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Cell Host & Microbe Nov 2022Gut-microbiota membership is associated with diverse neuropsychological outcomes, including substance use disorders (SUDs). Here, we use mice colonized with Citrobacter...
Gut-microbiota membership is associated with diverse neuropsychological outcomes, including substance use disorders (SUDs). Here, we use mice colonized with Citrobacter rodentium or the human γ-Proteobacteria commensal Escherichia coli HS as a model to examine the mechanistic interactions between gut microbes and host responses to cocaine. We find that cocaine exposure increases intestinal norepinephrine levels that are sensed through the bacterial adrenergic receptor QseC to promote intestinal colonization of γ-Proteobacteria. Colonized mice show enhanced host cocaine-induced behaviors. The neuroactive metabolite glycine, a bacterial nitrogen source, is depleted in the gut and cerebrospinal fluid of colonized mice. Systemic glycine repletion reversed, and γ-Proteobacteria mutated for glycine uptake did not alter the host response to cocaine. γ-Proteobacteria modulated glycine levels are linked to cocaine-induced transcriptional plasticity in the nucleus accumbens through glutamatergic transmission. The mechanism outline here could potentially be exploited to modulate reward-related brain circuits that contribute to SUDs.
Topics: Mice; Humans; Animals; Cocaine; Proteobacteria; Citrobacter rodentium; Gastrointestinal Microbiome; Bacteria; Escherichia coli; Glycine
PubMed: 36323315
DOI: 10.1016/j.chom.2022.09.014 -
Current Biology : CB Mar 2023Muñoz-Gómez and Hess introduce purple photosymbioses, which involve a heterotrophic protist host and anoxygenic photosymbionts from the phylum Proteobacteria.
Muñoz-Gómez and Hess introduce purple photosymbioses, which involve a heterotrophic protist host and anoxygenic photosymbionts from the phylum Proteobacteria.
Topics: Proteobacteria; Symbiosis; Photosynthesis
PubMed: 36917934
DOI: 10.1016/j.cub.2023.01.015 -
Microbiology (Reading, England) Jun 2011The 'iron bacteria' are a collection of morphologically and phylogenetically heterogeneous prokaryotes. They include some of the first micro-organisms to be observed and... (Review)
Review
The 'iron bacteria' are a collection of morphologically and phylogenetically heterogeneous prokaryotes. They include some of the first micro-organisms to be observed and described, and continue to be the subject of a considerable body of fundamental and applied microbiological research. While species of iron-oxidizing bacteria can be found in many different phyla, most are affiliated with the Proteobacteria. The latter can be subdivided into four main physiological groups: (i) acidophilic, aerobic iron oxidizers; (ii) neutrophilic, aerobic iron oxidizers; (iii) neutrophilic, anaerobic (nitrate-dependent) iron oxidizers; and (iv) anaerobic photosynthetic iron oxidizers. Some species (mostly acidophiles) can reduce ferric iron as well as oxidize ferrous iron, depending on prevailing environmental conditions. This review describes what is currently known about the phylogenetic and physiological diversity of the iron-oxidizing proteobacteria, their significance in the environment (on the global and micro scales), and their increasing importance in biotechnology.
Topics: Biotechnology; Environmental Microbiology; Iron; Oxidation-Reduction; Phylogeny; Proteobacteria
PubMed: 21511765
DOI: 10.1099/mic.0.045344-0 -
Frontiers in Bioscience (Landmark... Jan 2012Spatial and temporal control of cell differentiation and morphogenesis plays a key role in prokaryotes as well as eukaryotes. This is particularly important for bacteria... (Review)
Review
Spatial and temporal control of cell differentiation and morphogenesis plays a key role in prokaryotes as well as eukaryotes. This is particularly important for bacteria that divide asymmetrically, as they generate two morphologically and functionally distinct daughter cells. Several alpha-proteobacteria, including the aquatic, free-living Caulobacter crescentus, the symbiotic rhizobia and the plant and animal pathogens Agrobacterium and Brucella, have been shown to undergo asymmetrical division. C. crescentus has become a model system for the study of the regulatory networks, in particular the control of the cell cycle, the cytokinetic machinery, the cytoskeleton and the functions required for duplication and differentiation in general. As the bulk of these regulatory networks and functions is conserved in most alpha-proteobacteria, we recapitulate the recent advances in understanding these spatially and temporally controlled processes, focusing on cell cycle progression, DNA replication and partitioning, cell division and regulation of specific phenotypes that vary during the cell cycle or in the case of different lifestyles (like extracellular polysaccharide production) in C. crescentus and other alpha-proteobacteria.
Topics: Alphaproteobacteria; Cell Cycle; Chromosomes, Bacterial
PubMed: 22201830
DOI: 10.2741/4013 -
Annual Review of Microbiology Sep 2018The stringent response to nutrient deprivation is a stress response found throughout the bacterial domain of life. Although first described in proteobacteria for... (Review)
Review
The stringent response to nutrient deprivation is a stress response found throughout the bacterial domain of life. Although first described in proteobacteria for matching ribosome synthesis to the cell's translation status and for preventing formation of defective ribosomal particles, the response is actually much broader, regulating many hundreds of genes-some positively, some negatively. Utilization of the signaling molecules ppGpp and pppGpp for this purpose is ubiquitous in bacterial evolution, although the mechanisms employed vary. In proteobacteria, the signaling molecules typically bind to two sites on RNA polymerase, one at the interface of the β' and ω subunits and one at the interface of the β' secondary channel and the transcription factor DksA. The β' secondary channel is targeted by other transcription regulators as well. Although studies on the transcriptional outputs of the stringent response date back at least 50 years, the mechanisms responsible are only now coming into focus.
Topics: DNA-Directed RNA Polymerases; Gene Expression Regulation, Bacterial; Guanosine Pentaphosphate; Guanosine Tetraphosphate; Proteobacteria; Stress, Physiological; Transcription Factors
PubMed: 30200857
DOI: 10.1146/annurev-micro-090817-062444 -
Environmental Microbiology Jan 2018The type VI secretion system (T6SS) is a bacterial nanomachine used to inject effectors into prokaryotic or eukaryotic cells and is thus involved in both host... (Review)
Review
The type VI secretion system (T6SS) is a bacterial nanomachine used to inject effectors into prokaryotic or eukaryotic cells and is thus involved in both host manipulation and interbacterial competition. The T6SS is widespread among Gram-negative bacteria, mostly within the Proteobacterium Phylum. This secretion system is commonly found in commensal and pathogenic plant-associated bacteria. Phylogenetic analysis of phytobacterial T6SS clusters shows that they are distributed in the five main clades previously described (group 1-5). The even distribution of the system among commensal and pathogenic phytobacteria suggests that the T6SS provides fitness and colonization advantages in planta and that the role of the T6SS is not restricted to virulence. This manuscript reviews the phylogeny and biological roles of the T6SS in plant-associated bacteria, highlighting a remarkable diversity both in terms of mechanism and function.
Topics: Bacterial Proteins; Phylogeny; Plant Diseases; Plants; Proteobacteria; Type VI Secretion Systems; Virulence
PubMed: 29027348
DOI: 10.1111/1462-2920.13956 -
Marine Drugs Sep 2013After years of inadequate use and the emergence of multidrug resistant (MDR) strains, the efficiency of "classical" antibiotics has decreased significantly. New drugs to... (Review)
Review
After years of inadequate use and the emergence of multidrug resistant (MDR) strains, the efficiency of "classical" antibiotics has decreased significantly. New drugs to fight MDR strains are urgently needed. Bacteria hold much promise as a source of unusual bioactive metabolites. However, the potential of marine bacteria, except for Actinomycetes and Cyanobacteria, has been largely underexplored. In the past two decades, the structures of several antimicrobial compounds have been elucidated in marine Proteobacteria. Of these compounds, polyketides (PKs), synthesised by condensation of malonyl-coenzyme A and/or acetyl-coenzyme A, and non-ribosomal peptides (NRPs), obtained through the linkage of (unusual) amino acids, have recently generated particular interest. NRPs are good examples of naturally modified peptides. Here, we review and compile the data on the antimicrobial peptides isolated from marine Proteobacteria, especially NRPs.
Topics: Animals; Anti-Infective Agents; Humans; Peptides; Proteobacteria; Seawater; Water Microbiology
PubMed: 24084784
DOI: 10.3390/md11103632 -
Genome Biology and Evolution Jun 2023The determination of the last common ancestor (LCA) of a group of species plays a vital role in evolutionary theory. Traditionally, an LCA is inferred by the rooting of...
The determination of the last common ancestor (LCA) of a group of species plays a vital role in evolutionary theory. Traditionally, an LCA is inferred by the rooting of a fully resolved species tree. From a theoretical perspective, however, inference of the LCA amounts to the reconstruction of just one branch-the root branch-of the true species tree and should therefore be a much easier task than the full resolution of the species tree. Discarding the reliance on a hypothesized species tree and its rooting leads us to reevaluate what phylogenetic signal is directly relevant to LCA inference and to recast the task as that of sampling the total evidence from all gene families at the genomic scope. Here, we reformulate LCA and root inference in the framework of statistical hypothesis testing and outline an analytical procedure to formally test competing a priori LCA hypotheses and to infer confidence sets for the earliest speciation events in the history of a group of species. Applying our methods to two demonstrative data sets, we show that our inference of the opisthokonta LCA is well in agreement with the common knowledge. Inference of the proteobacteria LCA shows that it is most closely related to modern Epsilonproteobacteria, raising the possibility that it may have been characterized by a chemolithoautotrophic and anaerobic life style. Our inference is based on data comprising between 43% (opisthokonta) and 86% (proteobacteria) of all gene families. Approaching LCA inference within a statistical framework renders the phylogenomic inference powerful and robust.
Topics: Phylogeny; Biological Evolution; Genomics; Genome; Eukaryota; Proteobacteria
PubMed: 37247390
DOI: 10.1093/gbe/evad096 -
Microbial Physiology 2021Heterotrophic Proteobacteria are versatile opportunists that have been extensively studied as model organisms in the laboratory, as both pathogens and beneficial...
Heterotrophic Proteobacteria are versatile opportunists that have been extensively studied as model organisms in the laboratory, as both pathogens and beneficial symbionts of plants and animals, and as ubiquitous organisms found free-living in many environments. Succeeding in these niches requires an ability to persist for potentially long periods of time in growth-arrested states when essential nutrients become limiting. The tendency of these bacteria to grow in dense biofilm communities frequently leads to the development of steep nutrient gradients and deprivation of interior cells even when the environment is nutrient rich. Surviving within host environments also likely requires tolerating growth arrest due to the host limiting access to nutrients and transitioning between hosts may require a period of survival in a nutrient-poor environment. Interventions to maximise plant-beneficial activities and minimise infections by bacteria will require a better understanding of metabolic and regulatory networks that contribute to starvation survival, and how these networks function in diverse organisms. Here we focus on carbon starvation as a growth-arresting condition that limits availability not only of substrates for biosynthesis but also of energy for ongoing maintenance of the electrochemical gradient across the cell envelope and cellular integrity. We first review models for studying bacterial starvation and known strategies that contribute to starvation survival. We then present the results of a survey of carbon starvation survival strategies and outcomes in ten bacterial strains, including representatives from the orders Enterobacterales and Pseudomonadales (both Gammaproteobacteria) and Burkholderiales (Betaproteobacteria). Finally, we examine differences in gene content between the highest and lowest survivors to identify metabolic and regulatory adaptations that may contribute to differences in starvation survival.
Topics: Adaptation, Physiological; Animals; Bacteria; Gammaproteobacteria; Heterotrophic Processes; Proteobacteria
PubMed: 34058747
DOI: 10.1159/000516215 -
Current Issues in Molecular Biology 2019Chloromethane is a halogenated volatile organic compound, produced in large quantities by terrestrial vegetation. After its release to the troposphere and transport to... (Review)
Review
Chloromethane is a halogenated volatile organic compound, produced in large quantities by terrestrial vegetation. After its release to the troposphere and transport to the stratosphere, its photolysis contributes to the degradation of stratospheric ozone. A better knowledge of chloromethane sources (production) and sinks (degradation) is a prerequisite to estimate its atmospheric budget in the context of global warming. The degradation of chloromethane by methylotrophic communities in terrestrial environments is a major underestimated chloromethane sink. Methylotrophs isolated from soils, marine environments and more recently from the phyllosphere have been grown under laboratory conditions using chloromethane as the sole carbon source. In addition to anaerobes that degrade chloromethane, the majority of cultivated strains were isolated in aerobiosis for their ability to use chloromethane as sole carbon and energy source. Among those, the Proteobacterium (recently reclassified as ) harbours the only characterisized 'chloromethane utilization' () pathway, so far. This pathway is not representative of chloromethane-utilizing populations in the environment as genes are rare in metagenomes. Recently, combined 'omics' biological approaches with chloromethane carbon and hydrogen stable isotope fractionation measurements in microcosms, indicated that microorganisms in soils and the phyllosphere (plant aerial parts) represent major sinks of chloromethane in contrast to more recently recognized microbe-inhabited environments, such as clouds. Cultivated chloromethane-degraders lacking the genes display a singular isotope fractionation signature of chloromethane. Moreover, 13CH3Cl labelling of active methylotrophic communities by stable isotope probing in soils identify taxa that differ from the taxa known for chloromethane degradation. These observations suggest that new biomarkers for detecting active microbial chloromethane-utilizers in the environment are needed to assess the contribution of microorganisms to the global chloromethane cycle.
Topics: Bacterial Proteins; Biodegradation, Environmental; Energy Metabolism; Geologic Sediments; Metabolic Networks and Pathways; Methanol; Methyl Chloride; Methylobacterium; Methylophilaceae; Methyltransferases; Proteobacteria; Soil Microbiology
PubMed: 31166190
DOI: 10.21775/cimb.033.149