Identification of genomic islands in the genome ofBacillus cereusby comparative analysis withBacillus anthracis

2003 ◽  
Vol 16 (1) ◽  
pp. 19-23 ◽  
Author(s):  
Ren Zhang ◽  
Chun-Ting Zhang
Keyword(s):  
Comparative Analysis ◽  
Integration Site ◽  
Gc Content ◽  
Genomic Islands ◽  
Gene Gain ◽  
Abrupt Changes ◽  
Phage Protein ◽  
Recombinase Gene ◽  
A Site ◽  
Genomic Gc Content

Horizontal gene transfer has been recognized as a universal event throughout bacterial evolution. The availability of both complete genome sequences of Bacillus cereus and B. anthracis provides the possibility to perform comparative analysis based on their genomes. By using a windowless method to display the distribution of the genomic GC content of B. cereus and B. anthracis, we have found three genomic islands in the genome of B. cereus, i.e., BCGI-1, BCGI-2, and BCGI-3, respectively, which are absent in the genome of B. anthracis. All the genomic islands have abrupt changes in GC content compared with that of surrounding regions. BCGI-1 has many conserved features of genomic islands, e.g., a Val-tRNA gene is utilized as the integration site, and a site-specific recombinase gene is located at the 3′ end. BCGI-2 has a large percentage of phage protein, suggesting a phage-related recombination is involved. BCGI-3 contains a ferric anguibactin transport system, which is likely to be involved in the iron transport that enables the bacterium to overcome the iron limitation in the host. In addition, BCGI-3 also contains a cluster of genes related to lantibiotics, which may play a role during the evolution of the genome. Furthermore, the integrations of the genomic islands, BCGI-1 and BCGI-3, result in deletions of DNA sequence fragments; therefore, such integrations lead to both gene gain and gene loss simultaneously.

scholarly journals Coupling Between Protein Level Selection and Codon Usage Optimization in the Evolution of Bacteria and Archaea

mBio ◽  
2014 ◽  
Vol 5 (2) ◽  
Author(s):  
Wenqi Ran ◽  
David M. Kristensen ◽  
Eugene V. Koonin
Keyword(s):  
Codon Usage ◽  
Protein Level ◽  
Codon Usage Bias ◽  
Protein Sequence ◽  
Gc Content ◽  
Protein Sequences ◽  
Microbial Evolution ◽  
Fine Tuning ◽  
Selection For ◽  
Genomic Gc Content

ABSTRACT The relationship between the selection affecting codon usage and selection on protein sequences of orthologous genes in diverse groups of bacteria and archaea was examined by using the Alignable Tight Genome Clusters database of prokaryote genomes. The codon usage bias is generally low, with 57.5% of the gene-specific optimal codon frequencies (F opt ) being below 0.55. This apparent weak selection on codon usage contrasts with the strong purifying selection on amino acid sequences, with 65.8% of the gene-specific dN/dS ratios being below 0.1. For most of the genomes compared, a limited but statistically significant negative correlation between F opt and dN/dS was observed, which is indicative of a link between selection on protein sequence and selection on codon usage. The strength of the coupling between the protein level selection and codon usage bias showed a strong positive correlation with the genomic GC content. Combined with previous observations on the selection for GC-rich codons in bacteria and archaea with GC-rich genomes, these findings suggest that selection for translational fine-tuning could be an important factor in microbial evolution that drives the evolution of genome GC content away from mutational equilibrium. This type of selection is particularly pronounced in slowly evolving, “high-status” genes. A significantly stronger link between the two aspects of selection is observed in free-living bacteria than in parasitic bacteria and in genes encoding metabolic enzymes and transporters than in informational genes. These differences might reflect the special importance of translational fine-tuning for the adaptability of gene expression to environmental changes. The results of this work establish the coupling between protein level selection and selection for translational optimization as a distinct and potentially important factor in microbial evolution. IMPORTANCE Selection affects the evolution of microbial genomes at many levels, including both the structure of proteins and the regulation of their production. Here we demonstrate the coupling between the selection on protein sequences and the optimization of codon usage in a broad range of bacteria and archaea. The strength of this coupling varies over a wide range and strongly and positively correlates with the genomic GC content. The cause(s) of the evolution of high GC content is a long-standing open question, given the universal mutational bias toward AT. We propose that optimization of codon usage could be one of the key factors that determine the evolution of GC-rich genomes. This work establishes the coupling between selection at the level of protein sequence and at the level of codon choice optimization as a distinct aspect of genome evolution.

scholarly journals Selection Maintains Low Genomic GC Content in Marine SAR11 Lineages

2015 ◽  
Vol 32 (10) ◽  
pp. 2738-2748 ◽  
Author(s):  
Haiwei Luo ◽  
Luke R. Thompson ◽  
Ulrich Stingl ◽  
Austin L. Hughes
Keyword(s):  
Gc Content ◽  
Genomic Gc Content

Introduction Tè glise, Continents à la dérive

2019 ◽  
pp. 1-26
Author(s):  
John Patrick Walsh
Keyword(s):  
Comparative Analysis ◽  
Environmental Injustice ◽  
Historical Awareness ◽  
Political Economies ◽  
Political Time ◽  
Slow Violence ◽  
Fault Lines ◽  
A Site ◽  
Dominant Narratives ◽  
Point Of Departure

The book opens with analysis of Yanick Lahens’ reflection on the disastrous convergence of geological and political time in the Haitian earthquake of 2010. Lahens contemplates the imbrication of geological, political, and social fault lines to complicate the exceptional image of Haiti as a site of disaster. The introduction considers Lahens’ understanding of fault lines, below and above ground, in light of Rob Nixon’s critique of the slow violence of environmental injustice and Michel Serres’ idea of a natural contract with the planet. It brings together Lahens, Nixon, and Serres to illustrate the different conceptions of time and space that inform the ecological thought of a Haitian writer, an American critic, and a French philosopher. Taking this comparative analysis as its point of departure, the introduction begins to develop a theory of an eco-archive as an ethical and imaginative writing on the environment. It merges ecocriticism with the historical awareness of Haitian studies to argue that Lahens and other Haitian writers challenge the neocolonial and neoliberal political economies that feed the dominant narratives of the Anthropocene.

scholarly journals Molecular Characterization and Antimicrobial Susceptibilities of Nocardia Species Isolated from the Soil; A Comparison with Species Isolated from Humans

2020 ◽  
Vol 8 (6) ◽  
pp. 900
Author(s):  
Gema Carrasco ◽  
Sara Monzón ◽  
María San Segundo ◽  
Enrique García ◽  
Noelia Garrido ◽  
...  
Keyword(s):  
16S Rrna ◽  
Topoisomerase Ii ◽  
Gc Content ◽  
Amino Acid Identity ◽  
Beta Lactams ◽  
Nocardia Species ◽  
Antimicrobial Susceptibilities ◽  
The Difference ◽  
Subunit B ◽  
Genomic Gc Content

Nocardia species, one of the most predominant Actinobacteria of the soil microbiota, cause infection in humans following traumatic inoculation or inhalation. The identification, typing, phylogenetic relationship and antimicrobial susceptibilities of 38 soil Nocardia strains from Lara State, Venezuela, were studied by 16S rRNA and gyrB (subunit B of topoisomerase II) genes, multilocus sequence analysis (MLSA), whole-genome sequencing (WGS), and microdilution. The results were compared with those for human strains. Just seven Nocardia species with one or two strains each, except for Nocardia cyriacigeorgica with 29, were identified. MLSA confirmed the species assignments made by 16S rRNA and gyrB analyses (89.5% and 71.0% respectively), and grouped each soil strain with its corresponding reference and clinical strains, except for 19 N. cyriacigeorgica strains found at five locations which grouped into a soil-only cluster. The soil strains of N. cyriacigeorgica showed fewer gyrB haplotypes than the examined human strains (13 vs. 17) but did show a larger number of gyrB SNPs (212 vs. 77). Their susceptibilities to antimicrobials were similar except for beta-lactams, fluoroquinolones, minocycline, and clarithromycin, with the soil strains more susceptible to the first three (p ≤ 0.05). WGS was performed on four strains belonging to the soil-only cluster and on two outside it, and the results compared with public N. cyriacigeorgica genomes. The average nucleotide/amino acid identity, in silico genome-to-genome hybridization similarity, and the difference in the genomic GC content, suggest that some strains of the soil-only cluster may belong to a novel subspecies or even a new species (proposed name Nocardia venezuelensis).

scholarly journals Purification and Characterization of the R64 Shufflon-Specific Recombinase

2000 ◽  
Vol 182 (10) ◽  
pp. 2787-2792 ◽  
Author(s):  
Atsuko Gyohda ◽  
Teruya Komano
Keyword(s):  
Electrophoretic Analysis ◽  
Recombination Reaction ◽  
Site Specific ◽  
Dna Inversion ◽  
Repeat Sequences ◽  
In Vitro Recombination ◽  
Recombinase Gene ◽  
A Site

ABSTRACT The shufflon, a multiple DNA inversion system in plasmid R64, consists of four invertible DNA segments which are separated and flanked by seven 19-bp repeat sequences. The product of a site-specific recombinase gene, rci, promotes site-specific recombination between any two of the inverted 19-bp repeat sequences of the shufflon. To analyze the molecular mechanism of this recombination reaction, Rci protein was overproduced and purified. The purified Rci protein promoted the in vitro recombination reaction between the inverted 19-bp repeats of supercoiled DNA of a plasmid carrying segment A of the R64 shufflon. The recombination reaction was enhanced by the bacterial host factor HU. Gel electrophoretic analysis indicated that the Rci protein specifically binds to the DNA segments carrying the 19-bp sequences. The binding affinity of the Rci protein to the four shufflon segments as well as four synthetic 19-bp sequences differed greatly: among the four 19-bp repeat sequences, the repeat-a and -d sequences displayed higher affinity to Rci protein. These results suggest that the differences in the affinity of Rci protein for the 19-bp repeat sequences determine the inversion frequencies of the four segments.

scholarly journals Genome Mining and Comparative Analysis of Streptococcus intermedius Causing Brain Abscess in a Child

Pathogens ◽  
2019 ◽  
Vol 8 (1) ◽  
pp. 22 ◽  
Author(s):  
Elio Issa ◽  
Tamara Salloum ◽  
Balig Panossian ◽  
David Ayoub ◽  
Edmond Abboud ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Metal Ions ◽  
Genome Evolution ◽  
Brain Abscess ◽  
Survival Rates ◽  
Genome Mining ◽  
Genomic Islands ◽  
Polymorphism Analysis ◽  
Streptococcus Intermedius ◽  
Pan Genome

Streptococcus intermedius (SI) is associated with prolonged hospitalization and low survival rates. The genetic mechanisms involved in brain abscess development and genome evolution in comparison to other members of the Streptococcus anginosus group are understudied. We performed a whole-genome comparative analysis of an SI isolate, LAU_SINT, associated with brain abscess following sinusitis with all SI genomes in addition to S. constellatus and S. anginosus. Selective pressure on virulence factors, phages, pan-genome evolution and single-nucleotide polymorphism analysis were assessed. The structural details of the type seven secretion system (T7SS) was elucidated and compared with different organisms. ily and nanA were both abundant and conserved. Nisin resistance determinants were found in 47% of the isolates. Pan-genome and SNPs-based analysis didn’t reveal significant geo-patterns. Our results showed that two SC isolates were misidentified as SI. We propose the presence of four T7SS modules (I–IV) located on various genomic islands. We detected a variety of factors linked to metal ions binding on the GIs carrying T7SS. This is the first detailed report characterizing the T7SS and its link to nisin resistance and metal ions binding in SI. These and yet uncharacterized T7SS transmembrane proteins merit further studies and could represent potential therapeutic targets.

scholarly journals Global Evolutionary Analysis of 11 Gene Families Part of Reactive Oxygen Species (ROS) Gene Network in Four Eucalyptus Species

Antioxidants ◽  
2020 ◽  
Vol 9 (3) ◽  
pp. 257
Author(s):  
Qiang Li ◽  
Hélène San Clemente ◽  
Yongrui He ◽  
Yongyao Fu ◽  
Christophe Dunand
Keyword(s):  
Reactive Oxygen Species ◽  
Comparative Analysis ◽  
Gene Network ◽  
Expression Patterns ◽  
Reactive Oxygen ◽  
Evolutionary Process ◽  
Gene Families ◽  
Eucalyptus Species ◽  
Gene Gain ◽  
Oxygen Species

Eucalyptus is a worldwide hard-wood species which increasingly focused on. To adapt to various biotic and abiotic stresses, Eucalyptus have evolved complex mechanisms, increasing the cellular concentration of reactive oxygen species (ROS) by numerous ROS controlling enzymes. To better analyse the ROS gene network and discuss the differences between four Eucalyptus species, ROS gene network including 11 proteins families (1CysPrx, 2CysPrx, APx, APx-R, CIII Prx, Diox, GPx, Kat, PrxII, PrxQ and Rboh) were annotated and compared in an expert and exhaustive manner from the genomic data available from E. camaldulensis, E. globulus, E. grandis, and E. gunnii. In addition, a specific sequencing strategy was performed in order to determine if the missed sequences in at least one organism are the results of gain/loss events or only sequencing gaps. We observed that the automatic annotation applied to multigenic families is the source of miss-annotation. Base on the family size, the 11 families can be categorized into duplicated gene families (CIII Prx, Kat, 1CysPrx, and GPx), which contain a lot of gene duplication events and non-duplicated families (APx, APx-R, Rboh, DiOx, 2CysPrx, PrxII, and PrxQ). The gene family sizes are much larger in Eucalyptus than most of other angiosperms due to recent gene duplications, which could give higher adaptability to environmental changes and stresses. The cross-species comparative analysis shows gene gain and loss events during the evolutionary process. The 11 families possess different expression patterns, while in the Eucalyptus genus, the ROS families present similar expression patterns. Overall, the comparative analysis might be a good criterion to evaluate the adaptation of different species with different characters, but only if data mining is as exhaustive as possible. It is also a good indicator to explore the evolutionary process.

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