Novel integrative elements and genomic plasticity in ocean ecosystems
作者: Thomas Hackl, Raphaël Laurenceau, Markus J. Ankenbrand, Christina Bliem, Zev Cariani, Elaina Thomas, Keven D. Dooley, Aldo A. Arellano, Shane L. Hogle, Paul Berube, Gabriel E. Leventhal, ElaineLuo, John M. Eppley, Ahmed A. Zayed, John Beaulaurier, Ramunas Stepanauskas, Matthew B. Sullivan, Edward F. DeLong, Steven J. Biller, Sallie W.Chisholm
期刊: Cell
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.
Figure 1. Structure and function of tycheposons in Prochlorococcus
(A and B) Examples of two types of tycheposons illustrating their modular structure: (A) cargo-carrying tycheposons selected here because of their clear ecological relevance in ocean ecosystems, and (B) satellite tycheposons, carrying either a terS or MCP viral-packaging gene likely used to hijack phage capsids for dispersal. Cargo modules were annotated with roles in nitrate assimilation,31 siderophore transport,18 phosphate assimilation,32 zinc homeostasis,33 and phosphite assimilation.34
Gene labels: full-length and partial tRNA genes are labeled with single-letter amino acid code and their anticodon, e.g., Stga, tRNA-serineTGA; YR, tyrosine recombinase; MCP, major capsid protein; terS, terminase small subunit; xis, excisionase; hel, helicase; top, topoisomerase; lig, ligase; reg, transcriptional regulator; pri, primase, primase/polymerase, or primase/helicase; end, endonuclease; SSR, small serine recombinase; unk, conserved unknown. Some annotations are further labeled with more specific subprofiles indicating specific families of helicases, for example (helDnaB or helVirE).
水平基因转移加速了微生物的进化。海洋微型蓝藻Prochlorococcus（原绿球藻）展示了高度的基因组可塑性，而潜在的机制尚不清楚。在此，我们报告了DNA转座子的一个新的家族——“tycheposons”——其中一些是病毒卫星，另一些则携带物质，比如获取营养的基因，这些基因决定了这个全球丰富的属的遗传变异性。Tycheposons 共享独特的与移动生命周期相关的标志基因，包括一个深分支位点特异性的酪氨酸重组酶。它们在tRNA基因上的切除和整合似乎驱动了基因组岛的重塑，这是细菌中灵活基因的关键库。在一个选择实验中，动态获得和丢去携带硝酸盐同化盒的tycheposons，从而促进了染色体的重新排列和宿主的适应。从海水中获得的囊泡和噬菌体颗粒中富含tycheposons，为其在野外的传播提供途径。类似的元件也在与原绿球藻共生的微生物中被发现，这意味着在广阔的寡营养海洋中有一种对于微生物多样化的共同机制。
（实习生熊坤编译）
