Scientists at Oregon State University have shed light on the evolutionary history of a soil-borne bacteria that is so dangerous to grazing animals it is kept behind lock-and-key to prevent its spread.

Somewhere along the way, Rathayibacter toxicus lost about one-third of its genes. Yet it persists in spite of its genome reduction and low genetic diversity. In a new study, researchers propose a process that emphasizes the importance of the bacteria's reaction to viral infection. At the center of that process is a clustered regularly interspaced short palindromic repeat (CRISPR) locus.

The U.S. government has declared R. toxicus to be a biological select agent for toxins and specimens are handled at highly secure federal facilties. There is no evidence of the bacterial species in Oregon but concerns are high because the worm that transports it to plants is found in the state. In addition, the worm and bacteria both infect grass seedheads. In 2017, hay and grass seed were the third- and fifth-largest agricultural commodities in Oregon, with a combined value of more than $1 billion.

"The ability to detect and preemptively prevent the movement of R. toxicus is vitally important," said Jeff Chang, a microbial genomicist in OSU's College of Agricultural Sciences and the study's corresponding author. "It's one thing to see an infected grass, it's another to detect microbes before you even see their effects. With genome-enabled epidemiology, we can track the movement of specific lineages of bacteria and try to stop them from moving around."

CRISPRs are used in genome editing technology but are less known for their ecological roles. In this study, the scientists relied on whole genome sequencing to understand how different species of Rathayibacter are related and how they evolve.

"Now that we have a whole genome sequenced and understand it, we can identify specific sequences that can be used for molecular diagnostics. That could be a powerful way to massively survey seed lots to find out if R. toxicus is present," Chang said.

In the study, the researchers used DNA extracted from R. toxicus collected during a 30-year period of sampling in three regions of Australia. Their analysis also included strains collected from seeds produced in Oregon. R. toxicus was not detected in seed samples from Oregon, and the two dominant species of Rathayibacter found in Oregon lack the genes necessary to make the toxin that has afflicted grazing animals in Australia.

More than 100 sequenced Rathayibacter genomes were analyzed. R. toxicus is the most genetically distant, and that's likely because it is the only Rathayibacter to have acquired a CRISPR adaptive immune system to protect against viruses, said Ed Davis, an OSU doctoral graduate and one of the study's co-lead authors.

"In its evolution, not only did it lose genes but it gained genes, including the CRISPR locus," Davis said. "It gained genes that other Rathayibacter bacteria don't have. Its genome is normal, except some sections were removed. This suggests that this species experienced a dramatic event in its evolution."

Read more at: https://phys.org/news/2018-10-crispr-genetic-diversity-deadly-bacteria.html#jCp

俄勒岡州立大學(xué)的科學(xué)家們揭示土傳細菌的進化歷史是如此危險的食草動物留下來鎖鑰,防止其擴散。一路走來,Rathayibacter toxicus損失了三分之一的基因。但它持續(xù)減少盡管基因組和遺傳多樣性較低。在一項新的研究中,研究人員提出一個過程,強調(diào)了細菌對病毒感染的反應(yīng)的重要性。這一過程的中心是一個經(jīng)常聚集空間短回文重復(fù)CRISPR位點。

美國政府已經(jīng)宣布r . toxicus生物選擇代理毒素,在高度安全的聯(lián)邦別的處理標(biāo)本。沒有證據(jù)的細菌物種在俄勒岡州但擔(dān)憂很高因為蠕蟲運輸?shù)街参镏邪l(fā)現(xiàn)。此外,蠕蟲病毒和細菌感染草seedheads。2017年,干草和草籽是第三和第五大農(nóng)產(chǎn)品在俄勒岡州,價值總計超過10億美元。

”的能力檢測和預(yù)先防止運動r . toxicus至關(guān)重要,”Jeff Chang說,微生物genomicist在俄勒岡州立大學(xué)農(nóng)業(yè)科學(xué)學(xué)院和該研究的通訊作者。“是一回事看到受感染的草,這是另一個檢測微生物甚至在你看到其效果。隨著基因組使流行病學(xué),我們可以跟蹤特定的運動血統(tǒng)的細菌,試圖阻止他們移動。”

CRISPRs用于基因組編輯技術(shù),但不太出名的生態(tài)角色。在這項研究中,科學(xué)家們依靠全基因組測序來了解不同種類的Rathayibacter相關(guān)以及如何演變。

“現(xiàn)在我們有一個全基因組測序和理解它,我們可以識別特定的序列,可以用于分子診斷。這可能是一個強大的種子很多大規(guī)模調(diào)查發(fā)現(xiàn)如果r . toxicus存在,”張說。

在這項研究中,研究人員使用DNA提取r . toxicus收集30年期間澳大利亞三個區(qū)域的抽樣。他們的分析還包括壓力來自俄勒岡州生產(chǎn)的種子。r . toxicus種子樣本中沒有檢測到俄勒岡州的兩個優(yōu)勢種Rathayibacter發(fā)現(xiàn)在俄勒岡州缺乏必要的基因,使毒素,折磨食草動物在澳大利亞。

超過100測序Rathayibacter基因組進行了分析。r . toxicus基因是最遙遠,這是可能的,因為它是唯一Rathayibacter獲得了CRISPR適應(yīng)性免疫系統(tǒng)來抵御病毒,俄勒岡州立大學(xué)的博士研究生和埃德·戴維斯說研究的聯(lián)合作者之一。

”在其進化,它不僅失去基因,但它得到了基因,包括CRISPR位點,”戴維斯說。“這,其他Rathayibacter細菌沒有獲得基因。其基因組是正常的,除了一些部分被刪除。這表明這個物種進化經(jīng)歷了戲劇性的事件。”