The Experts below are selected from a list of 216 Experts worldwide ranked by ideXlab platform
Guillermo Dávila - One of the best experts on this subject based on the ideXlab platform.
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RNA-Seq analysis of the Multipartite Genome of Rhizobium etli CE3 shows different replicon contributions under heat and saline shock
BMC Genomics, 2014Co-Authors: Gamaliel López-leal, Maria Luisa Tabche, Santiago Castillo-ramírez, Alfredo Mendoza-vargas, Miguel A Ramírez-romero, Guillermo DávilaAbstract:Background Regulation of transcription is essential for any organism and Rhizobium etli (a multi-replicon, nitrogen-fixing symbiotic bacterium) is no exception. This bacterium is commonly found in the rhizosphere (free-living) or inside of root-nodules of the common bean ( Phaseolus vulgaris ) in a symbiotic relationship. Abiotic stresses, such as high soil temperatures and salinity, compromise the genetic stability of R. etli and therefore its symbiotic interaction with P. vulgaris . However, it is still unclear which genes are up- or down-regulated to cope with these stress conditions. The aim of this study was to identify the genes and non-coding RNAs (ncRNAs) that are differentially expressed under heat and saline shock, as well as the promoter regions of the up-regulated loci. Results Analysing the heat and saline shock responses of R. etli CE3 through RNA-Seq, we identified 756 and 392 differentially expressed genes, respectively, and 106 were up-regulated under both conditions. Notably, the set of genes over-expressed under either condition was preferentially encoded on plasmids, although this observation was more significant for the heat shock response. In contrast, during either saline shock or heat shock, the down-regulated genes were principally chromosomally encoded. Our functional analysis shows that genes encoding chaperone proteins were up-regulated during the heat shock response, whereas genes involved in the metabolism of compatible solutes were up-regulated following saline shock. Furthermore, we identified thirteen and nine ncRNAs that were differentially expressed under heat and saline shock, respectively, as well as eleven ncRNAs that had not been previously identified. Finally, using an in silico analysis, we studied the promoter motifs in all of the non-coding regions associated with the genes and ncRNAs up-regulated under both conditions. Conclusions Our data suggest that the replicon contribution is different for different stress responses and that the heat shock response is more complex than the saline shock response. In general, this work exemplifies how strategies that not only consider differentially regulated genes but also regulatory elements of the stress response provide a more comprehensive view of bacterial gene regulation.
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rna seq analysis of the Multipartite Genome of rhizobium etli ce3 shows different replicon contributions under heat and saline shock
BMC Genomics, 2014Co-Authors: Gamaliel Lopezleal, Maria Luisa Tabche, Santiago Castilloramirez, Alfredo Mendozavargas, Miguel A Ramirezromero, Guillermo DávilaAbstract:Regulation of transcription is essential for any organism and Rhizobium etli (a multi-replicon, nitrogen-fixing symbiotic bacterium) is no exception. This bacterium is commonly found in the rhizosphere (free-living) or inside of root-nodules of the common bean (Phaseolus vulgaris) in a symbiotic relationship. Abiotic stresses, such as high soil temperatures and salinity, compromise the genetic stability of R. etli and therefore its symbiotic interaction with P. vulgaris. However, it is still unclear which genes are up- or down-regulated to cope with these stress conditions. The aim of this study was to identify the genes and non-coding RNAs (ncRNAs) that are differentially expressed under heat and saline shock, as well as the promoter regions of the up-regulated loci. Analysing the heat and saline shock responses of R. etli CE3 through RNA-Seq, we identified 756 and 392 differentially expressed genes, respectively, and 106 were up-regulated under both conditions. Notably, the set of genes over-expressed under either condition was preferentially encoded on plasmids, although this observation was more significant for the heat shock response. In contrast, during either saline shock or heat shock, the down-regulated genes were principally chromosomally encoded. Our functional analysis shows that genes encoding chaperone proteins were up-regulated during the heat shock response, whereas genes involved in the metabolism of compatible solutes were up-regulated following saline shock. Furthermore, we identified thirteen and nine ncRNAs that were differentially expressed under heat and saline shock, respectively, as well as eleven ncRNAs that had not been previously identified. Finally, using an in silico analysis, we studied the promoter motifs in all of the non-coding regions associated with the genes and ncRNAs up-regulated under both conditions. Our data suggest that the replicon contribution is different for different stress responses and that the heat shock response is more complex than the saline shock response. In general, this work exemplifies how strategies that not only consider differentially regulated genes but also regulatory elements of the stress response provide a more comprehensive view of bacterial gene regulation.
Hari S Misra - One of the best experts on this subject based on the ideXlab platform.
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Overlapping oriC and centromere-like functions in secondary Genome replicons determine their maintenance independent of chromosome I in Deinococcus radiodurans
bioRxiv, 2020Co-Authors: Ganesh K Maurya, Hari S MisraAbstract:The Deinococcus radiodurans Multipartite Genome system (MGS) consists of chromosome I (ChrI) and secondary Genome elements; Chr II and megaplasmid (MP). The sequences upstream to parAB operons in Chr II (cisII) and MP (cisMP) helped an E. coli plasmid maintenance in D. radiodurans and showed sequence specific interactions with DnaA and ParBs. The cells devoid of cisII (delcisII) or cisMP (delcisMP) showed reduced gamma radiation resistance and copy number of Chr II and MP. Fluorescent Reporter-Operator System (FROS) developed for ChrI, ChrII and MP in delcisII or delcisMP mutants showed no change in wild type pattern of Chr I localization. However, the relative copy numbers of Chr II and MP had reduced while anucleate cells had increased in mutants. These results suggested that cisII and cisMP elements contain both ori and centromere-like functions, and like other MGS bacteria, the Chr I and secondary Genome are maintained independently in D. radiodurans.
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characterisation of parb encoded on Multipartite Genome in deinococcus radiodurans and their roles in radioresistance
Microbiological Research, 2019Co-Authors: Swathi Kota, Ganesh K Maurya, Hari S MisraAbstract:Abstract The Deinococcus radiodurans Multipartite Genome consists of 2 chromosomes and 2 plasmids Its Genome encodes 4 ParA and 4 ParB proteins on different replicons. Multiple sequence alignments of ParBs encoded on these Genome elements showed that ParB of primary chromosome (ParB1) is close to chromosomal type ParB and is found to be different from ParBs encoded on chromosome II (ParB2) and megaplasmid (ParB3) elements. We observed that ParB1, ParB2 and ParB3 exist as dimer in solution and these proteins interact to self but not to its homologs in D. radiodurans, suggesting the specificity in ParBs dimerization. The parB1 deletion mutant showed slow growth under normal condition and relatively reduced resistance to γ-radiation as compared to wild type. The parB2 and parB3 mutants maintained without selection pressure showed loss of radioresistance, which was not observed when maintained with selection pressure. Nearly half of the populations of these mutants showed resistance to antibiotics marked to respective Genome elements. Interestingly, all the parB mutants showed increased copy numbers of cognate Genome element in cells maintained with antibiotics possibly due to arrest in Genome segregation. These results suggested that ParB proteins encoded on Multipartite Genome system in D. radiodurans form homodimer and not heterodimer with other ParB homologs, and they independently regulate the segregation of respective Genome elements. The roles of ParB1 proteins in normal as well as radiation stressed growth of this bacterium have also been ascertained.
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ParA proteins of secondary Genome elements cross-talk and regulate radioresistance through Genome copy number reduction in Deinococcus radiodurans.
Biochemical Journal, 2019Co-Authors: Ganesh K Maurya, Swathi Kota, Naveen Kumar, Raghvendra Tewari, Hari S MisraAbstract:Deinococcus radiodurans, an extremely radioresistant bacterium has Multipartite Genome system and ploidy. Mechanisms underlying such types of bacterial Genome maintenance and its role in extraordinary radioresistance are not known in this bacterium. Chromosome I (Chr I), chromosome II (Chr II) and megaplasmid (Mp) encode its own set of Genome partitioning proteins. Here, we have characterized P-loop ATPases of Chr II (ParA2) and Mp (ParA3) and their roles in the maintenance of Genome copies and extraordinary radioresistance. Purified ParA2 and ParA3 showed nearly similar polymerization kinetics and interaction patterns with DNA. Electron microscopic examination of purified proteins incubated with DNA showed polymerization on nicked circular dsDNA. ParA2 and ParA3 showed both homotypic and heterotypic interactions to each other, but not with ParA1 (ParA of Chr I). Similarly, ParA2 and ParA3 interacted with ParB2 and ParB3 but not with ParB1 in vivo . ParB2 and ParB3 interaction with cis elements located upstream to the corresponding parAB operon was found to be sequence specific. Unlike single mutant of parA2 and parA3, their double mutant (D parA2 D ParA3 ) affected copy number of cognate Genome elements and resistance to g-radiation as well as hydrogen peroxide in this bacterium. These results suggested that ParA2 and ParA3 are DNA binding ATPases producing higher order polymers on DNA and are functionally redundant in the maintenance of secondary Genome elements in D. radiodurans . The findings also suggest the involvement of secondary Genome elements such as Chr II and Mp in the extraordinary radioresistance of D. radiodurans .
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Divisome and segrosome components of Deinococcus radiodurans interact through cell division regulatory proteins.
Microbiology, 2016Co-Authors: Ganesh K Maurya, Kruti Modi, Hari S MisraAbstract:The Deinococcus radiodurans Genome encodes many of the known components of divisome as well as four sets of Genome partitioning proteins, ParA and ParB on its Multipartite Genome. Interdependent regulation of cell division and Genome segregation is not understood. In vivo interactions of D. radiodurans' sdivisome, segrosome and other cell division regulatory proteins expressed on multicopy plasmids were studied in Escherichia coli using a bacterial two-hybrid system and confirmed by co-immunoprecipitation with the proteins made in E. coli. Many of these showed interactions both with the self and with other proteins. For example, DrFtsA, DrFtsZ, DrMinD, DrMinC, DrDivIVA and all four ParB proteins individually formed at least homodimers, while DrFtsA interacted with DrFtsZ, DrFtsW, DrFtsE, DrFtsK and DrMinD. DrMinD also showed interaction with DrFtsW, DrFtsE and DrMinC. Interestingly, septum site determining protein, DrDivIVA showed interactions with secondary Genome ParAs as well as ParB1, ParB3 and ParB4 while DrMinC interacted with ParB1 and ParB3. PprA, a pleiotropic protein recently implicated in cell division regulation, neither interacted with divisome proteins nor ParBs but interacted at different levels with all four ParAs. These results suggest the formation of independent multiprotein complexes of ‘DrFts’ proteins, segrosome proteins and cell division regulatory proteins, and these complexes could interact with each other through DrMinC and DrDivIVA, and PprA in D. radiodurans.
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DNA Gyrase of Deinococcus radiodurans is characterized as Type II bacterial topoisomerase and its activity is differentially regulated by PprA in vitro
Extremophiles, 2016Co-Authors: Swathi Kota, Yogendra S. Rajpurohit, Vijaya K. Charaka, Katsuya Satoh, Issay Narumi, Hari S MisraAbstract:The Multipartite Genome of Deinococcus radiodurans forms toroidal structure. It encodes topoisomerase IB and both the subunits of DNA gyrase (DrGyr) while lacks other bacterial topoisomerases. Recently, PprA a pleiotropic protein involved in radiation resistance in D. radiodurans has been suggested for having roles in cell division and Genome maintenance. In vivo interaction of PprA with topoisomerases has also been shown. DrGyr constituted from recombinant gyrase A and gyrase B subunits showed decatenation, relaxation and supercoiling activities. Wild type PprA stimulated DNA relaxation activity while inhibited supercoiling activity of DrGyr. Lysine133 to glutamic acid (K133E) and tryptophane183 to arginine (W183R) replacements resulted loss of DNA binding activity in PprA and that showed very little effect on DrGyr activities in vitro. Interestingly, wild type PprA and its K133E derivative continued interacting with GyrA in vivo while W183R, which formed relatively short oligomers did not interact with GyrA. The size of nucleoid in PprA mutant (1.9564 ± 0.324 µm) was significantly bigger than the wild type (1.6437 ± 0.345 µm). Thus, we showed that DrGyr confers all three activities of bacterial type IIA family DNA topoisomerases, which are differentially regulated by PprA, highlighting the significant role of PprA in DrGyr activity regulation and Genome maintenance in D. radiodurans.
Turlough M Finan - One of the best experts on this subject based on the ideXlab platform.
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Creation and Characterization of a Genomically Hybrid Strain in the Nitrogen-Fixing Symbiotic Bacterium Sinorhizobium meliloti.
ACS Synthetic Biology, 2018Co-Authors: Alice Checcucci, George C Dicenzo, Turlough M Finan, Marco Bazzicalupo, Veronica Ghini, Anke Becker, Francesca Decorosi, Johannes Döhlemann, Camilla Fagorzi, Marco FondiAbstract:Many bacteria, often associated with eukaryotic hosts and of relevance for biotechnological applications, harbor a Multipartite Genome composed of more than one replicon. Biotechnologically relevant phenotypes are often encoded by genes residing on the secondary replicons. A synthetic biology approach to developing enhanced strains for biotechnological purposes could therefore involve merging pieces or entire replicons from multiple strains into a single Genome. Here we report the creation of a genomic hybrid strain in a model Multipartite Genome species, the plant-symbiotic bacterium Sinorhizobium meliloti. We term this strain as cis-hybrid, since it is produced by genomic material coming from the same species’ panGenome. In particular, we moved the secondary replicon pSymA (accounting for nearly 20% of total Genome content) from a donor S. meliloti strain to an acceptor strain. The cis-hybrid strain was screened for a panel of complex phenotypes (carbon/nitrogen utilization phenotypes, intra- and extrac...
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inter replicon gene flow contributes to transcriptional integration in the sinorhizobium meliloti Multipartite Genome
G3: Genes Genomes Genetics, 2018Co-Authors: George C Dicenzo, Brian G Golding, Deelaka Wellappili, Turlough M FinanAbstract:Integration of newly acquired genes into existing regulatory networks is necessary for successful horizontal gene transfer (HGT). Ten percent of bacterial species contain at least two DNA replicons over 300 kilobases in size, with the secondary replicons derived predominately through HGT. The Sinorhizobium meliloti Genome is split between a 3.7 Mb chromosome, a 1.7 Mb chromid consisting largely of genes acquired through ancient HGT, and a 1.4 Mb megaplasmid consisting primarily of recently acquired genes. Here, RNA-sequencing is used to examine the transcriptional consequences of massive, synthetic Genome reduction produced through the removal of the megaplasmid and/or the chromid. Removal of the pSymA megaplasmid influenced the transcription of only six genes. In contrast, removal of the chromid influenced expression of ∼8% of chromosomal genes and ∼4% of megaplasmid genes. This was mediated in part by the loss of the ETR DNA region whose presence on pSymB is due to a translocation from the chromosome. No obvious functional bias among the up-regulated genes was detected, although genes with putative homologs on the chromid were enriched. Down-regulated genes were enriched in motility and sensory transduction pathways. Four transcripts were examined further, and in each case the transcriptional change could be traced to loss of specific pSymB regions. In particularly, a chromosomal transporter was induced due to deletion of bdhA likely mediated through 3-hydroxybutyrate accumulation. These data provide new insights into the evolution of the Multipartite bacterial Genome, and more generally into the integration of horizontally acquired genes into the transcriptome.
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Creation and multi-omics characterization of a genomically hybrid strain in the nitrogen-fixing symbiotic bacterium Sinorhizobium meliloti
bioRxiv, 2018Co-Authors: Alice Checcucci, George C Dicenzo, Turlough M Finan, Marco Bazzicalupo, Veronica Ghini, Francesca Decorosi, Johannes Döhlemann, Camilla Fagorzi, Anke Beker, Marco FondiAbstract:Many bacteria, often associated with eukaryotic hosts and of relevance for biotechnological applications, harbour a Multipartite Genome composed by more than one replicon. Biotechnologically relevant phenotypes are often encoded by genes residing on the secondary replicons. A synthetic biology approach to developing enhanced strains for biotechnological purposes could therefore involve merging pieces or entire replicons from multiple strains into a single Genome. Here we report the creation of a genomic hybrid strain in a model Multipartite Genome species, the plant-symbiotic bacterium Sinorhizobium meliloti. In particular, we moved the secondary replicon pSymA (accounting for nearly 20% of total Genome content) from a donor S. meliloti strain to an acceptor strain. The cis-hybrid strain was screened for a panel of complex phenotypes (carbon/nitrogen utilization phenotypes, intra- and extra-cellular metabolomes, symbiosis, and various microbiological tests). Additionally, metabolic network reconstruction and constraint-based modelling were employed for in silico prediction of metabolic flux reorganization. Phenotypes of the cis-hybrid strain were in good agreement with those of both parental strains. Interestingly, the symbiotic phenotype showed a marked cultivar-specific improvement with the cis-hybrid strains compared to both parental strains. These results provide a proof-of-principle for the feasibility of Genome-wide replicon-based remodelling of bacterial strains for improved biotechnological applications in precision agriculture.
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The Divided Bacterial Genome: Structure, Function, and Evolution.
Microbiology and Molecular Biology Reviews, 2017Co-Authors: George C Dicenzo, Turlough M FinanAbstract:SUMMARY Approximately 10% of bacterial Genomes are split between two or more large DNA fragments, a Genome architecture referred to as a Multipartite Genome. This Multipartite organization is found in many important organisms, including plant symbionts, such as the nitrogen-fixing rhizobia, and plant, animal, and human pathogens, including the genera Brucella, Vibrio, and Burkholderia. The availability of many complete bacterial Genome sequences means that we can now examine on a broad scale the characteristics of the different types of DNA molecules in a Genome. Recent work has begun to shed light on the unique properties of each class of replicon, the unique functional role of chromosomal and nonchromosomal DNA molecules, and how the exploitation of novel niches may have driven the evolution of the Multipartite Genome. The aims of this review are to (i) outline the literature regarding bacterial Genomes that are divided into multiple fragments, (ii) provide a meta-analysis of completed bacterial Genomes from 1,708 species as a way of reviewing the abundant information present in these Genome sequences, and (iii) provide an encompassing model to explain the evolution and function of the Multipartite Genome structure. This review covers, among other topics, salient Genome terminology; mechanisms of Multipartite Genome formation; the phylogenetic distribution of Multipartite Genomes; how each part of a Genome differs with respect to genomic signatures, genetic variability, and gene functional annotation; how each DNA molecule may interact; as well as the costs and benefits of this Genome structure.
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examination of prokaryotic Multipartite Genome evolution through experimental Genome reduction
PLOS Genetics, 2014Co-Authors: George C Dicenzo, Allyson M Maclean, Branislava Milunovic, Brian G Golding, Turlough M FinanAbstract:Many bacteria carry two or more chromosome-like replicons. This occurs in pathogens such as Vibrio cholerea and Brucella abortis as well as in many N2-fixing plant symbionts including all isolates of the alfalfa root-nodule bacteria Sinorhizobium meliloti. Understanding the evolution and role of this Multipartite Genome organization will provide significant insight into these important organisms; yet this knowledge remains incomplete, in part, because technical challenges of large-scale Genome manipulations have limited experimental analyses. The distinct evolutionary histories and characteristics of the three replicons that constitute the S. meliloti Genome (the chromosome (3.65 Mb), pSymA megaplasmid (1.35 Mb), and pSymB chromid (1.68 Mb)) makes this a good model to examine this topic. We transferred essential genes from pSymB into the chromosome, and constructed strains that lack pSymB as well as both pSymA and pSymB. This is the largest reduction (45.4%, 3.04 megabases, 2866 genes) of a prokaryotic Genome to date and the first removal of an essential chromid. Strikingly, strains lacking pSymA and pSymB (ΔpSymAB) lost the ability to utilize 55 of 74 carbon sources and various sources of nitrogen, phosphorous and sulfur, yet the ΔpSymAB strain grew well in minimal salts media and in sterile soil. This suggests that the core chromosome is sufficient for growth in a bulk soil environment and that the pSymA and pSymB replicons carry genes with more specialized functions such as growth in the rhizosphere and interaction with the plant. These experimental data support a generalized evolutionary model, in which non-chromosomal replicons primarily carry genes with more specialized functions. These large secondary replicons increase the organism's niche range, which offsets their metabolic burden on the cell (e.g. pSymA). Subsequent co-evolution with the chromosome then leads to the formation of a chromid through the acquisition of functions core to all niches (e.g. pSymB).
George C Dicenzo - One of the best experts on this subject based on the ideXlab platform.
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Genomic Diversity and Evolution of Rhizobia
Microbial Diversity in the Genomic Era, 2020Co-Authors: Alice Checcucci, George C Dicenzo, Elena Perrin, Marco Bazzicalupo, Alessio MengoniAbstract:Abstract The rhizosphere is colonized by a large variety of bacterial community and, thanks to the attractive chemical composition of the root exudates, some of them can penetrate inside the tissues and colonize the plant. The rhizobia are bacteria able to establish a mutualistic nitrogen-fixing endosymbiosis with specific legumes forming root nodules on the host plant. They are spread throughout the α- and β-subdivision (classes) of Proteobacteria, which often are united by the Multipartite Genome structure, consisting in a chromosome and additional plasmid, acquired later, and enriched in dispensable genes that play a key role in the determination of bacterium fitness in different ecological niches. Presently, Sinorhizobium meliloti is the main representative of α-proteobacteria for studies on Multipartite Genome evolution and environmental adaptation, but Burkholderia and Cupriavirus may represent a new frontier for the β-rhizobia knowledge.
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Creation and Characterization of a Genomically Hybrid Strain in the Nitrogen-Fixing Symbiotic Bacterium Sinorhizobium meliloti.
ACS Synthetic Biology, 2018Co-Authors: Alice Checcucci, George C Dicenzo, Turlough M Finan, Marco Bazzicalupo, Veronica Ghini, Anke Becker, Francesca Decorosi, Johannes Döhlemann, Camilla Fagorzi, Marco FondiAbstract:Many bacteria, often associated with eukaryotic hosts and of relevance for biotechnological applications, harbor a Multipartite Genome composed of more than one replicon. Biotechnologically relevant phenotypes are often encoded by genes residing on the secondary replicons. A synthetic biology approach to developing enhanced strains for biotechnological purposes could therefore involve merging pieces or entire replicons from multiple strains into a single Genome. Here we report the creation of a genomic hybrid strain in a model Multipartite Genome species, the plant-symbiotic bacterium Sinorhizobium meliloti. We term this strain as cis-hybrid, since it is produced by genomic material coming from the same species’ panGenome. In particular, we moved the secondary replicon pSymA (accounting for nearly 20% of total Genome content) from a donor S. meliloti strain to an acceptor strain. The cis-hybrid strain was screened for a panel of complex phenotypes (carbon/nitrogen utilization phenotypes, intra- and extrac...
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emergence and features of the Multipartite Genome structure of the family burkholderiaceae revealed through comparative and evolutionary genomics
bioRxiv, 2018Co-Authors: George C Dicenzo, Alessio Mengoni, Elena PerrinAbstract:The Multipartite Genome structure is found in a diverse group of important symbiotic and pathogenic bacteria; however, the advantage of this Genome structure remains incompletely understood. Here, we perform comparative genomics of hundreds of finished β-proteobacterial Genomes to study the role and emergence of Multipartite Genomes. Nearly all essential secondary replicons (chromids) of the β-proteobacteria are found in the family Burkholderiaceae. These replicons arose from just two plasmid acquisition events, and they were likely stabilized early in their evolution by the presence of core genes, at least some of which were likely acquired through an inter-replicon translocation event. On average, Burkholderiaceae genera with Multipartite Genomes had a larger total Genome size, but smaller chromosome, than genera without secondary replicons. PanGenome-level functional enrichment analyses suggested that inter-replicon functional biases are partially driven by the enrichment of secondary replicons in the accessory panGenome fraction. Nevertheless, the small overlap in orthologous groups present in each replicon9s panGenome indicates a clear functional separation of the replicons. Chromids appeared biased to environmental adaptation, as the functional categories enriched on chromids were also over-represented on the chromosomes of the environmental genera (Paraburkholderia, Cupriavidus) compared to the pathogenic genera (Burkholderia, Ralstonia). Using ancestral state reconstruction, it was predicted that the rate of accumulation of modern-day genes by chromids was more rapid than the rate of gene accumulation by the chromosomes. Overall, the data are consistent with a model where the primary advantage of secondary replicons is in facilitating increased rates of gene acquisition through horizontal gene transfer, consequently resulting in a replicon enriched in genes associated with adaptation to novel environments.
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inter replicon gene flow contributes to transcriptional integration in the sinorhizobium meliloti Multipartite Genome
G3: Genes Genomes Genetics, 2018Co-Authors: George C Dicenzo, Brian G Golding, Deelaka Wellappili, Turlough M FinanAbstract:Integration of newly acquired genes into existing regulatory networks is necessary for successful horizontal gene transfer (HGT). Ten percent of bacterial species contain at least two DNA replicons over 300 kilobases in size, with the secondary replicons derived predominately through HGT. The Sinorhizobium meliloti Genome is split between a 3.7 Mb chromosome, a 1.7 Mb chromid consisting largely of genes acquired through ancient HGT, and a 1.4 Mb megaplasmid consisting primarily of recently acquired genes. Here, RNA-sequencing is used to examine the transcriptional consequences of massive, synthetic Genome reduction produced through the removal of the megaplasmid and/or the chromid. Removal of the pSymA megaplasmid influenced the transcription of only six genes. In contrast, removal of the chromid influenced expression of ∼8% of chromosomal genes and ∼4% of megaplasmid genes. This was mediated in part by the loss of the ETR DNA region whose presence on pSymB is due to a translocation from the chromosome. No obvious functional bias among the up-regulated genes was detected, although genes with putative homologs on the chromid were enriched. Down-regulated genes were enriched in motility and sensory transduction pathways. Four transcripts were examined further, and in each case the transcriptional change could be traced to loss of specific pSymB regions. In particularly, a chromosomal transporter was induced due to deletion of bdhA likely mediated through 3-hydroxybutyrate accumulation. These data provide new insights into the evolution of the Multipartite bacterial Genome, and more generally into the integration of horizontally acquired genes into the transcriptome.
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Creation and multi-omics characterization of a genomically hybrid strain in the nitrogen-fixing symbiotic bacterium Sinorhizobium meliloti
bioRxiv, 2018Co-Authors: Alice Checcucci, George C Dicenzo, Turlough M Finan, Marco Bazzicalupo, Veronica Ghini, Francesca Decorosi, Johannes Döhlemann, Camilla Fagorzi, Anke Beker, Marco FondiAbstract:Many bacteria, often associated with eukaryotic hosts and of relevance for biotechnological applications, harbour a Multipartite Genome composed by more than one replicon. Biotechnologically relevant phenotypes are often encoded by genes residing on the secondary replicons. A synthetic biology approach to developing enhanced strains for biotechnological purposes could therefore involve merging pieces or entire replicons from multiple strains into a single Genome. Here we report the creation of a genomic hybrid strain in a model Multipartite Genome species, the plant-symbiotic bacterium Sinorhizobium meliloti. In particular, we moved the secondary replicon pSymA (accounting for nearly 20% of total Genome content) from a donor S. meliloti strain to an acceptor strain. The cis-hybrid strain was screened for a panel of complex phenotypes (carbon/nitrogen utilization phenotypes, intra- and extra-cellular metabolomes, symbiosis, and various microbiological tests). Additionally, metabolic network reconstruction and constraint-based modelling were employed for in silico prediction of metabolic flux reorganization. Phenotypes of the cis-hybrid strain were in good agreement with those of both parental strains. Interestingly, the symbiotic phenotype showed a marked cultivar-specific improvement with the cis-hybrid strains compared to both parental strains. These results provide a proof-of-principle for the feasibility of Genome-wide replicon-based remodelling of bacterial strains for improved biotechnological applications in precision agriculture.
Maria Luisa Tabche - One of the best experts on this subject based on the ideXlab platform.
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RNA-Seq analysis of the Multipartite Genome of Rhizobium etli CE3 shows different replicon contributions under heat and saline shock
BMC Genomics, 2014Co-Authors: Gamaliel López-leal, Maria Luisa Tabche, Santiago Castillo-ramírez, Alfredo Mendoza-vargas, Miguel A Ramírez-romero, Guillermo DávilaAbstract:Background Regulation of transcription is essential for any organism and Rhizobium etli (a multi-replicon, nitrogen-fixing symbiotic bacterium) is no exception. This bacterium is commonly found in the rhizosphere (free-living) or inside of root-nodules of the common bean ( Phaseolus vulgaris ) in a symbiotic relationship. Abiotic stresses, such as high soil temperatures and salinity, compromise the genetic stability of R. etli and therefore its symbiotic interaction with P. vulgaris . However, it is still unclear which genes are up- or down-regulated to cope with these stress conditions. The aim of this study was to identify the genes and non-coding RNAs (ncRNAs) that are differentially expressed under heat and saline shock, as well as the promoter regions of the up-regulated loci. Results Analysing the heat and saline shock responses of R. etli CE3 through RNA-Seq, we identified 756 and 392 differentially expressed genes, respectively, and 106 were up-regulated under both conditions. Notably, the set of genes over-expressed under either condition was preferentially encoded on plasmids, although this observation was more significant for the heat shock response. In contrast, during either saline shock or heat shock, the down-regulated genes were principally chromosomally encoded. Our functional analysis shows that genes encoding chaperone proteins were up-regulated during the heat shock response, whereas genes involved in the metabolism of compatible solutes were up-regulated following saline shock. Furthermore, we identified thirteen and nine ncRNAs that were differentially expressed under heat and saline shock, respectively, as well as eleven ncRNAs that had not been previously identified. Finally, using an in silico analysis, we studied the promoter motifs in all of the non-coding regions associated with the genes and ncRNAs up-regulated under both conditions. Conclusions Our data suggest that the replicon contribution is different for different stress responses and that the heat shock response is more complex than the saline shock response. In general, this work exemplifies how strategies that not only consider differentially regulated genes but also regulatory elements of the stress response provide a more comprehensive view of bacterial gene regulation.
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rna seq analysis of the Multipartite Genome of rhizobium etli ce3 shows different replicon contributions under heat and saline shock
BMC Genomics, 2014Co-Authors: Gamaliel Lopezleal, Maria Luisa Tabche, Santiago Castilloramirez, Alfredo Mendozavargas, Miguel A Ramirezromero, Guillermo DávilaAbstract:Regulation of transcription is essential for any organism and Rhizobium etli (a multi-replicon, nitrogen-fixing symbiotic bacterium) is no exception. This bacterium is commonly found in the rhizosphere (free-living) or inside of root-nodules of the common bean (Phaseolus vulgaris) in a symbiotic relationship. Abiotic stresses, such as high soil temperatures and salinity, compromise the genetic stability of R. etli and therefore its symbiotic interaction with P. vulgaris. However, it is still unclear which genes are up- or down-regulated to cope with these stress conditions. The aim of this study was to identify the genes and non-coding RNAs (ncRNAs) that are differentially expressed under heat and saline shock, as well as the promoter regions of the up-regulated loci. Analysing the heat and saline shock responses of R. etli CE3 through RNA-Seq, we identified 756 and 392 differentially expressed genes, respectively, and 106 were up-regulated under both conditions. Notably, the set of genes over-expressed under either condition was preferentially encoded on plasmids, although this observation was more significant for the heat shock response. In contrast, during either saline shock or heat shock, the down-regulated genes were principally chromosomally encoded. Our functional analysis shows that genes encoding chaperone proteins were up-regulated during the heat shock response, whereas genes involved in the metabolism of compatible solutes were up-regulated following saline shock. Furthermore, we identified thirteen and nine ncRNAs that were differentially expressed under heat and saline shock, respectively, as well as eleven ncRNAs that had not been previously identified. Finally, using an in silico analysis, we studied the promoter motifs in all of the non-coding regions associated with the genes and ncRNAs up-regulated under both conditions. Our data suggest that the replicon contribution is different for different stress responses and that the heat shock response is more complex than the saline shock response. In general, this work exemplifies how strategies that not only consider differentially regulated genes but also regulatory elements of the stress response provide a more comprehensive view of bacterial gene regulation.