The selfish yeast plasmid utilizes the condensin complex and condensed chromatin for faithful partitioning

Kumar, Deepanshu; Prajapati, Hemant Kumar; Mahilkar, Anjali; Ma, Chien-Hui; Jayaram, Makkuni; Ghosh, Santanu

doi:10.1371/journal.pgen.1009660

Cited by 14 publications

(27 citation statements)

References 111 publications

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“…Current evidence supports a model for 2μm plasmid partitioning in which plasmids become attached to mitotic chromosomes in a way that enables roughly equal numbers to be segregated into the two products of cell division ( 20 , 34 , 35 , 37 , 55 ). Studies of a fluorescently-tagged single-copy 2μm reporter plasmid suggest this is achieved by two separate mechanisms, both dependent on the Rep protein complex formed at the plasmid STB locus.…”

Section: Discussionsupporting

confidence: 55%

“…Consistent with this model, conditions that destabilize the spindle apparatus or impair chromosome segregation also disrupt 2μm plasmid inheritance ( 29 , 33 ). Further support comes from the observed co-localization of plasmid foci with nuclear chromatin ( 31 , 32 ), and with meiotic ( 36 ) and mitotic ( 37 ) chromosomes. Whether these associations represent direct linkage of plasmids to the chromosomes has yet to be determined.…”

Section: Introductionmentioning

confidence: 97%

“…The presence of a functional RSC2 complex and both Rep proteins at STB are prerequisites for recruitment of other host factors needed for the 2μm plasmid to be efficiently partitioned. These include the centromere-specific histone H3, Cse4 ( 48 ), a kinesin family nuclear motor protein Kip1 ( 49 ), and two ring-shaped SMC (Structural Maintenance of Chromosomes) complexes, cohesin ( 32 , 47 ) and condensin ( 37 ). Cohesin and condensin both play critical roles in chromosome segregation and genome organization mediating inter- and intra-chromosomal linkages by topologically entrapping DNA strands ( 50–53 ).…”

Section: Introductionmentioning

confidence: 99%

“…Studies of a single-copy 2μm reporter plasmid indicate the RSC2 complex and Rep protein-dependent recruitment of cohesin to STB maintains cohesion between newly-replicated sister plasmids until anaphase, when their separation coincides with that of the segregating chromosomes, contributing to equal partitioning of the plasmid copies ( 32 , 47 , 54 , 55 ). Mis-segregation of a 2μm plasmid reporter plasmid when condensin was inactivated suggests condensin recruited to STB also contributes to 2μm plasmid inheritance, possibly by compacting the clusters of replicated sister plasmids into formations that favour symmetric attachment to sister chromatids or by directly bridging interaction with the chromosomes ( 37 ).…”

Section: Introductionmentioning

confidence: 99%

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The yeast 2-micron plasmid Rep2 protein has Rep1-independent partitioning function

Mereshchuk

Johnstone

Chew

et al. 2022

Nucleic Acids Research

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Equal partitioning of the multi-copy 2-micron plasmid of the budding yeast Saccharomyces cerevisiae requires association of the plasmid Rep1 and Rep2 proteins with the plasmid STB partitioning locus. Determining how the Rep proteins contribute has been complicated by interactions between the components. Here, each Rep protein was expressed fused to the DNA-binding domain of the bacterial repressor protein LexA in yeast harboring a replication-competent plasmid that had LexA-binding sites but lacked STB. Plasmid transmission to daughter cells was increased only by Rep2 fusion expression. Neither Rep1 nor a functional RSC2 complex (a chromatin remodeler required for 2-micron plasmid partitioning) were needed for the improvement. Deletion analysis showed the carboxy-terminal 65 residues of Rep2 were required and sufficient for this Rep1-independent inheritance. Mutation of a conserved basic motif in this domain impaired Rep1-independent and Rep protein/STB-dependent plasmid partitioning. Our findings suggest Rep2, which requires Rep1 and the RSC2 complex for functional association with STB, directly participates in 2-micron plasmid partitioning by linking the plasmid to a host component that is efficiently partitioned during cell division. Further investigation is needed to reveal the host factor targeted by Rep2 that contributes to the survival of these plasmids in their budding yeast hosts.

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Section: Discussionsupporting

confidence: 55%

Section: Introductionmentioning

confidence: 97%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

The yeast 2-micron plasmid Rep2 protein has Rep1-independent partitioning function

Mereshchuk

Johnstone

Chew

et al. 2022

Nucleic Acids Research

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“…present in <10 metagenomes). Indeed, we observed a trend where more prevalent systems exhibit less mutual exclusivity (R 2 =0.39) (Figure S11B). However, we identified many prevalent systems (e.g.…”

Section: Mainmentioning

confidence: 86%

The genetic and ecological landscape of plasmids in the human gut

Fogarty

Eren

2020

Preprint

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Plasmids play a critical role in rapid bacterial adaptation by encoding accessory functions that may increase the host's fitness. However, the diversity and ecology of plasmids is poorly understood due to computational and experimental challenges in plasmid identification. Here, we report the Plasmid Classification System (PCS), a machine learning classifier that recognizes plasmid sequences based on gene functions. To train PCS, we performed a large-scale discovery and comparison of gene functions in a reference set of >16,000 plasmids and >14,000 chromosomes. PCS accurately recognizes a diverse range of plasmid subtypes, and it outperforms the previous state-of-the-art approach based on k-mer decomposition of sequences. Armed with this model, we conducted, to our knowledge, the largest search for naturally occurring human gut plasmids in 406 publicly available metagenomes representing 5 countries. This search yielded 6,257 high-confidence predicted plasmids, of which 576 had evidence of a circular conformation based on pair-end mapping. These predicted plasmids were found to be highly prevalent across the metagenomes compared to the reference set of known plasmids, suggesting there is extensive and uncharacterized plasmid diversity in the human gut microbiome.

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