scholarly journals Genome Sequences of Three Agrobacterium Biovars Help Elucidate the Evolution of Multichromosome Genomes in Bacteria

2009 ◽  
Vol 191 (8) ◽  
pp. 2501-2511 ◽  
Author(s):  
Steven C. Slater ◽  
Barry S. Goldman ◽  
Brad Goodner ◽  
João C. Setubal ◽  
Stephen K. Farrand ◽  
...  
Keyword(s):  
Plant Pathogens ◽  
Biochemical Properties ◽  
Gene Content ◽  
Bacterial Genomes ◽  
Associated Bacteria ◽  
Narrow Host Range ◽  
Chromosome Architecture ◽  
The Family ◽  
Chromosome Formation ◽  
Conserved Gene

ABSTRACT The family Rhizobiaceae contains plant-associated bacteria with critical roles in ecology and agriculture. Within this family, many Rhizobium and Sinorhizobium strains are nitrogen-fixing plant mutualists, while many strains designated as Agrobacterium are plant pathogens. These contrasting lifestyles are primarily dependent on the transmissible plasmids each strain harbors. Members of the Rhizobiaceae also have diverse genome architectures that include single chromosomes, multiple chromosomes, and plasmids of various sizes. Agrobacterium strains have been divided into three biovars, based on physiological and biochemical properties. The genome of a biovar I strain, A. tumefaciens C58, has been previously sequenced. In this study, the genomes of the biovar II strain A. radiobacter K84, a commercially available biological control strain that inhibits certain pathogenic agrobacteria, and the biovar III strain A. vitis S4, a narrow-host-range strain that infects grapes and invokes a hypersensitive response on nonhost plants, were fully sequenced and annotated. Comparison with other sequenced members of the Alphaproteobacteria provides new data on the evolution of multipartite bacterial genomes. Primary chromosomes show extensive conservation of both gene content and order. In contrast, secondary chromosomes share smaller percentages of genes, and conserved gene order is restricted to short blocks. We propose that secondary chromosomes originated from an ancestral plasmid to which genes have been transferred from a progenitor primary chromosome. Similar patterns are observed in select Beta- and Gammaproteobacteria species. Together, these results define the evolution of chromosome architecture and gene content among the Rhizobiaceae and support a generalized mechanism for second-chromosome formation among bacteria.

scholarly journals Detection of and Response to Signals Involved in Host-Microbe Interactions by Plant-Associated Bacteria

2005 ◽  
Vol 69 (1) ◽  
pp. 155-194 ◽  
Author(s):  
Anja Brencic ◽  
Stephen C. Winans
Keyword(s):  
Pseudomonas Syringae ◽  
Plant Pathogens ◽  
Root Nodules ◽  
Complex Nature ◽  
Natural Environments ◽  
Associated Bacteria ◽  
Bacterial Physiology ◽  
The Family ◽  
Microbe Interactions ◽  
Host Detection

SUMMARY Diverse interactions between hosts and microbes are initiated by the detection of host-released chemical signals. Detection of these signals leads to altered patterns of gene expression that culminate in specific and adaptive changes in bacterial physiology that are required for these associations. This concept was first demonstrated for the members of the family Rhizobiaceae and was later found to apply to many other plant-associated bacteria as well as to microbes that colonize human and animal hosts. The family Rhizobiaceae includes various genera of rhizobia as well as species of Agrobacterium. Rhizobia are symbionts of legumes, which fix nitrogen within root nodules, while Agrobacterium tumefaciens is a pathogen that causes crown gall tumors on a wide variety of plants. The plant-released signals that are recognized by these bacteria are low-molecular-weight, diffusible molecules and are detected by the bacteria through specific receptor proteins. Similar phenomena are observed with other plant pathogens, including Pseudomonas syringae, Ralstonia solanacearum, and Erwinia spp., although here the signals and signal receptors are not as well defined. In some cases, nutritional conditions such as iron limitation or the lack of nitrogen sources seem to provide a significant cue. While much has been learned about the process of host detection over the past 20 years, our knowledge is far from being complete. The complex nature of the plant-microbe interactions makes it extremely challenging to gain a comprehensive picture of host detection in natural environments, and thus many signals and signal recognition systems remain to be described.

scholarly journals Evolutionary genomics of APSE: a tailed phage that lysogenically converts the bacterium Hamiltonella defensa into a heritable protective symbiont of aphids

2021 ◽  
Vol 18 (1) ◽  
Author(s):  
Bret M. Boyd ◽  
Germain Chevignon ◽  
Vilas Patel ◽  
Kerry M. Oliver ◽  
Michael R. Strand
Keyword(s):  
Enteric Bacteria ◽  
Gene Content ◽  
Comparative Genomic ◽  
Bacterial Genomes ◽  
Virion Assembly ◽  
Phylogenetic Studies ◽  
Double Stranded Dna ◽  
The Family ◽  
Hamiltonella Defensa ◽  
Insect Symbionts

Abstract Background Most phages infect free-living bacteria but a few have been identified that infect heritable symbionts of insects or other eukaryotes. Heritable symbionts are usually specialized and isolated from other bacteria with little known about the origins of associated phages. Hamiltonella defensa is a heritable bacterial symbiont of aphids that is usually infected by a tailed, double-stranded DNA phage named APSE. Methods We conducted comparative genomic and phylogenetic studies to determine how APSE is related to other phages and prophages. Results Each APSE genome was organized into four modules and two predicted functional units. Gene content and order were near-fully conserved in modules 1 and 2, which encode predicted DNA metabolism genes, and module 4, which encodes predicted virion assembly genes. Gene content of module 3, which contains predicted toxin, holin and lysozyme genes differed among haplotypes. Comparisons to other sequenced phages suggested APSE genomes are mosaics with modules 1 and 2 sharing similarities with Bordetella-Bcep-Xylostella fastidiosa-like podoviruses, module 4 sharing similarities with P22-like podoviruses, and module 3 sharing no similarities with known phages. Comparisons to other sequenced bacterial genomes identified APSE-like elements in other heritable insect symbionts (Arsenophonus spp.) and enteric bacteria in the family Morganellaceae. Conclusions APSEs are most closely related to phage elements in the genus Arsenophonus and other bacteria in the Morganellaceae.

scholarly journals Conserved Gene Clusters in Bacterial Genomes Provide Further Support for the Primacy of RNA

1997 ◽  
Vol 45 (5) ◽  
pp. 467-472 ◽  
Author(s):  
Janet L. Siefert ◽  
Kirt A. Martin ◽  
Fadi Abdi ◽  
William R. Widger ◽  
George E. Fox
Keyword(s):  
Gene Clusters ◽  
Bacterial Genomes ◽  
Conserved Gene

Subcellular localization and biochemical properties of the enzymes of carbamoyl phosphate and urea synthesis in the batrachoidid fishes Opsanus beta, Opsanus tau and Porichthys notatus

1995 ◽  
Vol 198 (3) ◽  
pp. 755-766 ◽  
Author(s):  
P Walsh
Keyword(s):  
Glutamine Synthetase ◽  
Subcellular Localization ◽  
Biochemical Properties ◽  
Nitrogen Excretion ◽  
Urea Synthesis ◽  
Carbamoyl Phosphate ◽  
Opsanus Beta ◽  
Opsanus Tau ◽  
Porichthys Notatus ◽  
The Family

The subcellular localization and biochemical properties of the enzymes of carbamoyl phosphate and urea synthesis were examined in three representatives of fishes of the family Batrachoididae, the gulf toadfish (Opsanus beta), the oyster toadfish (Opsanus tau) and the plainfin midshipman (Porichthys notatus). The primary objective of the study was to compare the biochemical characteristics of these fishes, which represent a range between ammoniotelism and ureotelism (O. beta being facultatively ureotelic), with previous patterns observed for an ammoniotelic teleost (Micropterus salmoides, the largemouth bass) and an obligate ureogenic elasmobranch (Squalus acanthias, the dogfish shark). The present study documents the expression of mitochondrial carbamoyl phosphate synthetase (CPSase) III and cytosolic CPSase II (and its associated enzymes of pyrimidine synthesis, dihydro-orotase and aspartate carbamoyltransferase) in the livers of all three batrachoidid species. Both mitochondrial and cytosolic activities of arginase were present in the livers of all three species, as were cytosolic glutamine synthetase and argininosuccinate synthetase and lyase. However, O. beta also showed mitochondrial glutamine synthetase activity and higher total hepatic levels of glutamine synthetase than either O. tau or P. notatus. Taken together, these observations confirm that the arrangement of these enzymes in the batrachoidid fishes has greater similarity to that of M. salmoides than to that of S. acanthias. However, differences within the family appear to coincide with the different nitrogen excretion strategies. O. tau and P. notatus are primarily ammoniotelic and most closely resemble the ammoniotelic M. salmoides, whereas ureotelism in O. beta is correlated with the presence of a mitochondrial glutamine synthetase and the ability to induce higher total glutamine synthetase activities than O. tau or P. notatus. Additionally, isolated mitochondria from O. beta were able to generate citrulline from glutamine, whereas those from O. tau were not. Also in contrast to S. acanthias, glutamine synthetase activities in the mitochondria of O. beta are consistently lower than those of CPSase III. This and other kinetic observations lend support to the hypothesis that glutamine synthetase may be an important regulatory control point in determining rates of ureogenesis in O. beta.

Multifaceted Impacts of Bacteriophages in the Plant Microbiome

2018 ◽  
Vol 56 (1) ◽  
pp. 361-380 ◽  
Author(s):  
Britt Koskella ◽  
Tiffany B. Taylor
Keyword(s):  
Host Plant ◽  
Future Study ◽  
Plant Pathogens ◽  
Ecological Interactions ◽  
Selection Pressures ◽  
Bacterial Populations ◽  
Associated Bacteria ◽  
Open Questions ◽  
Microbe Interactions ◽  
Plant Microbiome

Plant-associated bacteria face multiple selection pressures within their environments and have evolved countless adaptations that both depend on and shape bacterial phenotype and their interaction with plant hosts. Explaining bacterial adaptation and evolution therefore requires considering each of these forces independently as well as their interactions. In this review, we examine how bacteriophage viruses (phages) can alter the ecology and evolution of plant-associated bacterial populations and communities. This includes influencing a bacterial population's response to both abiotic and biotic selection pressures and altering ecological interactions within the microbiome and between the bacteria and host plant. We outline specific ways in which phages can alter bacterial phenotype and discuss when and how this might impact plant-microbe interactions, including for plant pathogens. Finally, we highlight key open questions in phage-bacteria-plant research and offer suggestions for future study.

scholarly journals Rhopalocnemis phalloides has one of the most reduced and mutated plastid genomes known

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7500 ◽  
Author(s):  
Mikhail I. Schelkunov ◽  
Maxim S. Nuraliev ◽  
Maria D. Logacheva
Keyword(s):  
Plant Species ◽  
Mutation Rate ◽  
Plastid Genome ◽  
Gene Content ◽  
High Mutation Rate ◽  
Base Pairs ◽  
Plastid Genomes ◽  
The Family

Although most plant species are photosynthetic, several hundred species have lost the ability to photosynthesize and instead obtain nutrients via various types of heterotrophic feeding. Their plastid genomes markedly differ from the plastid genomes of photosynthetic plants. In this work, we describe the sequenced plastid genome of the heterotrophic plant Rhopalocnemis phalloides, which belongs to the family Balanophoraceae and feeds by parasitizing other plants. The genome is highly reduced (18,622 base pairs vs. approximately 150 kbp in autotrophic plants) and possesses an extraordinarily high AT content, 86.8%, which is inferior only to AT contents of plastid genomes of Balanophora, a genus from the same family. The gene content of this genome is quite typical of heterotrophic plants, with all of the genes related to photosynthesis having been lost. The remaining genes are notably distorted by a high mutation rate and the aforementioned AT content. The high AT content has led to sequence convergence between some of the remaining genes and their homologs from AT-rich plastid genomes of protists. Overall, the plastid genome of R. phalloides is one of the most unusual plastid genomes known.

scholarly journals Identification and biochemical characterization of a novel PP2C-like Ser/Thr phosphatase inE. coli

2018 ◽  
Author(s):  
Krithika Rajagopalan ◽  
Jonathan Dworkin
Keyword(s):  
Biochemical Characterization ◽  
Regulatory Protein ◽  
Biochemical Properties ◽  
Bacterial Genomes ◽  
Phosphatase Inhibitors ◽  
E Coli ◽  
Specificity And Sensitivity ◽  
Genes Encoding ◽  
Number Of Bacteria

AbstractIn bacteria, signaling phosphorylation is thought to occur primarily on His and Asp residues. However, phosphoproteomic surveys in phylogenetically diverse bacteria over the past decade have identified numerous proteins that are phosphorylated on Ser and/or Thr residues. Consistently, genes encoding Ser/Thr kinases are present in many bacterial genomes such asE. coli,which encodes at least three Ser/Thr kinases. Since Ser/Thr phosphorylation is a stable modification, a dedicated phosphatase is necessary to allow reversible regulation. Ser/Thr phosphatases belonging to several conserved families are found in bacteria. One family of particular interest are Ser/Thr phosphatases which have extensive sequence and structural homology to eukaryotic Ser/Thr PP2C phosphatases. These proteins, called eSTPs (eukaryotic-like Ser/Thr phosphatases), have been identified in a number of bacteria, but not inE. coli.Here, we describe a previously unknown eSTP encoded by anE. coliORF,yegK,and characterize its biochemical properties including its kinetics, substrate specificity and sensitivity to known phosphatase inhibitors. We investigate differences in the activity of this protein in closely relatedE. colistrains. Finally, we demonstrate that this eSTP acts to dephosphorylate a novel Ser/Thr kinase which is encoded in the same operon.ImportanceRegulatory protein phosphorylation is a conserved mechanism of signaling in all biological systems. Recent phosphoproteomic analyses of phylogenetically diverse bacteria including the model Gram-negative bacteriumE. colidemonstrate that many proteins are phosphorylated on serine or threonine residues. In contrast to phosphorylation on histidine or aspartate residues, phosphorylation of serine and threonine residues is stable and requires the action of a partner Ser/Thr phosphatase to remove the modification. Although a number of Ser/Thr kinases have been reported inE. coli, no partner Ser/Thrphosphatases have been identified. Here, we biochemically characterize a novel Ser/Thr phosphatase that acts to dephosphorylate a Ser/Thr kinase that is encoded in the same operon.

scholarly journals Location and Survival of Leaf-Associated Bacteria in Relation to Pathogenicity and Potential for Growth within the Leaf

1999 ◽  
Vol 65 (4) ◽  
pp. 1435-1443 ◽  
Author(s):  
M. Wilson ◽  
S. S. Hirano ◽  
S. E. Lindow
Keyword(s):  
Pseudomonas Syringae ◽  
Plant Pathogens ◽  
Vacuum Infiltration ◽  
Associated Bacteria ◽  
Growth And Survival ◽  
Total Leaf ◽  
Spray Inoculation ◽  
Dry Conditions ◽  
Population Sizes ◽  
Better Than

ABSTRACT The growth and survival of pathogenic and nonpathogenicPseudomonas syringae strains and of the nonpathogenic species Pantoea agglomerans, Stenotrophomonas maltophilia, and Methylobacterium organophilum were compared in the phyllosphere of bean. In general, the plant pathogens survived better than the nonpathogens on leaves under environmental stress. The sizes of the total leaf-associated populations of the pathogenic P. syringae strains were greater than the sizes of the total leaf-associated populations of the nonpathogens under dry conditions but not under moist conditions. In these studies the surface sterilants hydrogen peroxide and UV irradiation were used to differentiate cells that were fully exposed on the surface from nonexposed cells that were in “protected sites” that were inaccessible to these agents. In general, the population sizes in protected sites increased with time after inoculation of plants. The proportion of bacteria on leaves that were in protected sites was generally greater for pathogens than for nonpathogens and was greater under dry conditions than under moist conditions. When organisms were vacuum infiltrated into leaves, the sizes of the nonexposed “internal” populations were greater for pathogenic P. syringae strains than for nonpathogenic P. syringaestrains. The sizes of the populations of the nonpathogenic species failed to increase or even decreased. The sizes of nonexposed populations following spray inoculation were correlated with the sizes of nonexposed, internal populations which developed after vacuum infiltration and incubation. While the sizes of the populations of the pathogenic P. syringae strains increased on leaves under dry conditions, the sizes of the populations of the nonpathogenic strains of P. syringae, P. agglomerans, andS. maltophilia decreased when the organisms were applied to plants. The sizes of the populations on dry leaves were also correlated with the sizes of the nonexposed populations that developed following vacuum infiltration. Although pathogenicity was not required for growth in the phyllosphere under high-relative-humidity conditions, pathogenicity apparently was involved in the ability to access and/or multiply in certain protected sites in the phyllosphere and in growth on dry leaves.

scholarly journals Metagenomic profiling of host-associated bacteria from 8 datasets of the red alga Porphyra purpurea, with MetaPhlAn 3.0

2020 ◽  
Author(s):  
Orestis Nousias ◽  
Federica Montesanto
Keyword(s):  
16S Rrna ◽  
Bacterial Species ◽  
Reference Database ◽  
Marker Genes ◽  
Specific Marker ◽  
Bacterial Genomes ◽  
Associated Bacteria ◽  
Pan Genome ◽  
Nucleotide Database ◽  
Porphyra Purpurea

AbstractMicrobial communities play a fundamental role in the association with marine algae, in fact they are recognized to be actively involved in growth and morphogenesis.Porphyra purpurea is a red algae commonly found in the intertidal zone with an high economical value, indeed several species belonging to the genus Porphyra are intensely cultivated in the Eastern Asian countries. Moreover, P. purpurea is widely used as model species in different fields, mainly due to its peculiar life cycle. Despite of that, little is known about the microbial community associated to this species. Here we report the microbial-associated diversity of P. purpurea in four different localities (Ireland, Italy United Kingdom and USA) through the analysis of eight metagenomic datasets obtained from the publicly available metagenomic nucleotide database (https://www.ebi.ac.uk/ena/). The metagenomic datasets were quality controlled with FastQC version 0.11.8, pre-processed with Trimmomatic version 0.39 and analysed with Methaplan 3.0, with a reference database containing clade specific marker genes from ~ 99.500 bacterial genomes, following the pan-genome approach, in order to identify the putative bacterial taxonomies and their relative abundances. Furthermore, we compared the results to the 16S rRNA metagenomic analysis pipeline of MGnify database to evaluate the effectiveness of the two methods. Out of the 43 bacterial species identified with MetaPhlAn 3.0 only 5 were common with the MGnify results and from the 21 genera, only 9 were common. This approach highlighted the different taxonomical resolution of a 16S rRNA OTU-based method in contrast to the pan-genome approach deployed by MetaPhlAn 3.0.

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