Comparative genome analysis reveals the presence of multiple quorum-sensing systems in plant pathogenic bacterium, Erwinia rhapontici

2021 ◽  
Author(s):  
Tomohiro Morohoshi ◽  
Kanako Nameki ◽  
Nobutaka Someya
Keyword(s):  
Gene Pair ◽  
Large Scale ◽  
Insertion Sequence ◽  
Plant Pathogenic Bacterium ◽  
Comparative Genome Analysis ◽  
Genome Sequences ◽  
Indigenous Plasmid ◽  
Acylhomoserine Lactone ◽  
Sensing Systems ◽  
Erwinia Rhapontici

Abstract We present the complete genome sequences of three Erwinia rhapontici strains, MAFF 311153, 311154, and 311155. These chromosome sequences contained variety types of luxI/luxR gene pair involved in acylhomoserine lactone (AHL) biosynthesis and reception. Large-scale insertion sequence was observed in the indigenous plasmid of MAFF 311154 and contained eraI3/eraR3 gene pair which make possible to produce acylhomoserine lactone.

scholarly journals Dynamics of Genome Architecture in Rhizobium sp. Strain NGR234

2002 ◽  
Vol 184 (1) ◽  
pp. 171-176 ◽  
Author(s):  
Patrick Mavingui ◽  
Margarita Flores ◽  
Xianwu Guo ◽  
Guillermo Dávila ◽  
Xavier Perret ◽  
...  
Keyword(s):  
Large Scale ◽  
Insertion Sequence ◽  
Biological Significance ◽  
Genome Architecture ◽  
Bacterial Genomes ◽  
Symbiotic Plasmid ◽  
Sequence Elements ◽  
Dynamic Structures ◽  
Genome Analyses ◽  
Insertion Sequence Elements

ABSTRACT Bacterial genomes are usually partitioned in several replicons, which are dynamic structures prone to mutation and genomic rearrangements, thus contributing to genome evolution. Nevertheless, much remains to be learned about the origins and dynamics of the formation of bacterial alternative genomic states and their possible biological consequences. To address these issues, we have studied the dynamics of the genome architecture in Rhizobium sp. strain NGR234 and analyzed its biological significance. NGR234 genome consists of three replicons: the symbiotic plasmid pNGR234a (536,165 bp), the megaplasmid pNGR234b (>2,000 kb), and the chromosome (>3,700 kb). Here we report that genome analyses of cell siblings showed the occurrence of large-scale DNA rearrangements consisting of cointegrations and excisions between the three replicons. As a result, four new genomic architectures have emerged. Three consisted of the cointegrates between two replicons: chromosome-pNGR234a, chromosome-pNGR234b, and pNGR234a-pNGR234b. The other consisted of a cointegrate of the three replicons (chromosome-pNGR234a-pNGR234b). Cointegration and excision of pNGR234a with either the chromosome or pNGR234b were studied and found to proceed via a Campbell-type mechanism, mediated by insertion sequence elements. We provide evidence showing that changes in the genome architecture did not alter the growth and symbiotic proficiency of Rhizobium derivatives.

scholarly journals New Insights into the Evolutionary and Genomic Landscape of Molluscum Contagiosum Virus (MCV) based on Nine MCV1 and Six MCV2 Complete Genome Sequences

Viruses ◽  
2018 ◽  
Vol 10 (11) ◽  
pp. 586 ◽  
Author(s):  
Tomaž Zorec ◽  
Denis Kutnjak ◽  
Lea Hošnjak ◽  
Blanka Kušar ◽  
Katarina Trčko ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Large Scale ◽  
Nk Cell ◽  
Molluscum Contagiosum ◽  
Molluscum Contagiosum Virus ◽  
Genome Sequences ◽  
Viral Interference ◽  
Genomic Landscape ◽  
Genetic Landscape ◽  
Common Skin

Molluscum contagiosum virus (MCV) is the sole member of the Molluscipoxvirus genus and the causative agent of molluscum contagiosum (MC), a common skin disease. Although it is an important and frequent human pathogen, its genetic landscape and evolutionary history remain largely unknown. In this study, ten novel complete MCV genome sequences of the two most common MCV genotypes were determined (five MCV1 and five MCV2 sequences) and analyzed together with all MCV complete genomes previously deposited in freely accessible sequence repositories (four MCV1 and a single MCV2). In comparison to MCV1, a higher degree of nucleotide sequence conservation was observed among MCV2 genomes. Large-scale recombination events were identified in two newly assembled MCV1 genomes and one MCV2 genome. One recombination event was located in a newly identified recombinant region of the viral genome, and all previously described recombinant regions were re-identified in at least one novel MCV genome. MCV genes comprising the identified recombinant segments have been previously associated with viral interference with host T-cell and NK-cell immune responses. In conclusion, the two most common MCV genotypes emerged along divergent evolutionary pathways from a common ancestor, and the differences in the heterogeneity of MCV1 and MCV2 populations may be attributed to the strictness of the constraints imposed by the host immune response.

scholarly journals Comparative Genome Analysis of Bacillus sporothermodurans with Its Closest Phylogenetic Neighbor, Bacillus oleronius, and Bacillus cereus and Bacillus subtilis Groups

2020 ◽  
Vol 8 (8) ◽  
pp. 1185
Author(s):  
Rodney Owusu-Darko ◽  
Mushal Allam ◽  
Arshad Ismail ◽  
Carlos A. S. Ferreira ◽  
Sílvia D. de Oliveira ◽  
...  
Keyword(s):  
Heat Shock ◽  
Heat Resistance ◽  
Genome Analysis ◽  
Bacillus Species ◽  
Whole Genome ◽  
Comparative Genome Analysis ◽  
Genome Sequences ◽  
Comparative Genome ◽  
P Gene ◽  
Phylogenetic Neighbor

Bacillus sporothermodurans currently possesses one of the most highly heat-resistant spores (HRS), which can withstand ultra-high temperature (UHT) processing. Determination of multiple whole genome sequences of B. sporothermodurans provided an opportunity to perform the first comparative genome analysis between strains and with B. oleronius, B. cereus, and B. subtilis groups. In this study, five whole genome sequences of B. sporothermodurans strains, including those belonging to the HRS clone (SAD and BR12) normally isolated from UHT milk, were compared with the aforementioned Bacillus species for gene clusters responsible for heat resistance. In the phylogenomic analysis, B. sporothermodurans, with its closest phylogenetic neighbor, B. oleronius, clustered with B. thermoamylovorans and B. thermotolerans. Heat shock proteins GrpE, GroES, GroEL, and DnaK presented identical sequences for all B. sporothermodurans strains, indicating that differences in functional efficiency are not involved in the thermal resistance variations. However, comparing all species evaluated, B. sporothermodurans exhibited a different gene configuration in the chromosomal region of the heat shock protein GrpE. Furthermore, only B. sporothermodurans strains presented the stage II sporulation protein P gene located in this region. Multisequence alignment and phylogenetic analysis of the ClpB protein showed differences for HRS and non-HRS strains. The study identified ClpC, ClpE, and ClpX as the three ATPases putatively involved in protein disaggregation in B. sporothermodurans. Bacillussporothermodurans exhibits high homology with other Bacillus species in the DnaK, DnaJ, GroEL, and GroES cluster of genes involved in heat resistance. The data presented here pave the way to select and evaluate the phenotypic effects of genes putatively involved in heat resistance.

scholarly journals Genomic Insights into Bifidobacteria

2010 ◽  
Vol 74 (3) ◽  
pp. 378-416 ◽  
Author(s):  
Ju-Hoon Lee ◽  
Daniel J. O'Sullivan
Keyword(s):  
Genome Analysis ◽  
Health Benefits ◽  
Gut Microflora ◽  
Comparative Genome Analysis ◽  
Human Milk Oligosaccharides ◽  
Genome Sequences ◽  
Potential Health ◽  
Intestinal Microbes ◽  
Breast Fed ◽  
Dairy Fermentation

SUMMARY Since the discovery in 1899 of bifidobacteria as numerically dominant microbes in the feces of breast-fed infants, there have been numerous studies addressing their role in modulating gut microflora as well as their other potential health benefits. Because of this, they are frequently incorporated into foods as probiotic cultures. An understanding of their full interactions with intestinal microbes and the host is needed to scientifically validate any health benefits they may afford. Recently, the genome sequences of nine strains representing four species of Bifidobacterium became available. A comparative genome analysis of these genomes reveals a likely efficient capacity to adapt to their habitats, with B. longum subsp. infantis exhibiting more genomic potential to utilize human milk oligosaccharides, consistent with its habitat in the infant gut. Conversely, B. longum subsp. longum exhibits a higher genomic potential for utilization of plant-derived complex carbohydrates and polyols, consistent with its habitat in an adult gut. An intriguing observation is the loss of much of this genome potential when strains are adapted to pure culture environments, as highlighted by the genomes of B. animalis subsp. lactis strains, which exhibit the least potential for a gut habitat and are believed to have evolved from the B. animalis species during adaptation to dairy fermentation environments.

IS1071-mediated recombinational equilibrium in Alcaligenes sp. BR60 carrying the 3-chlorobenzoate catabolic transposon Tn5271

1993 ◽  
Vol 39 (1) ◽  
pp. 92-100 ◽  
Author(s):  
James Ng ◽  
R. Campbell Wyndham
Keyword(s):  
Homologous Recombination ◽  
Parent Strain ◽  
Insertion Sequence ◽  
Class Ii ◽  
Indigenous Plasmid ◽  
Resistant Mutants ◽  
Selection For ◽  
Transposition Mechanism

In experiments designed to Tn5 mutagenize the indigenous plasmid pBRC60 of Alcaligenes sp. BR60, kanamycin-resistant mutants were isolated that were cured of this plasmid and that exhibited recombination of the plasmid-located chlorobenzoate catabolic transposon Tn5271 into the chromosome. These events were independent of the location of Tn5 insertions into the genome of strain BR60. The chromosomal recombinants carried at least two novel copies of IS1071, the class II insertion sequence flanking Tn5271, compared with the parent strain. Recombination of Tn5271 into the chromosome of Alcaligenes sp. BR60 was also detected following mating in of pBRC60-incompatible (IncP1) plasmids, R68 and pGS65. Chromosomal copies of Tn5271 could be mobilized between Alcaligenes strains via plasmids pBRC40 or R68. Conjugation of the incompatible plasmid pGS65 into Alcaligenes strains in the absence of selection for 3-chlorobenzoate catabolism resulted in the recovery of 85% of transconjugants in which the entire pBRC60 plasmid had integrated into the chromosome. These transconjugants exhibited complex rearrangements in chromosomal IS1071 copies. A model of recombinational equilibrium involving homologous recombination between plasmid and chromosomal copies of IS1071 is presented. The results are discussed in terms of the IS1071 (class II) transposition mechanism and the observed products of IS 1071-mediated recombination in natural recipients of pBRC60 in aquatic environments.Key words: transposon, 3-chlorobenzoate catabolism, rearrangement.

scholarly journals Regulation of Quorum Sensing by RpoS inPseudomonas aeruginosa

2000 ◽  
Vol 182 (15) ◽  
pp. 4356-4360 ◽  
Author(s):  
Marvin Whiteley ◽  
Matthew R. Parsek ◽  
E. P. Greenberg
Keyword(s):  
Gene Expression ◽  
Pseudomonas Aeruginosa ◽  
Quorum Sensing ◽  
Gene Transcription ◽  
Opportunistic Pathogen ◽  
Null Mutant ◽  
Global Regulators ◽  
Acylhomoserine Lactone ◽  
Sensing Systems

ABSTRACT The LasR-LasI and RhlR-RhlI quorum-sensing systems are global regulators of gene expression in the opportunistic pathogenPseudomonas aeruginosa. Previous studies suggest that the RhlR-RhlI system activates expression of rpoS. We constructed merodiploid strains of P. aeruginosa containing the native rpoS gene and an rpoS-lacZ fusion. Studies of lacZ transcription in these strains indicated that rpoS was not regulated by RhlR-RhlI. We also generated an rpoS null mutant. This rpoS mutant showed elevated levels of rhlI (but not rhlR) transcription, elevated levels of the RhlI-generated acylhomoserine lactone quorum-sensing signal, and elevated levels of RhlR-RhlI-regulated gene transcription. These findings indicate that there is a relationship between RpoS and quorum sensing, but rather than the RhlR-RhlI system influencing the expression ofrpoS, it appears that RpoS regulates rhlI.

Ancestral genome duplication in rice

Genome ◽  
2004 ◽  
Vol 47 (3) ◽  
pp. 610-614 ◽  
Author(s):  
Romain Guyot ◽  
Beat Keller
Keyword(s):  
Large Scale ◽  
Genome Duplication ◽  
Rice Genome ◽  
Block Size ◽  
Pairwise Comparisons ◽  
Comparative Genome Analysis ◽  
Important Species ◽  
Duplication Events ◽  
First Time ◽  
Grass Genomes

The recent availability of the pseudochromosome sequences of rice allows for the first time the investigation of the extent of intra-genomic duplications on a large scale in this agronomically important species. Using a dot-matrix plotter as a tool to display pairwise comparisons of ordered predicted coding sequences along rice pseudochromosomes, we found that the rice genome contains extensive chromosomal duplications accounting for 53% of the available sequences. The size of duplicated blocks is considerably larger than previously reported. In the rice genome, a duplicated block size of >1 Mb appears to be the rule and not the exception. Comparative mapping has shown high genetic colinearity among chromosomes of cereals, promoting rice as a model for studying grass genomes. Further comparative genome analysis should allow the study of the conservation and evolution of these duplication events in other important cereals such as rye, barley, and wheat.Key words: rice, genome duplication, genome evolution.

scholarly journals Retrieve-ensembl-seq: user-friendly and large-scale retrieval of single or multi-genome sequences from Ensembl

2009 ◽  
Vol 25 (20) ◽  
pp. 2739-2740 ◽  
Author(s):  
O. Sand ◽  
M. Thomas-Chollier ◽  
J. van Helden
Keyword(s):  
Large Scale ◽  
Genome Sequences ◽  
User Friendly

ADF: An Anomaly Detection Framework for Large-Scale PM2.5 Sensing Systems

2018 ◽  
Vol 5 (2) ◽  
pp. 559-570 ◽  
Author(s):  
Ling-Jyh Chen ◽  
Yao-Hua Ho ◽  
Hsin-Hung Hsieh ◽  
Shih-Ting Huang ◽  
Hu-Cheng Lee ◽  
...  
Keyword(s):  
Anomaly Detection ◽  
Large Scale ◽  
Sensing Systems
Sign in / Sign up

Export Citation Format

Share Document