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Molecular Microbiology Jul 1997Various bacteria are able to grow aerobically or anaerobically on malonate as sole source of carbon and energy. Independent of the mechanism for energy conservation, the... (Review)
Review
Various bacteria are able to grow aerobically or anaerobically on malonate as sole source of carbon and energy. Independent of the mechanism for energy conservation, the decarboxylation of malonate is the key reaction in the decomposition of this compound. To achieve malonate decarboxylation under physiological conditions, the substrate must be converted into an activated (thioester) derivative. We report here on the malonate decarboxylases of Malonomonas rubra and Klebsiella pneumoniae. These enzymes perform an interesting substrate activation mechanism by generating a malonyl thioester with the enzyme. Formation of the malonyl-S-enzyme involves an 'activation module' that comprises the acetylation of a specific thiol group of an acyl carrier protein (ACP) and the transfer of the ACP moiety to malonate, yielding malonyl-S-ACP and acetate. The malonyl-S-ACP is subsequently decarboxylated with regeneration of the acetyl-ACP. The malonate activation mechanism is related to the activation of citrate by citrate lyase. The relationship extends to the identical 2'-(5''-phosphoribosyl)-3'-dephospho-CoA thiol cofactor that is bound covalently to the corresponding ACP subunit. In Klebsiella pneumoniae, malonate is decarboxylated by a water-soluble enzyme complex. In the anaerobic bacterium Malonomonas rubra, malonate decarboxylation is catalysed by a set of water-soluble as well as membrane-bound enzymes that function together in converting the free energy of the decarboxylation reaction into delta muNa+. Therefore, this malonate decarboxylase includes a biotin carrier protein that accepts the CO2 moiety from malonyl-S-ACP and delivers it to a membrane-bound decarboxylase acting as a Na+ pump. Genes encoding the individual protein components that perform the decarboxylation of malonate in K. pneumoniae or M. rubra have been identified within the mdc and mad gene clusters respectively. The function of most of the derived proteins could be envisaged from sequence similarities with proteins of known functions. The genetic evidence firmly supports the idea that malonate decarboxylation is carried out by the two different decarboxylases, as deduced from the biochemical studies of the enzymes.
Topics: Bacterial Proteins; Carboxy-Lyases; Genes, Bacterial; Klebsiella pneumoniae; Malonates; Operon; Proteobacteria
PubMed: 11902724
DOI: 10.1046/j.1365-2958.1997.4611824.x -
Nature Microbiology Jul 2018Nitrogen fixation in the surface ocean impacts global marine nitrogen bioavailability and thus microbial primary productivity. Until now, cyanobacterial populations have...
Nitrogen fixation in the surface ocean impacts global marine nitrogen bioavailability and thus microbial primary productivity. Until now, cyanobacterial populations have been viewed as the main suppliers of bioavailable nitrogen in this habitat. Although PCR amplicon surveys targeting the nitrogenase reductase gene have revealed the existence of diverse non-cyanobacterial diazotrophic populations, subsequent quantitative PCR surveys suggest that they generally occur in low abundance. Here, we use state-of-the-art metagenomic assembly and binning strategies to recover nearly one thousand non-redundant microbial population genomes from the TARA Oceans metagenomes. Among these, we provide the first genomic evidence for non-cyanobacterial diazotrophs inhabiting surface waters of the open ocean, which correspond to lineages within the Proteobacteria and, most strikingly, the Planctomycetes. Members of the latter phylum are prevalent in aquatic systems, but have never been linked to nitrogen fixation previously. Moreover, using genome-wide quantitative read recruitment, we demonstrate that the discovered diazotrophs were not only widespread but also remarkably abundant (up to 0.3% of metagenomic reads for a single population) in both the Pacific Ocean and the Atlantic Ocean northwest. Our results extend decades of PCR-based gene surveys, and substantiate the importance of heterotrophic bacteria in the fixation of nitrogen in the surface ocean.
Topics: Atlantic Ocean; Bacterial Proteins; Metagenomics; Nitrogen Fixation; Oxidoreductases; Pacific Ocean; Phylogeny; Planctomycetales; Proteobacteria; Water Microbiology
PubMed: 29891866
DOI: 10.1038/s41564-018-0176-9 -
Scientific Reports Feb 2022Characterization of the microbial community is essential for understanding the symbiotic relationships between microbes and host insects. Chrysomya megacephala is a...
Characterization of the microbial community is essential for understanding the symbiotic relationships between microbes and host insects. Chrysomya megacephala is a vital resource, a forensic insect, a pollinator, and a vector for enteric bacteria, protozoa, helminths, and viruses. However, research on its microbial community is incomprehensive, particularly at the pupal stage, which comprises approximately half of the entire larval development stage and is important entomological evidence in forensic medicine. For the first time, this study investigated the bacterial communities of C. megacephala pupae at different ages using third-generation sequencing technology. The results showed that C. megacephala has a diverse and dynamic bacterial community. Cluster analysis at ≥ 97% similarity produced 154 operational taxonomic units (OTUs) that belonged to 10 different phyla and were distributed into 15 classes, 28 orders, 50 families, 88 genera, and 130 species. Overall, the number of bacterial OTUs increased with the development of pupae, and the relative abundance of Wolbachia in the Day5 group was significantly lower than that in the other groups. Within the pupal stage, Proteobacteria, Firmicutes, and Bacteroidetes were the dominant phyla of bacteria. At the genus level, Wolbachia and Ignatzschineria coexisted, a rarely known feature. In addition, we found Erysipelothrix rhusiopathiae, the etiological agent of swine erysipelas, which is rarely identified in insects. This study enriches the understanding of the microbial community of C. megacephala and provides a reference for better utilization and control of C. megacephala.
Topics: Animals; Bacteroidetes; Calliphoridae; Erysipelothrix; Firmicutes; Forensic Entomology; Gammaproteobacteria; Microbiota; Proteobacteria; Pupa; RNA, Bacterial; RNA, Ribosomal, 16S; Sequence Analysis, RNA; Symbiosis; Wolbachia
PubMed: 35132164
DOI: 10.1038/s41598-022-06311-7 -
Nature Communications Jun 2017It has been hypothesized that some antibiotic resistance genes (ARGs) found in pathogenic bacteria derive from antibiotic-producing actinobacteria. Here we provide...
It has been hypothesized that some antibiotic resistance genes (ARGs) found in pathogenic bacteria derive from antibiotic-producing actinobacteria. Here we provide bioinformatic and experimental evidence supporting this hypothesis. We identify genes in proteobacteria, including some pathogens, that appear to be closely related to actinobacterial ARGs known to confer resistance against clinically important antibiotics. Furthermore, we identify two potential examples of recent horizontal transfer of actinobacterial ARGs to proteobacterial pathogens. Based on this bioinformatic evidence, we propose and experimentally test a 'carry-back' mechanism for the transfer, involving conjugative transfer of a carrier sequence from proteobacteria to actinobacteria, recombination of the carrier sequence with the actinobacterial ARG, followed by natural transformation of proteobacteria with the carrier-sandwiched ARG. Our results support the existence of ancient and, possibly, recent transfers of ARGs from antibiotic-producing actinobacteria to proteobacteria, and provide evidence for a defined mechanism.
Topics: Acinetobacter; Actinobacteria; Anti-Bacterial Agents; Bacterial Proteins; DNA Transposable Elements; Drug Resistance, Microbial; Escherichia coli; Gene Transfer, Horizontal; Phylogeny; Proteobacteria; Streptomyces
PubMed: 28589945
DOI: 10.1038/ncomms15784 -
The ISME Journal Aug 2009Small subunit (16S) rRNA gene surveys generating near full-length 16S rRNA clones offer a unique opportunity for in-depth phylogenetic analysis to highlight the breadth...
Small subunit (16S) rRNA gene surveys generating near full-length 16S rRNA clones offer a unique opportunity for in-depth phylogenetic analysis to highlight the breadth of diversity within various major bacterial phyla encountered in soil. This study offers a detailed phylogenetic analysis of the Proteobacteria-affiliated clones identified from 13,001 nearly full-length 16S rRNA gene clones derived from Oklahoma tall-grass prairie soil. Proteobacteria was the most abundant phylum in the community, and comprised 25% of the total clones. The most abundant and diverse class within the Proteobacteria was Alphaproteobacteria, followed by the Delta-, Beta- and Gammaproteobacteria. Members of the Epsilon- and Zetaproteobacteria were not detected in the dataset. Our analysis identified 15 novel order-level and 48 novel family-level Proteobacteria lineages. In addition, we show that the majority of Proteobacteria clones in the dataset belong to orders and families containing no described cultivated representatives (50% and 65%, respectively). An examination of the ecological distribution of the six most abundant Proteobacteria lineages in this dataset with no characterized pure culture representatives provided important information regarding their global distribution and environmental preferences. This level of novel phylogenetic diversity indicates that our understanding of the functions of soil microorganisms, even those belonging to phyla with numerous and diverse well-characterized cultured representatives such as the Proteobacteria, remains far from adequate.
Topics: Biodiversity; Cluster Analysis; DNA, Bacterial; DNA, Ribosomal; Oklahoma; Phylogeny; Proteobacteria; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology
PubMed: 19404326
DOI: 10.1038/ismej.2009.43 -
FEMS Microbiology Reviews Jan 2015Recent data indicate that cell cycle transcription in many alpha-Proteobacteria is executed by at least three conserved functional modules in which pairs of antagonistic... (Review)
Review
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.
Topics: Alphaproteobacteria; Caulobacter crescentus; Cell Cycle Checkpoints; Gene Expression Regulation, Bacterial; Promoter Regions, Genetic
PubMed: 25793963
DOI: 10.1093/femsre/fuu002 -
International Journal of Environmental... Sep 2019The aim of the study was to analyze the microbiological biodiversity of human foot skin with respect to factors such as age, gender, frequency of foot washing and... (Comparative Study)
Comparative Study
The aim of the study was to analyze the microbiological biodiversity of human foot skin with respect to factors such as age, gender, frequency of foot washing and physical activity, and to select indicator species to be considered when designing textile materials with antimicrobial properties used for sock and insole production. The experiment was carried out on a group of 40 people. The number of microorganisms was determined using culture-dependent methods. Biodiversity was determined using culture followed by genetic identification based on 16S rRNA gene sequencing (bacteria), ITS region (fungi), or using Illumina next-generation sequencing (in a group of eight selected individuals). The total bacterial number on women's feet was on average 1.0 × 10 CFU/cm, and was not statistically significantly different than that of men's feet (mean 1.2 × 10 CFU/cm). The number of bacteria, in most cases, decreased with age and with increased frequency of physical activity. The number of bacteria increased with diminishing feet-washing frequency; however, statistically significant differences were found between groups. The number of fungi was not significantly different amongst groups. Bacteria belonging to the phyla Firmicutes, Proteobacteria and Actinobacteria constituted the main microorganisms of the foot skin. and predominated amongst the fungi. The presence of specific species varied in groups depending on the factors mentioned above. Two of the species identified were classified as pathogens ( and ). These findings suggest that it is necessary to extend the list of microorganisms tested on textiles with respect to hygienic properties.
Topics: Adolescent; Adult; Bacteria; Biodiversity; Child; Child, Preschool; Culture Techniques; Female; Foot; Fungi; High-Throughput Nucleotide Sequencing; Humans; Infant; Male; Microbiota; Middle Aged; Proteobacteria; RNA, Ribosomal, 16S; Skin; Young Adult
PubMed: 31546968
DOI: 10.3390/ijerph16183503 -
Communications Biology Jan 2022The deep biosphere is an energy constrained ecosystem yet fosters diverse microbial communities that are key in biogeochemical cycling. Whether microbial communities in...
The deep biosphere is an energy constrained ecosystem yet fosters diverse microbial communities that are key in biogeochemical cycling. Whether microbial communities in deep biosphere groundwaters are shaped by infiltration of allochthonous surface microorganisms or the evolution of autochthonous species remains unresolved. In this study, 16S rRNA gene amplicon analyses showed that few groups of surface microbes infiltrated deep biosphere groundwaters at the Äspö Hard Rock Laboratory, Sweden, but that such populations constituted up to 49% of the microbial abundance. The dominant persisting phyla included Patescibacteria, Proteobacteria, and Epsilonbacteraeota. Despite the hydrological connection of the Baltic Sea with the studied groundwaters, infiltrating microbes predominantly originated from deep soil groundwater. Most deep biosphere groundwater populations lacked surface representatives, suggesting that they have evolved from ancient autochthonous populations. We propose that deep biosphere groundwater communities in the Fennoscandian Shield consist of selected infiltrated and indigenous populations adapted to the prevailing conditions.
Topics: Bacteria; Ecosystem; Fresh Water; Groundwater; Microbiota; Proteobacteria; Sweden
PubMed: 35017653
DOI: 10.1038/s42003-021-02980-8 -
Environmental Microbiology Reports Oct 2015This review emphasizes the biological roles of the osmoregulated periplasmic glucans (OPGs). Osmoregulated periplasmic glucans occur in almost all α-, β- and... (Review)
Review
This review emphasizes the biological roles of the osmoregulated periplasmic glucans (OPGs). Osmoregulated periplasmic glucans occur in almost all α-, β- and γ-Proteobacteria. This polymer of glucose is required for full virulence. The roles of the OPGs are complex and vary depending on the species. Here, we outline the four major roles of the OPGs through four different pathogenic and one symbiotic bacterial models (Dickeya dadantii, Salmonella enterica, Pseudomonas aeruginosa, Brucella abortus and Sinorhizobium meliloti). When periplasmic, the OPGs are a part of the signal transduction pathway and indirectly regulate genes involved in virulence. The OPGs can also be secreted. When outside of the cell, they interact directly with antibiotics to protect the bacterial cell or interact with the host cell to facilitate the invasion process. When OPGs are not found, as in the ε-Proteobacteria, OPG-like oligosaccharides are present. Their presence strengthens the evidence that OPGs play an important role in virulence.
Topics: Alphaproteobacteria; Anti-Bacterial Agents; Gammaproteobacteria; Glucans; Osmoregulation; Periplasm; Signal Transduction; Virulence
PubMed: 26265506
DOI: 10.1111/1758-2229.12325 -
Molecular Microbiology Oct 2010In addition to stress-specific responses, most bacteria can mount a general stress response (GSR), which protects the cells against a wide range of unspecific stress...
In addition to stress-specific responses, most bacteria can mount a general stress response (GSR), which protects the cells against a wide range of unspecific stress conditions. The best-understood examples of GSR are the σ(B)-cascade of Bacillus subtilis and the RpoS response in Escherichia coli. While the latter is conserved in many other proteobacteria of the ß-, γ- and δ-clades, RpoS homologues are absent in α-proteobacteria and their GSR has long been a mystery. Recent publications finally unraveled the core of the GSR in this proteobacterial class, which is mediated by EcfG-like σ-factors. EcfG activity is controlled by NepR-like anti-σ factors and PhyR-like proteins that act as anti-anti-σ factors. These unusual hybrid proteins contain an N-terminal EcfG-like domain that acts as a docking interface for NepR, and a C-terminal receiver domain typical for bacterial response regulators. Upon phosphorylation, PhyR titrates NepR away from EcfG, thereby releasing the σ-factor to recruit RNA polymerase and initiate transcription of its target genes. In this issue of Molecular Microbiology, Herrou et al. describe the function and three-dimensional structure of PhyR from Caulobacter crescentus. This structure is key to understanding the mechanism of the reversible, phosphorylation-dependent partner switching module that orchestrates the GSR in α-proteobacteria.
Topics: Alphaproteobacteria; Bacterial Proteins; Gene Expression Regulation, Bacterial; Phosphorylation; Sigma Factor; Stress, Physiological
PubMed: 20979331
DOI: 10.1111/j.1365-2958.2010.07336.x