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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 -
BMC Microbiology Nov 2007Alpha proteobacteria are one of the largest and most extensively studied groups within bacteria. However, for these bacteria as a whole and for all of its major...
BACKGROUND
Alpha proteobacteria are one of the largest and most extensively studied groups within bacteria. However, for these bacteria as a whole and for all of its major subgroups (viz. Rhizobiales, Rhodobacterales, Rhodospirillales, Rickettsiales, Sphingomonadales and Caulobacterales), very few or no distinctive molecular or biochemical characteristics are known.
RESULTS
We have carried out comprehensive phylogenomic analyses by means of Blastp and PSI-Blast searches on the open reading frames in the genomes of several alpha-proteobacteria (viz. Bradyrhizobium japonicum, Brucella suis, Caulobacter crescentus, Gluconobacter oxydans, Mesorhizobium loti, Nitrobacter winogradskyi, Novosphingobium aromaticivorans, Rhodobacter sphaeroides 2.4.1, Silicibacter sp. TM1040, Rhodospirillum rubrum and Wolbachia (Drosophila) endosymbiont). These studies have identified several proteins that are distinctive characteristics of all alpha-proteobacteria, as well as numerous proteins that are unique repertoires of all of its main orders (viz. Rhizobiales, Rhodobacterales, Rhodospirillales, Rickettsiales, Sphingomonadales and Caulobacterales) and many families (viz. Rickettsiaceae, Anaplasmataceae, Rhodospirillaceae, Acetobacteraceae, Bradyrhiozobiaceae, Brucellaceae and Bartonellaceae). Many other proteins that are present at different phylogenetic depths in alpha-proteobacteria provide important information regarding their evolution. The evolutionary relationships among alpha-proteobacteria as deduced from these studies are in excellent agreement with their branching pattern in the phylogenetic trees and character compatibility cliques based on concatenated sequences for many conserved proteins. These studies provide evidence that the major groups within alpha-proteobacteria have diverged in the following order: (Rickettsiales(Rhodospirillales (Sphingomonadales (Rhodobacterales (Caulobacterales-Parvularculales (Rhizobiales)))))). We also describe two conserved inserts in DNA Gyrase B and RNA polymerase beta subunit that are distinctive characteristics of the Sphingomonadales and Rhodosprilllales species, respectively. The results presented here also provide support for the grouping of Hyphomonadaceae and Parvularcula species with the Caulobacterales and the placement of Stappia aggregata with the Rhizobiaceae group.
CONCLUSION
The alpha-proteobacteria-specific proteins and indels described here provide novel and powerful means for the taxonomic, biochemical and molecular biological studies on these bacteria. Their functional studies should prove helpful in identifying novel biochemical and physiological characteristics that are unique to these bacteria.
Topics: Alphaproteobacteria; Amino Acid Sequence; Bacterial Proteins; Evolution, Molecular; Molecular Sequence Data; Open Reading Frames; Phylogeny; Sequence Alignment
PubMed: 18045498
DOI: 10.1186/1471-2180-7-106 -
FEMS Microbiology Ecology May 2005This paper summarizes recent data on the occurrence and properties of lithotrophic prokaryotes found in extremely alkaline, saline (soda) lakes. Among the... (Review)
Review
This paper summarizes recent data on the occurrence and properties of lithotrophic prokaryotes found in extremely alkaline, saline (soda) lakes. Among the chemolithotrophs found in these lakes the obligately autotrophic sulfur-oxidizing bacteria were the dominant, most diverse group, best adapted to haloalkaline conditions. The culturable forms are represented by three new genera, Thioalkalimicrobium, Thioalkalivibrio and Thioalkalispira in the Gammaproteobacteria. Among them, the genus Thioalkalivibrio was most metabolically diverse, including denitrifying, thiocyanate-oxidizing and facultatively alkaliphilic species. Culturable methane-oxidizing populations in the soda lakes belong to the type I methanotroph group in the Gammaproteobacteria, mostly in the genus Methylomicrobium. The nitrifying bacteria in hyposaline soda lakes were represented by a new species Nitrobacter alkalicus (Alphaproteobacteria), and by an alkaliphilic subspecies of Nitrosomonas halophila (Betaproteobacteria). Both belonged to the low salt-tolerant alkaliphiles. The facultatively autotrophic haloalkaliphilic isolates able to grow with hydrogen as electron donor were identified as representatives of the alpha-3 subclass of the Proteobacteria (aerobic) and of the Natronolimnicola - Alkalispirillum group in the gammaproteobacteria (nitrate-reducing). While all chemolithotrophic isolates from soda lakes belong to the alkaliphiles with a pH optimum for growth around 10, only the sulfur-oxidizing group included species able to grow under hypersaline conditions. This indicates that carbon and nitrogen cycles in the hypersaline alkaline lakes might not be closed.
Topics: Fresh Water; Hydrogen; Hydrogen-Ion Concentration; Methane; Nitrates; Oxidation-Reduction; Proteobacteria; Sodium Chloride; Sulfur
PubMed: 16329914
DOI: 10.1016/j.femsec.2005.02.012 -
Scientific Reports Jan 2022Intestinal gluconeogenesis (IGN), gastric bypass (GBP) and gut microbiota positively regulate glucose homeostasis and diet-induced dysmetabolism. GBP modulates gut...
Intestinal gluconeogenesis (IGN), gastric bypass (GBP) and gut microbiota positively regulate glucose homeostasis and diet-induced dysmetabolism. GBP modulates gut microbiota, whether IGN could shape it has not been investigated. We studied gut microbiota and microbiome in wild type and IGN-deficient mice, undergoing GBP or not, and fed on either a normal chow (NC) or a high-fat/high-sucrose (HFHS) diet. We also studied fecal and urine metabolome in NC-fed mice. IGN and GBP had a different effect on the gut microbiota of mice fed with NC and HFHS diet. IGN inactivation increased abundance of Deltaproteobacteria on NC and of Proteobacteria such as Helicobacter on HFHS diet. GBP increased abundance of Firmicutes and Proteobacteria on NC-fed WT mice and of Firmicutes, Bacteroidetes and Proteobacteria on HFHS-fed WT mice. The combined effect of IGN inactivation and GBP increased abundance of Actinobacteria on NC and the abundance of Enterococcaceae and Enterobacteriaceae on HFHS diet. A reduction was observed in the amounf of short-chain fatty acids in fecal (by GBP) and in both fecal and urine (by IGN inactivation) metabolome. IGN and GBP, separately or combined, shape gut microbiota and microbiome on NC- and HFHS-fed mice, and modify fecal and urine metabolome.
Topics: Actinobacteria; Animals; DNA, Bacterial; Enterobacteriaceae; Enterococcaceae; Fatty Acids, Volatile; Firmicutes; Gastric Bypass; Gastrointestinal Microbiome; Gluconeogenesis; Intestines; Male; Metabolome; Mice; Mice, Inbred C57BL; Phylogeny; Proteobacteria; Stomach
PubMed: 35082330
DOI: 10.1038/s41598-022-04902-y -
Scientific Reports Aug 2023During the processing of tobacco leaves, flue-curing and redrying can affect the structure of bacterial community, having an effect on the aging quality of tobacco...
During the processing of tobacco leaves, flue-curing and redrying can affect the structure of bacterial community, having an effect on the aging quality of tobacco leaves. In order to characterize the effects of flue-curing and redrying on the bacterial community of tobacco leaves, the bacterial community of samples at different processing stages (before flue-curing, after flue-curing, before redrying and after redrying) was analyzed using Illumina sequencing. A total of 33 phyla, 79 classes, 195 orders, 344 families, 826 genera and 7922 ASVs were obtained from 36 samples. There was no significant difference in the core bacterial groups of tobacco leaf at four processing stages. Proteobacteria dominated at the phylum level. Sphingomonas, Pseudomonas and Methylobacterium were the main genera shared by all samples. The functional prediction by PICRUSt showed an increase in the relative abundance of pathway related to metabolism after flue-curing and pathway related to environmental information processing after redrying. This study, we analyzed the changes of bacterial community and structural composition of tobacco leaves from flue-curing to redrying, and found that flue-curing had a greater effect on the microbial community than redrying. This is conducive for the exploration of microbial resources and improvement of tobacco leaf quality.
Topics: Humans; Nicotiana; Plant Leaves; Proteobacteria; Aging; Cancer Vaccines
PubMed: 37587237
DOI: 10.1038/s41598-023-40502-0 -
Molecular Microbiology May 2010The recently identified type VI secretion systems (T6SSs) are present in many pathogenic proteobacteria and are encoded by a conserved gene cluster. T6SSs contribute to... (Review)
Review
The recently identified type VI secretion systems (T6SSs) are present in many pathogenic proteobacteria and are encoded by a conserved gene cluster. T6SSs contribute to virulence development of various pathogens and are often activated upon contact with target cells. Since the identification of the T6SS, substantial progress has been made at all levels, including gene regulation, its impact on bacterial virulence, the function of effector proteins and the mechanism of secretion. Recent structural and mechanistic studies revealed unique features of the T6SS that distinguish it from other secretion systems. Structural similarities between the T6SS-specific exoproteins Hcp and VgrG and components of the cell-puncturing device of tailed bacteriophages suggest that the T6SSs mimic a bacteriophage machinery to puncture target cell membranes and to translocate effector proteins, representing a novel mechanism of effector delivery. In bacteriophages contraction of the tail sheath, which engulfs the tail tube, causes ejection of the cell-puncturing machinery. The T6SS components VipA/VipB form tubular structures, which might function as tail sheaths by engulfing Hcp proteins. The severing of VipA/VipB complexes by the AAA+ chaperone ClpV is essential for type VI protein secretion and might be linked to VipA/VipB tubule contraction, leading to the export of Hcp and VgrG.
Topics: Bacterial Proteins; Bacteriophages; Protein Conformation; Protein Transport; Proteobacteria
PubMed: 20444095
DOI: 10.1111/j.1365-2958.2010.07171.x -
FEMS Microbiology Ecology Jun 2005This review summarizes the recent advances in understanding the ecophysiological role and structure-function features of methanotrophic bacteria living in various cold... (Review)
Review
This review summarizes the recent advances in understanding the ecophysiological role and structure-function features of methanotrophic bacteria living in various cold ecosystems. The occurrence of methanotrophs in a majority of psychrosphere sites was verified by direct measurement of their methane-utilizing activity, by electron microscopy and immunofluorescent observations, and analyses of specific signatures in cellular phospholipids and total DNAs extracted from environmental samples. Surprisingly, the phenotypic and genotypic markers of virtually all extant methanotrophs were detected in various cold habitats, such as underground waters, Northern taiga and tundra soils, polar lakes and permafrost sediments. Also, recent findings indicated that even after long-term storage in permafrost, some methanotrophs can oxidize and assimilate methane not only at positive but also at subzero temperatures. Pure cultures of psychrophilic and psychrotolerant methanotrophs were isolated and characterized as new genera and species: Methylobacter psychrophilus, Methylosphaera hansonii, Methylocella palustris, Methylocella silvestris, Methylocella tundrae, Methylocapsa acidiphila and Methylomonas scandinavica. However, our knowledge about their adaptive mechanisms and survival in cold ecosystems remains limited and needs to be established using both traditional and molecular microbiological methods.
Topics: Adaptation, Biological; Cold Temperature; Ecology; Ecosystem; Geography; Methane; Methylobacteriaceae; Phylogeny; Proteobacteria
PubMed: 16329925
DOI: 10.1016/j.femsec.2005.02.010 -
Journal of Bacteriology Jan 2019We used comparative genomics to reconstruct d-galacturonic and d-glucuronic acid catabolic pathways and associated transcriptional regulons involving the tripartite...
We used comparative genomics to reconstruct d-galacturonic and d-glucuronic acid catabolic pathways and associated transcriptional regulons involving the tripartite ATP-independent periplasmic (TRAP) family transporters that bind hexuronates in proteobacteria. The reconstructed catabolic network involves novel transcription factors, catabolic enzymes, and transporters for utilization of both hexuronates and aldarates (d-glucarate and -galactarate). The reconstructed regulons for a novel GntR family transcription factor, GguR, include the majority of hexuronate/aldarate utilization genes in 47 species from the , , , and families. GudR, GulR, and UdhR are additional local regulators of some hexuronate/aldarate utilization genes in some of the above-mentioned organisms. The predicted DNA binding motifs of GguR and GudR regulators from and were validated by binding assays. Genes from the GulR- and GguR-controlled loci were differentially expressed in grown on hexuronates and aldarates. By a combination of bioinformatics and experimental techniques we identified a novel variant of the oxidative pathway for hexuronate utilization, including two previously uncharacterized subfamilies of lactone hydrolases (UxuL and UxuF). The genomic context of respective genes and reconstruction of associated pathways suggest that both enzymes catalyze the conversion of d-galactaro- and d-glucaro-1,5-lactones to the ring-opened aldarates. The activities of the purified recombinant enzymes, UxuL and UxuF, from four proteobacterial species were directly confirmed and kinetically characterized. The inferred novel aldarate-specific transporter from the tripartite tricarboxylate transporter (TTT) family transporter TctC was confirmed to bind d-glucarate This study expands our knowledge of bacterial carbohydrate catabolic pathways by identifying novel families of catabolic enzymes, transcriptional regulators, and transporters. Hexuronate catabolic pathways and their transcriptional networks are highly variable among different bacteria. We identified novel transcriptional regulators that control the hexuronate and aldarate utilization genes in four families of proteobacteria. By regulon reconstruction and genome context analysis we identified several novel components of the common hexuronate/aldarate utilization pathways, including novel uptake transporters and catabolic enzymes. Two novel families of lactonases involved in the oxidative pathway of hexuronate catabolism were characterized. Novel transcriptional regulons were validated via binding assays and gene expression studies with and species. The reconstructed catabolic pathways are interconnected with each other metabolically and coregulated via the GguR regulons in proteobacteria.
Topics: Computational Biology; Gene Expression Regulation, Bacterial; Genomics; Hexuronic Acids; Metabolic Networks and Pathways; Proteobacteria; Regulon; Transcription, Genetic
PubMed: 30249705
DOI: 10.1128/JB.00431-18 -
International Journal of Chronic... 2018Bronchiectasis is a debilitating disease with chronic airway infection. , the dominant phylum, can be detected with high-throughput sequencing.
BACKGROUND
Bronchiectasis is a debilitating disease with chronic airway infection. , the dominant phylum, can be detected with high-throughput sequencing.
OBJECTIVE
To stratify compositions according to culture findings in bronchiectasis.
PATIENTS AND METHODS
We sampled sputum, split for culture and 16srRNA sequencing, from 106 patients with stable bronchiectasis and 17 healthy subjects. Paired sputa from 22 bronchiectasis patients were collected during exacerbations and convalescence.
RESULTS
Forty-five, 41, and 20 patients with clinically stable bronchiectasis had isolated (PA), other potentially pathogenic microorganisms, and commensals at the initial visit, respectively. The PA group (but not other groups) demonstrated significantly greater relative abundance of , and lower Shannon-Wiener Diversity Index, Simpson Diversity Index, and richness compared with healthy subjects. was the dominant genus that discriminated bronchiectasis patients (particularly in the PA group) from healthy subjects. Compared with baseline levels, community compositions in the PA group, but not in other groups, were more resilient during exacerbations and convalescence.
CONCLUSION
community compositions could be partially reflected by conventional sputum bacterial culture. Significantly altered community compositions - particularly, the increased relative abundance of and diminished community diversity - represent critical targets for novel interventions to restore normal airway microen-vironment in patients with bronchiectasis.
Topics: Adolescent; Adult; Aged; Bronchiectasis; Disease Progression; Female; High-Throughput Nucleotide Sequencing; Humans; Male; Middle Aged; Proteobacteria; Pseudomonas aeruginosa; RNA, Ribosomal, 16S; Sputum; Young Adult
PubMed: 30140149
DOI: 10.2147/COPD.S159335 -
Nature Reviews. Microbiology Dec 2020Escherichia coli is considered to be the best-known microorganism given the large number of published studies detailing its genes, its genome and the biochemical... (Review)
Review
Escherichia coli is considered to be the best-known microorganism given the large number of published studies detailing its genes, its genome and the biochemical functions of its molecular components. This vast literature has been systematically assembled into a reconstruction of the biochemical reaction networks that underlie E. coli's functions, a process which is now being applied to an increasing number of microorganisms. Genome-scale reconstructed networks are organized and systematized knowledge bases that have multiple uses, including conversion into computational models that interpret and predict phenotypic states and the consequences of environmental and genetic perturbations. These genome-scale models (GEMs) now enable us to develop pan-genome analyses that provide mechanistic insights, detail the selection pressures on proteome allocation and address stress phenotypes. In this Review, we first discuss the overall development of GEMs and their applications. Next, we review the evolution of the most complete GEM that has been developed to date: the E. coli GEM. Finally, we explore three emerging areas in genome-scale modelling of microbial phenotypes: collections of strain-specific models, metabolic and macromolecular expression models, and simulation of stress responses.
Topics: Actinobacteria; Computer Simulation; Cyanobacteria; Escherichia coli; Firmicutes; Gene Regulatory Networks; Genome, Bacterial; Genomics; Metabolic Networks and Pathways; Models, Genetic; Phenotype; Proteobacteria; Stress, Physiological; Thermotoga; Whole Genome Sequencing
PubMed: 32958892
DOI: 10.1038/s41579-020-00440-4