Maintenance of multipartite genome system and its functional significance in bacteria

Misra, Hari S.; Maurya, Ganesh Kumar; Kota, Swathi; Charaka, Vijaya

doi:10.1007/s12041-018-0969-x

Cited by 23 publications

(16 citation statements)

References 122 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…, cells contain one or more large replicons in addition to the chromosome ( Harrison et al 2010 ). The majority of bacteria with multipartite genomes are associated with high tolerance to abiotic stresses, or are associated with animals, human, or plants as pathogens or symbionts ( Misra et al 2018 ). This observation, in addition to other data, has prompted scientists to hypothesize that multipartite genomes play crucial roles in the successful spread and establishment of bacteria into a broad range of ecological niches ( Heidelberg et al 2000 ).…”

Section: Introductionmentioning

confidence: 99%

The Pseudoalteromonas multipartite genome: distribution and expression of pangene categories, and a hypothesis for the origin and evolution of the chromid

Sonnenberg

Haugen

2021

G3 Genes|Genomes|Genetics

View full text Add to dashboard Cite

Bacterial genomes typically consist of one large chromosome, but can also include secondary replicons. These so-called multipartite genomes are scattered on the bacterial tree of life with the majority of cases belonging to Proteobacteria. Within the class gamma-proteobacteria, multipartite genomes are restricted to the two families Vibrionaceae and Pseudoalteromonadaceae. Whereas the genome of vibrios is well studied, information on the Pseudoalteromonadaceae genome is much scarcer. We have studied Pseudoalteromonadaceae with respect to the origin of the chromid, how pangene categories are distributed, how genes are expressed relative to their genomic location, and identified chromid hallmark genes. We calculated the Pseudoalteromonadaceae pangenome based on 25 complete genomes and found that core/softcore are significantly overrepresented in late replicating sectors of the chromid, regardless of how the chromid is replicated. On the chromosome, core/softcore and shell/cloud genes are only weakly overrepresented at the chromosomal replication origin and termination sequences, respectively. Gene expression is trending downwards with increasing distance from the chromosomal oriC, whereas the chromidal expression pattern is more complex. Moreover, we identified 78 chromid hallmark genes, and BLASTp searches suggest that the majority of them were acquired from the ancestral gene pool of Alteromonadales. Finally, our data strongly suggest that the chromid originates from a plasmid that was acquired in a relatively recent event. In summary, this work extends our knowledge on multipartite genomes, and helps us understand how and why secondary replicons are acquired, why they are maintained, and how they are shaped by evolution.

show abstract

Section: Introductionmentioning

confidence: 99%

The Pseudoalteromonas multipartite genome: distribution and expression of pangene categories, and a hypothesis for the origin and evolution of the chromid

Sonnenberg

Haugen

2021

G3 Genes|Genomes|Genetics

View full text Add to dashboard Cite

show abstract

“…1A). Specifically, while only five of these genes were associated with partner quality in all four experiments, 55 candidates for contributing to partner quality in many conditions. We discuss these three types of genetic effects in turn, at the phenotypic, genomic (three elements in the tripartite genome), gene, and variant level, then conclude with the general implications of our findings for plant-microbe interactions and symbiosis evolution more broadly.…”

Section: Resultsmentioning

confidence: 90%

Genome-wide association studies across environmental and genetic contexts reveal complex genetic architecture of symbiotic extended phenotypes

Batstone

Lindgren

Allsup

et al. 2021

Preprint

View full text Add to dashboard Cite

A goal of modern biology is to develop the genotype-phenotype (G-P) map, a predictive understanding of how genomic information generates the organismal trait variation that forms the basis of both natural and managed communities. As microbiome research advances, however, it has become clear that many of these traits are governed by genetic variation encoded not only by the host's own genome, but also by the genomes of myriad cryptic symbionts. Thus many ecologically-important traits are likely symbiotic extended phenotypes, and this recognition adds even more complexity to our conceptions of the G-P map. In model symbioses such as the legume-rhizobium mutualism, host growth and fitness often depend on genetic variation in symbiont partner quality, and our ability to manipulate host and symbiont genotype combinations, combined with increasingly precise sequencing and mapping approaches, provides an opportunity to characterize the genetic nature of these symbiotic extended phenotypes. Here we use naturally-occurring genetic variation in 191 strains of the nitrogen-fixing symbiont Ensifer meliloti in four mapping experiments to study the genomic architecture of symbiotic partner quality within and across environmental contexts and host genotypes. We demonstrate the quantitative genetic nature of symbiotic extended phenotypes, including extensive context-dependency in both the identity and functions of symbiont loci that control host growth. We additionally resolve a core set of universal loci from populations in the native range that are likely important in all or most environments, and thus, serve as excellent targets both for genetic engineering and future coevolutionary studies of symbiosis.

show abstract

“…The multipartite genome with ploidy and toroidal shape of the nucleoid are the most interesting cytogenetic features of this extremophile and in many bacteria that are parasite to some forms of life 21 . In our opinion, this area of bacterial genome biology offers a great potential with a possible revisit of several paradigms set by working with bacteria harbouring single circular chromosome.…”

Section: Discussionmentioning

confidence: 99%

“…These plasmids were linearized with XmnI and transformed into D. radiodurans cells. The homozygous replacement of cisII and cisMP by nptII was achieved through several rounds of sub-culturing and ascertained by diagnostic PCR using flanking primers (Table S1) of the target as described earlier (Maurya et al, 2018). The confirmed mutant cells were maintained in the absence of selection pressure but ensured for antibiotic resistance before the experiments.…”

Section: Construction Of Deletion Mutants and Cell Survival Studiesmentioning

confidence: 99%

OverlappingoriCand centromere-like functions in secondary genome replicons determine their maintenance independent of chromosome I inDeinococcus radiodurans

Maurya

Misra

2020

Preprint

View full text Add to dashboard Cite

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 (△cisII) or cisMP (△cisMP) showed reduced γ radiation resistance and copy number of Chr II and MP. Fluorescent Reporter-Operator System (FROS) developed for ChrI, ChrII and MP in △ cisII or △ cisMP 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. been studied, the centromeric sequences are found close to ori. For instance, B. subtilis and C. crescentus, the primary parS sites are located with 8-10 kb from oriC 12 . Likewise, the segregation proteins interact directly with replication initiation protein DnaA in many bacteria 11,13 . The organisation and dynamics of nucleoid during growth have been studied using genetic, microscopy and chromosome conformation capture techniques in rod-or crescent-shaped bacteria like E. coli, B. subtilis and C. crescentus 1, 14-17 and in cocci like Streptococcus pneumonia 18 and Staphylococcus aureus 19,20 .Recently, many bacteria have been discovered with multiple copies of multipartite genome system comprising of more than one chromosome and megaplasmids 21 . Studies on genome maintenance in bacteria harbouring multipartite genome (MGH) are limited to a few examples like V. cholerae, Burkholderia cenocepacia and Rhodobacter sphearoides [22][23][24] . In these bacteria, the partitioning components of primary chromosome are phylogenetically similar with the chromosome of single circular chromosome harbouring bacteria but are different from the elements encoded on secondary genome elements. Since, the sizes of the secondary genome elements vary, the synchronization in their duplication and segregation with cytokinetic events of cell division is quite intriguing. However, the real time monitoring of DNA replication in V. cholerae harbouring multiple size genome elements have revealed staggered replication initiation for different elements to allow the replication termination roughly around the same time 25,26 . The nucleoids dynamics during genome segregation have also been studied in some MGH bacteria like V. cholerae, R. sphaeroides, Shinorhizobium meliloti and D. radiodurans 22, 24, 27,28 . D. radiodurans, a Gram-positive non-pathogenic bacterium characterized for extraordinary radioresistance, also harbours multipartite genome system comprised of chromosome I (2,648,638bp), chromosome II (412,348bp) and megaplasmid (177,466bp) 29 . Earlier, Minsky and colleagues demonstrated th...

show abstract

Maintenance of multipartite genome system and its functional significance in bacteria

Cited by 23 publications

References 122 publications

The Pseudoalteromonas multipartite genome: distribution and expression of pangene categories, and a hypothesis for the origin and evolution of the chromid

The Pseudoalteromonas multipartite genome: distribution and expression of pangene categories, and a hypothesis for the origin and evolution of the chromid

Genome-wide association studies across environmental and genetic contexts reveal complex genetic architecture of symbiotic extended phenotypes

OverlappingoriCand centromere-like functions in secondary genome replicons determine their maintenance independent of chromosome I inDeinococcus radiodurans

Contact Info

Product

Resources

About