Architecture of Burkholderia cepacia complex σ70 gene family: evidence of alternative primary and clade-specific factors, and genomic instability

<p>Abstract</p> <p>Background</p> <p>The <it>Burkholderia cepacia </it>complex (Bcc) groups bacterial species with beneficial properties that can improve crop yields or remediate polluted sites but can also lead to dramatic human clinical outcomes among cystic fibrosis (CF) or immuno-compromised individuals. Genome-wide regulatory processes of gene expression could explain parts of this bacterial duality. Transcriptional σ⁷⁰factors are components of these processes. They allow the reversible binding of the DNA-dependent RNA polymerase to form the holoenzyme that will lead to mRNA synthesis from a DNA promoter region. Bcc genome-wide analyses were performed to investigate the major evolutionary trends taking place in the σ⁷⁰family of these bacteria.</p> <p>Results</p> <p>Twenty σ⁷⁰paralogous genes were detected in the <it>Burkholderia cenocepacia </it>strain J2315 (<it>Bcen</it>-J2315) genome, of which 14 were of the ECF (extracytoplasmic function) group. Non-ECF paralogs were related to primary (<it>rpoD</it>), alternative primary, stationary phase (<it>rpoS</it>), flagellin biosynthesis (<it>fliA</it>), and heat shock (<it>rpoH</it>) factors. The number of σ⁷⁰genetic determinants among this genome was of 2,86 per Mb. This number is lower than the one of <it>Pseudomonas aeruginosa</it>, a species found in similar habitats including CF lungs. These two bacterial groups showed strikingly different σ⁷⁰family architectures, with only three ECF paralogs in common (<it>fecI</it>-like, <it>pvdS </it>and <it>algU</it>). <it>Bcen</it>-J2315 σ⁷⁰paralogs showed clade-specific distributions. Some paralogs appeared limited to the ET12 epidemic clone (<it>ecfA2</it>), particular Bcc species (<it>sigI</it>), the <it>Burkholderia </it>genus (<it>ecfJ</it>, <it>ecfF</it>, and <it>sigJ</it>), certain proteobacterial groups (<it>ecfA1</it>, <it>ecfC</it>, <it>ecfD</it>, <it>ecfE</it>, <it>ecfG</it>, <it>ecfL</it>, <it>ecfM </it>and <it>rpoS</it>), or were broadly distributed in the eubacteria (<it>ecfI</it>, <it>ecfK</it>, <it>ecfH</it>, <it>ecfB</it>, and <it>rpoD</it>-, <it>rpoH</it>-, <it>fliA</it>-like genes). Genomic instability of this gene family was driven by chromosomal inversion (<it>ecfA2</it>), recent duplication events (<it>ecfA </it>and <it>RpoD</it>), localized (<it>ecfG</it>) and large scale deletions (<it>sigI</it>, <it>sigJ</it>, <it>ecfC</it>, <it>ecfH</it>, and <it>ecfK</it>), and a phage integration event (<it>ecfE</it>).</p> <p>Conclusion</p> <p>The Bcc σ⁷⁰gene family was found to be under strong selective pressures that could lead to acquisition/deletion, and duplication events modifying its architecture. Comparative analysis of Bcc and <it>Pseudomonas aeruginosa </it>σ⁷⁰gene families revealed distinct evolutionary strategies, with the Bcc having selected several alternative primary factors, something not recorded among <it>P. aeruginosa </it>and only previously reported to occur among the actinobacteria.</p

L'infiltration des eaux pluviales en milieu urbain : conséquences sur l'écosystème aquatique souterrain

International audienceL'urbanisation induit une imperméabilisation des sols et une augmentation du ruissellement, réduisant ainsi la recharge de la nappe souterraine. La gestion des eaux de pluie consiste à les collecter et les infiltrer vers la nappe qui est protégée de la pollution par des processus auto-épurateurs localisés dans le sol et la zone insaturée. Les dynamiques de la matière organique et des micro-organismes ont été suivies dans les eaux de surface et les eaux souterraines en amont et en aval des trois systèmes d'infiltration (SI). Les teneurs en Carbone Organique dissous (COD) biodégradable et réfractaire ont été mesurées sur l'eau et la croissance des biofilms a été suivie à l'aide des substrats artificiels incubés dans le milieu. Le COD diminue fortement au cours de l'infiltration, mais sa fraction biodégradable demeure plus forte en aval de SI, tout comme les biofilms qui sont stimulés par les infiltrations en biomasse et en diversité. ABSTRACT Urbanization increases impervious surfaces and stormwater runoff reducing groundwater recharge. Stormwater management mainly consists in the collection of rain water and its infiltration to the aquifer, which is protected by the self-purification capacity of the soil and the unsaturated zone. The dynamics of organic matter and microorganisms were studied in surface water and in groundwater upstream and downstream of three stormwater infiltration systems (SIS). Dissolved Organic Carbon (DOC) concentrations were measured in surface and in ground waters, while biofilm dynamics were studied using artificial substrates incubated in the waters. DOC sharply decrease from surface water to the groundwater, but the biodegradable fraction of DOC was higher downstream than upstream of the SIS and the biofilms were stimulated by the infiltration for both biomass and bacterial diversity

Selection of nitrogen-fixing deficient Burkholderia vietnamiensis strains by cystic fibrosis patients: involvement of nif gene deletions and auxotrophic mutations

Burkholderia vietnamiensis is the third most prevalent species of the Burkholderia cepacia complex (Bcc) found in cystic fibrosis (CF) patients. Its ability at fixing nitrogen makes it one of the main Bcc species showing strong filiations with environmental reservoirs. In this study, 83% (29 over 35) of the B. vietnamiensis CF isolates and 100% of the environmental ones (over 29) were found expressing the dinitrogenase complex (encoded by the nif cluster) which is essential in N 2 fixation. Among the deficient strains, two were found growing with ammonium chloride suggesting that they were defective in N 2 fixation, and four with amino acids supplements suggesting that they were harbouring auxotrophic mutations. To get insights about the genetic events that led to the emergence of the N 2 -fixing defective strains, a genetic analysis of B. vietnamiensis nitrogen-fixing property was undertaken. A 40-kb-long nif cluster and nif regulatory genes were identified within the B. vietnamiensis strain G4 genome sequence, and analysed. Transposon mutagenesis and nifH genetic marker exchanges showed the nif cluster and several other genes like gltB (encoding a subunit of the glutamate synthase) to play a key role in B. vietnamiensis ability at growing in nitrogen-free media. nif cluster DNA probings of restricted genomic DNA blots showed a full deletion of the nif cluster for one of the N 2 -fixing defective strain while the other one showed a genetic organization similar to the one of the G4 strain. For 17% of B. vietnamiensis clinical strains, CF lungs appeared to have favoured the selection of mutations or deletions leading to N 2 -fixing deficiencies.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/75167/1/j.1462-2920.2007.01240.x.pd

Enkele proeven over de invloed van de stikstofvorm op het optreden van stip bij paprika

<p><b>Copyright information:</b></p><p>Taken from "Architecture of complex σgene family: evidence of alternative primary and clade-specific factors, and genomic instability"</p><p>http://www.biomedcentral.com/1471-2164/8/308</p><p>BMC Genomics 2007;8():308-308.</p><p>Published online 4 Sep 2007</p><p>PMCID:PMC2194791.</p><p></p>mes using ACT [36]. -J2315 ORF annotations were assigned using other annotated genomes. ORF numbers assigned by the Sanger Institute are indicated. Dashes indicate missing regions. Phage DNA in (c) indicates a potential phage insertion. Arrows indicating ORF of sigma factors are filled with dots, and of anti-sigma factors are filled with vertical bars

Genome characteristics of facultatively symbiotic Frankia sp. strains reflect host range and host plant biogeography

Soil bacteria that also form mutualistic symbioses in plants encounter two major levels of selection. One occurs during adaptation to and survival in soil, and the other occurs in concert with host plant speciation and adaptation. Actinobacteria from the genus Frankia are facultative symbionts that form N2-fixing root nodules on diverse and globally distributed angiosperms in the “actinorhizal” symbioses. Three closely related clades of Frankia sp. strains are recognized; members of each clade infect a subset of plants from among eight angiosperm families. We sequenced the genomes from three strains; their sizes varied from 5.43 Mbp for a narrow host range strain (Frankia sp. strain HFPCcI3) to 7.50 Mbp for a medium host range strain (Frankia alni strain ACN14a) to 9.04 Mbp for a broad host range strain (Frankia sp. strain EAN1pec.) This size divergence is the largest yet reported for such closely related soil bacteria (97.8%–98.9% identity of 16S rRNA genes). The extent of gene deletion, duplication, and acquisition is in concert with the biogeographic history of the symbioses and host plant speciation. Host plant isolation favored genome contraction, whereas host plant diversification favored genome expansion. The results support the idea that major genome expansions as well as reductions can occur in facultative symbiotic soil bacteria as they respond to new environments in the context of their symbioses

Freshwater Bacteria Can Methylate Selenium through the Thiopurine Methyltransferase Pathway

Involvement of the bacterial thiopurine methyltransferase (bTPMT) in natural selenium methylation by freshwater was investigated. A freshwater environment that had no known selenium contamination but exhibited reproducible emission of dimethyl selenide (DMSe) or dimethyl diselenide (DMDSe) when it was supplemented with an organic form of selenium [(methyl)selenocysteine] or an inorganic form of selenium (sodium selenite) was used. The distribution of the bTPMT gene (tpm) in the microflora was studied. Freshwater bacteria growing on 10 μM sodium selenite and 10 μM sodium selenate were isolated, and 4.5 and 10% of the strains, respectively, were shown by colony blot hybridization to hybridize with a Pseudomonas syringae tpm DNA probe. Ribotyping showed that these strains are closely related. The complete rrs sequence of one of the strains, designated Hsa.28, was obtained and analyzed. Its closest phyletic neighbor was found to be the Pseudomonas anguilliseptica rrs sequence. The Hsa.28 strain grown with sodium selenite or (methyl)selenocysteine produced significant amounts of DMSe and DMDSe. The Hsa.28 tpm gene was isolated by genomic DNA library screening and sequencing. BLASTP comparisons of the deduced Hsa.28 bTPMT sequence with P. syringae, Pseudomonas aeruginosa, Vibrio cholerae, rat, and human thiopurine methyltransferase sequences revealed that the levels of similarity were 52 to 71%. PCR-generated Escherichia coli subclones containing the Hsa.28 tpm open reading frame were constructed. E. coli cells harboring the constructs and grown with sodium selenite or (methyl)selenocysteine produced significant levels of DMSe and DMDSe, confirming that the gene plays a role in selenium methylation. The effect of strain Hsa.28 population levels on freshwater DMSe and DMDSe emission was investigated. An increase in the size of the Hsa.28 population was found to enhance significantly the emission of methyl selenides by freshwater samples supplemented with sodium selenite or (methyl)selenocysteine. These data suggest that bTPMT can play a role in natural freshwater selenium methylation processes

Molecular phylogeny of the symbiotic actinomycetes of the genus Frankia matches host-plant infection processes.

International audienceNucleotide sequences of approximately 213 bp of the nif H-D intergene and the beginning of nifD were determined for symbiotic Frankia isolates from the major host-infectivity groups. This region of the nif operon is variable enough to classify most infective Frankia strains at the species level. Phylogenetic inferences from these sequences are in agreement with the 16S rRNA-derived phylogeny of the genus and, thus, are in favor of an intrageneric evolution of nif genes by orthology. Phylogenetic lineages derived from combined nifH-D intergene and partial nifD and 16S rRNA sequences are supported for at least 93% of bootstrap replicates and are useful for investigating evolutionary relationships of the genus and symbiotic properties of this microorganism. The genus Frankia is divided into two major phylogenetic clusters that match with the separation of species according to the mechanism of infection of actinorhizal plants. One cluster groups species strictly adapted to the mechanism of root hair infection (RHI), and the other groups species adapted to the mechanism of direct intercellular penetration. In the RHI cluster, the species infective on Casuarina plants appears to have emerged from strains infective on Alnus. The concordance between the symbiotic properties and the molecular phylogeny of Frankia strains indicates a major role for the host plant in the evolution and speciation of the genus Frankia

Genome Sequences of Three Strains of the Pseudomonas aeruginosa PA7 Clade

International audienceDraft genome sequences of three P. aeruginosa strains from the PA7 clade are presented here. Their lengths are 6.36 (EML528), 6.44 (EML545), and 6.33 Mb (EML548). Comparisons with the PA7 genome showed 5,113 conserved coding sequences (CDSs), and significant numbers of strain-specific CDSs. Their analysis will improve our understanding of this highly divergent clade