鄭 姚 吳開年 王 利 魏 勇
枯草芽孢桿菌對(duì)氨氮應(yīng)答的轉(zhuǎn)錄組及sRNA分析*
鄭 姚1吳開年1王 利1①魏 勇2
(1. 西南民族大學(xué) 青藏高原動(dòng)物遺傳資源保護(hù)與利用教育部和四川省重點(diǎn)實(shí)驗(yàn)室 成都 610041; 2. 四川省畜牧科學(xué)研究院 成都 610041)
為探索枯草芽孢桿菌()脫氮的分子機(jī)制,篩選枯草芽孢桿菌對(duì)氨氮的分子生態(tài)學(xué)應(yīng)答相關(guān)候選基因及small RNA(sRNA),本研究對(duì)處于富含氨氮環(huán)境和對(duì)照組的枯草芽孢桿菌R47進(jìn)行原核鏈特異性轉(zhuǎn)錄組及sRNA分析,并采用Real-time PCR方法檢測(cè)差異表達(dá)基因的相對(duì)表達(dá)量。結(jié)果顯示,平均每個(gè)測(cè)序樣本得到約1.40×107條reads。對(duì)照組與處理組DESeq2分析得到3918個(gè)差異表達(dá)基因,并富集在KEGG數(shù)據(jù)庫中的176個(gè)信號(hào)通路,其中,包括8個(gè)與適應(yīng)富含氨氮環(huán)境相關(guān)的信號(hào)通路(細(xì)菌雙組分系統(tǒng)通路、精氨酸生物合成、嘌呤代謝等),同時(shí)發(fā)現(xiàn),、和基因可能參與枯草芽孢桿菌對(duì)氨氮的應(yīng)答過程。經(jīng)sRNA分析獲得已注釋的枯草芽孢桿菌sRNA 62條。對(duì)sRNA靶基因的分析結(jié)果顯示,其有3960個(gè)對(duì)應(yīng)的潛在靶基因,主要參與碳水化合物運(yùn)輸和新陳代謝、氨基酸轉(zhuǎn)運(yùn)和代謝、轉(zhuǎn)錄過程,其中,sRNA2073和sRNA2182對(duì)應(yīng)的靶基因分別為和。Real-time PCR結(jié)果顯示,、、、和基因的相對(duì)表達(dá)量變化與轉(zhuǎn)錄組測(cè)序結(jié)果一致。本研究為進(jìn)一步探究枯草芽孢桿菌污水脫氮的分子機(jī)理提供參考數(shù)據(jù)。
枯草芽孢桿菌;氨氮應(yīng)答;轉(zhuǎn)錄組;差異表達(dá)基因;sRNA分析
生活污水排放量的劇增、部分工廠未正確處理工業(yè)廢水等原因使水體中含氮有害物質(zhì)積累,導(dǎo)致水體氨氮污染,這對(duì)水生生物的生存造成威脅(Liu, 2004)。因此,水體凈化已是養(yǎng)殖業(yè)的關(guān)注焦點(diǎn),當(dāng)前主要提倡微生物脫氮,以微生物作為生態(tài)調(diào)節(jié)劑來維持水生態(tài)平衡,不僅效率高、成本低,而且不易造成二次污染(康傳磊等, 2018)。
枯草芽孢桿菌()為革蘭氏陽性菌,其抗逆性強(qiáng)、環(huán)境兼容性好,優(yōu)異的蛋白質(zhì)分泌功能使其成為生產(chǎn)抗生素、藥用蛋白和工業(yè)酶的重要宿主(Kewcharoen, 2019; 王成強(qiáng)等, 2019)??莶菅挎邨U菌因具有多種優(yōu)良特性而在水產(chǎn)養(yǎng)殖中得到廣泛應(yīng)用??莶菅挎邨U菌HAINUP40可降低模擬廢水及養(yǎng)殖廢水水體中氨氮含量,是凈化水質(zhì)的一種良好生物制劑(劉樹彬等, 2018)??莶菅挎邨U菌對(duì)氨的利用途徑為谷氨酰胺合成酶/谷氨酸合成酶(Glutamine synthetase/glutamate synthase, GS/GOGAT)途徑(Magasanik, 1982)。本研究以枯草芽孢桿菌R47為研究對(duì)象,以(NH4)2SO4作為水體氨氮污染來源,模擬富含氨氮污水,采用高通量測(cè)序技術(shù)建立富含氨氮條件下枯草芽孢桿菌轉(zhuǎn)錄組數(shù)據(jù)庫,初步篩選參與枯草芽孢桿菌響應(yīng)富含氨氮環(huán)境的相關(guān)基因及通路,為進(jìn)一步探究其對(duì)氨氮應(yīng)答的分子機(jī)制提供數(shù)據(jù)支撐。
枯草芽孢桿菌R47分離于鯽魚()糞便,保存于西南民族大學(xué)青藏高原動(dòng)物遺傳資源保護(hù)與利用教育部和四川省重點(diǎn)實(shí)驗(yàn)室。
將枯草芽孢桿菌R47接種于LB液體培養(yǎng)基,37℃培養(yǎng),待菌液濃度達(dá)1.4×108CFU/ml時(shí),取10 ml菌液加入100 ml水樣中,分別于6、18和24 h取樣,根據(jù)水質(zhì)檢測(cè)試劑盒(杭州陸恒生物科技有限公司)操作指南測(cè)定氨氮含量(mg/L)。
1.3.1 測(cè)序樣品制備及測(cè)序 以(NH4)2SO4為氨氮污染來源,模擬富含氨氮污水。將枯草芽孢桿菌R47接種于LB液體培養(yǎng)基,37℃培養(yǎng),待菌液濃度達(dá)1.4×108CFU/ml時(shí),向LB液體培養(yǎng)基中添加(NH4)2SO4,對(duì)照組(C)和處理組(T)的(NH4)2SO4濃度分別為0和40 mmol/L,37℃ 180 r/min培養(yǎng)24 h后,4℃ 12000 r/min離心2 min,收集菌體沉淀,–80℃中保存。每個(gè)樣品3個(gè)生物學(xué)重復(fù)。參照細(xì)菌總RNA提取試劑盒(北京天根生化科技有限公司)提取2組細(xì)菌總RNA,經(jīng)NanoDrop ND-1000核酸檢測(cè)儀(LabTech, 美國(guó))檢測(cè)RNA的濃度與純度。基于Illumina二代高通量測(cè)序平臺(tái)(HiSeq 4000)測(cè)序,由上海美吉生物醫(yī)藥科技有限公司完成。
1.3.2 轉(zhuǎn)錄組數(shù)據(jù)處理與分析 將質(zhì)控后的原始數(shù)據(jù),即Clean data,與參考基因組使用軟件Bowtie進(jìn)行比對(duì),獲得用于后續(xù)分析的Mapped data,同時(shí),對(duì)本次轉(zhuǎn)錄組測(cè)序的比對(duì)結(jié)果進(jìn)行質(zhì)量評(píng)估,Reads在參考基因組不同區(qū)域分布以及Reads在不同染色體分布分析,以此獲得各樣品Reads的比對(duì)效率和Reads在基因組上的位置信息。比對(duì)參考基因組進(jìn)行基礎(chǔ)功能注釋,基于蛋白序列與NR庫(Non-Redundant Protein Database)、Swiss-prot庫(Swissprotein sequence database)、Pfam數(shù)據(jù)庫、COG數(shù)據(jù)庫(Cluster of Orthologous Groups of proteins)和KEGG數(shù)據(jù)庫(Kyoto Encyclopedia of Genes and Genomes) 6大數(shù)據(jù)庫進(jìn)行比對(duì),得到相應(yīng)的功能注釋信息,綜合NR、Swiss-Prot、KEGG、COG和Pfam數(shù)據(jù)庫的注釋結(jié)果,選擇最佳的Unigene進(jìn)行分析。利用軟件RSEM(RNA-Seq expression estimation by Expectation-Maximization)以TPM為定量指標(biāo)對(duì)基因的表達(dá)水平進(jìn)行定量分析?;谪?fù)二項(xiàng)分布的DESeq2軟件對(duì)Raw counts進(jìn)行組間表達(dá)差異的基因統(tǒng)計(jì)分析,標(biāo)準(zhǔn)為對(duì)比組樣品間表達(dá)倍數(shù)(Fold Change)≥2和錯(cuò)誤發(fā)現(xiàn)率(False Discover Rate,F(xiàn)DR)<0.05&|log2FC|>1。采用軟件Goatools對(duì)差異表達(dá)基因進(jìn)行GO和KEGG Pathway富集分析,預(yù)測(cè)其可能參與的生物學(xué)過程和功能。
1.3.3 small RNA(sRNA)分析 采用軟件Rockhopper獲得sRNA預(yù)測(cè)結(jié)果后,使用Blast及公共數(shù)據(jù)sRNAMap、sRNATarBase、SIPHT及Rfam資源對(duì)鑒定到的sRNA進(jìn)行注釋。采用RNAplex和IntaRNA分別對(duì)sRNA靶基因預(yù)測(cè),然后對(duì)潛在靶基因的功能進(jìn)行分析。
使用PrimeScriptTM1ststrand cDNA Sythesis Kit試劑盒(TaKaRa公司)制備cDNA。選擇了5個(gè)差異表達(dá)基因,以高水平、恒定表達(dá)的16基因?yàn)閮?nèi)參基因,設(shè)計(jì)特異性引物(表1)。以合成的cDNA為模板,使用TB GreenTMPremix ExTMⅡ試劑盒(TaKaRa公司)進(jìn)行實(shí)時(shí)熒光定量分析,檢測(cè)其mRNA水平的相對(duì)表達(dá)量,采用2–??法分析結(jié)果。Real-TimePCR結(jié)果與轉(zhuǎn)錄組測(cè)序數(shù)據(jù)結(jié)果均以|Log2FC|表示。
表1 Real-Time PCR引物
枯草芽孢桿菌菌株R47對(duì)氨氮的應(yīng)答實(shí)驗(yàn)結(jié)果顯示,在6 h后水樣中氨氮含量從0.8降至0.01 mg/L,18和24 h后,水樣中氨氮含量也均維持在0.01 mg/L,這表明枯草芽孢桿菌R47可明顯降低氨氮含量,可能存在同化吸收作用。
平均每個(gè)測(cè)序樣本得到約1.40×107條reads。質(zhì)控后堿基錯(cuò)誤率(Clean Error Rate)為0.01%,堿基質(zhì)量值大于20的占99.24%,大于30的占97.55%,GC含量為43.51%。以上結(jié)果顯示,轉(zhuǎn)錄組測(cè)序結(jié)果質(zhì)量較高。將各樣本比對(duì)到參考基因組上的Reads (Mapped Reads)占Clean Reads的百分比均大于80%,表明所選參考基因組組裝可以滿足信息分析的需求。
分別基于NR、Swiss-prot、Pfam、COG、GO和KEGG數(shù)據(jù)庫進(jìn)行總Unigene注釋,注釋到NR庫的基因占比最高,高達(dá)96.95%,注釋到KEGG庫的基因占總基因數(shù)最少,為42.51%。6個(gè)數(shù)據(jù)庫總計(jì)能注釋的Unigene數(shù)目為4420。
轉(zhuǎn)錄組測(cè)序數(shù)據(jù)相關(guān)性檢查結(jié)果顯示,每組樣品間基因表達(dá)水平皮爾遜相關(guān)系數(shù)的平方(2)均大于0.65,即各組樣品之間表達(dá)模式的相似度較高,增加了實(shí)驗(yàn)的可靠性。將2個(gè)組基因表達(dá)水平分析中得到的數(shù)據(jù)采用DESeq2進(jìn)行分析,結(jié)果顯示,與對(duì)照組相比,處理組共篩選出3918條差異表達(dá)基因(Differentially expressed genes, DEGs),其中,包括1887個(gè)DEGs上調(diào)表達(dá),2031個(gè)DEGs下調(diào)表達(dá)。利用KEGG數(shù)據(jù)庫,可將DEGs按照參與的Pathway通路或行使的功能進(jìn)行分類,結(jié)果發(fā)現(xiàn),表達(dá)下調(diào)基因主要參與氨基酸代謝、碳水化合物代謝、膜運(yùn)輸過程,上調(diào)基因則主要參與碳水化合物代謝、氨基酸代謝與輔助因子和維生素的代謝等過程。
采用軟件Goatools對(duì)差異表達(dá)基因進(jìn)行GO富集分析,獲得差異表達(dá)基因主要具有的GO功能(圖1)。上調(diào)基因中對(duì)與氨氮代謝功能有關(guān)的GO條目及候選基因進(jìn)行篩選,共得到1個(gè)GO條目,包含37個(gè)DEGs。下調(diào)基因中GO條目及候選基因篩選共得到13個(gè)GO條目,包含574個(gè)DEGs。將DEGs標(biāo)注到KEGG數(shù)據(jù)庫中,對(duì)基因進(jìn)行KEGG Pathway富集分析,結(jié)果顯示,共富集到176個(gè)信號(hào)通路,上調(diào)基因與下調(diào)基因共同信號(hào)通路有130個(gè)。在差異基因KEGG富集結(jié)果中,挑選了富集最顯著的20條通路在圖形中展示(圖2)。在所有KEGG通路中,對(duì)參與枯草芽孢桿菌氨氮代謝通路及候選基因篩選,共得到8個(gè)信號(hào)通路,包含260個(gè)DEGs (表2)。根據(jù)對(duì)差異表達(dá)基因GO與KEGG富集分析中篩選出9個(gè)與枯草芽孢桿菌R47對(duì)水中氨氮應(yīng)答的相關(guān)基因(表3)。
去除接頭并濾去低質(zhì)量數(shù)據(jù)后,獲得3348條長(zhǎng)度為50~500 nt的sRNA序列,其中,以50~100 nt的序列居多。用Blast及公共數(shù)據(jù)庫sRNA Map、sRNA TarBase、SIPHT及Rfam資源對(duì)鑒定到的sRNA進(jìn)行注釋,被注釋到的sRNA總數(shù)為62。
對(duì)sRNA靶基因的分析結(jié)果顯示,其有3960個(gè)對(duì)應(yīng)的潛在靶基因。KEGG數(shù)據(jù)庫將潛在的靶基因分為代謝、環(huán)境信息處理等6大類(表4)。這些潛在靶基因涉及較廣的生物學(xué)過程及功能,其中主要參與碳水化合物運(yùn)輸和新陳代謝、氨基酸轉(zhuǎn)運(yùn)和代謝、轉(zhuǎn)錄過程等,但由于數(shù)據(jù)有限,有1285個(gè)靶基因功能不明確。根據(jù)富集分析所得9個(gè)相關(guān)基因中,其中,和分別是sRNA2073和sRNA2182的靶基因。
為評(píng)估轉(zhuǎn)錄組測(cè)序結(jié)果的可靠性,隨機(jī)挑選、、、和共5個(gè)基因進(jìn)行Real-time PCR分析。相關(guān)性分析結(jié)果顯示,皮爾遜相關(guān)系數(shù)為0.947,<0.05,Real-time PCR與轉(zhuǎn)錄組測(cè)序結(jié)果具有一致性,表明基于轉(zhuǎn)錄組分析差異表達(dá)基因的表達(dá)結(jié)果較為可靠(圖3)。
微生物可參與水環(huán)境中的物質(zhì)代謝,將有機(jī)和無機(jī)污染物轉(zhuǎn)化為無毒化合物,從而達(dá)到改善水質(zhì)的作用(Hu, 2012)。比較來自海水分離的枯草芽孢桿菌、糞產(chǎn)堿桿菌()和綠膿桿菌(),枯草芽孢桿菌所分泌的酶具有最高的活性,去除污漬能力最強(qiáng)(Marathe, 2018)。分離于水產(chǎn)養(yǎng)殖水體及底泥中枯草芽孢桿菌B7具有良好的水質(zhì)調(diào)控作用,對(duì)水體中氨氮的去除率大于80%(陳靜, 2008)。鯽魚糞便中分離的枯草芽孢桿菌R47對(duì)氨氮具有相似響應(yīng),在一定時(shí)間內(nèi)可降低氨氮含量,從而改善水質(zhì)。
圖1 差異表達(dá)基因GO富集散點(diǎn)圖
生物體對(duì)某一刺激作出反應(yīng)時(shí),闡明其生物功能涉及的信號(hào)通路是至關(guān)重要的。本研究在GO富集分析的基礎(chǔ)上,進(jìn)一步開展了KEGG信號(hào)通路分析,發(fā)現(xiàn)DEGs富集最多的候選信號(hào)通路為細(xì)菌雙組分系統(tǒng)(Two component system, TCS)。TCS在細(xì)菌、古細(xì)菌中均有發(fā)現(xiàn),是其對(duì)環(huán)境刺激作出反應(yīng)的多種信號(hào)轉(zhuǎn)導(dǎo)過程??莶菅挎邨U菌通過TCS來應(yīng)對(duì)高濃度氨氮環(huán)境,得以在逆境中生存(Galperin, 2018; Krell, 2010)。、和參與枯草芽孢桿菌對(duì)高濃度氨氮的應(yīng)激反應(yīng)。TCS可影響細(xì)菌的生物膜形成(Plate, 2012)。枯草芽孢桿菌生物被膜的胞外基質(zhì)主要由胞外多糖和胞外蛋白質(zhì)TasA 2個(gè)主要組分組成,分別由操縱子和操縱子誘導(dǎo)合成(Kolodkin, 2010; Nagorska, 2010)。SinR是枯草芽孢桿菌生物被膜形成過程中重要的調(diào)控蛋白,通過抑制胞外多糖和胞外蛋白TasA的合成,進(jìn)而抑制生物被膜的形成(Kearns, 2005)。差異表達(dá)分析結(jié)果顯示,和均表現(xiàn)出下調(diào)趨勢(shì),而表現(xiàn)出上調(diào)趨勢(shì)。這可能是因?yàn)榭莶菅挎邨U菌R47正處于高濃度氨氮水體的初級(jí)適應(yīng)階段。
圖2 差異表達(dá)基因KEGG富集散點(diǎn)圖
表2 氨氮代謝相關(guān)差異表達(dá)基因KEGG富集通路
Tab.2 The enrichment pathway of ammonia nitrogen metabolism related DEGs
表3 氨氮代謝相關(guān)差異表達(dá)基因
Tab.3 DEGs related ammonia nitrogen metabolism
表4 sRNA潛在靶基因的KEGG代謝通路分類統(tǒng)計(jì)
Tab.4 Classification of KEGG metabolic pathways of sRNA potential target genes
枯草芽孢桿菌沒有谷氨酸脫氫酶活性,通過GS/GOGAT途徑同化氨,、、和參與此過程。基因編碼的蛋白是氮代謝全局調(diào)控因子(Global nitrogen regulator, GlnR),一種轉(zhuǎn)錄調(diào)控因子??莶菅挎邨U菌氮代謝途徑的谷氨酰胺合成酶基因受GlnR的調(diào)節(jié)(楊帆等, 2019),這一觀點(diǎn)在本研究也得以證實(shí)。位于上游,參與雙順反子glnRA操縱子的組成。具有一個(gè)α-螺旋–轉(zhuǎn)角–螺旋結(jié)構(gòu)域的GlnR形成二聚體后,結(jié)合到操縱子上,在氮源豐富時(shí)抑制轉(zhuǎn)錄,降低谷氨酸合成酶的活性(Brown, 1996; Wray, 2008),同時(shí),GlnR也能抑制脲酶操縱子的轉(zhuǎn)錄,作為阻遏物阻礙基因表達(dá)(Brandenburg, 2002; Randazzo, 2017)。差異表達(dá)基因分析結(jié)果顯示,、和呈下調(diào)趨勢(shì),與其保持一致??莶菅挎邨U菌對(duì)氨氮的應(yīng)答是一個(gè)復(fù)雜反應(yīng),多個(gè)信號(hào)通路相互協(xié)調(diào)完成。本研究?jī)H對(duì)枯草芽孢桿菌R47的雙組分系統(tǒng)與部分基因進(jìn)行了探討,還需深入開展研究。
sRNA介導(dǎo)的轉(zhuǎn)錄后基因調(diào)控是生物體的一種新型基因調(diào)控機(jī)制,它在有機(jī)體適應(yīng)環(huán)境、調(diào)節(jié)生命活動(dòng)等生物過程中有極為重要的作用。氮脅迫誘導(dǎo)RNA1和RNA4可調(diào)節(jié)念珠藻()和藍(lán)細(xì)菌()對(duì)氮的可利用性(álvarez-Escribano, 2018; Kl?hn, 2018)。Gaimster等(2019)發(fā)現(xiàn),副球菌() sRNA29的過表達(dá)下調(diào)亞硝酸鹽還原酶并限制細(xì)胞產(chǎn)生NO和N2O。本研究對(duì)樣本sRNA的靶基因進(jìn)行預(yù)測(cè)分析,sRNA2073和sRNA2182所介導(dǎo)的調(diào)控通路可能是枯草芽孢桿菌R47進(jìn)行氮代謝的重要輔助。
本研究利用Illumina二代高通量測(cè)序技術(shù)對(duì)在富含氨氮環(huán)境中枯草芽孢桿菌R47進(jìn)行測(cè)序,并初步分析發(fā)現(xiàn)細(xì)菌雙組分系統(tǒng)和、、、、、、等基因可能參與枯草芽孢桿菌R47對(duì)氨氮應(yīng)答過程,同時(shí)進(jìn)行了sRNA分析,為后續(xù)深入探討枯草芽孢桿菌的脫氮分子機(jī)理提供數(shù)據(jù)支撐。
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Transcriptome and sRNA Analyses of the Response ofto Ammonia Nitrogen
ZHENG Yao1, WU Kainian1, WANG Li1①, WEI Yong2
(1. Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education and Sichuan Province, Southwest Minzu University, Chengdu 610041; 2. Animal Science Academy of Sichuan Province, Chengdu 610041)
To explore the molecular mechanism of denitrification byand screen out candidate genes and small RNA (sRNA) related to the response ofto ammonia nitrogen. Transcriptome sequencing and sRNA analysis were performed onin both an ammonia-rich environment and a control group. The relative expression changes in differentially expressed genes were analyzed using real-time PCR. The results showed that each sequencing sample yielded approximately 1.40 × 107reads on average. There were 3918 differentially expressed genes in the control and treatment groups as per DESeq2 analysis, which enriched 176 signaling pathways in the KEGG database, including eight signaling pathways (bacterial two-component system pathway, arginine biosynthesis, purine metabolism, and so on) adapted to the ammonia-rich environment. We found that,,,,,, andgenes may be involved in the response ofto ammonia nitrogen in water. Sixty-two annotated strains ofsRNA were obtained. The prediction and analysis results of sRNA target genes revealed that there are 3960 potential target genes involved in carbohydrate transport and metabolism, amino acid transport and metabolism, and transcription processes. Among them, the target genes corresponding to sRNA2073 and sRNA2182 wereand, respectively. Real-time PCR analysis showed that the relative expression changes of,,andwere consistent with transcriptome sequencing. These results provide reference data for further exploring the molecular mechanism of nitrogen removal byin wastewater.
; Response to ammonia nitrogen; Transcriptome; Differentially expressed genes; sRNA analysis
WANG Li, E-mail: qinxin916@aliyun.com
Q933
A
2095-9869(2021)02-0147-08
10.19663/j.issn2095-9869.20200205001
http://www.yykxjz.cn/
鄭姚, 吳開年, 王利, 魏勇. 枯草芽孢桿菌對(duì)氨氮應(yīng)答的轉(zhuǎn)錄組及sRNA分析. 漁業(yè)科學(xué)進(jìn)展, 2021, 42(2): 147–154
Zheng Y, Wu KN, Wang L, Wei Y. Transcriptome and sRNA analyses of the response ofto ammonia nitrogen. Progress in Fishery Sciences, 2021, 42(2): 147–154
* 四川省農(nóng)業(yè)科技成果轉(zhuǎn)化資金項(xiàng)目(2018NZZJ008)、四川省科技支撐項(xiàng)目(2016NZ0044)和四川肉羊創(chuàng)新團(tuán)隊(duì)防疫崗位共同資助 [This work was supported by Sichuan Agricultural Science and Technology Achievement Transformation Fund Project (2018NZZJ008), Sichuan Province Science and Technology Support Project (2016NZ0044), and Sichuan Meat Sheep Innovation Team Epidemic Prevention Post]. 鄭 姚,E-mail: 1793946322@qq.com
王 利,教授,E-mail: qinxin916@aliyun.com
2020-02-05,
2020-03-11
(編輯 馮小花)