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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 -
Scientific Reports Sep 2021Soda lakes are saline and alkaline ecosystems that are considered to have existed since the first geological records of the world. These lakes support the growth of...
Soda lakes are saline and alkaline ecosystems that are considered to have existed since the first geological records of the world. These lakes support the growth of ecologically and economically important microorganisms due to their unique geochemistry. Microbiota members of lakes are valuable models to study the link between community structure and abiotic parameters such as pH and salinity. Lake Van is the largest endroheic lake and in this study, bacterial diversity of lake water, sediment, and pearl mullet (inci kefali; Alburnus tarichi), an endemic species of fish which are collected from different points of the lake, are studied directly and investigated meticulously using a metabarcoding approach after pre-enrichment. Bacterial community structures were identified using Next Generation Sequencing of the 16S rRNA gene. The analysis revealed that the samples of Lake Van contain high level of bacterial diversity. Direct water samples were dominated by Proteobacteria, Cyanobacteria, and Bacteroidota, on the other hand, pre-enriched water samples were dominated by Proteobacteria and Firmicutes at phylum-level. In direct sediment samples Proteobacteria, whereas in pre-enriched sediment samples Firmicutes and Proteobacteria were determined at highest level. Pre-enriched fish samples were dominated by Proteobacteria and Firmicutes at phylum-level. In this study, microbiota members of Lake Van were identified by taxonomic analysis.
Topics: Animals; Firmicutes; Fishes; Geologic Sediments; Lakes; Microbiota; Proteobacteria; RNA, Ribosomal, 16S
PubMed: 34526632
DOI: 10.1038/s41598-021-97980-3 -
BMC Genomics Sep 2009Peptidase family A1, to which pepsin belongs, had been assumed to be restricted to eukaryotes. The tertiary structure of pepsin shows two lobes with similar folds and it...
BACKGROUND
Peptidase family A1, to which pepsin belongs, had been assumed to be restricted to eukaryotes. The tertiary structure of pepsin shows two lobes with similar folds and it has been suggested that the gene has arisen from an ancient duplication and fusion event. The only sequence similarity between the lobes is restricted to the motif around the active site aspartate and a hydrophobic-hydrophobic-Gly motif. Together, these contribute to an essential structural feature known as a psi-loop. There is one such psi-loop in each lobe, and so each lobe presents an active Asp. The human immunodeficiency virus peptidase, retropepsin, from peptidase family A2 also has a similar fold but consists of one lobe only and has to dimerize to be active. All known members of family A1 show the bilobed structure, but it is unclear if the ancestor of family A1 was similar to an A2 peptidase, or if the ancestral retropepsin was derived from a half-pepsin gene. The presence of a pepsin homologue in a prokaryote might give insights into the evolution of the pepsin family.
RESULTS
Homologues of the aspartic peptidase pepsin have been found in the completed genomic sequences from seven species of bacteria. The bacterial homologues, unlike those from eukaryotes, do not possess signal peptides, and would therefore be intracellular acting at neutral pH. The bacterial homologues have Thr218 replaced by Asp, a change which in renin has been shown to confer activity at neutral pH. No pepsin homologues could be detected in any archaean genome.
CONCLUSION
The peptidase family A1 is found in some species of bacteria as well as eukaryotes. The bacterial homologues fall into two groups, one from oceanic bacteria and one from plant symbionts. The bacterial homologues are all predicted to be intracellular proteins, unlike the eukaryotic enzymes. The bacterial homologues are bilobed like pepsin, implying that if no horizontal gene transfer has occurred the duplication and fusion event might be very ancient indeed, preceding the divergence of bacteria and eukaryotes. It is unclear whether all the bacterial homologues are derived from horizontal gene transfer, but those from the plant symbionts probably are. The homologues from oceanic bacteria are most closely related to memapsins (or BACE-1 and BACE-2), but are so divergent that they are close to the root of the phylogenetic tree and to the division of the A1 family into two subfamilies.
Topics: Amino Acid Sequence; Bacterial Proteins; Evolution, Molecular; Genome, Bacterial; Humans; Molecular Sequence Data; Pepsin A; Phylogeny; Proteobacteria; Sequence Alignment
PubMed: 19758436
DOI: 10.1186/1471-2164-10-437 -
BMC Microbiology Oct 2021The Rhizobiales (Proteobacteria) order is an abundant and diverse group of microorganisms, being extensively studied for its lifestyle based on the association with...
BACKGROUND
The Rhizobiales (Proteobacteria) order is an abundant and diverse group of microorganisms, being extensively studied for its lifestyle based on the association with plants, animals, and humans. New studies have demonstrated that the last common ancestor (LCA) of Rhizobiales had a free-living lifestyle, but the phylogenetic and metabolism characterization of basal lineages remains unclear. Here, we used a high-resolution phylogenomic approach to test the monophyly of the Aestuariivirgaceae family, a new taxonomic group of Rhizobiales. Furthermore, a deep metabolic investigation provided an overview of the main functional traits that can be associated with its lifestyle. We hypothesized that the presence of pathways (e.g., Glycolysis/Gluconeogenesis) and the absence of pathogenic genes would be associated with a free-living lifestyle in Aestuariivirgaceae.
RESULTS
Using high-resolution phylogenomics approaches, our results revealed a clear separation of Aestuariivirgaceae into a distinct clade of other Rhizobiales family, suggesting a basal split early group and corroborate the monophyly of this group. A deep functional annotation indicated a metabolic versatility, which includes putative genes related to sugar degradation and aerobic respiration. Furthermore, many of these traits could reflect a basal metabolism and adaptations of Rhizobiales, as such the presence of Glycolysis/Gluconeogenesis pathway and the absence of pathogenicity genes, suggesting a free-living lifestyle in the Aestuariivirgaceae members.
CONCLUSIONS
Aestuariivirgaceae (Rhizobiales) family is a monophyletic taxon of the Rhizobiales with a free-living lifestyle and a versatile metabolism that allows these microorganisms to survive in the most diverse microbiomes, demonstrating their adaptability to living in systems with different conditions, such as extremely cold environments to tropical rivers.
Topics: Evolution, Molecular; Geologic Sediments; Metabolic Networks and Pathways; Metagenome; Metagenomics; Phylogeny; Proteobacteria; Seawater
PubMed: 34711170
DOI: 10.1186/s12866-021-02354-4 -
Applied and Environmental Microbiology Sep 2019Microorganisms that release plant-available phosphate from natural soil phosphate stores may serve as biological alternatives to costly and environmentally damaging...
Microorganisms that release plant-available phosphate from natural soil phosphate stores may serve as biological alternatives to costly and environmentally damaging phosphate fertilizers. To explore this possibility, we engineered a collection of root bacteria to release plant-available orthophosphate from phytate, an abundant phosphate source in many soils. We identified 82 phylogenetically diverse phytase genes, refactored their sequences for optimal expression in , and then synthesized and engineered them into the genomes of three root-colonizing bacteria. Liquid culture assays revealed 41 engineered strains with high levels of phytate hydrolysis. Among these, we identified 12 strains across three bacterial hosts that confer a growth advantage on the model plant when phytate is the sole phosphate source. These data demonstrate that DNA synthesis approaches can be used to generate plant-associated strains with novel phosphate-solubilizing capabilities. Phosphate fertilizers are essential for high-yield agriculture yet are costly and environmentally damaging. Microbes that release soluble phosphate from naturally occurring sources in the soil are appealing, as they may reduce the need for such fertilizers. In this study, we used synthetic biology approaches to create a collection of engineered root-associated microbes with the ability to release phosphate from phytate. We demonstrate that these strains improve plant growth under phosphorus-limited conditions. This represents a first step in the development of phosphate-mining bacteria for future use in crop systems.
Topics: Arabidopsis; Microorganisms, Genetically-Modified; Phosphates; Phytic Acid; Plant Roots; Proteobacteria
PubMed: 31285192
DOI: 10.1128/AEM.01210-19 -
Gut Microbes Sep 2020The understanding of the effects of compounds on the gut microbiome is limited. In particular, it is unclear whether structurally similar compounds would have similar or...
The understanding of the effects of compounds on the gut microbiome is limited. In particular, it is unclear whether structurally similar compounds would have similar or distinct effects on the gut microbiome. Here, we selected berberine (BBR), an isoquinoline quaternary alkaloid, and 16 structural analogs and evaluated their effects on seven individual gut microbiomes cultured . The responses of the individual microbiomes were evaluated by metaproteomic profiles and by assessing butyrate production. We show that both interindividual differences and compound treatments significantly contributed to the variance of metaproteomic profiles. BBR and eight analogs led to changes in proteins involved in microbial defense and stress responses and enrichment of proteins from Verrucomicrobia, Proteobacteria, and Bacteroidetes phyla. It also led to a decrease in proteins from the Firmicutes phylum and its Clostridiales order which correlated to decrease proteins involved in the butyrate production pathway and butyrate concentration. Three of the compounds, sanguinarine, chelerythrine, and ethoxysanguinarine, activated bacterial protective mechanisms, enriched Proteobacteria, increased opacity proteins, and markedly reduced butyrate production. Dihydroberberine had a similar function to BBR in enriching the genus. In addition, it showed less overall adverse impacts on the functionality of the gut microbiome, including a better maintenance of the butyrate level. Our study shows that microbiome assay can assess differential regulating effects of compounds with subtle differences and reveals that compound analogs can have distinct effects on the microbiome.
Topics: Bacterial Proteins; Bacteroidetes; Berberine; Biological Variation, Population; Butyrates; Firmicutes; Gastrointestinal Microbiome; Humans; Metabolic Networks and Pathways; Molecular Structure; Proteobacteria; Proteomics; Verrucomicrobia
PubMed: 32372706
DOI: 10.1080/19490976.2020.1755413 -
PloS One 2020Management practices such as tillage, crop rotation, irrigation, organic and inorganic inputs application are known to influence diversity and function of soil microbial...
Management practices such as tillage, crop rotation, irrigation, organic and inorganic inputs application are known to influence diversity and function of soil microbial populations. In this study, we investigated the effect of conventional versus organic farming systems at low and high input levels on structure and diversity of prokaryotic microbial communities. Soil samples were collected from the ongoing long-term farming system comparison trials established in 2007 at Chuka and Thika in Kenya. Physicochemical parameters for each sample were analyzed. Total DNA and RNA amplicons of variable region (V4-V7) of the 16S rRNA gene were generated on an Illumina platform using the manufacturer's instructions. Diversity indices and statistical analysis were done using QIIME2 and R packages, respectively. A total of 29,778,886 high quality reads were obtained and assigned to 16,176 OTUs at 97% genetic distance across both 16S rDNA and 16S rRNA cDNA datasets. The results pointed out a histrionic difference in OTUs based on 16S rDNA and 16S rRNA cDNA. Precisely, while 16S rDNA clustered by site, 16S rRNA cDNA clustered by farming systems. In both sites and systems, dominant phylotypes were affiliated to phylum Actinobacteria, Proteobacteria and Acidobacteria. Conventional farming systems showed a higher species richness and diversity compared to organic farming systems, whilst 16S rRNA cDNA datasets were similar. Physiochemical factors were associated differently depending on rRNA and rDNA. Soil pH, electrical conductivity, organic carbon, nitrogen, potassium, aluminium, zinc, iron, boron and micro-aggregates showed a significant influence on the observed microbial diversity. The observed higher species diversity in the conventional farming systems can be attributed to the integration of synthetic and organic agricultural inputs. These results show that the type of inputs used in a farming system not only affect the soil chemistry but also the microbial population dynamics and eventually the functional roles of these microbes.
Topics: Acidobacteria; Agriculture; DNA, Bacterial; Kenya; Microbiota; Organic Agriculture; Proteobacteria; RNA, Ribosomal, 16S; Soil Microbiology
PubMed: 32790770
DOI: 10.1371/journal.pone.0236574 -
International Journal of Environmental... Sep 2017Hot spring water may harbour emerging waterborne opportunistic pathogens that can cause infections in humans. We have investigated the diversity and antimicrobial...
Hot spring water may harbour emerging waterborne opportunistic pathogens that can cause infections in humans. We have investigated the diversity and antimicrobial resistance of culturable emerging and opportunistic bacterial pathogens, in water and sediment of hot springs located in Limpopo, South Africa. Aerobic bacteria were cultured and identified using 16S ribosomal DNA (rDNA) gene sequencing. The presence of spp. was investigated using real-time polymerase chain reaction. Isolates were tested for resistance to ten antibiotics representing six different classes: β-lactam (carbenicillin), aminoglycosides (gentamycin, kanamycin, streptomycin), tetracycline, amphenicols (chloramphenicol, ceftriaxone), sulphonamides (co-trimoxazole) and quinolones (nalidixic acid, norfloxacin). Gram-positive sp. and sp. and gram-negative sp., sp., sp., sp., sp. and sp. were isolated, all recognised as emerging food-borne pathogens. spp. was not detected throughout the study. Isolates of , and and an unknown species of the class Gammaproteobacteria were resistant to two antibiotics in different combinations of carbenicillin, ceftriaxone, nalidixic acid and chloramphenicol. sp. was sensitive to all ten antibiotics. This study suggests that hot springs are potential reservoirs for emerging opportunistic pathogens, including multiple antibiotic resistant strains, and highlights the presence of unknown populations of emerging and potential waterborne opportunistic pathogens in the environment.
Topics: Actinobacteria; Anti-Bacterial Agents; DNA, Ribosomal; Drug Resistance, Bacterial; Environmental Monitoring; Geologic Sediments; Hot Springs; Phylogeny; Proteobacteria; South Africa; Water Pollutants
PubMed: 28914802
DOI: 10.3390/ijerph14091070 -
Applied and Environmental Microbiology Aug 2011Members of the neutrophilic iron-oxidizing candidate class Zetaproteobacteria have predominantly been found at sites of microbially mediated iron oxidation in marine...
Members of the neutrophilic iron-oxidizing candidate class Zetaproteobacteria have predominantly been found at sites of microbially mediated iron oxidation in marine environments around the Pacific Ocean. Eighty-four full-length (>1,400-bp) and 48 partial-length Zetaproteobacteria small-subunit (SSU) rRNA gene sequences from five novel clone libraries, one novel Zetaproteobacteria isolate, and the GenBank database were analyzed to assess the biodiversity of this burgeoning class of the Proteobacteria and to investigate its biogeography between three major sampling regions in the Pacific Ocean: Loihi Seamount, the Southern Mariana Trough, and the Tonga Arc. Sequences were grouped into operational taxonomic units (OTUs) on the basis of a 97% minimum similarity. Of the 28 OTUs detected, 13 were found to be endemic to one of the three main sampling regions and 2 were ubiquitous throughout the Pacific Ocean. Additionally, two deeply rooted OTUs that potentially dominate communities of iron oxidizers originating in the deep subsurface were identified. Spatial autocorrelation analysis and analysis of molecular variance (AMOVA) showed that geographic distance played a significant role in the distribution of Zetaproteobacteria biodiversity, whereas environmental parameters, such as temperature, pH, or total Fe concentration, did not have a significant effect. These results, detected using the coarse resolution of the SSU rRNA gene, indicate that the Zetaproteobacteria have a strong biogeographic signal.
Topics: Base Sequence; Biodiversity; DNA, Bacterial; Iron; Molecular Sequence Data; Oxidation-Reduction; Pacific Ocean; Phylogeny; Phylogeography; Proteobacteria; RNA, Ribosomal; Seawater; Sequence Analysis, DNA
PubMed: 21666021
DOI: 10.1128/AEM.00533-11 -
Microbiology and Molecular Biology... Mar 2001The P(II) family of signal transduction proteins are among the most widely distributed signal proteins in the bacterial world. First identified in 1969 as a component of... (Review)
Review
The P(II) family of signal transduction proteins are among the most widely distributed signal proteins in the bacterial world. First identified in 1969 as a component of the glutamine synthetase regulatory apparatus, P(II) proteins have since been recognized as playing a pivotal role in control of prokaryotic nitrogen metabolism. More recently, members of the family have been found in higher plants, where they also potentially play a role in nitrogen control. The P(II) proteins can function in the regulation of both gene transcription, by modulating the activity of regulatory proteins, and the catalytic activity of enzymes involved in nitrogen metabolism. There is also emerging evidence that they may regulate the activity of proteins required for transport of nitrogen compounds into the cell. In this review we discuss the history of the P(II) proteins, their structures and biochemistry, and their distribution and functions in prokaryotes. We survey data emerging from bacterial genome sequences and consider other likely or potential targets for control by P(II) proteins.
Topics: Bacteria; Bacterial Proteins; Biological Transport; Carrier Proteins; Cyanobacteria; Glutamate-Ammonia Ligase; Nitrogen; PII Nitrogen Regulatory Proteins; Phosphorylation; Plant Proteins; Proteobacteria; Signal Transduction; Structure-Activity Relationship; Transcription Factors
PubMed: 11238986
DOI: 10.1128/MMBR.65.1.80-105.2001