Antoine Danchin

..The discussion ends with the central question of evolvability of artificial constructs and to suggest that combining in vivo Synthetic Biology with biochemical reactors might be an efficient way forward...

..It has an urgent need to design novel antibiotics against staphylococci infections, especially those can kill cells embedded in biofilm...

..Acid resistance in E. coli is hierarchically controlled by numerous regulators among which are small noncoding RNAs (sncRNA)...

..Traditional investigations stress differences in gene content. We focused on conserved genes that have accumulated small mutation differences during the transition...

..The consequence is that genes acquired by horizontal transfer as well as viruses will tend to perpetuate in niches where they are functional, creating recurrent conditions for emergence of diseases...

..This permits living systems to accumulate information over generations, but has the drawback, in multicellular organisms, to open the door for immortalisation, leading to cancer...

..The paleome also possesses genes that enable information to accumulate in a ratchet-like process down the generations. The systems biology must include the dynamics of information creation in its future developments...

..This scenario of constraints imposed by efficient influx of metabolites provides us with a model that should be followed when constructing synthetic cells...

..Synthetic biology faces a dilemma: it will either implement the corresponding genes, and cells will evolve in an unpredictable manner, or omit them, and cells will age and have to be reconstructed periodically...

..We suggest that the program of life codes for processes meant to trap information which comes from the context provided by the environment of the machine...

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..The expression of the ytmI operon and the yhcL gene was regulated in response to sulfur availability, while the level of expression of the yckK gene remained low under all the conditions tested...

..However, genomes harbor two very different categories of genes: those genes present in a majority of organisms - persistent genes - and those present in very few organisms - rare genes...

..Transcriptome analysis of a delta cymR mutant and the wild-type strain also brought out significant changes in the expression level of a large set of genes related to stress response or to transition toward anaerobiosis...

..luminescens virulence. Our results also highlight the power of proteomic analysis for detecting unexpected links between different, concomitant processes in bacteria...

..The addition of O-acetyl-serine prevented the formation of this protein-DNA complex...

..As a consequence, the uvrY-deficient strain exhibited a decreased killing of insect cells and a reduced growth on insect cells culture, suggesting a UvrY role in the adaptation of P. luminescens inside the insect...

..These results, along with the G+C signature of the chromosomal region, support the existence of a fitness island for acid adaptation on the E. coli chromosome...

..In addition, we showed that H-NS positively affects motility via the flhDC master operon repression by RcsB. This substantiates the central role of RcsB in H-NS-mediated control of motility and acid stress resistance...

..coli. An ytqI mutant in B. subtilis shows impairment of growth in the absence of cysteine, a phenotype resembling that of a cysQ mutant in E. coli. Phylogenetic distribution of YtqI, Orn and CysQ supports bifunctionality of YtqI...

..The link between AstRS-dependent stationary-phase adaptation and phenotypic variation is discussed...

..Finally, we showed that the luxS-deficient strain had attenuated virulence against the lepidopteran Spodoptera littoralis. We concluded that AI-2 is involved mainly in early steps of insect invasion in P. luminescens...

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..A common motif, AT(A/T)ATTCCTAT, was found in the promoter region of the ytlI and lmo2352 genes. Deletion of part of this motif or the introduction of point mutations in this sequence confirmed its involvement in ytlI regulation...

..This suggests that CA is consumed via at least two separate pathways in P. luminescens: the biosynthesis of ST and a pathway involving the Hca and Mhp enzymes...

..We proposed a regulatory model in which the antisense RNA controlled the expression of the ubiG operon in cis via transcriptional interference at the ubiG locus...

..The expression of genes encoding transporters (yhcL, ytmJKLMN, and yxeMO) was high when the sulfur source was methionine or taurine and reduced when it was sulfate...

..Overall, despite a very high gene flow, genes co-exist in an organised genome...

..The transcriptome data also indicated that processes other than iron uptake might be involved in the cellular response to exogenous pyrophosphate or methylenediphosphonic acid...

..These results indicate that essentiality plays a fundamental role in the distribution of genes in most bacterial genomes...

..Other uptake systems are therefore present for these two compounds. In contrast, the Yus ABC transporter corresponds to the sole d-methionine uptake system. We propose to rename yusC, yusB and yusA as metN, metP and metQ, respectively...

..They should then be regarded as truly essential genes...

..subtilis is an epiphyte). This should permit investigators to make reliable inferences to prepare validation experiments in a variety of domains of bacterial growth and development as well as build up accurate phylogenies...

..Methionine sulfoxide reductases are enzymes able to regenerate methionine and restore protein function after oxidative damage...

..Further analysis suggests that RNA degradation, associated to the presence of iron, still plays a role in extant metabolism, including the evolution of genome structures...

..We propose an original model, supported by the determination of the intracellular concentrations of the different partners, by which CysK positively regulates CymR in sensing the bacterial cysteine pool...

..This leads to a twofold reduction in the global amount of Enzyme IIA(Glc), the adenylate cyclase activator, responsible for the decrease in adenylate cyclase activity observed in the hns crp strain...

..It is argued that a sizeable contribution to this effect comes from the dynamical compartimentalization induced by the recycling of tRNAs, leading to gene expression rates dependent on their genomic and expression context...

..Replication is a highly unsymmetrical process, and the presence of two polymerases is therefore not unexpected. Using comparative genomics, we explored whether other processes have evolved in parallel with each polymerase...

..coli and Acinetobacter proteins, the alpha-helical domain displays weaker intermolecular interactions in the Psychrobacter protein, which may account for the low thermal stability observed at 37 degrees C...

..The expression of hcaR was repressed in the absence of oxygen by the ArcA/ArcB two-component system...

..Moreover, newly identified insecticidal proteins may be effective alternatives for the control of insect pests...

..We conclude that, unlike in E. coli, degradation of nanoRNA is performed in a redundant fashion in B. subtilis...

..Finally, the presence of a similar regulatory region in several Gram-negative bacteria implies that this mechanism is largely conserved...

..They also indicate that when a control for this variable is included, essentiality plays no significant role in the rate of protein evolution in bacteria, as is the case in eukaryotes...

..coli cysQ mutant. Here, we show that SMU.1297 can complement an E. coli orn(-) mutant, suggesting that having both pAp-phosphatase and nanoRNase activity is a common feature of NrnA homologs...

..We show that the model is consistent with the asymmetric distribution of highly expressed genes and of stress response genes in Escherichia coli and Bacillus subtilis. The model offers a framework for interpreting data from genomics...

..Mg(2+)-regulated gene expression of pbgP1 was absent in the mutant and was restored when phoPQ was complemented in trans. This finding highlights the essential role played by PhoPQ in the virulence of an entomopathogen...

..A further problem is that most existing methods are optimized for Escherichia coli data sets; applying these methods to newly sequenced bacterial genomes may not result in an equivalent level of accuracy...

..The transport and binding of iron, sugars and amino acids were also affected and molecular chaperones were strongly down-regulated. A potential role for H-NS in phenotypic variation control is discussed...

..This is the first report of a regulator of some of the genes involved in cysteine biosynthesis in B. subtilis...

..From these results, we propose that pAp might be a physiological regulator of PARP-1 activity...

..H-NS regulates the acid stress resistance. The present study aimed to characterize the H-NS-dependent cascade governing the acid stress resistance pathways and to define the interplay between the different regulators...

..The importance of this carbapenem production in the ecology of P. luminescens is discussed...

..subtilis and E. coli enzymes...

..Our findings point to remarkable conservation of the connection between sulfur- and RNA metabolism between E.coli and humans...

..Here we show, however, that in Bacillus subtilis and Escherichia coli, essentiality (the transcript product), not expressiveness (the collision rate), selectively drives the biased gene distribution...

..ebi.ac.uk/chebi/). The newly annotated sequence is deposited at the International Nucleotide Sequence Data Collaboration with accession number AL009126.4...

..This bias is present throughout a given genome, both in coding and non-coding sequences. Until now this bias remained of unknown origin...

..Such rules could aid the understanding of common properties and essential differences corresponding to elusive functions, or of still unknown bacterial biotopes...

..Our results suggest that V. cholerae is able to sense a moderate decrease in pH and to modify accordingly its structure and physiology...

..The recent identification of novel activities in these organisms, stresses the (underestimated) importance of degradation of very short RNAs, as well as 5'-3' degradative processes in Bacteria...

..This hypothesis is discussed in terms of the relative geochemical distribution of Se and As...

..When methionine levels were limiting, the amount of the full-length transcript increased. These results substantiate a model of regulation by transcription antitermination...

..SubtiList is accessible at http://genolist.pasteur.fr/SubtiList/. Similar bacterial databases are accessible at http://genolist.pasteur.fr/...

..The enormous amount of genome sequence data asks for user-oriented databases to manage sequences and annotations. Queries must include search tools permitting function identification through exploration of related objects...

..Such a microbial mechanism of detoxification, which is possibly exploitable for bioremediation applications of contaminated sites, may have played a crucial role in the occupation of ancient ecological niches on earth...

..This suggests the existence of alternative mechanisms contributing to CpG deficiency in bacteria...

..A remarkable role of aromatic amino acids was uncovered. Expressed orphan proteins are enriched in these residues, suggesting that they might participate in a process of gain of function during evolution...

..Given the increasing biological relevance of secondary DNA structures, these findings should facilitate further studies on the evolution, dynamics and expression of the genetic information stored in bacterial genomes...

..We suggest that the higher energy cost and limited availability of G and C over A and T/U could be a basis for the understanding of these differences...

..Some allow identification of species-specific functions or localisation such as surface or exported proteins. Errors in genome annotations are also revealed by correspondence analysis, making it useful for quality control and correction...