How Virus-like ‘Jumping Genes’ Became Our Partners in Evolution

A DNA transposon is a kind of mobile genetic element that can pop out of one chromosome and paste itself into a new location on another.

DNA转座子是一种可移动的遗传元件，它可以从一条染色体中弹出，并将自身粘贴到另一条染色体上的新位置。

Samuel Velasco/ Quanta Magazine

塞缪尔·贝拉斯科/广达杂志

You might imagine that the DNA in your cells has a simple history.

您可能会想象细胞中的 DNA 有着简单的历史。

Even though it’s been recombined in every generation through sex and gained the occasional mutation, on the whole the genome has been stable and has been passed down reliably from your ancestors.

尽管它在每一代中都会通过性重组并偶尔发生突变，但总体而言，基因组一直是稳定的，并且已经从祖先那里可靠地传承下来。

But that’s not the entire story.

但这还不是故事的全部。

Nearly half of your genome is a wild drama: mobile, repetitive, disruptive, even viral.

你的基因组中有近一半是一场狂野的戏剧：移动的、重复的、破坏性的，甚至是病毒式的。

This half is the result of genetic material that can clip itself out of the DNA sequence, float off, and re-root somewhere else.

这一半是遗传物质的结果，它可以将自身从 DNA 序列中剪掉，漂浮起来，然后在其他地方重新扎根。

These sequences can multiply and expand, inflating the genome from within.

这些序列可以繁殖和扩展，从内部膨胀基因组。

They can hop into the middle of another sequence and break it.

他们可以跳到另一个序列的中间并打破它。

They can also be fertile soil for new adaptations to grow.

它们也可以成为新适应物生长的肥沃土壤。

“Jumping genes” can cut and paste themselves into new locations in the genome.

“跳跃基因”可以将自身剪切并粘贴到基因组中的新位置。

But they’re more than parasites or genetic junk.

但它们不仅仅是寄生虫或基因垃圾。

These unruly genetic fragments are known as transposable elements, or transposons for short.

这些难以驾驭的遗传片段被称为转座元件，简称转座子。

Often called jumping genes for their ability to relocate in a genome, they may seem pathological — indeed, many have viral origins — or perhaps little more than junk.

它们通常被称为跳跃基因，因为它们能够在基因组中重新定位，它们可能看起来是病态的——事实上，许多基因都有病毒起源——或者可能只不过是垃圾。

But transposons are increasingly understood to be a key feature of many genetic tool kits.

但人们越来越认识到转座子是许多遗传工具包的关键特征。

Their connections to the evolution of everything from moths to wombs, and even to the fundamental biological processes that turn genes off and on, suggest that the relationship between host genome and transposon is best understood as a deep coevolutionary entanglement.

它们与从飞蛾到子宫的万物进化的联系，甚至与关闭和打开基因的基本生物过程的联系，表明宿主基因组和转座子之间的关系最好被理解为一种深层的共同进化纠缠。

The first hints of transposons’ existence were uncovered more than 80 years ago by the geneticist Barbara McClintock while she was studying color variation in corn kernels at the Cold Spring Harbor Laboratory in New York.

80 多年前，遗传学家芭芭拉·麦克林托克 (Barbara McClintock) 在纽约冷泉港实验室研究玉米粒的颜色变化时首次发现了转座子存在的迹象。

She worked with a corn strain whose kernels were typically solid purple, but some were speckled, with purple pigment spattering a yellow base.

她研究了一种玉米品种，其籽粒通常是纯紫色的，但也有一些有斑点，紫色颜料溅落在黄色的底座上。

She hoped to explain how genes produced this color variation.

她希望解释基因如何产生这种颜色变化。

McClintock’s explanation would challenge geneticists’ understanding of how the genome works.

麦克林托克的解释将挑战遗传学家对基因组如何运作的理解。

She discovered genetic elements that could move: They could excise themselves from one location and insert themselves into another on the same chromosome or a different one.

她发现了可以移动的遗传元件：它们可以从一个位置切除自己，并将自己插入到同一染色体或不同染色体上的另一个位置。

Sometimes, these genetic acrobats would jump into the middle of a purple pigment gene and interfere with its function, producing a speckled cell.

有时，这些基因杂技演员会跳到紫色素基因的中间并干扰其功能，产生斑点细胞。

If it jumped out again, the pigment gene would be restored, making a purple cell.

如果它再次跳出来，色素基因就会恢复，形成紫色细胞。

Barbara McClintock’s description of mobile genetic sequences in 1944 was initially treated with skepticism.

Barbara McClintock 在 1944 年对可移动基因序列的描述最初受到了怀疑。

She was awarded a Nobel Prize in 1983.

她于1983年获得诺贝尔奖。

Smithsonian Institution Science Service; Restored by Adam Cuerden

史密森学会科学服务处；亚当·库尔登修复

McClintock called these mobile genes “controlling elements” for their dominion over the expression of the color-producing genes; today we call them transposons for their ability to transpose themselves, or change positions, within a genome.

麦克林托克将这些可移动基因称为“控制元件”，因为它们对产生颜色的基因的表达具有支配作用。今天，我们称它们为转座子，因为它们能够在基因组内自行转位或改变位置。

Three decades later, in 1983, McClintock was awarded a Nobel Prize for her discovery, which showed that genes are not fixed in place.

三十年后的 1983 年，麦克林托克因其发现而获得了诺贝尔奖，该发现表明基因并非固定在某个位置。

Since then, researchers have uncovered transposons in organisms across the tree of life and described a whole taxonomy of subtypes that cluster into two main groups.

从那时起，研究人员在生命之树的生物体中发现了转座子，并描述了亚型的完整分类，这些亚型分为两个主要组。

The transposons McClintock discovered are DNA transposons, so called because they travel as a DNA molecule.

麦克林托克发现的转座子是 DNA 转座子，之所以如此命名是因为它们以 DNA 分子的形式传播。

Transposons in this class jump by means of “cut and paste.” Enzymes called transposases bind to the ends of the DNA transposon and splice it free.

此类转座子通过“剪切和粘贴”的方式跳跃。称为转座酶的酶与 DNA 转座子的末端结合并将其自由剪接。

The liberated bundle then touches down somewhere else in the genome, where native DNA repair processes paste it in.

然后，被释放的束落在基因组的其他地方，本地 DNA 修复过程将其粘贴进去。

A second class of transposons, known as retrotransposons, aren’t cut directly out of the genome.

第二类转座子，称为逆转录转座子，并不是直接从基因组中切除的。

Instead, the DNA sequence is copied into RNA, a molecular strand that is flexible and mobile by nature.

相反，DNA 序列被复制到 RNA，这是一种本质上灵活且可移动的分子链。

Liberated from the genome, the sequence in the RNA copy is then reverse-transcribed into DNA at a different location.

RNA 拷贝中的序列从基因组中释放出来，然后在不同位置反转录成 DNA。

By copying themselves instead of cutting, retrotransposons can easily flood a genome with many iterations of themselves.

通过复制自身而不是切割，逆转录转座子可以轻松地用自身的许多迭代淹没基因组。

Over time, this has led retrotransposons to make up large proportions of a host genome in some cases; for example, nearly half of the human genome is retrotransposons.

随着时间的推移，这导致逆转录转座子在某些情况下占据了宿主基因组的很大一部分。例如，近一半的人类基因组是逆转录转座子。

McClintock’s curiosity about which genes create purple or yellow kernels on the same cob of multicolored corn led to her uncovering a fundamental mechanism of genetics.

麦克林托克对哪些基因在同一根彩色玉米棒上产生紫色或黄色玉米粒的好奇心使她发现了遗传学的基本机制。

Eerily, many retrotransposons are related to viruses; biologists debate which came first.

奇怪的是，许多反转录转座子与病毒有关。生物学家争论哪个先出现。

These viruses, known as retroviruses, insert a DNA copy of their RNA sequence into the host cell’s genome, hijacking the cell’s resources to reproduce themselves.

这些病毒被称为逆转录病毒，将其 RNA 序列的 DNA 副本插入宿主细胞的基因组中，劫持细胞资源进行自我繁殖。

The most widely known example is HIV, which invades the genomes of infection-fighting white blood cells.

最广为人知的例子是艾滋病毒，它会侵入抗感染白细胞的基因组。

If they don’t kill their host, retroviruses’ genetic legacy can be left behind in the host genome afterward, like splinters lodged in a finger.

如果它们不杀死宿主，逆转录病毒的遗传遗产可能会留在宿主基因组中，就像手指上的碎片一样。

This viral scar tissue can accumulate over millions of years: In humans, these viral ghosts make up an estimated 8% of the total genome.

这种病毒疤痕组织可以积累数百万年：在人类中，这些病毒鬼魂估计占总基因组的 8%。

That means we are in no small part made of virus.

这意味着我们在很大程度上是由病毒组成的。

The same features that allow DNA transposons and retrotransposons to move within a genome also predispose them to moving between genomes.

允许 DNA 转座子和反转录转座子在基因组内移动的相同特征也使它们易于在基因组之间移动。

By hitchhiking on a passing virus, transposons can defy species boundaries and land in a totally new evolutionary setting.

通过搭上路过的病毒的便车，转座子可以打破物种界限，进入一个全新的进化环境。

“Virtually all of the [transposon types] we know can apparently go from species to species,” said Cedric Feschotte , a geneticist at Cornell University.

“几乎我们所知道的所有[转座子类型]显然都可以从一个物种转移到另一个物种，”康奈尔大学的遗传学家塞德里克·费肖特说。

Initially, these “horizontally transferred” transposons were thought to be a rare exception to normal biology.

最初，这些“水平转移”的转座子被认为是正常生物学的罕见例外。

But by now, thousands of examples have been reported, Feschotte said, in species that run the gamut from fungal pathogens to snakes to cows.

但到目前为止，已经报道了数千个例子，费肖特说，涉及从真菌病原体到蛇到牛的各种物种。

In 2020, researchers described nearly 1,000 independent horizontal transfer events in 307 vertebrate genomes, predominantly in fish.

2020 年，研究人员描述了 307 个脊椎动物基因组中的近 1,000 个独立水平转移事件，主要是鱼类。

Given their self-replicating, virus-like behavior, it’d be understandable to consider transposons as something between benign bloat and selfish parasite.

考虑到它们的自我复制、类似病毒的行为，将转座子视为介于良性膨胀和自私寄生虫之间的东西是可以理解的。

But researchers are increasingly finding that, as in the case of McClintock’s corn kernels, they can be a source of meaningful evolutionary material.

但研究人员越来越多地发现，就像麦克林托克的玉米粒一样，它们可以成为有意义的进化材料的来源。

Around 200 years ago, the peppered moths of England were readily identifiable by their black-speckled white wings, which camouflaged well with pale tree bark.

大约 200 年前，英格兰的胡椒蛾很容易通过它们带有黑斑的白色翅膀来识别，这些翅膀用浅色树皮很好地伪装起来。

But after the Industrial Revolution, when pollution from coal-powered factories darkened the trees, black wings came to dominate the population.

但工业革命之后，当燃煤工厂的污染使树木变暗时，黑翅开始在种群中占主导地位。

Evolutionary biologists later explained that in the new, sootier environment, white moths were easily spotted by predatory birds, while black moths blended in with the darkened bark.

进化生物学家后来解释说，在新的、烟熏味更重的环境中，白色飞蛾很容易被掠食性鸟类发现，而黑色飞蛾则与变黑的树皮融为一体。

The white moths had lost their survival advantage, and black moths survived better and reproduced.

白蛾失去了生存优势，黑蛾则更好地生存并繁衍。

Life marched on.

生活继续前行。

This story about the dark-winged peppered moths is now considered a textbook example of natural selection.

这个关于黑翅胡椒蛾的故事现在被认为是自然选择的教科书例子。

However, it wasn’t until 2016 that researchers uncovered the genetic mechanism behind the wardrobe change.

然而，直到 2016 年，研究人员才发现了衣柜变化背后的遗传机制。

By sequencing hundreds of peppered moth genomes, the geneticists found a significant and consistent difference in a gene called cortex involved in wing development.

通过对数百个胡椒蛾基因组进行测序，遗传学家发现参与翅膀发育的称为皮质的基因存在显着且一致的差异。

A transposon, absent in the white-winged moths, had been inserted into the beginning of this gene in nearly all the black moths and had led, through an unknown mechanism, to the production of dark-colored wings.

白翅蛾中不存在的转座子被插入到几乎所有黑蛾的该基因的开头，并通过一种未知的机制导致深色翅膀的产生。

The black morph of the peppered moth evolved when a transposon inserted itself into a gene that controls wing pattern.

当转座子将自身插入到控制翅膀图案的基因中时，胡椒蛾的黑色形态就进化了。

The authors estimated that this transposition occurred in 1819 — after the rise in pollution levels had started to alter the moth’s habitat.

作者估计这种转变发生在 1819 年——污染水平的上升开始改变飞蛾的栖息地之后。

“This is completely changing how we see rapid adaptation,” said Pierre Baduel , a geneticist at the French National Center for Scientific Research in Paris.

“这彻底改变了我们对快速适应的看法，”巴黎法国国家科学研究中心的遗传学家皮埃尔·巴杜尔说。

It is typically thought that generating new traits takes long periods of evolutionary time.

人们通常认为产生新特征需要很长的进化时间。

In this case, a transposon created a new trait that was immediately selected for.

在这种情况下，转座子创造了一种新的性状，并立即被选择。

These types of insertions may happen frequently.

这些类型的插入可能经常发生。

But to be passed on to the next generation, they need to occur in the reproductive cells.

但要传递给下一代，它们需要发生在生殖细胞中。

Any insertions that have large, immediate, and potentially negative effects on an organism are usually rapidly weeded out by natural selection.

任何对生物体产生巨大、直接和潜在负面影响的插入通常都会被自然选择迅速淘汰。

“The genome is just constantly bombarded by gene insertion, and then most of them are removed,” Baduel said.

巴杜尔说：“基因组不断受到基因插入的轰炸，然后大部分基因被删除。”

“If the environment has changed and suddenly they become adaptive, then they stick.”

“如果环境发生了变化，它们突然变得适应性强，那么它们就会坚持下去。”

Sometimes, instead of changing an existing gene, a transposon in a new context can be co-opted over time to generate something new.

有时，随着时间的推移，新环境中的转座子可以被选择以产生新的东西，而不是改变现有的基因。

For instance, a transposon fused in the right location can, by chance, create a novel protein that goes on to regulate other genes spread throughout the genome.

例如，融合在正确位置的转座子可以偶然产生一种新的蛋白质，该蛋白质可以继续调节分布在整个基因组中的其他基因。

This is completely changing how we see rapid adaptation.

这彻底改变了我们对快速适应的看法。

Pierre Baduel, French National Center for Scientific Research

Pierre Baduel，法国国家科学研究中心

This process of tweaking genes to establish new traits is thought to have catalyzed evolutionary novelty in animals .

这种调整基因以建立新性状的过程被认为催化了动物的进化新颖性。

Transposable elements are linked to the evolution of animal eyes as well as the adaptive immune system in jawed vertebrates.

转座因子与动物眼睛的进化以及有颌脊椎动物的适应性免疫系统有关。

The domestication of transposons for new purposes has also been implicated in the evolution of the placenta — a defining feature of nearly all mammals.

为了新目的而对转座子进行的驯化也与胎盘的进化有关——胎盘是几乎所有哺乳动物的一个决定性特征。

That means that a transposon is partly responsible for the months-long process of development in utero that’s typical for our lineage, humans included.

这意味着转座子对子宫内长达数月的发育过程负有部分责任，这对于我们的血统（包括人类）来说是典型的。

Even when the effects are more subtle, the relationship between genome and transposon seems to sometimes go deeper than that of a host adapting to an invading, self-interested genetic force.

即使影响更加微妙，基因组和转座子之间的关系有时似乎比宿主适应入侵的、自私的遗传力量的关系还要深入。

In many cases, it could be considered more of a coevolutionary arrangement, Feschotte said.

费肖特说，在许多情况下，这可以被认为更像是一种共同进化的安排。

Some products made by transposons may do the same jobs as native proteins, and over time, the host genome may become dependent on the transposon and its products, a situation he compared to an addiction.

转座子产生的一些产品可能与天然蛋白质发挥相同的作用，随着时间的推移，宿主基因组可能会变得依赖于转座子及其产品，他将这种情况比作成瘾。

This drive for coexistence may undergird fundamental aspects of how genomes regulate themselves.

这种共存的驱动力可能会巩固基因组如何自我调节的基本方面。

The disruptive nature of transposons may have required organisms to evolve new methods of shutting off their activity.

转座子的破坏性可能要求生物体进化出新的方法来关闭其活动。

Epigenetic control — the means by which an organism can dial the expression of its genetic repertoire up or down, or shut off the expression of some genes entirely — may have evolved first to bring transposons to heel.

表观遗传控制——有机体通过其调高或调低其遗传库的表达，或完全关闭某些基因的表达的手段——可能首先进化到让转座子屈服。

“One of the models is that relatively simple organisms evolved epigenetic silencing to silence their transposons,” said Susan Wessler , a geneticist emerita at the University of California, Riverside and vice president of the National Academy of Sciences.

“其中一个模型是，相对简单的生物体进化出表观遗传沉默，以沉默它们的转座子，”加州大学河滨分校的荣休遗传学家、美国国家科学院副院长苏珊·韦斯勒（Susan Wessler）说。

Under this theory, organisms figured out how to turn genes off to get these unruly genetic parasites under control.

根据这一理论，生物体找到了如何关闭基因以控制这些难以驾驭的遗传寄生虫的方法。

Then evolutionary processes repurposed those controls to turn all sorts of genes off, leading to regulatory processes that, for example, produce dozens of cell types from the same genome.

然后，进化过程重新利用这些控制来关闭各种基因，从而导致调节过程，例如，从同一基因组产生数十种细胞类型。

This coevolutionary perspective is a more neutral take on the relationship between transposon and host genome, Feschotte said, compared to how they’ve been viewed in the recent past, as “selfish,” “parasitic,” or “junk” DNA.

Feschotte 说，与最近人们对转座子和宿主基因组之间关系的看法相比，这种共同进化的观点是一种更加中立的观点，即“自私”、“寄生”或“垃圾”DNA。

Now, the emerging understanding that transposons are intimately interwoven within the regulatory workings of the host genome is rehabilitating their reputation as critical sources of evolutionary innovation.

现在，人们逐渐认识到转座子与宿主基因组的调控运作密切相关，正在恢复其作为进化创新关键来源的声誉。

“We are all influenced by the terms that we use,” Feschotte said.

“我们都受到我们使用的术语的影响，”费肖特说。

“[Transposons] are not just passengers.

“[转座子]不仅仅是乘客。

They’ve been coevolving with organisms from the beginning.”

它们从一开始就与生物体共同进化。”

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