CHINH SACH v n QURN LV
METAGENOMICS VA VIEC KHAI THAC
TIEM NANG DA DANG SINH HOC NGUON GEN VI SINH VAT CUA VIET NAM
Metagenomics
Metagenomics la phudng phap nghien cdu (phSn tich) da h§ gen (metagenome) cua tat ci cdc vi sinh vat thu nhan true tie'p tU miu moi truflng tiJ nhien ma khong thong qua nu6i cay. Thuc chSt, metagenomics ia thuat ngO Mtjc siI dung d l mo tJ m6t itnh vUc nghien cUu l<hoa hoc va cac l<y thu§t cho phep piian tich toan the vi sinh vat song trong bat l<y moi trudng tu nhien nao. Metagenomics bat nguon tu y tudng tach dong DNA true tiep tU cac mSu moi trudng cua Pace (Dai hpc Colorado - Hoa Ky) vao nam 1991. Nam 1995, Heaiy va cong sU (Bai hoc Florida - Hoa Ky) da xSy dung thanh cong mot thu vien DNA da he gen tU h8n hop cSc sinh vat trong c6 kh6 va tim dU(?c 14 dong co hoat tinh ceilulase tij thu vien. Sau thanh cong cua Heaiy va cpng sU, rat nhieu thu vien DNA metagenome cua vi sinh vat trong cac moi trudng song da duoc xay dung nh^m khai thac gen cung nhu nghi§n cUu su da dang vi sinh vat. Sau hon 20 nam phat trien, Metagenomics da trS thanh mpt cong cu manh me dUdc sit dung rat rdng rai de nghien cUu sU da dang cija vi sinh vat.
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Metagenomics (nghien cHu da he gen) da t^o nSn nhitng tiSn bo virdt bSc trong viSc nghiin cifu vS' sinh thai hgc, tie'n hda va da dang vi sinh vSt. D3y la djnh hirdng nghien ctfu mdi, quan trgng da trd thanh chie'n lifdc trong phat tri^n kinh te'bin vifng, an ninh quO'c phong, bio v$ si}c khde va moi trUtrng cija nhie'u qufi'c gia trfin the' gidi. 0 Viet Nam, metagenomics budc dau dugc triln khai ii giii cac bai toan cd tfnh chS't ting the, nhim xay diTng car sd diF lieu v l da dang sinh hgc cua cac he vi sinh v3t cd gla trj.
Hinh 1: cic ptiUdng ptiip tiep can chinti cua metagenomics de tim gen mdi
Lich sill pliat liian va ilng dung metagenomics Thuat ngO metagenomics ian dIu tien dUdc sii dung va cong b6 vao nam 1985 xuat phat tO y tudng nghiSn cCfii phan tich thong tin di truyen ciia mdt he sinh vSt. Hidn nay, metagenomics dUdc md rpng sD dyng dua vao cac cdng nghe hien dai de nghien cLfu cac loai vi sinh vat trong cac phiJc hdp vi sinh vat thu true tiep td mdi trudng tu nhidn ma khdng can nudi cay. Cac nha nghien cUu v^ vi sinh v&t cho biet, sd iUdng vi sinh vat tdn tai tu nhien la vd cung idn va rat phong phu vd thanhi phan ioai song phan Idn chung lai khdng the nudi cay tren mdi trudng nhdn tao, do dd khd
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(tham chf la khong the) xac djnh trinh tM DNA cung nhJ nghien ciru phan tich chLJng. NhOng nghidn ciifu dau tien ve metagenomics da tap trung phan tfch trinh tM 16S rRNA duac tim tha'y l<h6ng thuoc ve bat ky loai nao da dMdc phan lap va nghien cijfu trudc day. Dieu nay cho thay, da co rat nhieu loai vi sinh vat bj b6 sot, khong dUdc nghien cMu. Vdi ket qu^ phSn tfch trinh ta cac doan 16S rRNA thu triJc tiep ta moi tradng ttJ nhien cho th^y, neu chi sii dyng phadng phap nuoi truyen thong, chung ta chf co thi nghien cau dadc 1%
so ladng cac loai vi sinh vat t6n tai trong miu ta nhien ndi chung; 0,001-0,1% cac loalvisinh vat biln; 0,25%
cac loai vi sinh v§t nUdc ngpt; 0,25% vi sinh vat trong tr^m tfch; 0,3% vi sinh vat dat. Mgt nghien cOu da minh chufng cho thdng tin nay: nam 2002, Mya Breitbart (Dai hpc South Florida - Hoa Ky) va Forest Rohwer (Dai hpc San Diego State - Hoa Ky) cung cac dong nghi§p da sD dung cong nghe metagenomics cho thay, trong 200 lit nadc biln co chaa hdn 5.000 loai virus khac nhau. Torsvik (Dgi hpc Bergen - Na Uy), Turnbaugh (Dai hpc Harvard - Hoa Ky), Tringe (Vien Nghien cQu Genome - Hoa Ky) va cdng sa cung stf dung cdng ngh§ metagenomics cho thay, co tren 1 trieu loai virus khac nhau cho mdi kg tram tfch bien (bao gom c^ thac khuan thi). Cong nghe metagenomics ra ddi da khac phLic dupe nhQng han che cua cac phadng phap truyen thong, hudng si/ tap trung nghien ciiu vao cac vi sinh v&t chaa dapc chD y d^n hoac chua biet den. Bang each phan lap va nghien cilu trac tilp genome cOa toan bp cac vi sinh vat trong mot mdi trudng nghien cau, ta cd the cd thdng tin di truyen cua he vl sinh v§t d do ma khdng can phk\ phan lap va nudi cay tCtng te bao rieng Id.
PhUdng phip tiep c$n tim gen mdi bang metagenomics
Metagenomics nghi§n ciiu da he gen quan xa vi sinh vat thdng qua ba bade: 1) tach chiet DNA da he gen cCia vi sinh vat trong mau thu thap; 2) thiet lap thu vien DNA da he gen hoac glal trinh ta DNA da he gen va 3) sang Ipc ho§c ph§n lap gen mong mud'n.
Metagenomics tilp can da he gen theo hal phUdng phap chfnh la phan lap gen daa tren vi§c thiet lap tha vien DNA da he gen va khai thac trinh td DNA, phan lap gen daa tren dQ li§u giki trinh tU DNA da he gen.
Trong do, each tiep can di/a vao chac nang dang ngay cang phdbien.
Phan lap gen tCf thd vien DNA cua da he gen Trong giai doan dSu phat triln cdng nghe metagenomics, each tiep can da he gen la phan lap gen di/a vao tha vien DNA da he gen. Theo c^ch nay,
trade het, DNA da he gen dadc tach chiet trac tiep ta miu mdi trddng. Bade tiep theo la toan bg DNA da he gen se dadc phan eSt bang enzyme han che d l tao thanh cac doan DNA cd kfch thadc du de chda dUdc trpn ven trinh tii cua gen mong mud'n. Sau dd, cae doan DNA nay dapc gan vao vector thi'ch hpp va chuyin vao chung vi sinh vat chu. Vdi so' lupng ddng du Idn, tha vien cd the chMa dadc toan bp cac gen cua da he gen. Cac ddng bleu hien protein ngoai lai sau do se dupe sang Igc hoat tfnh (vf dy nhu san xuat vitamin, chat khang khang sinh, enzyme...) tr§n moi tradng co cd chat dac hieu. Ta do cac ddng mang gen ma hda cho tinh trang mong muon se dapc lua chon, g\k\ trinh ty de thu dUdc trinh ty gen. Nhieu cellulose da dadc phat hien nhd phadng phap nay (ta tha vien DNA da he gen cua vi sinh vat trong dg eo trau eo 61 ddng khac nhau cd hogt tfnh cellulose da dapc ph&n \kp, trong dd 13 ddng cd hoat tfnh endoglucanase; ta thu vien DNA he gen cua vi sinh vat sd'ng trong ehat th^i cCia nha may giay ed 2 ddng cd hoat tfnh endoglucanase, 3 ddng cd hoat tfnh exoglucanase va 2 dong cd hoat tinh p- glucosidase da dape phan lap..). Tuy nhien, viec phan lap gen daa tren viec sang Ipc tha vien DNA da he gen tren moi tradng cd cd chat thadng to'n rat nhieu thdi gian va cdng sufc do phai sang loe mdt khd'i lapng Idn cae ddng trong tha vien. Hdn nQa, each tie'p can nay cdn yeu cau sd lapng dong thd vien phai rat Idn va chat lapng thu vien ph&i eao. Ngay nay, vdi sU phat triln vUpt bac cija khoa hoc va cong nghe, viec Q\ki trinh ty toan bp he gen da trd nen khk thi hdn (tilt kiem thdi gian va kinh phi hdn). Do do, metagenomics khai thac gen eung nhu danh gia sy da dang vi sinh vat deu dya trdn trinh ta DNA da he gen cija vi sinh vat.
Khai thac va phan l$p gen tif dCf lieu trinh ti/DNA da he gen
Trong nhOng nam gan dky, ky thuSt gl^i trinh ta thdng lUdng cao (High Throughput Sequencing - HTS) dapc ang dung rdng rai trong viec giai trinh ty DNA da hd gen cua quan xa vi sinh vat song trong mdi trddng sd'ng nhat dinh. Diem khac biet quan trpng giSa HTS va ky thuat giai trinh ty Sanger truyen thd'ng la dung ladng. Trong khi mot Sanger diln hinh tao ra dapc 102 trinh ty (vdi do dai 600-900 bp) thi HTS (vi du 454 va lllumina) cd the sinh ra 106-109 trinh ty (vdi dp dai 100-700 bp) cho mdi lan chay. Vdi liu diem giai trinh ty nhanh va chinh xac, ky thuat gi^i trinh ty HTS dypc sii dung rat pho bien de g\k\ trinh ta DNA da he gen cua vi sinh vat trong mdi tradng sd'ng. DNA da he gen sau khi dadc giai trinh ty la mdt hdn hdp cac doan trinh tu rieng re, vi vay, cac trinh tu nay se dapc sap xep lai va dadc xii ly bang cac phSn mIm chuyen dung nha
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SOAPdenovo, BWA, FragGeneScan, MetageneMark, MetageneAnnotator (MGA)/Metagene, Orpheiia,. de cd dUdc trinh tu DNA da he gen hoan chinh. Trinh tu hoan chinh nay se dUdc dU doan chUc nang sinh hoc va ddn vj phan loai dua vao mUc dp tudng ddng cua trinh tu vdi nhieu cdsddQ iieu tham khcio cd sSn se dua ra thdng tin ve chUc nang cua gen, nhu KEGG (Kyoto Encyciopedia of Genes and Genomes, ia cd sd dO iieu true tuyen iien quan den he gen, cac con dudng enzyme va cac s^n ph^m sinh lioc), eggNOG (evoiutionary genealogy ol genes: Non-supervised Orthologous Groups, la cd sd dQ iieu chCfa cac nhdm orthologous), COG/KOG (COG • Clusters of Orthologous Group, ia cd sd do lieu protein cua sinh vat nhan sd, nhan ciiuan ddn bao; KOG - eukaryotic orthologous groups, la cd sd do lieu tu 7 he gen sinh vat nhan chuan: 3 loai dpng vat, 1 ipai thuc vat, Arabidopsis tltaliana, 2 ioai nam va cac ky sinh trung ndi bao), PFAM va TiGHFAM (la cd sd do lieu cac hp protein). Tuy nhien, khdng cd cd sd do iieu tham khko nao chOa day du cac thdng tin ve ChOc nang sinh hpc, ve ioai... Vi vay, de dat dUdc ket qua tdt nhat thi tat ch cac co sd dO lieu c^n dupe si!f dung.
Ijfng di^ng cua metagenomics trong lihal thie gen mdi vi dinh gii si/da d^ng vi sinh v$t
Trong nhieu mdi trudng, sd vi sinh vat khdng the nudi cay dUdc bang cdng nghe chiem khoang 99%. Vi v|y, cac phuong phap nghidn cdu su da dang dl truyen cua vi sinh vat, cau true quan the va vai trd sinh thai cija cac VI sinh vat khdng thdng qua nudi cay vi sinh vdt la rat can thidt. Metagenomics, thdng qua viec giai trinh tu loan bd DNA da he gen, la mdt phuong phap hieu qua cho phep nghien cOu su da dang loai cung nhu khai thac cac enzyme vdi hoat tinh xuc tac sinh hpc mdi cua cac vi khuan khdng nudi cay dupe tO he sinh thai trong cac mdi trudng tu nhien. Chlnii vi vay, sd IUdng cac nghidn cOu da hd gen cija khu he vi sinli vat dua tren vide giji ma toan bd he gen bang may giai trinh tu thd he mdi khdng ngOng gia tang ke 10 khi DNA da hd gen dSu tien cua cac vi sinh vat sdng trong he thong thoat nudc cOa md axit dupe giai trinh tU. Cho den nay, nhieu DNAda he gen cua vi sinh vat S cdc mdi trudng khac nhau da dUdc danh gia da dang vi sinh vdt cung nhu da dang di truyen nhu mdi trudng nudc bien, rudt ngudi, da cd bd, phan compost va dat... Phan Hcii trinh tu DNA da he gen vi sinh vat cua 33 mau dat lay to dat trdng cd, dat rOng, dat sa mac, dat Arctic va dat rOng ngap man cho thay, vi sinh vat cd mat trong ddt gdm 11 nganh va 53 chi. Trong dd, Proteobacteria id nganh chiem ty Id cao nhat trong quan xa vi sinh vdt cua dat (trO mSu dat sa mac), d dat sa mac, ca 2
nganh Proteobacteria va Actinobacteria chiem Uu thd:
30% Proteobacteria va 29% Actinobacteria. Ngoai ra, Firmicutes va Bacteroidetes ia hai nganh chinh chiem uu the d qudn xa vi sinh vat dudng rudt ngudi khdng cd mat thudng xuyen trong cac quan xa vi sinh v§t dat. Bang phuong phap giai trinh tU gen tren cac thiet bj the he mdi cCia lllumina Inc/Gencme Analysis, DNA da he gen cija toan bd vi sinh vat cd trong 124 mdu phan ngudi chdu Au da dUdc giai trinh tu. Ke't qua xii ly va phan tich trinh tU cho thay, kich tiiudc DNA da he gen Idn den 576,7 gigabase (Gb), cd 3,3 trieu gen vi sinh vat (Idn hdn gan 150 lan so vdi sd gen cua 1 he gen ngudi hoan chinh) da dUdc xac dinh dac diem.
Trong dd, hon 90% gen la ci!la vi khuan, phan cdn lai chd ye'u ia gen cCia vi khuan co, chf 1 % la gen ci!ia sinh vat nhan chuan va virus. Kd't qua phan tich cijng cho thay, hdn 99% gen vi khuan thudc trong nhdm 1.000 va 1.150 loai vi khuan phd bid'n va mdi cd the ngudi CO it nhat 160 ioai nhu vay. Ngoai ra, cijng rat nhieu enzyme chuyen hda iignoceiiuose dUdc tim tha'y tO cac he tu nhien khac nhu trong da co trau bd hay miu nudc hd va da't rOng ngdp man. Vide tim kiem cac enzyme mdi ma hda cho he enzyme celiuiase chuydn hda iignoceiluiose tO mdt sd he mini sinh thai bang phUdng phap metagenomic hidn dang cd xu hudng phdt trien, giup kham pha ra nhieu enzyme mdi vdi dap tinh qu;^, gidm gia thanh trong qua trinh Ong dung cdng nghiep va dap Ung nhu cau ve viec sdn xud't nang iuong sach trong tuong iai.
Dinh lulling ngliien cilu, ilng dung metagenomics tien tlie giAi va viec tiien liliai tai Viet Nam
Metagenomics da tao nen nhUng tien bd vUdt bac trong sinh thai hoc, tien hda va da dang vi sinh vdt.
Bay la djnh hudng mdi, quan trong va trd thanh chidn iuoc trong phat trie'n kinh te ben vBng, an ninh qudc phdng, bao ve sUc khde va mdi trudng trdn the gidi hieri nay. Metagenomics la cdng cu mdi, td hpp rat nhidu ky thuat sinh hpc ket hpp tin - sinh hoc de phan tich sang ipc, xay dung thu vidn metagenomics, quan ly va khai thac cho mdi trudng tu nhien, co t h i ngudi, ddng vat, thuc vat khdng thdng qua nudi cay.
Metagenomics dupe Ong dung va mang lai hieu qui cho phat trien kinh te, an sinh xa hdi va mdi trudng, nhu trpng iinh vuc khpa hpc trai dat: phat trien me hinh genome tren co sd sinh thai vi sinh vat nham md td va du bao cac qua trinh mdi trudng loan cau, thay ddi khi hau va su ben vOng cCia trai dat. Trong linh vuc khoa hoc su sdng: cac hoc thuyet mdi trinh dd tien tien dU bao trudc cac nang iuc sinh hpc quan tiie vi sinh vdt
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gdc, sinh thai va sy tie'n hda. Trong fi'nh vdc y - sinh hpc: xae djnh rd mac dp toan cau sy ddng gdp cua he vi sinh vat cho sac khde, phat lilen va dieu tri benh cho cac ca t h i , cpng dong ngddi, dgng vat, thyc vat; phat trien cac pliadng phap dieu trj mdi tren cd sd cae kien thac metagenomics. Trong ITnh vyc nang lapng: phat tnen h§ vi sinh vat va cac qua trinh cho nguon nang lapng sinh hpc mdi cd hieu qua kinh te, mdi tradng ben vOng hdn va cd kha nang phuc hoi nhanh vdl cac bien dgng xau cCia trai dat. Trong ITnh vac mdi tradng: phat trien cac cdng cy de quan trac moi tradng kh\c6 sy cd d tat ca cac mdc do, ta thay doi khf hau den rd rl khf dot, hda chat, dau ta kho chda va cae phadng phap vi sinh vat cd ban dapc gpi la phddng phap xanh phuc vu viec duy tri eac he sinh thai.
De tilp can dddc vdi nhQng thanh tau cua the gidi, tao dieu kien khai thac hieu qua nguon gen vl sinh v§t phong phij va da dang cua Viet Nam ang dyng vao nhieu ITnh vac thac tiln khac nhau, ngay 23.4.2014, 86 tradng Bo Khoa hpe va Cdng nghe da ban hanh Quyet djnh so 826/QD-BKHCN phe duyet Danh myc dat hang dy an khoa hpc va cdng nghe cap quo'c gia "Nghien cdu metagenome eCia vi sinli vat ta mpt so mdi tradng dac thu nham tim kiem cac gen, enzyme, chat xuc tac sinh hpc mdi de s^n xuat eac ehe pham sinh hgc phuc vu ddi sd'ng, b^o ve sdc khde con ngadi va mdi trudng" vdi mye tieu dat ra la: sCf dyng metagenomics d l khai thac cac vat li$u di truyen mdi ma hda cac enzyme, cac chat ed hoat tfnh sinh hgc, cae chat xuc tac, cac chat khang u...
cd tiem nang cong nghe trong san xuat thude, tgo kit chan doan b§nh, phat trien cay tring, v§t nudi cd gia trj kinh te, gdp phan bko ve sac khde cpng dong, ph^t triln kinh te b i n vijfng, bao ve mdi tradng.
Dy an khoa hgc va cong nghe tren da dapc dat hang va giao cho Vien Han \km Khoa hoc va Cdng nghe Viet Nam ehu tri vdi 5 djnh hudng nghien ciiu ehfnh gom: 1) Nghien ciiu metagenome cua vi sinh vat vijng dat 6 nhilm chat diet co/dioxin nham tim kiem cac gen mdi cd khk nang phan huy dioxin; 2]
Nghien cau metagenome cua vi sinh vat dat vung re mpt sd' dai dien cay trong d Viet Nam: cay thud'c cd cu (cay nghe), cky cdng nghiep (ca ph§, lac) nhlm tang nang suat va chat lapng cay trong; 3) Nghien eau metagenome cua ba he mini sinh thai tiem nang nhlm khai thac cac gen mdi ma hda he enzyme chuyen hda hieu quk Iignoceiluiose; 4) Nghien eQu metagenome eua vi sinh vat trong cac dam nudi tdm, gdp phan tao ed sd khoa hgc de phat trien nghe nudi torn d Viet Nam; 5) Nghien ciiu metagenome ctia vi
sinh vat lien ke't h^l midn tai bien mien Trung Viet Nam nham phat hien va sang Igc cac chat hogt tfnh sinh hge mdi.
6 Viet Nam, day la nhdng nghien ciiu dau tien ang dung cdng nghe metagenomics d l g\k\ cae bai toan cd tinh chat tong the, cap thiet, md ra mgt each nhin toan dien v l mgt dd'i tUdng cu t h i ndi rieng cung nhu cac mat xich trong he sinh thai ndi chung, ta dd xay dang cd sd dO lieu ve da dgng sinh hgc cua cae he vi sinh vat cd gia tri, lam cd sd cho viee khai thac va ang dung trong cac nghien cau ve sinh hgc he thd'ng sau nay.
NhOng nghien cdu danh gla da dgng va tilm nang di truyen cua vi sinh vSt ta h§ sinh thai cua Viet Nam se gdp phan dang ke vao sy phat trien kinh te dua tren nen tang sinh hgc ben vOng ciia dat nadc. Kit qua nghien cdu thu dadc cd the thay doi phddng thdc canh tac d l dat hieu qua cao nha't nham phat triln ben vOfng nen ndng nghiep eung nhu nguon cay nguyen lieu phuc vu phat triln cdng nghi§p dadc cua Vidt Nam trong tadng lai .s^
T a i lieu tham khao
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