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 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):  
Comparative Genomics ◽  
Microcystis Aeruginosa ◽  
Phylogenetic Trees ◽  
Environmental Changes ◽  
Second Messengers ◽  
Guanosine Monophosphate ◽  
Cyanobacterial Blooms ◽  
Forming Mechanism ◽  
Regulatory Processes ◽  
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 (4.97 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 congruence between the two types of phylogenetic trees based on 31 highly conserved protein-coding genes and sensor domain-coding genes. 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.

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

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Meng Chen ◽  
Chun-Yang Xu ◽  
Xu Wang ◽  
Chong-Yang Ren ◽  
Jiao Ding ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Microcystis Aeruginosa ◽  
Comparative Genomics Analysis

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 Chemical Characterization of Microcystis aeruginosa for Feed and Energy Uses

Energies ◽  
2021 ◽  
Vol 14 (11) ◽  
pp. 3013
Author(s):  
Larissa Souza Passos ◽  
Éryka Costa Almeida ◽  
Claudio Martin Pereira de Pereira ◽  
Alessandro Alberto Casazza ◽  
Attilio Converti ◽  
...  
Keyword(s):  
Microcystis Aeruginosa ◽  
Animal Feed ◽  
Renewable Energy Sources ◽  
Chemical Characterization ◽  
Cyanobacterial Blooms ◽  
Energy Sources ◽  
Carbohydrate Source ◽  
Heating Value ◽  
Adverse Health Effects ◽  
Degradation Reactions

Cyanobacterial blooms and strains absorb carbon dioxide, drawing attention to its use as feed for animals and renewable energy sources. However, cyanobacteria can produce toxins and have a low heating value. Herein, we studied a cyanobacterial strain harvested during a bloom event and analyzed it to use as animal feed and a source of energy supply. The thermal properties and the contents of total nitrogen, protein, carbohydrate, fatty acids, lipid, and the presence of cyanotoxins were investigated in the Microcystis aeruginosa LTPNA 01 strain and in a bloom material. Microcystins (hepatotoxins) were not detected in this strain nor in the bloom material by liquid chromatography coupled to mass spectrometry. Thermogravimetric analysis showed that degradation reactions (devolatilization) initiated at around 180 °C, dropping from approximately 90% to 20% of the samples’ mass. Our work showed that despite presenting a low heating value, both biomass and non-toxic M. aeruginosa LTPNA 01 could be used as energy sources either by burning or producing biofuels. Both can be considered a protein and carbohydrate source similar to some microalgae species as well as biomass fuel. It could also be used as additive for animal feed; however, its safety and potential adverse health effects should be further investigated.

scholarly journals Evidence of Quorum Sensing in Cyanobacteria by Homoserine Lactones: The Origin of Blooms

Water ◽  
2021 ◽  
Vol 13 (13) ◽  
pp. 1831
Author(s):  
Natalia Herrera ◽  
Fernando Echeverri
Keyword(s):  
Cell Proliferation ◽  
Quorum Sensing ◽  
Microcystis Aeruginosa ◽  
Industrial Effluents ◽  
Cyanobacterial Blooms ◽  
Cylindrospermopsis Raciborskii ◽  
Bacterial Communication ◽  
Homoserine Lactones ◽  
Exogenous Compounds ◽  
Almost All

Although several theories have been postulated to explain cyanobacterial blooms, their biochemical origin has not yet been found. In this work, we explore the existence of bacterial communication, called quorum sensing, in Microcystis aeruginosa and Cylindrospermopsis raciborskii. Thus, the application of several known acylhomoserine lactones to cultures of both cyanobacteria causes profound metabolic. At 72 h post-application, some of them produced substantial increases in cell proliferation, while others were inhibitors. There was a correlation with colony-forming activity for most of them. According to ELISA analysis, the microcystin levels were increased with some lactones. However, there was a clear difference between M. aeruginosa and C. raciborskii culture since, in the first one, there was an inducing effect on cell proliferation, while in C. raciborskii, the effects were minor. Besides, there were compound inhibitors and inducers of microcystins production in M. aeruginosa, but almost all compounds were only inducers of saxitoxin production in C. raciborskii. Moreover, each lactone appears to be involved in a specific quorum sensing process. From these results, the formation of cyanobacterial blooms in dams and reservoirs could be explained since lactones may come from cyanobacteria and other sources as bacterial microflora-associated or exogenous compounds structurally unrelated to lactones, such as drugs, industrial effluents, and agrochemicals.

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