海洋生态系统中的新型整合元件与基因组可塑性

Novel integrative elements and genomic plasticity in ocean ecosystems.

作者信息

Hackl Thomas, Laurenceau Raphaël, Ankenbrand Markus J, Bliem Christina, Cariani Zev, Thomas Elaina, Dooley Keven D, Arellano Aldo A, Hogle Shane L, Berube Paul, Leventhal Gabriel E, Luo Elaine, Eppley John M, Zayed Ahmed A, Beaulaurier John, Stepanauskas Ramunas, Sullivan Matthew B, DeLong Edward F, Biller Steven J, Chisholm Sallie W

机构信息

Massachusetts Institute of Technology, Department of Civil and Environmental Engineering, Cambridge, MA 02139, USA; Groningen Institute for Evolutionary Life Sciences, University of Groningen, 9700CC Groningen, the Netherlands.

Massachusetts Institute of Technology, Department of Civil and Environmental Engineering, Cambridge, MA 02139, USA.

出版信息

Cell. 2023 Jan 5;186(1):47-62.e16. doi: 10.1016/j.cell.2022.12.006.

DOI:10.1016/j.cell.2022.12.006

PMID:36608657

Abstract

Horizontal gene transfer accelerates microbial evolution. The marine picocyanobacterium Prochlorococcus exhibits high genomic plasticity, yet the underlying mechanisms are elusive. Here, we report a novel family of DNA transposons-"tycheposons"-some of which are viral satellites while others carry cargo, such as nutrient-acquisition genes, which shape the genetic variability in this globally abundant genus. Tycheposons share distinctive mobile-lifecycle-linked hallmark genes, including a deep-branching site-specific tyrosine recombinase. Their excision and integration at tRNA genes appear to drive the remodeling of genomic islands-key reservoirs for flexible genes in bacteria. In a selection experiment, tycheposons harboring a nitrate assimilation cassette were dynamically gained and lost, thereby promoting chromosomal rearrangements and host adaptation. Vesicles and phage particles harvested from seawater are enriched in tycheposons, providing a means for their dispersal in the wild. Similar elements are found in microbes co-occurring with Prochlorococcus, suggesting a common mechanism for microbial diversification in the vast oligotrophic oceans.

摘要

水平基因转移加速微生物进化。海洋聚球藻属蓝细菌表现出高度的基因组可塑性，但其潜在机制尚不清楚。在此，我们报道了一个新的DNA转座子家族——“幸运转座子”，其中一些是病毒卫星，而另一些携带货物，如营养获取基因，这些基因塑造了这个全球丰富属的遗传变异性。幸运转座子共享独特的与移动生命周期相关的标志性基因，包括一个深度分支的位点特异性酪氨酸重组酶。它们在tRNA基因处的切除和整合似乎驱动了基因组岛的重塑，而基因组岛是细菌中灵活基因的关键储存库。在一项选择实验中，携带硝酸盐同化盒的幸运转座子动态获得和丢失，从而促进染色体重排和宿主适应。从海水中收获的囊泡和噬菌体颗粒富含幸运转座子，为它们在野外的传播提供了一种方式。在与聚球藻属共生的微生物中也发现了类似的元件，这表明在广阔的贫营养海洋中微生物多样化存在一种共同机制。