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(xì)菌的進(jìn)化歷史是如此危險(xiǎn)的食草動(dòng)物留下來(lái)鎖鑰,防止其擴(kuò)散。一路走來(lái),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(xiàng)新的研究中,研究人員提出一個(gè)過(guò)程,強(qiáng)調(diào)了細(xì)菌對(duì)病毒感染的反應(yīng)的重要性。這一過(guò)程的中心是一個(gè)經(jīng)常聚集空間短回文重復(fù)CRISPR位點(diǎn)。

美國(guó)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(méi)有證據(jù)的細(xì)菌物種在俄勒岡州但擔(dān)憂(yōu)很高因?yàn)槿湎x(chóng)運(yùn)輸?shù)街参镏邪l(fā)現(xiàn)。此外,蠕蟲(chóng)病毒和細(xì)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(jià)值總計(jì)超過(guò)10億美元。

”的能力檢測(cè)和預(yù)先防止運(yùn)動(dòng)r . toxicus至關(guān)重要,”Jeff Chang說(shuō),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(gè)檢測(cè)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(yùn)動(dòng)血統(tǒng)的細(xì)菌,試圖阻止他們移動(dòng)。”

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(xiàng)研究中,科學(xué)家們依靠全基因組測(cè)序來(lái)了解不同種類(lèi)的Rathayibacter相關(guān)以及如何演變。

“現(xiàn)在我們有一個(gè)全基因組測(cè)序和理解它,我們可以識(shí)別特定的序列,可以用于分子診斷。這可能是一個(gè)強(qiáng)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(shuō)。

在這項(xiàng)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(gè)區(qū)域的抽樣。他們的分析還包括壓力來(lái)自俄勒岡州生產(chǎn)的種子。r . toxicus種子樣本中沒(méi)有檢測(cè)到俄勒岡州的兩個(gè)優(yōu)勢(shì)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(dòng)物在澳大利亞。

超過(guò)100測(cè)序Rathayibacter基因組進(jìn)行了分析。r . toxicus基因是最遙遠(yuǎn),這是可能的,因?yàn)樗俏ㄒ籖athayibacter獲得了CRISPR適應(yīng)性免疫系統(tǒng)來(lái)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(shuō)研究的聯(lián)合作者之一。

”在其進(jìn)化,它不僅失去基因,但它得到了基因,包括CRISPR位點(diǎn),”戴維斯說(shuō)。“這,其他Rathayibacter細(xì)菌沒(méi)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(gè)物種進(jìn)化經(jīng)歷了戲劇性的事件。”