scholarly journals Phylogeny and Comparative Genomics Unveil Independent Diversification Trajectories ofqnrBand Genetic Platforms within Particular Citrobacter Species

2015 ◽  
Vol 59 (10) ◽  
pp. 5951-5958 ◽  
Author(s):  
Teresa G. Ribeiro ◽  
Ângela Novais ◽  
Raquel Branquinho ◽  
Elisabete Machado ◽  
Luísa Peixe
Keyword(s):  
Phylogenetic Analysis ◽  
Comparative Genomics ◽  
Pulsed Field Gel Electrophoresis ◽  
Divergent Evolution ◽  
High Identity ◽  
Content Type ◽  
Clonal Relatedness ◽  
Intergenic Regions ◽  
Genetic Sequences ◽  
Comparative Genomics Analysis

ABSTRACTTo gain insights into the diversification trajectories ofqnrBgenes, a phylogenetic and comparative genomics analysis of these genes and their surrounding genetic sequences was performed. For this purpose,Citrobactersp. isolates (n= 21) and genome or plasmid sequences (n= 56) available in public databases harboring complete or truncatedqnrBgenes were analyzed.Citrobacterspecies identification was performed by phylogenetic analysis of different genotypic markers. The clonal relatedness among isolates, the location ofqnrBgenes, and the genetic surroundings ofqnrBgenes were investigated by pulsed-field gel electrophoresis (PFGE), S1-/I-CeuI-PFGE and hybridization, and PCR mapping and sequencing, respectively. Identification ofCitrobacterisolates was achieved usingleuSandrecNgene sequences, and isolates characterized in this study were diverse and harbored chromosomalqnrBgenes. Phylogenetic analysis of all knownqnrBgenes revealed seven main clusters and two branches, with most of them included in two clusters. Specific platforms (comprisingpspFandsapAand varying in synteny and/or identity of other genes and intergenic regions) were associated with each one of theseqnrBclusters, and the reliable identification of allCitrobacterisolates revealed that each platform evolved in different recognizable (Citrobacter freundii,C. braakii,C. werkmanii, andC. pasteurii) and putatively new species. A high identity was observed between some of the platforms identified in the chromosome ofCitrobacterspp. and in different plasmids ofEnterobacteriaceae. Our data corroborateCitrobacteras the origin ofqnrBand further suggest divergent evolution of closely relatedqnrBgenes/platforms in particularCitrobacterspp., which were delineated using particular genotypic markers.

scholarly journals Diversity and evolution of the emerging Pandoraviridae family

2017 ◽  
Author(s):  
Matthieu Legendre ◽  
Elisabeth Fabre ◽  
Olivier Poirot ◽  
Sandra Jeudy ◽  
Audrey Lartigue ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
De Novo ◽  
Gene Duplications ◽  
Statistical Features ◽  
Strong Component ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Intergenic Regions ◽  
Comparative Genomics Analysis ◽  
Horizontal Transfers

AbstractWith DNA genomes up to 2.5 Mb packed in particles of bacterium-like shape and dimension, the first two Acanthamoeba-infectingPandoravirusesremained the most spectacular viruses since their description in 2013. Our isolation of three new strains from distant locations and environments allowed us to perform the first comparative genomics analysis of the emerging worldwide-distributed Pandoraviridae family. Thorough annotation of the genomes combining transcriptomic, proteomic, and bioinformatic analyses, led to the discovery of many non-coding transcripts while significantly reducing the former set of predicted protein-coding genes. We found that the Pandoraviridae exhibit an open pan genome, the enormous size of which is not adequately explained by gene duplications or horizontal transfers. As most of the strain specific genes have no extant homolog and exhibit statistical features comparable to intergenic regions, we suggests thatde novogene creation is a strong component in the evolution of the giant Pandoravirus genomes.

scholarly journals Comparative genomics analysis of c-di-GMP metabolism and regulation in Microcystis aeruginosa

2019 ◽  
Author(s):  
Meng Chen ◽  
Chun-Yang Xu ◽  
Xu Wang ◽  
Chong-Yang Ren ◽  
Jiao Ding ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Comparative Genomics ◽  
Microcystis Aeruginosa ◽  
Environmental Changes ◽  
Guanosine Monophosphate ◽  
Cyanobacterial Blooms ◽  
Medium Size ◽  
Pan Genome ◽  
Diguanylate Cyclases ◽  
Comparative Genomics Analysis

Abstract Background: Cyanobacteria are of special concern because they proliferate in eutrophic water bodies worldwide and affect water quality. As an ancient photosynthetic microorganism, cyanobacteria can survive in ecologically diverse habitats because of their capacity to rapidly respond to environmental changes through a web of complex signaling networks, including using second messengers to regulate physiology or metabolism. A ubiquitous second messenger, bis-(3′,5′)-cyclic-dimeric-guanosine monophosphate (c-di-GMP), has been found to regulate essential behaviors in a few cyanobacteria but not Microcystis, which are the most dominant species in cyanobacterial blooms. In this study, comparative genomics analysis was performed to explore the genomic basis of c-di-GMP signaling in Microcystis aeruginosa. Results: General characterization along with a pan-genome analysis showed that M. aeruginosa have a medium size genome (4.99 Mb in average), a conserved core genome, and an expansive pan-genome. Phylogenetic analysis showed good overall congruence between the two types of phylogenetic trees based on 31 highly conserved protein-coding genes and pan-genome matrix. Furthermore, phylogenetic analysis revealed no correlation between geographic distribution and phylogenetic relationships of the M. aeruginosa strains isolated from different regions. Moreover, proteins involved in c-di-GMP metabolism and regulation, such as diguanylate cyclases, phosphodiesterases, and PilZ-containing proteins, were encoded in M. aeruginosa genomes. It was revealed that the numbers of genes that encode diguanylate cyclases, phosphodiesterases, and hybrid proteins with GGDEF-EAL domains in M. aeruginosa might result from environment-specific adaptation. Bioinformatics and structure analysis of c-di-GMP signal-related GGDEF, EAL and GGDEF-EAL domains revealed that they all possess essential conserved amino acid residues that bind the substrate. In addition, it was also found that all selected M. aeruginosa genomes encode PilZ domain containing proteins. Conclusions: Comparative genomics analysis of c-di-GMP metabolism and regulation in M. aeruginosa strains helped elucidate the genetic basis of c-di-GMP signaling pathways in M. aeruginosa. Knowledge of c-di-GMP metabolism and relevant signal regulatory processes in cyanobacteria can enhance our understanding of their adaptability to various environments and bloom-forming mechanism. Keywords: Microcystis aeruginosa, Comparative genomics, c-di-GMP, Phylogenetic analysis, GGDEF, EAL, PilZ

scholarly journals Comparative genomics analysis of c-di-GMP metabolism and regulation in Microcystis aeruginosa

2020 ◽  
Author(s):  
Meng Chen ◽  
Chun-Yang Xu ◽  
Xu Wang ◽  
Chong-Yang Ren ◽  
Jiao Ding ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Comparative Genomics ◽  
Microcystis Aeruginosa ◽  
Phylogenetic Trees ◽  
Environmental Changes ◽  
Second Messengers ◽  
Guanosine Monophosphate ◽  
Cyanobacterial Blooms ◽  
Pan Genome ◽  
Comparative Genomics Analysis

Abstract Background: Cyanobacteria are of special concern because they proliferate in eutrophic water bodies worldwide and affect water quality. As an ancient photosynthetic microorganism, cyanobacteria can survive in ecologically diverse habitats because of their capacity to rapidly respond to environmental changes through a web of complex signaling networks, including using second messengers to regulate physiology or metabolism. A ubiquitous second messenger, bis-(3′,5′)-cyclic-dimeric-guanosine monophosphate (c-di-GMP), has been found to regulate essential behaviors in a few cyanobacteria but not Microcystis, which are the most dominant species in cyanobacterial blooms. In this study, comparative genomics analysis was performed to explore the genomic basis of c-di-GMP signaling in Microcystis aeruginosa. Results: Proteins involved in c-di-GMP metabolism and regulation, such as diguanylate cyclases, phosphodiesterases, and PilZ-containing proteins, were encoded in M. aeruginosa genomes. However, the number of identified protein domains involved in c-di-GMP signaling was not proportional to the size of M. aeruginosa genomes (4.99 Mb in average). Pan-genome analysis showed that genes involved in c-di-GMP metabolism and regulation are conservative in M. aeruginosa strains. Phylogenetic analysis showed good overall congruence between the three types of phylogenetic trees based on 31 highly conserved protein-coding genes, sensor domain-coding genes, and pan-genome matrix. Propensity for gene loss analysis revealed that most of genes involved in c-di-GMP signaling are stable in M. aeruginosa strains. Moreover, bioinformatics and structure analysis of c-di-GMP signal-related GGDEF and EAL domains revealed that they all possess essential conserved amino acid residues that bind the substrate. In addition, it was also found that all selected M. aeruginosa genomes encode PilZ domain containing proteins. Conclusions: Comparative genomics analysis of c-di-GMP metabolism and regulation in M. aeruginosa strains helped elucidating the genetic basis of c-di-GMP signaling pathways in M. aeruginosa. Knowledge of c-di-GMP metabolism and relevant signal regulatory processes in cyanobacteria can enhance our understanding of their adaptability to various environments and bloom-forming mechanism. Keywords: Microcystis aeruginosa, Comparative genomics, c-di-GMP, Phylogenetic analysis, GGDEF, EAL, HD-GYP, PilZ

scholarly journals OXA-48-Like-Producing Klebsiella pneumoniae in Southern Spain in 2014–2015

2018 ◽  
Vol 63 (1) ◽  
Author(s):  
Jesús Machuca ◽  
Lorena López-Cerero ◽  
Felipe Fernández-Cuenca ◽  
Laura Mora-Navas ◽  
Concepción Mediavilla-Gradolph ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Gel Electrophoresis ◽  
Pulsed Field Gel Electrophoresis ◽  
Southern Spain ◽  
Clinical Samples ◽  
Sequencing Analysis ◽  
Content Type ◽  
Clonal Relatedness ◽  
Sequence Types

ABSTRACT The aim of this study was to characterize the population structure of 56 OXA-48-like-producing Klebsiella pneumoniae isolates, as well as extended-spectrum β-lactamase (ESBL) and carbapenemase genes, recovered in 2014 and 2015 from 16 hospitals in southern Spain. XbaI pulsed-field gel electrophoresis and multilocus sequence typing were performed to assess clonal relatedness. Representative isolates belonging to OXA-48-like-producing and CTX-M-15-coproducing pulsotypes were selected for characterization of blaOXA-48-like- and blaCTX-M-15-carrying plasmids by PCR-based replicon typing, IncF subtyping, whole-genome sequencing analysis, and typing of Tn1999 structures. Forty-three OXA-48-producing isolates (77%) were recovered from clinical samples and 13 from rectal swabs. All isolates showed ertapenem MIC values of ≥1 mg/liter, although 70% remained susceptible to imipenem and meropenem. Forty-nine isolates (88%) produced OXA-48, 5 produced OXA-245, and 2 produced OXA-181. Twenty-eight different pulsotypes (5 detected in more than 1 hospital) and 16 sequence types (STs) were found. The most prevalent clones were ST15 (29 isolates [52%]) and ST11 (7 isolates [13%]). Forty-five (80%) isolates were also blaCTX-M-15 carriers. The blaCTX-M-15 gene was mostly (82%) located on IncR plasmids, although ST15 and ST11 isolates also carried this gene on IncF plasmids. The composite transposon variant Tn1999.2-like was the most frequent. Among ST15 and ST11 isolates, different transposon variants were observed. The blaOXA-48 gene was mainly located on IncL plasmids, although IncM plasmids were also observed. The spread of OXA-48-like-producing K. pneumoniae in southern Spain is mainly due to ST15 and ST11 clones. Variation within clonal lineages could indicate different acquisition events for both ESBL and carbapenemase traits.

scholarly journals Complete Genome Sequence of Brucella canis BCB018, a Strain Isolated from a Human Patient

2012 ◽  
Vol 194 (23) ◽  
pp. 6697-6698 ◽  
Author(s):  
Yufei Wang ◽  
Yuehua Ke ◽  
Qing Zhen ◽  
Xitong Yuan ◽  
Jie Xu ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Draft Genome ◽  
Human Brucellosis ◽  
Presumptive Diagnosis ◽  
Human Patient ◽  
Content Type ◽  
Brucella Canis ◽  
Comparative Genomics Analysis

ABSTRACTBrucella canisis considered a rare cause of human brucellosis because of difficulties in presumptive diagnosis and underestimation of the incidence. Here, we report the draft genome sequence of aBrucella canisisolate, BCB018, isolated from a human patient, providing precious resources for comparative genomics analysis ofBrucellafield strains.

scholarly journals Novel Transcriptional Regulons for Autotrophic Cycle Genes in Crenarchaeota

2015 ◽  
Vol 197 (14) ◽  
pp. 2383-2391 ◽  
Author(s):  
Semen A. Leyn ◽  
Irina A. Rodionova ◽  
Xiaoqing Li ◽  
Dmitry A. Rodionov
Keyword(s):  
Carbon Dioxide ◽  
Transcriptional Regulation ◽  
Comparative Genomics ◽  
Dna Binding ◽  
Transcriptional Control ◽  
Binding Assays ◽  
Promoter Regions ◽  
Content Type ◽  
Genome Context

ABSTRACTAutotrophic microorganisms are able to utilize carbon dioxide as their only carbon source, or, alternatively, many of them can grow heterotrophically on organics. Different variants of autotrophic pathways have been identified in various lineages of the phylumCrenarchaeota. Aerobic members of the orderSulfolobalesutilize the hydroxypropionate-hydroxybutyrate cycle (HHC) to fix inorganic carbon, whereas anaerobicThermoprotealesuse the dicarboxylate-hydroxybutyrate cycle (DHC). Knowledge of transcriptional regulation of autotrophic pathways inArchaeais limited. We applied a comparative genomics approach to predict novel autotrophic regulons in theCrenarchaeota. We report identification of two novel DNA motifs associated with the autotrophic pathway genes in theSulfolobales(HHC box) andThermoproteales(DHC box). Based on genome context evidence, the HHC box regulon was attributed to a novel transcription factor from the TrmB family named HhcR. Orthologs of HhcR are present in allSulfolobalesgenomes but were not found in other lineages. A predicted HHC box regulatory motif was confirmed byin vitrobinding assays with the recombinant HhcR protein fromMetallosphaera yellowstonensis. For the DHC box regulon, we assigned a different potential regulator, named DhcR, which is restricted to the orderThermoproteales. DhcR inThermoproteus neutrophilus(Tneu_0751) was previously identified as a DNA-binding protein with high affinity for the promoter regions of two autotrophic operons. The global HhcR and DhcR regulons reconstructed by comparative genomics were reconciled with available omics data inMetallosphaeraandThermoproteusspp. The identified regulons constitute two novel mechanisms for transcriptional control of autotrophic pathways in theCrenarchaeota.IMPORTANCELittle is known about transcriptional regulation of carbon dioxide fixation pathways inArchaea. We previously applied the comparative genomics approach for reconstruction of DtxR family regulons in diverse lineages ofArchaea. Here, we utilize similar computational approaches to identify novel regulatory motifs for genes that are autotrophically induced in microorganisms from two lineages ofCrenarchaeotaand to reconstruct the respective regulons. The predicted novel regulons in archaeal genomes control the majority of autotrophic pathway genes and also other carbon and energy metabolism genes. The HhcR regulon was experimentally validated by DNA-binding assays inMetallosphaeraspp. Novel regulons described for the first time in this work provide a basis for understanding the mechanisms of transcriptional regulation of autotrophic pathways inArchaea.

scholarly journals Categorization of Orthologous Gene Clusters in 92 Ascomycota Genomes Reveals Functions Important for Phytopathogenicity

2021 ◽  
Vol 7 (5) ◽  
pp. 337
Author(s):  
Daniel Peterson ◽  
Tang Li ◽  
Ana M. Calvo ◽  
Yanbin Yin
Keyword(s):  
Comparative Genomics ◽  
Orthologous Gene ◽  
Gene Clusters ◽  
Phytopathogenic Fungi ◽  
Secreted Proteins ◽  
Economic Losses ◽  
Comparative Genomic ◽  
Signal Peptides ◽  
Comparative Genomics Analysis

Phytopathogenic Ascomycota are responsible for substantial economic losses each year, destroying valuable crops. The present study aims to provide new insights into phytopathogenicity in Ascomycota from a comparative genomic perspective. This has been achieved by categorizing orthologous gene groups (orthogroups) from 68 phytopathogenic and 24 non-phytopathogenic Ascomycota genomes into three classes: Core, (pathogen or non-pathogen) group-specific, and genome-specific accessory orthogroups. We found that (i) ~20% orthogroups are group-specific and accessory in the 92 Ascomycota genomes, (ii) phytopathogenicity is not phylogenetically determined, (iii) group-specific orthogroups have more enriched functional terms than accessory orthogroups and this trend is particularly evident in phytopathogenic fungi, (iv) secreted proteins with signal peptides and horizontal gene transfers (HGTs) are the two functional terms that show the highest occurrence and significance in group-specific orthogroups, (v) a number of other functional terms are also identified to have higher significance and occurrence in group-specific orthogroups. Overall, our comparative genomics analysis determined positive enrichment existing between orthogroup classes and revealed a prediction of what genomic characteristics make an Ascomycete phytopathogenic. We conclude that genes shared by multiple phytopathogenic genomes are more important for phytopathogenicity than those that are unique in each genome.

scholarly journals A Novel Hydrolase Identified by Genomic-Proteomic Analysis of Phenylurea Herbicide Mineralization by Variovorax sp. Strain SRS16

2011 ◽  
Vol 77 (24) ◽  
pp. 8754-8764 ◽  
Author(s):  
Karolien Bers ◽  
Baptiste Leroy ◽  
Philip Breugelmans ◽  
Pieter Albers ◽  
Rob Lavigne ◽  
...  
Keyword(s):  
Proteomic Analysis ◽  
Krebs Cycle ◽  
Divergent Evolution ◽  
Phenylurea Herbicides ◽  
Transcription Analysis ◽  
Content Type ◽  
First Report ◽  
Phenylurea Herbicide ◽  
Hydrolyzing Enzymes ◽  
Krebs Cycle Intermediates

ABSTRACTThe soil bacterial isolateVariovoraxsp. strain SRS16 mineralizes the phenylurea herbicide linuron. The proposed pathway initiates with hydrolysis of linuron to 3,4-dichloroaniline (DCA) andN,O-dimethylhydroxylamine, followed by conversion of DCA to Krebs cycle intermediates. Differential proteomic analysis showed a linuron-dependent upregulation of several enzymes that fit into this pathway, including an amidase (LibA), a multicomponent chloroaniline dioxygenase, and enzymes associated with a modified chlorocatecholortho-cleavage pathway. Purified LibA is a monomeric linuron hydrolase of ∼55 kDa with aKmand aVmaxfor linuron of 5.8 μM and 0.16 nmol min−1, respectively. This novel member of the amidase signature family is unrelated to phenylurea-hydrolyzing enzymes from Gram-positive bacteria and lacks activity toward other tested phenylurea herbicides. Orthologues oflibAare present in all other tested linuron-degradingVariovoraxstrains with the exception ofVariovoraxstrains WDL1 and PBS-H4, suggesting divergent evolution of the linuron catabolic pathway in differentVariovoraxstrains. The organization of the linuron degradation genes identified in the draft SRS16 genome sequence indicates that gene patchwork assembly is at the origin of the pathway. Transcription analysis suggests that a catabolic intermediate, rather than linuron itself, acts as effector in activation of the pathway. Our study provides the first report on the genetic organization of a bacterial pathway for complete mineralization of a phenylurea herbicide and the first report on a linuron hydrolase in Gram-negative bacteria.

scholarly journals Mobile Genetic Elements Related to the Diffusion of Plasmid-Mediated AmpC β-Lactamases or Carbapenemases from Enterobacteriaceae: Findings from a Multicenter Study in Spain

2015 ◽  
Vol 59 (9) ◽  
pp. 5260-5266 ◽  
Author(s):  
L. Zamorano ◽  
E. Miró ◽  
C. Juan ◽  
L. Gómez ◽  
G. Bou ◽  
...  
Keyword(s):  
Southern Hybridization ◽  
Mobile Genetic Elements ◽  
Pulsed Field Gel Electrophoresis ◽  
Content Type ◽  
Genetic Elements ◽  
Chromosomal Origin ◽  
Class 1 ◽  
Rapid Dissemination ◽  
Large Plasmids ◽  
Genetic Context

ABSTRACTWe examined the genetic context of 74 acquiredampCgenes and 17 carbapenemase genes from 85 of 640Enterobacteriaceaeisolates collected in 2009. Using S1 pulsed-field gel electrophoresis and Southern hybridization, 37 of 74blaAmpCgenes were located on large plasmids of different sizes belonging to six incompatibility groups. We used sequencing and PCR mapping to investigate the regions flanking the acquiredampCgenes. TheblaCMY-2-like genes were associated with ISEcp1; the surroundingblaDHAgenes were similar toKlebsiella pneumoniaeplasmid pTN60013 associated with IS26and thepspandsapoperons; and theblaACC-1genes were associated with IS26elements inserted into ISEcp1. All of the carbapenemase genes (blaVIM-1,blaIMP-22, andblaIMP-28) were located in class 1 integrons. Therefore, although plasmids are the main cause of the rapid dissemination ofampCgenes amongEnterobacteriaceae, we need to be aware that other mobile genetic elements, such as insertion sequences, transposons, or integrons, can be involved in the mobilization of these genes of chromosomal origin. Additionally, three new integrons (In846 to In848) are described in this study.

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