scholarly journals Sinorhizobium meliloti: chromosomal types and genomic islands

2019 ◽  
Vol 17 (3) ◽  
pp. 23-38
Author(s):  
Mariia E. Cherkasova ◽  
Victoria S. Muntyan ◽  
Alla S. Saksaganskaia ◽  
Boris V. Simarov ◽  
Marina L. Roumiantseva
Keyword(s):  
Sinorhizobium Meliloti ◽  
Core Genome ◽  
Introgressive Hybridization ◽  
Genomic Islands ◽  
Aral Sea ◽  
Polymorphism Analysis ◽  
Gene Markers ◽  
Intergenic Sequences ◽  
Clonal Lines ◽  
Chromosomal Type

Background. Polymorphism analysis was done for the core genome sequences of nodule bacteria of S. meliloti species in order to identify chromosomal types and to evaluate the occurrence of accessory elements (genomic islands) in them. Materials and methods. Chromosomal studied loci were: betBC (marker M-I) and SMc04407-SMc04881 (marker M-II) both are related to metabolic processes and stress tolerance, and 16S-23S intergenic sequences (marker M-III) to search phylogenetical distance at intraspecies level. Results. Significant differences between the occurrence of alleles of gene-markers M-I/M-II and MIII were determined between strains related to tested the 5 typical groups and 9 subgroups of strains differing by geographical region/source (nodule, soil) of isolation, as well as by salt tolerance. Four chromosomal types were identified among tested S. meliloti native isolates and a preference occurence of one of the three islands Rm1021 in links with particular chromosomal type was shown. The significant prevalence of strains with particular chromosomal type was shown for S. meliloti populations native to centers of alfalfa diversity at the NE of Caucasus, as well as at NE of Kazakhstan (Aral sea related region), as well as in agrocenoses. Conclusion. It was predicted that strains inherited altered markers M-I/M-II may belong to divergent clonal lines occured in both centers of alfalfa diversity, while strains with altered sequences of all three markers could be a representatives of a new S. meliloti biovar(s), the formation of which is occurred much more intensively at the modern center of the introgressive hybridization of alfalfa at NE of Kazakhstan.

scholarly journals Expression of Medicago truncatula Genes Responsive to Nitric Oxide in Pathogenic and Symbiotic Conditions

2008 ◽  
Vol 21 (6) ◽  
pp. 781-790 ◽  
Author(s):  
Alberto Ferrarini ◽  
Matteo De Stefano ◽  
Emmanuel Baudouin ◽  
Chiara Pucciariello ◽  
Annalisa Polverari ◽  
...  
Keyword(s):  
Nitric Oxide ◽  
Medicago Truncatula ◽  
Regulatory Networks ◽  
Sinorhizobium Meliloti ◽  
Biotic Interactions ◽  
Hypersensitive Reaction ◽  
Nodule Formation ◽  
Polymorphism Analysis ◽  
Symbiotic Interaction ◽  
Physiological Relevance

Nitric oxide (NO) is involved in diverse physiological processes in plants, including growth, development, response to pathogens, and interactions with beneficial microorganisms. In this work, a dedicated microarray representing the widest database available of NO-related transcripts in plants has been produced with 999 genes identified by a cDNA amplified fragment length polymorphism analysis as modulated in Medicago truncatula roots treated with two NO donors. The microarray then was used to monitor the expression of NO-responsive genes in M. truncatula during the incompatible interaction with the foliar pathogen Colletotrichum trifolii race 1 and during the symbiotic interaction with Sinorhizobium meliloti 1021. A wide modulation of NO-related genes has been detected during the hypersensitive reaction or during nodule formation and is discussed with special emphasis on the physiological relevance of these genes in the context of the two biotic interactions. This work clearly shows that NO-responsive genes behave differently depending on the plant organ and on the type of interaction, strengthening the need to consider regulatory networks, including different signaling molecules.

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 Sequencing and Functional Annotation of Avian Pathogenic Escherichia coli Serogroup O78 Strains Reveal the Evolution of E. coli Lineages Pathogenic for Poultry via Distinct Mechanisms

2012 ◽  
Vol 81 (3) ◽  
pp. 838-849 ◽  
Author(s):  
Francis Dziva ◽  
Heidi Hauser ◽  
Thomas R. Connor ◽  
Pauline M. van Diemen ◽  
Graham Prescott ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Core Genome ◽  
Systemic Disease ◽  
Genomic Islands ◽  
Content Type ◽  
E Coli ◽  
Group 4 ◽  
Pathogenic Escherichia Coli ◽  
Transposon Mutants ◽  
Avian Disease

ABSTRACTAvian pathogenicEscherichia coli(APEC) causes respiratory and systemic disease in poultry. Sequencing of a multilocus sequence type 95 (ST95) serogroup O1 strain previously indicated that APEC resemblesE. colicausing extraintestinal human diseases. We sequenced the genomes of two strains of another dominant APEC lineage (ST23 serogroup O78 strains χ7122 and IMT2125) and compared them to each other and to the reannotated APEC O1 sequence. For comparison, we also sequenced a human enterotoxigenicE. coli(ETEC) strain of the same ST23 serogroup O78 lineage. Phylogenetic analysis indicated that the APEC O78 strains were more closely related to human ST23 ETEC than to APEC O1, indicating that separation of pathotypes on the basis of their extraintestinal or diarrheagenic nature is not supported by their phylogeny. The accessory genome of APEC ST23 strains exhibited limited conservation of APEC O1 genomic islands and a distinct repertoire of virulence-associated loci. In light of this diversity, we surveyed the phenotype of 2,185 signature-tagged transposon mutants of χ7122 following intra-air sac inoculation of turkeys. This procedure identified novel APEC ST23 genes that play strain- and tissue-specific roles during infection. For example, genes mediating group 4 capsule synthesis were required for the virulence of χ7122 and were conserved in IMT2125 but absent from APEC O1. Our data reveal the genetic diversity ofE. colistrains adapted to cause the same avian disease and indicate that the core genome of the ST23 lineage serves as a chassis for the evolution ofE. colistrains adapted to cause avian or human disease via acquisition of distinct virulence genes.

scholarly journals Polymorphism among Sinorhizobium meliloti isolates native to the origins of alfalfa diversity differed in soil-climate characteristics

2009 ◽  
Vol 7 (2) ◽  
pp. 19-25
Author(s):  
Marina L Roumiantseva ◽  
Olga P Onishchuk ◽  
Viktoriya S Belova ◽  
Oksana N Kurchak ◽  
Boris V Simarov
Keyword(s):  
Salt Tolerance ◽  
Medicago Sativa ◽  
Sinorhizobium Meliloti ◽  
Aral Sea ◽  
Salt Tolerant ◽  
Central Asian ◽  
Symbiotic Properties ◽  
Adaptation Processes ◽  
Soil Climate ◽  
Tolerance To Salinity

Sinorhizoboium meliloti populations native to the 4 distinct gene centers (GC) of alfalfa were explored toward the tolerance to salinity, cryptic plasmid profiles and symbiotic properties. The significant correlations detected among nodule (N) and trapped (T) isolates related to the similar or distinct populations. more than 60 % N- and 77 % T-isolates tolerant to 3,5 % NaCl; salt tolerant N-isolates formed effective symbiosis with Medicago sativa and M. truncatula significantly more often. Isolates native to the GC area next to aral Sea had possessed the reduced level of salt tolerance in comparison with the isolates originated from Central asian, North-Caucasian and Europe-Siberian GC; that, has related to adaptation processes, which have ensured their viability in extremely salted soils.<img src="http://elibrary.ru/pic/1pix.gif" />

scholarly journals Comparative genome analysis of Salmonella enterica serovar Gallinarum biovars Pullorum and Gallinarum decodes strain specific genes

PLoS ONE ◽  
2021 ◽  
Vol 16 (8) ◽  
pp. e0255612
Author(s):  
Rajesh Kumar Vaid ◽  
Zoozeal Thakur ◽  
Taruna Anand ◽  
Sanjay Kumar ◽  
Bhupendra Nath Tripathi
Keyword(s):  
Genome Analysis ◽  
Salmonella Enterica ◽  
Core Genome ◽  
Genomic Islands ◽  
Economic Losses ◽  
Genotypic Differences ◽  
Comparative Genome Analysis ◽  
Comparative Genome ◽  
Genomic Features ◽  
Antimicrobial Resistance Genes

Salmonella enterica serovar Gallinarum biovar Pullorum (bvP) and biovar Gallinarum (bvG) are the etiological agents of pullorum disease (PD) and fowl typhoid (FT) respectively, which cause huge economic losses to poultry industry especially in developing countries including India. Vaccination and biosecurity measures are currently being employed to control and reduce the S. Gallinarum infections. High endemicity, poor implementation of hygiene and lack of effective vaccines pose challenges in prevention and control of disease in intensively maintained poultry flocks. Comparative genome analysis unravels similarities and dissimilarities thus facilitating identification of genomic features that aids in pathogenesis, niche adaptation and in tracing of evolutionary history. The present investigation was carried out to assess the genotypic differences amongst S.enterica serovar Gallinarum strains including Indian strain S. Gallinarum Sal40 VTCCBAA614. The comparative genome analysis revealed an open pan-genome consisting of 5091 coding sequence (CDS) with 3270 CDS belonging to core-genome, 1254 CDS to dispensable genome and strain specific genes i.e. singletons ranging from 3 to 102 amongst the analyzed strains. Moreover, the investigated strains exhibited diversity in genomic features such as virulence factors, genomic islands, prophage regions, toxin-antitoxin cassettes, and acquired antimicrobial resistance genes. Core genome identified in the study can give important leads in the direction of design of rapid and reliable diagnostics, and vaccine design for effective infection control as well as eradication. Additionally, the identified genetic differences among the S. enterica serovar Gallinarum strains could be used for bacterial typing, structure based inhibitor development by future experimental investigations on the data generated.

scholarly journals Genome analysis of Campylobacter concisus strains from patients with inflammatory bowel disease and gastroenteritis provides new insights into pathogenicity

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Heung Kit Leslie Chung ◽  
Alfred Tay ◽  
Sophie Octavia ◽  
Jieqiong Chen ◽  
Fang Liu ◽  
...  
Keyword(s):  
Inflammatory Bowel Disease ◽  
Core Genome ◽  
Secretion System ◽  
Effector Proteins ◽  
Type Iv Secretion ◽  
Genomic Islands ◽  
Type Iv Secretion System ◽  
Campylobacter Concisus ◽  
Type Iv ◽  
Inflammatory Bowel

Abstract Campylobacter concisus is an oral bacterium that is associated with inflammatory bowel disease. C. concisus has two major genomospecies, which appear to have different enteric pathogenic potential. Currently, no studies have compared the genomes of C. concisus strains from different genomospecies. In this study, a comparative genome analysis of 36 C. concisus strains was conducted including 27 C. concisus strains sequenced in this study and nine publically available C. concisus genomes. The C. concisus core-genome was defined and genomospecies-specific genes were identified. The C. concisus core-genome, housekeeping genes and 23S rRNA gene consistently divided the 36 strains into two genomospecies. Two novel genomic islands, CON_PiiA and CON_PiiB, were identified. CON_PiiA and CON_PiiB islands contained proteins homologous to the type IV secretion system, LepB-like and CagA-like effector proteins. CON_PiiA islands were found in 37.5% of enteric C. concisus strains (3/8) isolated from patients with enteric diseases and none of the oral strains (0/27), which was statistically significant. This study reports the findings of C. concisus genomospecies-specific genes, novel genomic islands that contain type IV secretion system and putative effector proteins, and other new genomic features. These data provide novel insights into understanding of the pathogenicity of this emerging opportunistic pathogen.

scholarly journals Long-read viral metagenomics captures abundant and microdiverse viral populations and their niche-defining genomic islands

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6800 ◽  
Author(s):  
Joanna Warwick-Dugdale ◽  
Natalie Solonenko ◽  
Karen Moore ◽  
Lauren Chittick ◽  
Ann C. Gregory ◽  
...  
Keyword(s):  
High Throughput ◽  
Low Cost ◽  
Host Community ◽  
Genomic Islands ◽  
Viral Metagenomics ◽  
Viral Gene ◽  
Gene Markers ◽  
Short Read ◽  
Viral Genomes ◽  
Long Read

Marine viruses impact global biogeochemical cycles via their influence on host community structure and function, yet our understanding of viral ecology is constrained by limitations in host culturing and a lack of reference genomes and ‘universal’ gene markers to facilitate community surveys. Short-read viral metagenomic studies have provided clues to viral function and first estimates of global viral gene abundance and distribution, but their assemblies are confounded by populations with high levels of strain evenness and nucleotide diversity (microdiversity), limiting assembly of some of the most abundant viruses on Earth. Such features also challenge assembly across genomic islands containing niche-defining genes that drive ecological speciation. These populations and features may be successfully captured by single-virus genomics and fosmid-based approaches, at least in abundant taxa, but at considerable cost and technical expertise. Here we established a low-cost, low-input, high throughput alternative sequencing and informatics workflow to improve viral metagenomic assemblies using short-read and long-read technology. The ‘VirION’ (Viral, long-read metagenomics via MinION sequencing) approach was first validated using mock communities where it was found to be as relatively quantitative as short-read methods and provided significant improvements in recovery of viral genomes. We then then applied VirION to the first metagenome from a natural viral community from the Western English Channel. In comparison to a short-read only approach, VirION: (i) increased number and completeness of assembled viral genomes; (ii) captured abundant, highly microdiverse virus populations, and (iii) captured more and longer genomic islands. Together, these findings suggest that VirION provides a high throughput and cost-effective alternative to fosmid and single-virus genomic approaches to more comprehensively explore viral communities in nature.

scholarly journals Integrase-Controlled Excision of Metal-Resistance Genomic Islands in Acinetobacter baumannii

Genes ◽  
2018 ◽  
Vol 9 (7) ◽  
pp. 366 ◽  
Author(s):  
Zaaima AL-Jabri ◽  
Roxana Zamudio ◽  
Eva Horvath-Papp ◽  
Joseph Ralph ◽  
Zakariya AL-Muharrami ◽  
...  
Keyword(s):  
Heavy Metal ◽  
Acinetobacter Baumannii ◽  
Core Genome ◽  
Susceptibility Testing ◽  
Gene Clusters ◽  
Heavy Metal Resistance ◽  
Metal Resistance ◽  
Genomic Islands ◽  
Genome Plasticity ◽  
E Coli

Genomic islands (GIs) are discrete gene clusters encoding for a variety of functions including antibiotic and heavy metal resistance, some of which are tightly associated to lineages of the core genome phylogenetic tree. We have investigated the functions of two distinct integrase genes in the mobilization of two metal resistant GIs, G08 and G62, of Acinetobacter baumannii. Real-time PCR demonstrated integrase-dependent GI excision, utilizing isopropyl β-d-1-thiogalactopyranoside IPTG-inducible integrase genes in plasmid-based mini-GIs in Escherichia coli. In A. baumannii, integrase-dependent excision of the original chromosomal GIs could be observed after mitomycin C induction. In both E. coli plasmids and A. baumannii chromosome, the rate of excision and circularization was found to be dependent on the expression level of the integrases. Susceptibility testing in A. baumannii strain ATCC 17978, A424, and their respective ΔG62 and ΔG08 mutants confirmed the contribution of the GI-encoded efflux transporters to heavy metal decreased susceptibility. In summary, the data evidenced the functionality of two integrases in the excision and circularization of the two Acinetobacter heavy-metal resistance GIs, G08 and G62, in E. coli, as well as when chromosomally located in their natural host. These recombination events occur at different frequencies resulting in genome plasticity and may participate in the spread of resistance determinants in A. baumannii.

scholarly journals Horizontally Acquired Homologs of Xenogeneic Silencers: Modulators of Gene Expression Encoded by Plasmids, Phages and Genomic Islands

Genes ◽  
2020 ◽  
Vol 11 (2) ◽  
pp. 142 ◽  
Author(s):  
Alejandro Piña-Iturbe ◽  
Isidora D. Suazo ◽  
Guillermo Hoppe-Elsholz ◽  
Diego Ulloa-Allendes ◽  
Pablo A. González ◽  
...  
Keyword(s):  
Regulatory Networks ◽  
Core Genome ◽  
Current Knowledge ◽  
Genomic Islands ◽  
Expression Of Genes ◽  
Genes Encoding ◽  
Related Group ◽  
Bacterial Fitness ◽  
Foreign Dna ◽  
Horizontal Acquisition

Acquisition of mobile elements by horizontal gene transfer can play a major role in bacterial adaptation and genome evolution by providing traits that contribute to bacterial fitness. However, gaining foreign DNA can also impose significant fitness costs to the host bacteria and can even produce detrimental effects. The efficiency of horizontal acquisition of DNA is thought to be improved by the activity of xenogeneic silencers. These molecules are a functionally related group of proteins that possess affinity for the acquired DNA. Binding of xenogeneic silencers suppresses the otherwise uncontrolled expression of genes from the newly acquired nucleic acid, facilitating their integration to the bacterial regulatory networks. Even when the genes encoding for xenogeneic silencers are part of the core genome, homologs encoded by horizontally acquired elements have also been identified and studied. In this article, we discuss the current knowledge about horizontally acquired xenogeneic silencer homologs, focusing on those encoded by genomic islands, highlighting their distribution and the major traits that allow these proteins to become part of the host regulatory networks.

scholarly journals Comparative Genomic Analysis of Rhodococcus equi: An Insight into Genomic Diversity and Genome Evolution

2019 ◽  
Vol 2019 ◽  
pp. 1-14
Author(s):  
Jianchao Ying ◽  
Jun Ye ◽  
Teng Xu ◽  
Qian Wang ◽  
Qiyu Bao ◽  
...  
Keyword(s):  
Core Genome ◽  
Genomic Analysis ◽  
Rhodococcus Equi ◽  
Comparative Genomic Analysis ◽  
Genomic Islands ◽  
Genomic Diversity ◽  
Comparative Genomic ◽  
Niche Adaptation ◽  
Genomic Studies ◽  
Insight Into

Rhodococcus equi, a member of the Rhodococcus genus, is a gram-positive pathogenic bacterium. Rhodococcus possesses an open pan-genome that constitutes the basis of its high genomic diversity and allows for adaptation to specific niche conditions and the changing host environments. Our analysis further showed that the core genome of R. equi contributes to the pathogenicity and niche adaptation of R. equi. Comparative genomic analysis revealed that the genomes of R. equi shared identical collinearity relationship, and heterogeneity was mainly acquired by means of genomic islands and prophages. Moreover, genomic islands in R. equi were always involved in virulence, resistance, or niche adaptation and possibly working with prophages to cause the majority of genome expansion. These findings provide an insight into the genomic diversity, evolution, and structural variation of R. equi and a valuable resource for functional genomic studies.

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