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ABSTRACTThe nitrogen (N) status transduced via the NtrBC two-component system is a major signaling cue in the root nodule endosymbiosis of diazotrophic rhizobia with legumes. NtrBC is upregulated in the N-limiting rhizosphere environment at the onset of nodulation but silenced in nodules to favor the assimilation of the fixed N into plant biomass. We reported that the trans-acting sRNA NfeR1 (Nodule Formation Efficiency RNA) broadly influences the symbiotic performance of the α-rhizobium Sinorhizobium meliloti. Here, we show that NfeR1 is indeed an N-responsive sRNA that fine-tunes NtrBC output during the symbiotic transition. Biochemical and genetic approaches unveiled that NtrC and the LysR-type symbiotic regulator LsrB bind at distinct nearby sites in the NfeR1 promoter, acting antagonistically as repressor and activator of transcription, respectively. This complex transcriptional control specifies peak NfeR1 steady-state levels in N-starved and endosymbiotic bacteria. Furthermore, NfeR1 base pairs the translation initiation region of the histidine kinase coding mRNA ntrB, causing a decrease in both NtrB and NtrC abundance as assessed by double-plasmid genetic assays. In the context of endogenous regulation, NfeR1-mediated ntrBC silencing most likely amends the effective strength of the known operon autorepression exerted by NtrC. Accordingly, a lack of NfeR1 shifts the wild-type NtrBC output, restraining the fitness of free-living rhizobia under N stress and plant growth upon nodulation. The mixed NtrBC-NfeR1 double-negative feedback loop is thus an unprecedented adaptive network motif that helps α-rhizobia adjust N metabolism to the demands of an efficient symbiosis with legume plants.IMPORTANCERoot nodule endosymbioses between diazotrophic rhizobia and legumes provide the largest input of combined N to the biosphere, thus representing an alternative to harmful chemical fertilizers for sustainable crop production. Rhizobia have evolved intricate strategies to coordinate N assimilation for their own benefit with N2 fixation to sustain plant growth. The rhizobial N status is transduced by the NtrBC two-component system, the seemingly ubiquitous form of N signal transduction in Proteobacteria. Here, we show that the regulatory sRNA NfeR1 (nodule formation efficiency RNA) of the alfalfa symbiont Sinorhizobium meliloti is transcribed from a complex promoter repressed by NtrC in a N-dependent manner and feedback silences ntrBC by complementary base-pairing. These findings unveil a more prominent role of NtrC as a transcriptional repressor than hitherto anticipated and a novel RNA-based mechanism for NtrBC regulation. The NtrBC-NfeR1 double-negative feedback loop accurately rewires symbiotic S. meliloti N metabolism and is likely conserved in α-rhizobia.

Simple Summary: Wolbachia are obligate intracellular bacteria that occur in insects and filarial worms. Strains that infect insects have genomes that encode mobile genetic elements that are typically lost as obligate intracellular bacteria undergo genomic streamlining. These mobile elements include diverse lambda-like prophages that package an approximately 65 kb viral genome called Phage WO, which includes a unique eukaryotic association module, or EAM. The EAM encodes unusually large proteins thought to mediate interactions between the bacterium, its virus, and the host eukaryotic cell. We propose that in addition to conventional bacteriophages, Wolbachia also encode smaller gene transfer agents (GTAs). From two independent preparations, we recovered an identical 15.6 kb sequence that lacks an EAM. Its small size and gene composition suggest that the element is a GTA, which may participate in the horizontal transfer of random DNA from the Wolbachia genome. Although functional proof of GTA activity remains to be obtained, these data provide a useful framework for future analysis of mobile genetic elements encoded by Wolbachia genomes. Wolbachia are obligate intracellular bacteria that occur in insects and filarial worms. Strains that infect insects have genomes that encode mobile genetic elements, including diverse lambda-like prophages called Phage WO. Phage WO packages an approximately 65 kb viral genome that includes a unique eukaryotic association module, or EAM, that encodes unusually large proteins thought to mediate interactions between the bacterium, its virus, and the eukaryotic host cell. The Wolbachia supergroup B strain, wStri from the planthopper Laodelphax striatellus, produces phage-like particles that can be recovered from persistently infected mosquito cells by ultracentrifugation. Illumina sequencing, assembly, and manual curation of DNA from two independent preparations converged on an identical 15,638 bp sequence that encoded packaging, assembly, and structural proteins. The absence of an EAM and regulatory genes defined for Phage WO from the wasp, Nasonia vitripennis, was consistent with the possibility that the 15,638 bp sequence represents an element related to a gene transfer agent (GTA), characterized by a signature head–tail region encoding structural proteins that package host chromosomal DNA. Future investigation of GTA function will be supported by the improved recovery of physical particles, electron microscopic examination of potential diversity among particles, and rigorous examination of DNA content by methods independent of sequence assembly. [ABSTRACT FROM AUTHOR]

Genes of unknown function constitute a considerable fraction of most bacterial genomes. In a Tn5-based search for stress response genes in the nitrogen-fixing facultative endosymbiont Sinorhizobium (Ensifer) meliloti, we identified a previously uncharacterized gene required for growth on solid media with increased NaCl concentrations. The encoded protein carries a predicted thioredoxin fold and deletion of the gene also results in increased sensitivity to hydrogen peroxide and cumene hydroperoxide. We have designated the gene srlA (stress resistance locus A) based on these phenotypes. A deletion mutant yields phenotypic revertants on high salt medium and genome sequencing revealed that all revertants carry a mutation in genes homologous to either cenK or cenR. srlA promoter activity is abolished in these revertant host backgrounds and in a strain carrying a deletion in cenK. We also observed that the srlA promoter is autoregulated, displaying low activity in a wildtype (wt) host background and high activity in the srl deletion mutant background. The srlA promoter includes a conserved inverted repeat directly upstream of the predicted -35 subsequence. A mutational analysis demonstrated that the site is required for the high promoter activity in the srlA deletion background. Electromobility shift assays using purified wildtype CenR response regulator and a D55E phosphomimetic derivative suggest this protein acts as a likely Class II activator by binding promoter DNA. These results document the first identified CenK--CenR regulon member in S. meliloti and demonstrate this two-component regulatory system and gene srlA influences cellular growth and persistence under certain stress-inducing conditions. [ABSTRACT FROM AUTHOR]

Genes of unknown function constitute a considerable fraction of most bacterial genomes. In a Tn5-based search for stress response genes in the nitrogen-fixing facultative endosymbiont Sinorhizobium (Ensifer) meliloti, we identified a previously uncharacterized gene required for growth on solid media with increased NaCl concentrations. The encoded protein carries a predicted thioredoxin fold and deletion of the gene also results in increased sensitivity to hydrogen peroxide and cumene hydroperoxide. We have designated the gene srlA (stress resistance locus A) based on these phenotypes. A deletion mutant yields phenotypic revertants on high salt medium and genome sequencing revealed that all revertants carry a mutation in genes homologous to either cenK or cenR. srlA promoter activity is abolished in these revertant host backgrounds and in a strain carrying a deletion in cenK. We also observed that the srlA promoter is autoregulated, displaying low activity in a wildtype (wt) host background and high activity in the srl deletion mutant background. The srlA promoter includes a conserved inverted repeat directly upstream of the predicted −35 subsequence. A mutational analysis demonstrated that the site is required for the high promoter activity in the srlA deletion background. Electromobility shift assays using purified wildtype CenR response regulator and a D55E phosphomimetic derivative suggest this protein acts as a likely Class II activator by binding promoter DNA. These results document the first identified CenK–CenR regulon member in S. meliloti and demonstrate this two-component regulatory system and gene srlA influences cellular growth and persistence under certain stress-inducing conditions.

ABSTRACT Flavoproteins are a diverse class of proteins that are mostly enzymes and contain as cofactors flavin mononucleotide (FMN) and/or flavin adenine dinucleotide (FAD), which enable them to participate in a wide range of physiological reactions. We have compiled 78 potential proteins building the flavoproteome of Brucella ovis (B. ovis), the causative agent of ovine brucellosis. The curated list of flavoproteins here reported is based on (i) the analysis of sequence, structure and function of homologous proteins, and their classification according to their structural domains, clans, and expected enzymatic functions; (ii) the constructed phylogenetic trees of enzyme functional classes using 19 Brucella strains and 26 pathogenic and/or biotechnological relevant alphaproteobacteria together with B. ovis; and (iii) the evaluation of the genetic context for each entry. Candidates account for ∼2.7% of the B. ovis proteome, and 75% of them use FAD as cofactor. Only 55% of these flavoproteins belong to the core proteome of Brucella and contribute to B. ovis processes involved in maintenance activities, survival and response to stress, virulence, and/or infectivity. Several of the predicted flavoproteins are highly divergent in Brucella genus from revised proteins and for them it is difficult to envisage a clear function. This might indicate modified catalytic activities or even divergent processes and mechanisms still not identified. We have also detected the lack of some functional flavoenzymes in B. ovis, which might contribute to it being nonzoonotic. Finally, potentiality of B. ovis flavoproteome as the source of antimicrobial targets or biocatalyst is discussed. IMPORTANCE Some microorganisms depend heavily on flavin-dependent activities, but others maintain them at a minimum. Knowledge about flavoprotein content and functions in different microorganisms will help to identify their metabolic requirements, as well as to benefit either industry or health. Currently, most flavoproteins from the sheep pathogen Brucella ovis are only automatically annotated in databases, and only two have been experimentally studied. Indeed, certain homologues with unknown function are not characterized, and they might relate to still not identified mechanisms or processes. Our research has identified 78 members that comprise its flavoproteome, 76 of them flavoenzymes, which mainly relate to bacteria survival, virulence, and/or infectivity. The list of flavoproteins here presented allows us to better understand the peculiarities of Brucella ovis and can be applied as a tool to search for candidates as new biocatalyst or antimicrobial targets.

Cyclic‐di‐GMP plays crucial role in the cell cycle regulation of the α‐ProteobacteriumCaulobacter crescentus. Here we investigated its role in the α‐ProteobacteriumBrucella abortus, a zoonotic intracellular pathogen. Surprisingly, deletion of all predicted cyclic‐di‐GMP synthesizing or degrading enzymes did not drastically impair the growth of B. abortus, nor its ability to grow inside cell lines. As other Rhizobiales, B. abortus displays unipolar growth from the new cell pole generated by cell division. We found that the phosphodiesterase PdeA, the ortholog of the essential polar growth factor RgsP of the Rhizobiale Sinorhizobium meliloti, is required for rod shape integrity but is not essential for B. abortus growth. Indeed, the radius of the pole is increased by 31 ± 1.7% in a ΔpdeA mutant, generating a coccoid morphology. A mutation in the cyclic‐di‐GMP phosphodiesterase catalytic site of PdeA does not generate the coccoid morphology and the ΔpdeA mutant kept the ability to recruit markers of new and old poles. However, the presence of PdeA is required in an intra‐nasal mouse model of infection. In conclusion, we propose that PdeA contributes to bacterial morphology and virulence in B. abortus, but it is not crucial for polarity and asymmetric growth. [ABSTRACT FROM AUTHOR]

The MucR/Ros family protein is conserved in alpha-proteobacteria and characterized by its zinc-finger motif that has been proposed as the ancestral domain from which the eukaryotic C2H2 zinc-finger structure evolved. In the past decades, accumulated evidences have revealed MucR as a pleiotropic transcriptional regulator that integrating multiple functions such as virulence, symbiosis, cell cycle and various physiological processes. Scattered reports indicate that MucR mainly acts as a repressor, through oligomerization and binding to multiple sites of AT-rich target promoters. The N-terminal region and zinc-finger bearing C-terminal region of MucR mediate oligomerization and DNA-binding, respectively. These features are convergent to those of xenogeneic silencers such as H-NS, MvaT, Lsr2 and Rok, which are mainly found in other lineages. Phylogenetic analysis of MucR homologs suggests an ancestral origin of MucR in alpha- and delta-proteobacteria. Multiple independent duplication and lateral gene transfer events contribute to the diversity and phyletic distribution of MucR. Finally, we posed questions which remain unexplored regarding the putative roles of MucR as a xenogeneic silencer and a general manager in balancing adaptation and regulatory integration in the pangenome context.

BackgroundSpecialized interactions help structure communities, but persistence of specialized organisms is puzzling because a generalist can occupy more environments and partake in more beneficial interactions. The "Jack-of-all-trades is a master of none" hypothesis asserts that specialists persist because the fitness of a generalist utilizing a particular habitat is lower than that of a specialist adapted to that habitat. Yet, there are many reasons to expect that mutualists will generalize on partners.Plant-soil feedbacks help to structure plant and microbial communities, but how frequently are soil-based symbiotic mutualistic interactions sufficiently specialized to influence species distributions and community composition? To address this question, we quantified realized partner richness and phylogenetic breadth of four wild-grown native legumes (Lupinus bicolor, L. arboreus, Acmispon strigosus and A. heermannii) and performed inoculation trials to test the ability of two hosts (L. bicolor and A. strigosus) to nodulate (fundamental partner richness), benefit from (response specificity), and provide benefit to (effect specificity) 31 Bradyrhizobium genotypes.ResultsIn the wild, each Lupinus species hosted a broader genetic range of Bradyrhizobium than did either Acmispon species, suggesting that Acmispon species are more specialized. In the greenhouse, however, L. bicolor and A. strigosus did not differ in fundamental association specificity: all inoculated genotypes nodulated both hosts. Nevertheless, A. strigosus exhibited more specificity, i.e., greater variation in its response to, and effect on, Bradyrhizobium genotypes. Lupinus bicolor benefited from a broader range of genotypes but averaged less benefit from each. Both hosts obtained more fitness benefit from symbionts isolated from conspecific hosts; those symbionts in turn gained greater fitness benefit from hosts of the same species from which they were isolated.ConclusionsThis study affirmed two important tenets of evolutionary theory. First, as predicted by the Jack-of-all-trades is a master of none hypothesis, specialist A. strigosus obtained greater benefit from its beneficial symbionts than did generalist L. bicolor. Second, as predicted by coevolutionary theory, each test species performed better with partner genotypes isolated from conspecifics. Finally, positive fitness feedback between the tested hosts and symbionts suggests that positive plant-soil feedback could contribute to their patchy distributions in this system.

The alpha-proteobacterium Zymomonas mobilis is a promising biofuel producer, based on its native metabolism that efficiently converts sugars to ethanol. Therefore, it has a high potential for industrial-scale biofuel production. Two previous studies suggested that Z. mobilis strain Zm4 might not be monoploid. However, a systematic analysis of the genome copy number is still missing, in spite of the high potential importance of Z. mobilis. To get a deep insight into the ploidy level of Z. mobilis and its regulation, the genome copy numbers of three strains were quantified. The analyses revealed that, during anaerobic growth, the lab strain Zm6, the Zm6 type strain obtained from DSMZ (German Collection of Microorganisms), and the lab strain Zm4, have copy numbers of 18.9, 22.3 and 16.2, respectively, of an origin-adjacent region. The copy numbers of a terminus-adjacent region were somewhat lower with 9.3, 15.8, and 12.9, respectively. The values were similar throughout the growth curves, and they were only slightly downregulated in late stationary phase. During aerobic growth, the copy numbers of the lab strain Zm6 were much higher with around 40 origin-adjacent copies and 17 terminus-adjacent copies. However, the cells were larger during aerobic growth, and the copy numbers per μm3 cell volume were rather similar. Taken together, this first systematic analysis revealed that Z. mobilis is polyploid under regular laboratory growth conditions. The copy number is constant during growth, in contrast to many other polyploid bacteria. This knowledge should be considered in further engineering of the strain for industrial applications.

The alpha-proteobacterium Zymomonas mobilis is a promising biofuel producer, based on its native metabolism that efficiently converts sugars to ethanol. Therefore, it has a high potential for industrial-scale biofuel production. Two previous studies suggested that Z. mobilis strain Zm4 might not be monoploid. However, a systematic analysis of the genome copy number is still missing, in spite of the high potential importance of Z. mobilis. To get a deep insight into the ploidy level of Z. mobilis and its regulation, the genome copy numbers of three strains were quantified. The analyses revealed that, during anaerobic growth, the lab strain Zm6, the Zm6 type strain obtained from DSMZ (German Collection of Microorganisms), and the lab strain Zm4, have copy numbers of 18.9, 22.3 and 16.2, respectively, of an origin-adjacent region. The copy numbers of a terminus-adjacent region were somewhat lower with 9.3, 15.8, and 12.9, respectively. The values were similar throughout the growth curves, and they were only slightly downregulated in late stationary phase. During aerobic growth, the copy numbers of the lab strain Zm6 were much higher with around 40 origin-adjacent copies and 17 terminus-adjacent copies. However, the cells were larger during aerobic growth, and the copy numbers per μm3 cell volume were rather similar. Taken together, this first systematic analysis revealed that Z. mobilis is polyploid under regular laboratory growth conditions. The copy number is constant during growth, in contrast to many other polyploid bacteria. This knowledge should be considered in further engineering of the strain for industrial applications. [ABSTRACT FROM AUTHOR]

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Acidocalcisomes are membrane-enclosed, polyphosphate-containing acidic organelles in lower Eukaryota but have been described likewise for Agrobacterium tumefaciens (Seufferheld, M., Vieira, M., Ruiz, F. A., Rodrigues, C. O., Moreno, S., & Docampo, R. 2003. J. Biol. Chem. 278:29971-29978). This study aimed at the characterization of polyphosphate-containing acidocalcisomes in this -proteobacterium. Unexpectedly, fluorescence microscopical investigation of A. tumefaciens cells using fluorescent dyes and localization of constructed fusions of polyphosphate kinases (PPKs) and of vacuolar H+45 -translocating pyrophosphatase (HppA) with enhanced yellow fluorescent protein (eYFP) suggested that acidocalcisomes and polyphosphate are different subcellular structures. Acidocalcisomes and polyphosphate granules were frequently located closely together and both near the cell poles. However, they never shared the same position. Mutant strains of A. tumefaciens with deletions of both ppk genes (Δppk1, Δppk2) were unable to form polyphosphate, but still showed cell pole-located eYFP-HppA-foci and could be stained with MitoTracker. In conclusion, A. tumefaciens forms polyP granules that are free of a surrounding membrane and thus resemble polyP granules of Ralstonia eutropha and other bacteria. The composition, contents and function of the subcellular structures that are stainable with MitoTracker and harbor eYFP-HppA remain unclear. [ABSTRACT FROM AUTHOR]

Intracellular bacteria of the genus Wolbachia (α-Proteobacteria) are the most widespread endosymbionts of insects. Host infection is usually associated with alterations in reproduction, such as cytoplasmic incompatibility, the induction of parthenogenesis and offspring sex ratio bias: all phenomena that may influence host speciation. In the present study, by using well-established molecular tools, we investigated the presence of Wolbachia in leaf beetles of the genus Crioceris and their host plants, which are various species of Asparagus. Multilocus sequence typing of bacterial genes showed that despite their occurrence in the same habitat and feeding on the same plant, two species of Crioceris, C. quinquepunctata and C. quatuordecimpunctata, are infected by two different strains of Wolbachia. C. asparagi, C. paracenthesis and C. duodecimpunctata, which are sympatric with the infected species, do not harbour the bacterium. Interestingly, DNA of Wolbachia was detected in host plant tissues that are exploited by the beetles, providing evidence for the horizontal transmission of the bacterium between beetles and their host plants. Moreover, Wolbachia was detected in species of Crioceris that are not closely related.

The obligate intracellular microbe, Wolbachia pipientis (Rickettsiales; Anaplasmataceae), is a Gram-negative member of the alpha proteobacteria that infects arthropods and filarial worms. Although closely related to the genera Anaplasma and Ehrlichia, which include pathogens of humans, Wolbachia is uniquely associated with invertebrate hosts in the clade Ecdysozoa. Originally described in Culex pipiens mosquitoes, Wolbachia is currently represented by 17 supergroups and is believed to occur in half of all insect species. In mosquitoes, Wolbachia acts as a gene drive agent, with the potential to modify vector populations; in filarial worms, Wolbachia functions as a symbiont, and is a target for drug therapy. A small number of Wolbachia strains from supergroups A, B, and F have been maintained in insect cell lines, which are thought to provide a more permissive environment than the natural host. When transferred back to an insect host, Wolbachia produced in cultured cells are infectious and retain reproductive phenotypes. Here, I review applications of insect cell lines in Wolbachia research and describe conditions that facilitate Wolbachia infection and replication in naive host cells. Progress in manipulation of Wolbachia in vitro will enable genetic and biochemical advances that will facilitate eventual genetic engineering of this important biological control agent.

The di‐copper center CuA is an essential metal cofactor in cytochrome oxidase (Cox) of mitochondria and many prokaryotes, mediating one‐electron transfer from cytochrome c to the site for oxygen reduction. CuA is located in subunit II (CoxB) of Cox and protrudes into the periplasm of Gram‐negative bacteria or the mitochondrial intermembrane space. How the two copper ions are brought together to build CoxB·CuA is the subject of this review. It had been known that the reductase TlpA and the metallochaperones ScoI and PcuC are required for CuA formation in bacteria, but the mechanism of copper transfer has emerged only recently for the Bradyrhizobium diazoefficiens system. It consists of the following steps: (a) TlpA keeps the active site cysteine pair of CoxB in its dithiol state as a prerequisite for metal insertion; (b) ScoI·Cu2+ rapidly forms a transient complex with apo‐CoxB; (c) PcuC, loaded with Cu1+ and Cu2+, dissociates this complex to CoxB·Cu2+, and a second PcuC·Cu1+·Cu2+ transfers Cu1+ to CoxB·Cu2+, yielding mature CoxB·CuA. Variants of this pathway might exist in other bacteria or mitochondria. [ABSTRACT FROM AUTHOR]

The α-proteobacteria are a fascinating group of free-living, symbiotic and pathogenic organisms, including the Brucella genus, which is responsible for a worldwide zoonosis. One common feature of α-proteobacteria is the presence of a conserved response regulator called CtrA, first described in the model bacterium Caulobacter crescentus , where it controls gene expression at different stages of the cell cycle. Here, we focus on Brucella abortus and other intracellular α-proteobacteria in order to better assess the potential role of CtrA in the infectious context. Comparative genomic analyses of the CtrA control pathway revealed the conservation of specific modules, as well as the acquisition of new factors during evolution. The comparison of CtrA regulons also suggests that specific clades of α-proteobacteria acquired distinct functions under its control, depending on the essentiality of the transcription factor. Other CtrA-controlled functions, for instance motility and DNA repair, are proposed to be more ancestral. Altogether, these analyses provide an interesting example of the plasticity of a regulation network, subject to the constraints of inherent imperatives such as cell division and the adaptations to diversified environmental niches. [ABSTRACT FROM AUTHOR]

Unisexual Trichogramma forms have attracted much attention due to their potential advantages as biocontrol agents. Fitness studies have been performed and understanding the cost that Wolbachia may inflict on their hosts will help in deciding if Wolbachia infected (unisexual) forms are indeed better than sexual forms when used in biological control programmes. The influence of Wolbachia on the foraging behaviour (including walking activity and speed) of T. atopovirilia is reported in this paper. Temperature strongly affected T. atopovirilia female walking activity, but Wolbachia infected and uninfected females differed in none of the behavioural components that were measured such as walking activity and walking speed. Walking activity was highest at 25 ºC and differed significantly from that at 20 and 15 ºC. Trichogramma wasps were highly affected at 15 ºC. Behaviour analysis with females showed that female wasps spend most of the time on drilling + ovipositing on host eggs followed by host drumming and walking while drumming. The parasitism rate and number of offspring did not differ significantly between infected and cured Trichogramma females. Biological control implications of these findings are discussed.Formas unissexuais de Trichogramma têm despertado a atenção de pesquisadores devido as potenciais vantagens deste parasitóide como agente de controle biológico. O estudo do "Fitness" tem sido avaliado e entender o custo de ser infectado por Wolbachia ajudará em determinar se formas infectadas por Wolbachia (unisexuais) são realmente melhores que as sexuadas quando utilizadas em programas de controle biológico. A influência de Wolbachia no comportamento de procura (incluindo a atividade e a velocidade de caminhamento) de T. atopovirilia é relatada neste artigo. A temperatura afetou grandemente a atividade de caminhamento de fêmeas de T. atopovirilia, entretanto os componentes de comportamento tais como a atividade e a velocidade de caminhamento não diferiram em relação às fêmeas infectadas e não infectadas. A atividade de caminhamento foi maior a 25 ºC e diferiu significativamente de 20 e 15 ºC. Fêmeas de Trichogramma foram altamente afetados a 15 ºC. Em função da análise do comportamento com fêmeas, pode-se verificar que houve maior tempo gasto no processo de oviposição, seguido pelo toque com as antenas sobre os ovos dos hospedeiros e do caminhamento ao mesmo tempo que toca os ovos com as antenas. A taxa de parasitismo e o número de descendentes não diferiram significativamente entre fêmeas de Trichogramma infectadas e curadas da infecção por Wolbachia. As implicações dos resultados obtidos sobre o controle biológico são discutidas.

The brucellae are α-Proteobacteriacausing brucellosis, an important zoonosis. Although multiplying in endoplasmic reticulum-derived vacuoles, they cause no cell death, suggesting subtle but efficient use of host resources. Brucellae are amino-acid prototrophs able to grow with ammonium or use glutamate as the sole carbon–nitrogen sourcein vitro. They contain more than twice amino acid/peptide/polyamine uptake genes than the amino-acid auxotrophLegionella pneumophila, which multiplies in a similar vacuole, suggesting a different nutritional strategy. During these two last decades, many mutants of key actors in nitrogen metabolism (transporters, enzymes, regulators, etc.) have been described to be essential for full virulence of brucellae. Here, we review the genomic and experimental data onBrucellanitrogen metabolism and its connection with virulence. An analysis of various aspects of this metabolism (transport, assimilation, biosynthesis, catabolism, respiration and regulation) has highlighted differences and similarities in nitrogen metabolism with other α-Proteobacteria. Together, these data suggest that, during their intracellular life cycle, the brucellae use various nitrogen sources for biosynthesis, catabolism and respiration following a strategy that requires prototrophy and a tight regulation of nitrogen use. [ABSTRACT FROM AUTHOR]

The aim of this work was using the legume plant Anthyllis vulneraria L. (ecotype metallicolous) as a trap plant, in order to isolate metal-tolerant rhizobial strains from metal-contaminated soils from Morocco, with pollution indexes spanning three orders of magnitude. As bioindicator, soil bacterial density was inversely correlated to the pollution index. Forty-three bulk soil bacteria and sixty two bacteria from nodules were isolated. The resistance of bacteria from nodules to heavy metals was four to ten times higher than that of bulk soil bacteria, reaching high maximum tolerable concentrations for Cd (2 mM), Cu (2 mM), Pb (7 mM), and Zn (3 mM). Besides, some strains show multiple metal-tolerant abilities and great metal biosorption onto the bacterial surface. Amplification and restriction analysis of ribosomal 16S rDNA (ARDRA) and 16S ribosomal DNA (rDNA) sequencing were used to assess biodiversity and phylogenetic position among bacteria present in nodules. Our results suggest that a great diversity of non-rhizobial bacteria (alpha- and gamma-proteobacteria) colonize nodules of Anthyllis plants in contaminated soils. Taking together, our results evidence that, in polluted soils, rhizobia can be displaced by non-rhizobial (and hence, non-fixing) strains from nodules. Thus, the selection of metal-resistant rhizobia is a key step for using A. vulneraria symbioses for in situ phytoremediation. [ABSTRACT FROM AUTHOR]

The maintenance of large plasmid in a wide variety of alpha-proteobacteria depends on the repABC replication/segregation unit. The intergenic repB-repC region of these plasmids encodes a countertranscribed RNA (ctRNA) that modulates the transcription/translation rate of RepC, the initiator protein. The ctRNA acts as a strong incompatibility factor when expressed in trans . We followed a site directed mutagenesis approach to map those sequences of the ctRNA that are required for plasmid incompatibility and for plasmid replication control. We found that the first three nucleotides of the 5′-end of the ctRNA are essential for interactions with its target RNA. We also found that stretches of 4–5 nucleotides of non-complementarity within the first 10 nucleotides of the left arm of the ctRNA and the target RNA are sufficient to avoid plasmid incompatibility. Additionally, miniplasmid derivatives expressing ctRNAs with mutations in the 5′ end or small deletions in the ctRNA are capable of controlling their own replication and coexisting with the parental plasmid. We suggest that a mechanism that could have a crucial role in the speciation process of repABC plasmids is to accumulate enough changes in this small region of the ctRNA gene to disrupt heteroduplex formation between the target RNA of one plasmid and the ctRNA of the other. Plasmids carrying these changes will not have defects in their maintenance. [ABSTRACT FROM AUTHOR]

Beta-oxidation of fatty acids and detoxification of reactive oxygen species are generally accepted as being fundamental functions of peroxisomes. Additionally, these pathways might have been the driving force favoring the selection of this compartment during eukaryotic evolution. Here we performed phylogenetic analyses of enzymes involved in beta-oxidation of fatty acids in Bacteria, Eukaryota, and Archaea. These imply an alpha-proteobacterial origin for three out of four enzymes. By integrating the enzymes' history into the contrasting models on the origin of eukaryotic cells, we conclude that peroxisomes most likely evolved non-symbiotically and subsequent to the acquisition of mitochondria in an archaeal host cell. [ABSTRACT FROM AUTHOR]

Recent data indicate that cell cycle transcription in many alpha-Proteobacteria is executed by at least three conserved functional modules in which pairs of antagonistic regulators act jointly, rather than in isolation, to control transcription in S-, G2- or G1-phase. Inactivation of module components often results in pleiotropic defects, ranging from cell death and impaired cell division to fairly benign deficiencies in motility. Expression of module components can follow systemic (cell cycle) or external (nutritional/cell density) cues and may be implemented by auto-regulation, ancillary regulators or other (unknown) mechanisms. Here, we highlight the recent progress in understanding the molecular events and the genetic relationships of the module components in environmental, pathogenic and/or symbiotic alpha-proteobacterial genera. Additionally, we take advantage of the recent genome-wide transcriptional analyses performed in the model alpha-Proteobacterium Caulobacter crescentus to illustrate the complexity of the interactions of the global regulators at selected cell cycle-regulated promoters and we detail the consequences of (mis-)expression when the regulators are absent. This review thus provides the first detailed mechanistic framework for understanding orthologous operational principles acting on cell cycle-regulated promoters in other alpha-Proteobacteria. [ABSTRACT FROM AUTHOR]

In α-proteobacteria, strict regulation of cell cycle progression is necessary for the specific cellular differentiation required for adaptation to diverse environmental niches. The symbiotic lifestyle of Sinorhizobium meliloti requires a drastic cellular differentiation that includes genome amplification. To achieve polyploidy, the S. meliloti cell cycle program must be altered to uncouple DNA replication from cell division. In the α-proteobacterium Caulobacter crescentus, cell cycle-regulated transcription plays an important role in the control of cell cycle progression but this has not been demonstrated in other α-proteobacteria. Here we describe a robust method for synchronizing cell growth that enabled global analysis of S. meliloti cell cycle-regulated gene expression. This analysis identified 462 genes with cell cycle-regulated transcripts, including several key cell cycle regulators, and genes involved in motility, attachment, and cell division. Only 28% of the 462 S. meliloti cell cycle-regulated genes were also transcriptionally cell cycle-regulated in C. crescentus. Furthermore, CtrA- and DnaA-binding motif analysis revealed little overlap between the cell cycle-dependent regulons of CtrA and DnaA in S. meliloti and C. crescentus. The predicted S. meliloti cell cycle regulon of CtrA, but not that of DnaA, was strongly conserved in more closely related α-proteobacteria with similar ecological niches as S. meliloti, suggesting that the CtrA cell cycle regulatory network may control functions of central importance to the specific lifestyles of α-proteobacteria. [ABSTRACT FROM AUTHOR]

Abstract: The repABC replication/partitioning systems are commonly found in alpha-proteobacteria plasmids and in secondary chromosomes. All of the elements required for their replication and stable maintenance are encoded within a single transcription unit: the repABC operon. The repC gene encodes an initiator protein, while RepA, RepB and centromere-like sequence (parS) direct plasmid segregation. Strains containing two or more repABC plasmids are a common feature in some alpha proteobacteria groups, indicating that the repABC plasmid family embraces several incompatibility groups. Genes encoded within repABC operons are highly dynamic: each one possess its own distinctive phylogeny and homologous recombination events are common within these operons. Additionally, alpha-proteobacterial genomes contain repAB genes not associated with the ctRNA or with repC as well as plasmids whose replication depends on a ctRNA-repC module without the participation of repAB genes. Some alphaproteobacteria have repC genes clustered with other genes that are not involved in replication/partitioning functions. These atypical associations of genes could have an important role in the origin and diversification of new plasmids. Here we evaluated the functionality and possible evolutionary consequences of one of these atypical gene associations: the repAC genes present in the Rhizobium leguminosarum plasmid pRL7. The repAC genes are organized in an operon and they are capable of sustaining replication but in an unstable manner. RepC was essential for replication, and the origin of replication resides within its coding region. In contrast, RepA plays a minor role in the negative regulation of its own transcription. [Copyright &y& Elsevier]

Abstract: Fusarium solani strain FsK (FsK), isolated from a plant pathogen-suppressive compost, grows endophytically in tomato roots and controls infestations by Fusarium oxysporum f.sp. radicis-lycopersici (FORL). The effect of root colonization by the two fungi on the diversity of rhizosphere microbial community was studied. Tomato plants were inoculated with FsK and/or FORL and rhizosphere soil was collected 8, 15 and 30 days post inoculation (dpi) and analyzed by denaturating gradient gel electrophoresis (DGGE) of PCR-amplified internal transcribed spacer (ITS) sequences of fungi and 16S rRNA gene sequences of common rhizosphere bacterial guilds like alpha-proteobacteria and pseudomonads. Cluster analysis of DGGE fingerprints showed that FsK had a transient impact on the fungal and alpha-proteobacterial community only during its endophytic stage (15 dpi), while FORL had a readily distinguished and persistent effect on the fungal community. The changes observed in the rhizosphere fungal and bacterial communities may depict the interactions of the two fungal inocula with the plant. Cloning of selected DGGE bands stimulated by FsK showed that the responsive bacteria were closely related to species known to include biological control agents (BCA). Overall, the inoculation of FsK in tomato rhizosphere did not appear to have a significant impact on the diversity of non-target microbial groups inhabiting plant rhizosphere. [Copyright &y& Elsevier]

2D and 3D cryo-electron microscopy, together with adsorption kinetics assays of ΦCb13 and ΦCbK phage-infected Caulobacter crescentus, provides insight into the mechanisms of infection. ΦCb13 and ΦCbK actively interact with the flagellum and subsequently attach to receptors on the cell pole. We present evidence that the first interaction of the phage with the bacterial flagellum takes place through a filament on the phage head. This contact with the flagellum facilitates concentration of phage particles around the receptor (i.e., the pilus portals) on the bacterial cell surface, thereby increasing the likelihood of infection. Phage head filaments have not been well characterized and their function is described here. Phage head filaments may systematically underlie the initial interactions of phages with their hosts in other systems and possibly represent a widespread mechanism of efficient phage propagation. [ABSTRACT FROM AUTHOR]

Abstract: Bacterial endosymbionts gave rise to mitochondria in a process that depended on the acquisition of protein import pathways. Modification and in some cases major re-tooling of the endosymbiont''s cellular machinery produced these pathways, establishing mitochondria as organelles common to all eukaryotic cells. The legacy of this evolutionary tinkering can be seen in the homologies and structural similarities between mitochondrial protein import machinery and modern day bacterial proteins. Comparative analysis of these systems is revealing both possible routes for the evolution of the mitochondrial membrane translocases and a greater understanding of the mechanisms behind mitochondrial protein import. This article is part of a Special Issue entitled Protein translocation across or insertion into membranes. [Copyright &y& Elsevier]

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Several closely related Mn(II)-oxidizing alpha-Proteobacteria were isolated from very different marine environments: strain SI85-9A1 from the oxic/anoxic interface of a stratified Canadian fjord, strain HTCC 2156 from the surface waters off the Oregon coast, and strain AE01 from the dorsal surface of a hydrothermal vent tubeworm. 16S rRNA analysis reveals that these isolates are part of a tight phylogenetic cluster with previously characterized members of the genus Aurantimonas. Other organisms within this clade have been isolated from disparate environments such as surface waters of the Arctic and Mediterranean seas, a deep-sea hydrothermal plume, and a Caribbean coral. Further analysis of all these strains revealed that many of them are capable of oxidizing dissolved Mn(II) and producing particulate Mn(III/IV) oxides. Strains SI85-9A1 and HTCC 2156 were characterized further. Despite sharing nearly identical 16S rRNA gene sequences with the previously described Aurantimonas coralicida, whole genome DNA-DNA hybridization indicated that their overall genomic similarity is low. Polyphasic phenotype characterization further supported distinguishing characteristics among these bacteria. Thus SI85-9A1 and HTCC 2156 are described as two new species within the family 'Aurantimonadaceae': Aurantimonas manganoxydans sp. nov. and Aurantimonas litoralis sp. nov. This clade of bacteria is widely distributed around the globe and may be important contributors to Mn cycling in many environments. Our results highlight the difficulty in utilizing 16S rRNA-based approaches to investigate the microbial ecology of Mn(II) oxidation. [ABSTRACT FROM AUTHOR]

Aims: Comparison of the microbial composition and process performance between laboratory scale processes treating domestic and vegetable oil wastewaters. Methods and Results: Two laboratory scale modified Ludzack–Ettinger processes were operated under similar operating conditions. One process was fed domestic wastewater and the other an industrial wastewater, vegetable oil effluent. Nitrogen removal capacities of the processes were similar. The industrial process exhibited a lower COD removal capacity and oxygen utilization rate, although a greater mixed liquor volatile suspended solids concentration was observed in the industrial process. Fluorescent in situ hybridization (FISH) with probes EUBmix, ALF1b, BET42a, GAM42a and HGC69a revealed that 81% and 72% of total cells stained with 4′, 6-diamidino-2-phenylindole (DAPI) within the domestic and industrial processes respectively bound to EUBmix. This indicated a slightly lower Eubacterial population within the industrial process. The alpha-proteobacteria was the dominant community in the industrial process (31% of EUBmix), while the beta-proteobacteria dominated the domestic process (33% of EUBmix). Conclusions: The findings served to establish a difference in the microbial population between the processes. Therefore, the class alpha-proteobacteria could play a primary role in the degradation of vegetable oil effluent. Significance and Impact of the Study: This research will aid in process design and retrofitting of biological processes treating vegetable oil effluent. [ABSTRACT FROM AUTHOR]

Amblyomma triste is the most prevalent tick species reported in human tick bites in Uruguay and has been found to be infected with Rickettsia parkeri, but no other microorganisms have been reported from this tick. A sample of 254 adults of A. triste was collected by flagging on vegetation in suburban areas in southern Uruguay. Pools of five ticks were assembled and a screening for the DNA from the resulting 51 pools was realized by PCR assays using primers for amplifying a fragment of 16S rRNA gene for members of Anaplasmataceae. Seventeen pools were positive (33%) and the sequenciation of the gene fragment amplified revealed the presence of a putative new Alpha-Proteobacterium (denominated Atri-uru). The phylogenetic analysis showed that this microorganism is closely related to the symbiont of I. ricinus denominated 'Candidatus Midichloria mitochondrii' and other associated organisms. This rickettsial symbiont of ticks is included in a recent new clade proposed for the Alpha subclass of the Proteobacteria. The discovery of this bacterium in A. triste is the first evidence of this group of Rickettsiales detected in the Genus Amblyomma, and the first record in South America. Also, in two of 17 positive samples a Gamma-Proteobacterium related to Francisella-like organisms was detected. [ABSTRACT FROM AUTHOR]

Abstract: Mitochondria are eukaryotic organelles that originated from a single bacterial endosymbiosis some 2 billion years ago. The transition from the ancestral endosymbiont to the modern mitochondrion has been accompanied by major changes in its protein content, the so-called proteome. These changes included complete loss of some bacterial pathways, amelioration of others and gain of completely new complexes of eukaryotic origin such as the ATP/ADP translocase and most of the mitochondrial protein import machinery. This renewal of proteins has been so extensive that only 14–16% of modern mitochondrial proteome has an origin that can be traced back to the bacterial endosymbiont. The rest consists of proteins of diverse origin that were eventually recruited to function in the organelle. This shaping of the proteome content reflects the transformation of mitochondria into a highly specialized organelle that, besides ATP production, comprises a variety of functions within the eukaryotic metabolism. Here we review recent advances in the fields of comparative genomics and proteomics that are throwing light on the origin and evolution of the mitochondrial proteome. [Copyright &y& Elsevier]

The alpha-proteobacteria displayed diverse and often unconventional life-styles. In particular, they keep close relationships with the eucaryotic cell. Their genomic organization is often atypical. Indeed, complex genomes, with two or more chromosomes that could be linear and sometimes associated with plasmids larger than one megabase, have been described. Moreover, polymorphism in genome size and topology as well as in replicon number was observed among very related bacteria, even in a same species. Alpha-proteobacteria provide a good model to study the reductive evolution, the role and origin of multiple chromosomes, and the genomic fluidity. The amount of new data harvested in the last decade should lead us to better understand emergence of bacterial life-styles and to build the conceptual basis to improve the definition of the bacterial species. [ABSTRACT FROM AUTHOR]

While much work has been carried out on cave communities that obtain energy from measurable exogenous energy sources (surface organics, sulfide or nitrite), very little work has been carried out on communities that subsist in regions of nutrient scarcity. In this study we generated a 16S SSU-rDNA clone library from an oligotrophic, bacterial community that occurs on a wall in Fairy Cave, Glenwood Springs, Colorado, in the absence of observable energy sources. Thirty-eight unique phylotypes based on restriction fragment length polymorphisms were identified and sequenced. Phylogenetic analysis of the sequences revealed that these phylotypes did not correspond to any known sequence, but were related to organisms in the bacterial divisions Proteobacteria, Actinobacteria, Cytophagales and the Low G+C gram-positive bacterial relatedness group. Comparative metabolic analysis suggests that the bacterial community subsists using a complex metabolic network, with input from trace organics within the environment or fixation of atmospheric gases using lithotrophic metabolism. Community distribution of these phylotypes is unique from previous observations in caves using cultivation, suggesting that many of the species identified are sufficiently adapted to the oligotrophic lifestyle and thus remain resistant to cultivation using standard techniques. Such oligotrophic microbial communities may reflect the principal form of life in subaerial cave environments. [ABSTRACT FROM AUTHOR]

The genus Brucella contains alpha-Proteobacteria adapted to intracellular life within cells of a variety of mammals. Controversy has arisen concerning Brucella internal taxonomy, and it has been proposed that the DNA–DNA hybridization-based genomospecies concept be applied to the genus. According to this view, only one species, Brucella melitensis, should be recognized, and the classical species should be considered as biovars (B. melitensis biovar melitensis; B. melitensis biovar abortus; etc.). However, a critical reappraisal of the species concept, a review of the population structure of bacteria and the analysis of Brucella genetic diversity by methods other than DNA–DNA hybridization show that there are no scientific grounds to apply the genomospecies concept to this genus. On the other hand, an enlarged biological species concept allows the definition of Brucella species that are consistent with molecular analyses and support the taxonomical standing of most classical species. Both the host range as a long-recognized biological criterion and the presence of species-specific markers in outer membrane protein genes and in other genes show that B. melitensis, B. abortus, B. ovis, B. canis and B. neotomae are not mere pathovars (or nomenspecies) but biologically meaningful species. The status of B. suis is, however, less clear. These approaches should be useful to define species for the marine mammal Brucella isolates, as illustrated by the grouping of the isolates from pinnipeds or from cetaceans by omp2 gene analysis. It is shown that a correct Brucella species definition is important to understand the evolution of the genus. [Copyright &y& Elsevier]

The palymerase chain reaction (PCR) was used to amplify eubacterial smaIl-subu nit (16S) ribosomal DNA (rDVA) genes from galls of the marine red alga Prionitis la nceolata Harvey (Gigartinales). These tumors consist of hypertrophied algal cells containing large number of intercellular bacteria that remain uncoltivable. PCR-amplified 16S rDNA, from surface-sterilized gall tissue plugs were cloned, sequenced, and analyzed by alignment to available small-subunit rRNA sequence (University of Illinois Ribosomal Database Project). Variable regions were identified and used to construct of fluorescently labeled, species-specific oligodeoxynucleotide probe for whole cells in situ hybridization to the gall symbiont. Probe 949 (PLANC. 949) localized the P. lanceolata bacterial symbiont in preparations from mature gall tissue. This probe did not hybridize to the rDNA of closely related bacteria included as controls in the same hybridization reactions. ln situ hybridization revealed the presence of the same bacterium in association with P. laneceolata gall formation from three central California localities. Distance and parsimony anaIyses suggest that this organism is a member of the Proteobacteria (alpha subdivision: Rhodobacter group) and is most dosely related to Roseobacrer denitrificans. [ABSTRACT FROM AUTHOR]

A broad range of Bacteria either synthesizes the compatible solutes ectoine and hydroxyectoine or employ specialized transporters for their uptake to ameliorate high osmolarity stress. Through bioinformatics of all sequenced microbial genomes, more than 4000 putative ectoine producing bacteria were recently identified (Czech et al., 2018). A subset of these putative ectoine producers encodes different types of transporters in the direct gene neighborhood of the core biosynthetic genes (ectABCD) for ectoines. Using Hyphomonas neptunium and Novosphingobium sp. LH128 as model organisms, we analyzed the synthesis, uptake and excretion of ectoines as these alphaproteobacteria possess novel types of ect gene clusters that harbor a different set of transporter genes, and in the case of Novosphingobium, also a mscS-like mechanosensitive channel gene. Here we show that H. neptunium harbors a novel sodium solute superfamily importer (EctI) exhibiting a substrate spectrum for a variety of compatible solutes. Novosphingobium sp. LH128, a pure hydroxyectoine producer, employs a major facilitator superfamily importer (EctU) with substrate-specificity for ectoine and hydroxyectoine. We were able to study the putative substrate-binding site of EctI and EctU for the substrates glycine betaine, ectoine and hydroxyectoine by modeling and docking studies, and through site-directed mutagenesis. In case of Novosphingobium sp. LH128, we showed that a knock-out mutant of EctU resulted in an hydroxyectoine secreting strain, highlighting the role of this substrate-specific importer in the recycling of the compatible solute hydroxyectoine. Furthermore, we reveal here for the first time that EctE from Novosphingobium sp. LH128 probably serves as a specific exporter for ectoines. [ABSTRACT FROM AUTHOR]

Simple Summary: Wolbachia is an intracellular bacterium that occurs in arthropods and in filarial worms. First described nearly a century ago in the reproductive tissues of Culex pipiens mosquitoes, Wolbachia is now known to occur in roughly 50% of insect species, and has been considered the most abundant intracellular bacterium on earth. In insect hosts, Wolbachia modifies reproduction in ways that facilitate spread of the microbe within the host population, but otherwise is relatively benign. In this "gene drive" capacity, Wolbachia provides a tool for manipulating mosquito populations. In mosquitoes, Wolbachia causes cytoplasmic incompatibility, in which the fusion of egg and sperm nuclei is disrupted, and eggs fail to hatch, depending on the presence/absence of Wolbachia in the parent insects. Recent findings demonstrate that Wolbachia from infected insects can be transferred into mosquito species that do not host a natural infection. When transinfected into Aedes aegypti, an important vector of dengue and Zika viruses, Wolbachia causes cytoplasmic incompatibility and, in addition, decreases the mosquito's ability to transmit viruses to humans. This review addresses the maintenance of Wolbachia in insect cell lines, which provide a tool for high-level production of infectious bacteria. In vitro technologies will improve use of Wolbachia for pest control, and provide the microbiological framework for genetic engineering of this promising biocontrol agent. The obligate intracellular microbe, Wolbachia pipientis (Rickettsiales; Anaplasmataceae), is a Gram-negative member of the alpha proteobacteria that infects arthropods and filarial worms. Although closely related to the genera Anaplasma and Ehrlichia, which include pathogens of humans, Wolbachia is uniquely associated with invertebrate hosts in the clade Ecdysozoa. Originally described in Culex pipiens mosquitoes, Wolbachia is currently represented by 17 supergroups and is believed to occur in half of all insect species. In mosquitoes, Wolbachia acts as a gene drive agent, with the potential to modify vector populations; in filarial worms, Wolbachia functions as a symbiont, and is a target for drug therapy. A small number of Wolbachia strains from supergroups A, B, and F have been maintained in insect cell lines, which are thought to provide a more permissive environment than the natural host. When transferred back to an insect host, Wolbachia produced in cultured cells are infectious and retain reproductive phenotypes. Here, I review applications of insect cell lines in Wolbachia research and describe conditions that facilitate Wolbachia infection and replication in naive host cells. Progress in manipulation of Wolbachia in vitro will enable genetic and biochemical advances that will facilitate eventual genetic engineering of this important biological control agent. [ABSTRACT FROM AUTHOR]