Genome of Herbaspirillum seropedicae Strain SmR1, a Specialized Diazotrophic Endophyte of Tropical Grasses

The molecular mechanisms of plant recognition, colonization, and nutrient exchange between diazotrophic endophytes and plants are scarcely known. Herbaspirillum seropedicae is an endophytic bacterium capable of colonizing intercellular spaces of grasses such as rice and sugar cane. The genome of H. seropedicae strain SmR1 was sequenced and annotated by The Paraná State Genome Programme—GENOPAR. The genome is composed of a circular chromosome of 5,513,887 bp and contains a total of 4,804 genes. The genome sequence revealed that H. seropedicae is a highly versatile microorganism with capacity to metabolize a wide range of carbon and nitrogen sources and with possession of four distinct terminal oxidases. The genome contains a multitude of protein secretion systems, including type I, type II, type III, type V, and type VI secretion systems, and type IV pili, suggesting a high potential to interact with host plants. H. seropedicae is able to synthesize indole acetic acid as reflected by the four IAA biosynthetic pathways present. A gene coding for ACC deaminase, which may be involved in modulating the associated plant ethylene-signaling pathway, is also present. Genes for hemagglutinins/hemolysins/adhesins were found and may play a role in plant cell surface adhesion. These features may endow H. seropedicae with the ability to establish an endophytic life-style in a large number of plant species

The complete genome sequence of Chromobacterium violaceum reveals remarkable and exploitable bacterial adaptability

Chromobacterium violaceum is one of millions of species of free-living microorganisms that populate the soil and water in the extant areas of tropical biodiversity around the world. Its complete genome sequence reveals (i) extensive alternative pathways for energy generation, (ii) ≈500 ORFs for transport-related proteins, (iii) complex and extensive systems for stress adaptation and motility, and (iv) wide-spread utilization of quorum sensing for control of inducible systems, all of which underpin the versatility and adaptability of the organism. The genome also contains extensive but incomplete arrays of ORFs coding for proteins associated with mammalian pathogenicity, possibly involved in the occasional but often fatal cases of human C. violaceum infection. There is, in addition, a series of previously unknown but important enzymes and secondary metabolites including paraquat-inducible proteins, drug and heavy-metal-resistance proteins, multiple chitinases, and proteins for the detoxification of xenobiotics that may have biotechnological applications

Peptide utilization by Prevotella spp. and its impact on ruminal nitrogen metabolism

Two aspects of peptide metabolism in Prevotella spp., uptake and degradation, were investigated. Oligopeptides containing the amino acid analogs oxalysine and ethionine inhibited growth of several Prevotella species, and the inhibition could be reversed by the inclusion of nutritional peptides in the growth medium. Based on the mode of action of the toxic amino acid mimetics in other microorganisms, these results demonstrate the use of the smugglin concept in rumen bacteria: inhibitory compounds incorporated into larger molecules that are normally transported were used to inhibit growth of Prevotella spp. The characterization of the mode of action of protamine, a 32-amino acid polycationic peptide, on Prevotella spp. was conducted to determine its applicability as a smugglin. Protamine exerted its toxic effects by disrupting the outer membrane, which was demonstrated by: (i) an increased sensitivity to hydrophobic antibiotics (novobiocin and monensin), and; (ii) release of the periplasmic enzyme alkaline phosphatase following short-term exposure to protamine. As such, it is unlikely that protamine could be used as a smugglin. Studies of a dipeptidyl peptidase activity from Prevotella bryantii strain B\sb14 using enzyme inhibitors revealed that the enzyme responsible for much of the Gly-Arg-MNAse (PrtA) activity in cell extracts is similar to gingipain R, member of a novel family of calcium-dependent cysteine proteases isolated from various strains of Porphyromonas gingivalis. Chemical mutagenesis was used to generate two mutant strains defective in PrtA. An ecological role for the PrtA activity was demonstrated in co-culture experiments with Gram-positive, ammonia-producing ruminal bacteria. The rate and extent of ammonia production was reduced by approximately 25% in co-cultures containing the mutants when compared with wild-type-containing cultures. PrtA enrichment studies were undertaken, and multiple peaks of Gly-Arg-MNAse activity following ion-exchange chromatography of the cytoplasmic/periplasmic fraction of P. bryantii B\sb14 were obtained. Peaks of activity possessed different sensitivities to oxygen, and this result led to a further characterization of the PrtA activities. Studies with Triton X-100 and the effect of aerobiosis indicated that at least two Gly-Arg-MNAse activities are present in P. bryantii B\sb14: PrtA is the predominant, intracellular, O\sb2-sensitive enzyme, whereas PrtB is a membrane-associated activity that O\sb2-insensitive

Phenotypic and Genotypic Characterization of Group B Streptococcal Isolates in Southern Brazil ▿

One-hundred sixty-eight group B streptococcal (GBS) isolates from a Brazilian hospital were phenotypically and genotypically characterized. Isolates were recovered from human sources from April 2006 to May 2008 and classified as either invasive, noninvasive, or colonizing isolates. Classical methods for serotyping and antibiotic resistance profiling were employed. Clonal groups were also defined by pulsed-field gel electrophoresis (PFGE). Results showed that susceptibility to beta-lactam antimicrobials was predominant among the isolates. Only 4.7% were resistant to erythromycin and clindamycin. The erm(B) gene was widely detected in our GBS isolates, according to our phenotypic results (constitutive macrolide-lincosamide-streptogramin B [cMLSB] resistance phenotype), and the erm(A) gene was also detected in some isolates. MLSB resistance was restricted to strains isolated from patients with noninvasive infections and carriers. Serotype Ia was predominant (38.1%), serotype IV isolates were found at a high frequency (13.1%), and few isolates of serotype III were identified (3%). Pulsed-field gel electrophoresis results revealed a variety of types, reflecting the substantial genetic diversity among GBS strains, although a great number of isolates could be clustered into two major groups with a high degree of genetic relatedness. Three main PFGE clonal groups were found, and isolates sharing the same PFGE type were grouped into different serotypes. Furthermore, in a few cases, isolates from the same patients and possessing the same PFGE type were of different serotypes. These findings could be related to the occurrence of capsular switching by horizontal transfer of capsular genes

The type III secretion system is necessary for the development of a pathogenic and endophytic interaction between <it>Herbaspirillum rubrisubalbicans</it> and Poaceae

Abstract Background Herbaspirillum rubrisubalbicans was first identified as a bacterial plant pathogen, causing the mottled stripe disease in sugarcane. H. rubrisubalbicans can also associate with various plants of economic interest in a non pathogenic manner. Results A 21 kb DNA region of the H. rubrisubalbicans genome contains a cluster of 26 hrp/hrc genes encoding for the type three secretion system (T3SS) proteins. To investigate the contribution of T3SS to the plant-bacterial interaction process we generated mutant strains of H. rubrisubalbicans M1 carrying a Tn5 insertion in both the hrcN and hrpE genes. H. rubrisulbalbicans hrpE and hrcN mutant strains of the T3SS system failed to cause the mottled stripe disease in the sugarcane susceptible variety B-4362. These mutant strains also did not produce lesions on Vigna unguiculata leaves. Oryza sativa and Zea mays colonization experiments showed that mutations in hrpE and hrcN genes reduced the capacity of H. rubrisulbalbicans to colonize these plants, suggesting that hrpE and hrcN genes are involved in the endophytic colonization. Conclusions Our results indicate that the T3SS of H. rubrisubalbicans is necessary for the development of the mottled stripe disease and endophytic colonization of rice.</p

Swine and Poultry Pathogens: the Complete Genome Sequences of Two Strains of Mycoplasma hyopneumoniae and a Strain of Mycoplasma synoviae

This work reports the results of analyses of three complete mycoplasma genomes, a pathogenic (7448) and a nonpathogenic (J) strain of the swine pathogen Mycoplasma hyopneumoniae and a strain of the avian pathogen Mycoplasma synoviae; the genome sizes of the three strains were 920,079 bp, 897,405 bp, and 799,476 bp, respectively. These genomes were compared with other sequenced mycoplasma genomes reported in the literature to examine several aspects of mycoplasma evolution. Strain-specific regions, including integrative and conjugal elements, and genome rearrangements and alterations in adhesin sequences were observed in the M. hyopneumoniae strains, and all of these were potentially related to pathogenicity. Genomic comparisons revealed that reduction in genome size implied loss of redundant metabolic pathways, with maintenance of alternative routes in different species. Horizontal gene transfer was consistently observed between M. synoviae and Mycoplasma gallisepticum. Our analyses indicated a likely transfer event of hemagglutinin-coding DNA sequences from M. gallisepticum to M. synoviae

Molecular mechanisms probably involved in plant colonization and plant growth promotion identified in the <i>H. seropedicae</i> SmR1 genome.

<p>Plant signals can modulate the expression of bacterial genes coding for adhesins, type IV <i>pili</i> and enzymes of lipopolysaccharide (LPS) synthesis, triggering bacterial attachment to root surfaces. The molecular communication involves bacterial protein secretion and phytohormones to stimulate plant growth and modulate plant defense response. In addition, modulation of plant ethylene levels by ACC deaminase may contribute to plant growth promotion. The success of the endophytic association depends on a compatible genetic background that leads to benefits for both organisms.</p