Coordinated regulation of core and accessory genes in the multipartite genome of Sinorhizobium fredii.
Prokaryotes benefit from having accessory genes, but it is unclear how accessory genes can be linked with the core regulatory network when developing adaptations to new niches. Here we determined hierarchical core/accessory subsets in the multipartite pangenome (composed of genes from the chromosome...
| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2018-05-01
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| Series: | PLoS Genetics |
| Online Access: | http://europepmc.org/articles/PMC5991415?pdf=render |
| _version_ | 1818179164140732416 |
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| author | Jian Jiao Meng Ni Biliang Zhang Ziding Zhang J Peter W Young Ting-Fung Chan Wen Xin Chen Hon-Ming Lam Chang Fu Tian |
| author_facet | Jian Jiao Meng Ni Biliang Zhang Ziding Zhang J Peter W Young Ting-Fung Chan Wen Xin Chen Hon-Ming Lam Chang Fu Tian |
| author_sort | Jian Jiao |
| collection | DOAJ |
| description | Prokaryotes benefit from having accessory genes, but it is unclear how accessory genes can be linked with the core regulatory network when developing adaptations to new niches. Here we determined hierarchical core/accessory subsets in the multipartite pangenome (composed of genes from the chromosome, chromid and plasmids) of the soybean microsymbiont Sinorhizobium fredii by comparing twelve Sinorhizobium genomes. Transcriptomes of two S. fredii strains at mid-log and stationary growth phases and in symbiotic conditions were obtained. The average level of gene expression, variation of expression between different conditions, and gene connectivity within the co-expression network were positively correlated with the gene conservation level from strain-specific accessory genes to genus core. Condition-dependent transcriptomes exhibited adaptive transcriptional changes in pangenome subsets shared by the two strains, while strain-dependent transcriptomes were enriched with accessory genes on the chromid. Proportionally more chromid genes than plasmid genes were co-expressed with chromosomal genes, while plasmid genes had a higher within-replicon connectivity in expression than chromid ones. However, key nitrogen fixation genes on the symbiosis plasmid were characterized by high connectivity in both within- and between-replicon analyses. Among those genes with host-specific upregulation patterns, chromosomal znu and mdt operons, encoding a conserved high-affinity zinc transporter and an accessory multi-drug efflux system, respectively, were experimentally demonstrated to be involved in host-specific symbiotic adaptation. These findings highlight the importance of integrative regulation of hierarchical core/accessory components in the multipartite genome of bacteria during niche adaptation and in shaping the prokaryotic pangenome in the long run. |
| first_indexed | 2024-12-11T20:59:31Z |
| format | Article |
| id | doaj.art-6a0c93bd3a7b41ed859b91100c9123dd |
| institution | Directory Open Access Journal |
| issn | 1553-7390 1553-7404 |
| language | English |
| last_indexed | 2024-12-11T20:59:31Z |
| publishDate | 2018-05-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Genetics |
| spelling | doaj.art-6a0c93bd3a7b41ed859b91100c9123dd2022-12-22T00:51:01ZengPublic Library of Science (PLoS)PLoS Genetics1553-73901553-74042018-05-01145e100742810.1371/journal.pgen.1007428Coordinated regulation of core and accessory genes in the multipartite genome of Sinorhizobium fredii.Jian JiaoMeng NiBiliang ZhangZiding ZhangJ Peter W YoungTing-Fung ChanWen Xin ChenHon-Ming LamChang Fu TianProkaryotes benefit from having accessory genes, but it is unclear how accessory genes can be linked with the core regulatory network when developing adaptations to new niches. Here we determined hierarchical core/accessory subsets in the multipartite pangenome (composed of genes from the chromosome, chromid and plasmids) of the soybean microsymbiont Sinorhizobium fredii by comparing twelve Sinorhizobium genomes. Transcriptomes of two S. fredii strains at mid-log and stationary growth phases and in symbiotic conditions were obtained. The average level of gene expression, variation of expression between different conditions, and gene connectivity within the co-expression network were positively correlated with the gene conservation level from strain-specific accessory genes to genus core. Condition-dependent transcriptomes exhibited adaptive transcriptional changes in pangenome subsets shared by the two strains, while strain-dependent transcriptomes were enriched with accessory genes on the chromid. Proportionally more chromid genes than plasmid genes were co-expressed with chromosomal genes, while plasmid genes had a higher within-replicon connectivity in expression than chromid ones. However, key nitrogen fixation genes on the symbiosis plasmid were characterized by high connectivity in both within- and between-replicon analyses. Among those genes with host-specific upregulation patterns, chromosomal znu and mdt operons, encoding a conserved high-affinity zinc transporter and an accessory multi-drug efflux system, respectively, were experimentally demonstrated to be involved in host-specific symbiotic adaptation. These findings highlight the importance of integrative regulation of hierarchical core/accessory components in the multipartite genome of bacteria during niche adaptation and in shaping the prokaryotic pangenome in the long run.http://europepmc.org/articles/PMC5991415?pdf=render |
| spellingShingle | Jian Jiao Meng Ni Biliang Zhang Ziding Zhang J Peter W Young Ting-Fung Chan Wen Xin Chen Hon-Ming Lam Chang Fu Tian Coordinated regulation of core and accessory genes in the multipartite genome of Sinorhizobium fredii. PLoS Genetics |
| title | Coordinated regulation of core and accessory genes in the multipartite genome of Sinorhizobium fredii. |
| title_full | Coordinated regulation of core and accessory genes in the multipartite genome of Sinorhizobium fredii. |
| title_fullStr | Coordinated regulation of core and accessory genes in the multipartite genome of Sinorhizobium fredii. |
| title_full_unstemmed | Coordinated regulation of core and accessory genes in the multipartite genome of Sinorhizobium fredii. |
| title_short | Coordinated regulation of core and accessory genes in the multipartite genome of Sinorhizobium fredii. |
| title_sort | coordinated regulation of core and accessory genes in the multipartite genome of sinorhizobium fredii |
| url | http://europepmc.org/articles/PMC5991415?pdf=render |
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