suggests that variant signals (including the common AUUAAA) are processed less efficiently than the canonical signal and could therefore be selected for regulatory purposes. However, the position of the site in the untranslated region may also play a role in polyadenylation rate.

EST databases as multi-conditional gene expression datasets.

Large-scale expression data, such as that generated by hybridization to microarrays, is potentially a rich source of information on gene function and regulation. By clustering genes according to their expression profiles, groups of genes involved in the same pathways or sharing common regulatory mechanisms may be identified. Publicly-available EST collections are a largely unexplored source of expression data. We previously used a sample of rice ESTs to generate 'digital expression profiles' by counting the frequency of tags for different genes sequenced from different cDNA libraries. A simple statistical test was used to associate genes or cDNA libraries having similar expression profiles. Here we further validate this approach using larger samples of ESTs from the UniGene projects (clustered human, mouse and rat ESTs). Our results show that genes clustered on the basis of expression profile may represent genes implicated in similar pathways or coding for different subunits of multi-component enzyme complexes. In addition we suggest that comparison of clusters from different species, may be useful for confirmation or prediction of orthologs.