Looking Back 3.8 Billion Years
Into the Root of the 'Tree of Life'
回溯38億年直達「生命樹」的根源
NASA-funded researchers at the Georgia
Institute of Technology are tapping information found in the cells of all life
on Earth, and using it to trace life's evolution. They have learned that life
is a master stenographer -- writing, rewriting and recording its history in
elaborate biological structures.
喬治亞理工學院的研究團隊在NASA資助下，正在一一寫下從地球上所有生命的細胞中發現的資訊，並用此來追溯生命演化的過程。他們從中認識到生命實為速記高手，將它在規畫生物藍圖過程中的點點滴滴詳細記錄、修改並重新編撰。
Some of the keys to unlocking the origin of life lie encrypted in the ribosome, life's oldest and most universal assembly of molecules. Today's ribosome converts genetic information (RNA) into proteins that carry out various functions in an organism. But the ribosome itself has changed over time. Its history shows how simple molecules joined forces to invent biology, and its current structure records ancient biological processes that occurred at the root of the Tree of Life, some 3.8 billion years ago.
核醣體為生命中最古老，也是最常見的分子複合體，其中隱含著要解開生命起源這項謎題的部分關鍵。現今核醣體的主要功能是將基因含有的資訊轉譯成蛋白質，而這些蛋白質在生命體內可以展現出各式各樣的功能。但核醣體本身也會隨著時間而逐漸改變。從它的歷史中我們可以得知簡單的小分子如何齊心協力發明出生命，而它今日的構造也記載著在38億年前，生命樹的根基曾經進行過何種生物作用。
By examining variations in the ribosomal RNA contained in modern cells, scientists can visualize the timeline of life far back in history, elucidating molecular structures, reactions and events near the biochemical origins of life.
藉由檢視現今細胞中核醣體RNA的變異，科學家可以描繪出直達遙遠過去的時間線，而釐清將近生命起源時，有何生化反應發生，而參與其中的分子架構又是如何。
"Biology is a great keeper of records," said Loren Williams, a professor in the Georgia Tech School of Chemistry and Biochemistry, and principal investigator for the NASA Astrobiology Institute's Georgia Tech Center for Ribosome Adaptation and Evolution from 2009-2014. "We are figuring out how to read some of the oldest records in biology to understand pre-biological processes, the origin of life, and the evolution of life on Earth."
「生物是各種歷史紀錄的保管者。」喬治亞理工學院化學與生化學院的教授Loren Williams說，她也於2009年至2014年在NASA天體生物學研究所的喬治亞理工學院核醣體適應與演化中心擔任計畫主持人。「我們正尋找方法來解讀生命中某些最古老的資訊，以瞭解地球生命起源之前的化學反應、生命如何開始和生物如何演化。」
The study is scheduled to be reported November 30 in the Early Edition of the journal Proceedings of the National Academy of Sciences.
本研究預計於11月30日刊登在期刊《美國國家科學院院刊》的早版。
Like rings in the trunk of a tree, the ribosome contains components that functioned early on in its history. The center of the trunk records the tree's youth, and successive rings represent each year of the tree's life, with the outermost layer recording the present. Just as the core of a tree's trunk remains unchanged over time, all modern ribosomes contain a common core dating back 3.8 billion years. This common core is the same in all living organisms, including humans.
就像樹幹中的年輪一樣，核醣體仍保有某些在歷史早期擁有功能的部分。樹輪的中心記載著樹木的童年，一輪一輪往外則代表著往後的每一年，而最外層正在記錄著當下發生的種種事蹟。如同樹輪的中心在時光洪流中仍能保持原貌，現今所有的核醣體都會擁有在38億年前便已經形成的核心。包含人類在內的生物全體，核醣體共有的核心都會是一模一樣的。
"The ribosome recorded its history," said Williams. "It accreted and got bigger and bigger over time. But the older parts were continually frozen after they accreted, just like the rings of a tree. As long as that tree lives, the inner rings will not change. The very core of the ribosome is older than biology, produced by evolutionary processes that we still don't understand very well."
「核醣體會記錄自己的歷史軌跡。」Williams說。「隨著時間它會逐漸生長並越變越大。但就像年輪一樣，雖然核醣體會持續成長，其核心仍然完好如初。只要樹還活著，年輪內層就不會改變。核醣體最深的核心地帶比生命本身還要古老，而形成核心的演化過程我們仍然所知甚少。」
While exploiting this record-keeping ability of the ribosome reveals how biology has changed over time, it can also point to the environmental conditions on Earth in which that biology evolved, and help inform our search for life elsewhere in the Universe.
利用核醣體會記錄自身歷史的能力，我們不但可以知道生物如何隨著時間演變，也能了解生物出現當時地球的環境條件，而這有助於我們尋找宇宙他處的生命。
"This work enables us to look back in time past the root of the tree of life -- the ancestor of all modern cells -- to a time when proteins and nucleic acids had not yet become the basis for all biochemistry," said Carl Pilcher, interim director of the NASA Astrobiology Institute. "It helps us understand some of the earliest stages in the development of life on Earth, and can guide our search for extraterrestrial environments where life may have developed."
「這項研究讓我們能追溯過往直至生命樹的根基，也就是當今所有細胞的祖先出現的時刻。當時蛋白質和核苷酸尚未成為所有生化作用的基礎。」NASA天體生物學研究所的代理所長Carl Pilcher說。「這有利於我們了解地球生命發展過程中一些最早的階段，同時也可以指引我們尋找可能有生命發育其中的地外環境。」
By rewinding, reverse engineering, and replaying this ancient ribosomal tape, researchers are uncovering the secrets of creation and are answering foundational, existential questions about our place in the Universe.
藉著解開、還原並重播這捲記錄在核醣體中的古老錄像，研究人員能挖掘出生物創始當時的秘密，並回答這項由來已久，有關人類存在本質的問題：我們在宇宙中的定位為何？
By studying more additions to the ribosome, the research team -- with key contributions by Georgia Tech Research Scientist Anton Petrov -- found "molecular fingerprints" that show where insertions were made, allowing them to discern the rules by which it grew. Using a technique they call the Structural Comparative Method, the researchers were able to model the ribosome's development in great detail.
在喬治亞理工學院的研究員Anton Petrov做出的重要貢獻下，研究團隊得以對核醣體的增長研究得更加透徹。他們發現了可以顯示插入序列形成位置的「分子指紋」，使他們得以辨識出核醣體成長的規則。利用他們稱作比對結構法的技術，研究人員能夠非常精細的模擬核醣體的演變過程。
"By taking ribosomes from a number of species -- humans, yeast, various bacteria and archaea -- and looking at the outer portions that are variable, we saw that there were very specific rules governing how they change," said Williams. "We took those rules and applied them to the common core, which allowed us to see all the way back to the first pieces of RNA."
「我們採集了許多物種身上的核醣體，包括人類、酵母菌還有各式各樣的細菌與古菌，並且觀察這些核醣體外層有所差異的部分，我們發現這些變化遵循著特定的規則。」Williams說。「我們收集這些規則並將之套用在核醣體共同的核心上，如此我們便能從各種面向回溯至第一段RNA的誕生。」
Some clues along the way helped. For instance, though RNA is now responsible for creating proteins, the very earliest life had no proteins. By looking for regions of the ribosome that contain no proteins, the researchers could determine that those elements existed before the advent of proteins. "Once the ribosome gained a certain capability, that changed its nature," Williams said.
某些推裡邏輯至始至終都很有幫助。舉例來說，雖然RNA現今的作用是負責製造蛋白質，但十分早期的生命體內是沒有蛋白質的。因此研究人員可以觀察核醣體中並未含有蛋白質的區域，來了解蛋白質出現以前核醣體就已經擁有的零件。「核醣體一旦增加了某項新功能，它的樣貌也會隨之改變。」Williams說。
While the ribosomal core is the same across species, what's added on top differs. Humans have the largest ribosome, encompassing some 7,000 nucleotides representing dramatic growth from the hundred or so base pairs at the beginning.
雖然核醣體的核心在各種物種身上皆如出一轍，但增建在其上的構造卻大異其趣。人類擁有最大的核醣體，大致上由7000個核苷酸分子組成。這顯示從一開始僅僅數百個左右的鹼基對，歷經了相當劇烈的增長才有現今的樣貌。
"What we're talking about is going from short oligomers, short pieces of RNA, to the biology we see today," said Williams. "The increase in size and complexity is mind-boggling."
「我們正在談論的是現今我們看到的生物，是如何從那些短小的寡聚物(oligomer)和RNA碎片演變而成。」Williams說。「這些由小至大、由簡至繁的過程變化之劇烈，實在是令人難以想像。」
The researchers obtained their ribosomes from structure and sequence databases that have been produced to help scientists identify new species. Ribosomes can be crystallized, which reveals their three dimensional structures.
研究團隊從幫助科學家辨認新物種用的核醣體結構與序列資料庫，來獲取他們需要的資料。核醣體可以形成結晶，可以被用來辨識出核醣體本身的三維構造。
Beyond understanding how evolution played out over time, this knowledge of the ribosome's development could have more practical modern-day health applications.
除了可以了解隨著時間進行演化如何作用之外，這項核醣體演變的知識也能實際應用在當代醫學。
"The ribosome is one of the primary target for antibiotics, so understanding its architecture and consistently throughout biology could be of great benefit," said Williams. "By studying the ribosome, we can start thinking about biology in a different way. We can see the symbiotic relationship between RNA and proteins."
「由於核醣體是抗生素作用的主要目標之一，因此了解它的結構和它在所有生物身上皆有的共通性質會有很大的益處。」Williams說。「藉由研究核醣體，我們可以看到RNA和蛋白質之間的共生關係，而能夠從另外一個角度來思考生命科學。」
As a next step, Williams and colleagues are now using experiments to verify what their model shows.
Williams和其同僚正在進行的下一步是利用實驗來驗證他們的模型呈現出來的結果。
"We have a coherent and consistent model that accounts for all the data we have going all the way back to a form of biology that is very primitive compared to what we have now," Williams explained. "We plan to continue testing the predictions of the model."
「與現有的方式相比，我們的模型一路模擬回至非常原始的生命形式時，可以得到相當一致且合理的數據。」Williams解釋。「我們接下來的計劃是繼續去驗證模型得到的預測結果。」
In addition to those already named, the research included Burak Gulen, Ashlyn Norris, Chad Bernier, Nicholas Kovacs, Kathryn Lanier, Stephen Harvey, Roger Wartell and Nicholas Hud from Georgia Tech, and George Fox from the University of Houston.
除了以上提到的人名之外，其他的研究人員包括喬治亞理工學院的Burak Gulen、Ashlyn Norris、Chad Bernier、Nicholas Kovacs、Kathryn Lanier、Stephen Harvey、Roger Wartell和Nicholas Hud，以及休士頓大學的George Fox。
This research was funded in part by the NASA Astrobiology Institute under grant NNA09DA78A. The content is solely the responsibility of the authors and does not necessarily represent the official views of NASA.
此研究部分由NASA天體生物學研究所資助，計畫編號為NNA09DA78A。內容責任歸屬為作者獨有，並不全然代表NASA的官方立場。
引用自：Georgia Institute of Technology. "Looking Back 3.8 Billion Years Into the Root of the 'Tree of Life'." ScienceDaily. ScienceDaily, 30 November 2015.
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