I HC QUC GIA H NI TRNG I HC KHOA HC T NHIấN Nguyn Th Tho NGHIấN CU GEN M HểA ENZYME THAM GIA THY PHN CELLULOSE T KHU H VI KHUN TRONG RUT MI BNG K THUT METAGENOMICS LUN N TIN S SINH HC H Ni - Nm 2015 I HC QUC GIA H NI TRNG I HC KHOA HC T NHIấN Nguyn Th Tho NGHIấN CU GEN M HểA ENZYME THAM GIA THY PHN CELLULOSE T KHU H VI KHUN RUT MI BNG K THUT METAGENOMICS LUN N TIN S SINH HC Chuyờn ngnh: Di truyn hc Mó s: 62 42 01 21 NGI HNG DN KHOA HC: GS TS Trng Nam Hi TS Th Huyn H Ni - Nm 2015 LI CAM OAN Tụi xin cam oan: õy l cụng trỡnh nghiờn cu ca tụi v mt s kt qu cựng cng tỏc vi cỏc cng s khỏc Cỏc s liu v kt qu trỡnh by lun ỏn l trung thc, mt phn ó c cụng b trờn cỏc khoa hc chuyờn ngnh vi s ng ý v cho phộp ca cỏc ng tỏc gi Phn cũn li cha c tỏc gi no cụng b bt kỡ cụng trỡnh no khỏc H Ni, ngy thỏng nm 2015 Tỏc gi Nguyn Th Tho LI CM N Tụi xin by t lũng bit n sõu sc ti GS.TS Trng Nam Hi v TS Th Huyn phũng K thut di truyn, Vin Cụng ngh sinh hc, Vin Hn lõm Khoa hc v Cụng ngh Vit Nam ó thu nhn, hng dn tn tỡnh, quan tõm ht mc v to mi iu kin cho tụi hon thnh lun ỏn ny Lun ỏn c thc hin ti phũng K thut di truyn Phũng Thớ nghim trng im Cụng ngh Gen, Vin Cụng ngh sinh hc, Vin Hn lõm Khoa hc v Cụng ngh Vit Nam v c h tr bi ti Ngh nh th vi Nht Bn: Phõn lp h gen mó húa cho enzyme thy phõn lignocellulose t khu h vi sinh rut mi Vit Nam bng k thut Metagenomics Trong thi gian hc v nghiờn cu ti phũng K thut di truyn, tụi ó nhn c s giỳp v s ch bo tn tỡnh v chuyờn mụn ca th cỏn b nghiờn cu ca phũng Tụi xin chõn thnh cm n s giỳp quý bỏu ú! Tụi xin by t lũng cm n sõu sc n cỏc thy cụ giỏo Khoa Sinh hc, i hc Khoa hc T nhiờn, i hc Quc gia H Ni ó ging dy v ch bo cho tụi nhng kin thc chuyờn mụn v k nng cn thit hon thnh lun ỏn, tụi ó nhn c nhiu s giỳp quý bỏu v nhit tỡnh ca cỏc ng nghip cụng tỏc ti khoa Sinh hc, Trng i hc Vinh, tụi xin chõn thnh cm n s giỳp quý bỏu ú! Vi tt c lũng bit n, tụi xin dnh cho gia ỡnh, b m, chng v con, nhng ngi thõn ó thụng cm, ng viờn, to iu kin v chia s khú khn cựng tụi thi gian qua! Nguyn Th Tho MC LC M U 14 Tớnh cp thit ca ti 18 Mc tiờu ca ti 20 i tng v phm vi nghiờn cu 20 Ni dung nghiờn cu 20 í ngha khoa hc v thc tin ca ti 20 úng gúp mi ca ti 20 Chng TNG QUAN TI LIU 21 1.1 GII THIU CHUNG V LIGNOCELLULOSE 21 1.1.1 Cellulose 22 1.1.2 Hemicellulose 23 1.1.3 Lignin 24 1.2 GII THIU CHUNG V CELLULASE 24 1.2.1 C ch hot ng ca cellulase v s thy phõn cellulose 24 1.2.2 Cu trỳc ca cellulase 26 1.2.2.1 Cu trỳc chung ca cellulase 26 1.2.2.2 Cellulosome thy phõn cellulose 27 1.3 CELLULASE CA VI KHUN 28 1.3.1 S lc v h cellulase 28 1.3.2 Cellulase ca vi khun v vi khun c 30 1.3.2.1 Cellulase vi khun v vi khun c a m 30 1.3.2.2 Cellulase vi khun v vi khun c a nhit 31 1.3.3 ng dng ca cellulase 31 1.3.3.1 ng dng ca cellulase cụng ngh sn xut bia, ru vang, ch bin thc phm v thc n 32 1.3.3.2 ng dng cellulase dt may 33 1.3.3.3 ng dng cellulase ch bin bt giy v giy 33 1.3.3.4 ng dng ca cellulase sn xut cn sinh hc 34 1.4 MI V H VI SINH VT RUT MI LIấN QUAN N S THY PHN LIGNOCELLULOSE 35 1.4.1 S lc v mi v a dng mi Vit Nam 35 1.4.2 H vi sinh vt rut mi bc thp 36 1.4.3 S tiờu húa lignocellulose ca mi 38 1.4.4 Tỡnh hỡnh nghiờn cu gen mó húa cellulase ca sinh vt ng rut mi bc thp 39 1.5 KHI QUT CHUNG V METAGENOMICS 41 1.5.1 Phng phỏp tip cn tỡm gen mi bng Metagenomics 42 1.5.2 Phõn lp gen t th vin DNA a h gen 43 1.5.3 Khai thỏc v phõn lp gen t d liu trỡnh t DNA a h gen 45 1.5.3.1 Phng phỏp gii trỡnh t ca mt s h thng mỏy th h mi 45 1.5.3.2 Tp hp cỏc read thnh contig 47 1.5.4 ng dng ca Metagenomics 50 1.5.4.1 ng dng ca Metagenomics khai thỏc gen mi v ỏnh giỏ s a dng vi sinh vt 50 1.5.4.2 Tim nng ng dng ca Metagenomics 53 Chng I TNG V PHNG PHP NGHIấN CU 55 2.1 I TNG, VT LIU, HểA CHT V THIT B MY MểC 55 2.1.1 i tng v vt liu 55 2.1.2 Húa cht v thit b mỏy múc 56 2.2 PHNG PHP NGHIấN CU 58 2.2.1 Cỏc phng phỏp vi sinh 59 2.2.2 Cỏc phng phỏp sinh hc phõn t 59 2.2.2.1 Tỏch chit DNA h gen ca mi 59 2.2.2.2 Phng phỏp thu nhn vi khun rut mi v tỏch chit DNA a h gen ca chỳng 59 2.2.2.3 Tinh sch DNA a h gen bng phng phỏp mỏng n (troughing) 60 2.2.2.4 Gii trỡnh t DNA a h gen bng mỏy gii trỡnh t th h mi HiSeq2000 ca Illumina 61 2.2.2.5 Phng phỏp bin np DNA plasmid vo vi khun E coli bng sc nhit 62 2.2.2.6 Phng phỏp tỏch chit DNA plasmid t t bo vi khun E coli 63 2.2.2.7 Phng phỏp ct v ghộp ni gen 63 2.2.2.8 Phng phỏp tinh sch DNA t gel agarose bng QIAquick Gel Extraction kit 64 2.2.2.9 K thut PCR 64 2.2.2.10 Thit k vector biu hin pET22b(+) mang gen egc 66 2.2.2.11 in di DNA trờn gel agarose 66 2.2.2.12 Phng phỏp biu hin gen 66 2.2.2.13 in di bin tớnh protein trờn gel polyacrylamide-SDS 67 2.2.2.14 in di protein trờn gel polyacrylamide khụng SDS 68 2.2.3 Cỏc phng phỏp húa sinh protein 68 2.2.3.1 Phng phỏp tinh ch protein bng sc kớ ỏi lc his-tag 68 2.2.3.2 nh lng protein bng phng phỏp Bradford 69 2.2.3.3 nh lng ng kh bng phng phỏp DNS 69 2.2.3.4 Phng phỏp xỏc nh hot tớnh endoglucanase 70 2.2.3.5 Phng phỏp xỏc nh hot tớnh -glucosidase v -xylosidase 71 2.2.3.6 Xỏc nh nh hng ca nhit , pH, cỏc ion kim loi v mt s húa cht lờn hot tớnh endoglucanase 72 2.2.3.7 Xỏc nh bn ca enzyme 72 2.2.3.8 Xỏc nh thụng s ng hc ca enzyme 72 2.2.4 Cỏc phng phỏp tin sinh hc v x lý s liu bng phn mm sinh hc 73 2.2.4.1 Phõn tớch trỡnh t DNA a h gen vi khun rut mi 73 2.2.4.2 So sỏnh trỡnh t ORF ca d liu DNA a h gen vi CSDL ca NCBI 74 2.2.4.3 Thit k mi bng phn mm FastPCR 75 2.2.4.4 Kim tra v trớ ca cỏc enzyme hn ch trờn gen quan tõm bng phn mm trc tuyn RestrictionMapper 75 2.2.4.5 Chuyn mó trỡnh t DNA sang trỡnh t axit amin bng chng trỡnh dch mó ExPASy 75 2.2.4.6 Xõy dng cõy phỏt sinh loi ca loi mi nghiờn cu vi cỏc loi mi khỏc bng phn mm Genedoc v MEGA5 75 2.2.4.7 D oỏn cu trỳc ca EGC bng phn mm Phyre2 76 Chng KT QU V THO LUN 77 3.1 KT QU NH LOI MI NGHIấN CU BNG PHNG PHP PHN T 77 3.1.1 Tỏch chit DNA h gen ca mi 79 3.1.2 PCR khuch i on DNA ca gen mó húa RNA ribosome 16S ti th mi 79 3.1.3 Phõn tớch sn phm PCR 76 3.2 TCH CHIT, C V PHN TCH TRèNH T DNA A H GEN VI KHUN RUT MI C gestroi 86 3.2.1 Tỏch chit v tinh sch DNA a h gen vi khun rut mi C gestroi 86 3.2.2 c v phõn tớch trỡnh t DNA a h gen vi khun rut mi C gestroi 87 3.2.2.1 Tp hp trỡnh t v xỏc nh gen 87 3.2.2.2 a dng vi sinh vt rut mi C gestroi 90 3.3 GEN M HểA ENZYME THU PHN CELLULOSE CA VI KHUN RUT MI C gestroi 96 3.3.1 D oỏn chc nng gen ca DNA a h gen vi khun rut mi C gestroi 96 3.3.2 Gen mó húa enzyme phõn hy cellulose 98 3.3.3 La chn ORF cellulase biu hin 100 3.4 TCH DếNG GEN egc 104 3.4.1 Trỡnh t ORF GL0130684 105 3.4.2 Khuch i gen egc 105 3.4.3 Ghộp ni sn phm khuch i gen egc vo vector tỏch dũng pJET1.2/blunt 106 3.4.4 Bin np sn phm ghộp ni vo t bo E coli DH10b 107 3.4.5 Ct kim tra plasmid tỏi t hp bng enzyme hn ch 108 3.4.6 Phõn tớch trỡnh t gen wegc phõn lp c t DNA a h gen vi khun rut mi C gestroi 108 3.4.7 Khuch i gen egc khụng cha tớn hiu tit t khuụn pJET-wegc 111 3.4.8 Thit k vector biu hin gen egc 111 3.4.8.1 Ghộp ni gen egc vo vector biu hin 111 3.4.8.2 Ct kim tra plasmid tỏi t hp pET22-egc 113 3.5 BIU HIN GEN egc TRONG VI KHUN E coli BL21(DE3) 114 3.5.1 Chn dũng biu hin gen egc t bo E coli BL21(DE3) 114 3.5.2 nh hng ca nhit n s biu hin gen egc t bo E coli BL21(DE3) 116 3.5.3 nh hng ca nng IPTG n hiu qu cm ng 117 3.5.4 in di v kim tra hot tớnh endoglucanase ca EGC 119 3.5.5 Tinh ch protein EGC bng ct sc kớ ỏi lc His-tag 120 3.5.6 Tớnh c hiu c cht ca EGC 124 3.5.7 nh hng ca nhit n hot tớnh endoglucanase ca EGC 126 3.5.8 nh hng ca pH n hot tớnh ca EGC 127 3.5.9 bn nhit ca EGC 128 3.5.10 nh hng ca mt s ion kim loi v húa cht lờn hot tớnh ca EGC 128 3.5.11 c im ng hc ca EGC 132 KT LUN V KIN NGH 135 TI LIU THAM KHO 138 DANH MC K HIU V CH VIT TT Tờn vit tt BglB BglF BglG Tờn ting Anh Beta-glucosidase B Beta-glucosidase F Beta-glucosidase G BLAST Basic Local Alignment Search Tool bp BSA Base pair Bovine serum albumin BWA Burrows-Wheeler Aligner CD Carbohydrate binding domain Catalytic domain cDNA Complementary DNA CBD Cel12A Cel45A (EGV) Cel48A Cel5A Cel6A (CBHII) Cel6B (EGVI) Cel7A (CBHI) Tờn ting 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