Functional characterization of cellulases identified from the cow rumen fungus <b><it>Neocallimastix patriciarum </it></b>W5 by transcriptomic and secretomic analyses
<p>Abstract</p> <p>Background</p> <p><it>Neocallimastix patriciarum</it> is one of the common anaerobic fungi in the digestive tracts of ruminants that can actively digest cellulosic materials, and its cellulases have great potential for hydrolyzing cellulos...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2011-08-01
|
| Series: | Biotechnology for Biofuels |
| Subjects: | |
| Online Access: | http://www.biotechnologyforbiofuels.com/content/4/1/24 |
| _version_ | 1811340434537971712 |
|---|---|
| author | Wang Tzi-Yuan Chen Hsin-Liang Lu Mei-Yeh J Chen Yo-Chia Sung Huang-Mo Mao Chi-Tang Cho Hsing-Yi Ke Huei-Mien Hwa Teh-Yang Ruan Sz-Kai Hung Kuo-Yen Chen Chih-Kuan Li Jeng-Yi Wu Yueh-Chin Chen Yu-Hsiang Chou Shao-Pei Tsai Ya-Wen Chu Te-Chin Shih Chun-Chieh A Li Wen-Hsiung Shih Ming-Che |
| author_facet | Wang Tzi-Yuan Chen Hsin-Liang Lu Mei-Yeh J Chen Yo-Chia Sung Huang-Mo Mao Chi-Tang Cho Hsing-Yi Ke Huei-Mien Hwa Teh-Yang Ruan Sz-Kai Hung Kuo-Yen Chen Chih-Kuan Li Jeng-Yi Wu Yueh-Chin Chen Yu-Hsiang Chou Shao-Pei Tsai Ya-Wen Chu Te-Chin Shih Chun-Chieh A Li Wen-Hsiung Shih Ming-Che |
| author_sort | Wang Tzi-Yuan |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p><it>Neocallimastix patriciarum</it> is one of the common anaerobic fungi in the digestive tracts of ruminants that can actively digest cellulosic materials, and its cellulases have great potential for hydrolyzing cellulosic feedstocks. Due to the difficulty in culture and lack of a genome database, it is not easy to gain a global understanding of the glycosyl hydrolases (<it>GHs</it>) produced by this anaerobic fungus.</p> <p>Results</p> <p>We have developed an efficient platform that uses a combination of transcriptomic and proteomic approaches to <it>N. patriciarum </it>to accelerate gene identification, enzyme classification and application in rice straw degradation. By conducting complementary studies of transcriptome (Roche 454 GS and Illumina GA IIx) and secretome (ESI-Trap LC-MS/MS), we identified 219 putative <it>GH </it>contigs and classified them into 25 <it>GH</it> families. The secretome analysis identified four major enzymes involved in rice straw degradation: β-glucosidase, endo-1,4-β-xylanase, xylanase B and Cel48A exoglucanase. From the sequences of assembled contigs, we cloned 19 putative cellulase genes, including the <it>GH1</it>, <it>GH3</it>, <it>GH5</it>, <it>GH6</it>, <it>GH9</it>, <it>GH18</it>, <it>GH43 </it>and <it>GH48 </it>gene families, which were highly expressed in <it>N. patriciarum </it>cultures grown on different feedstocks.</p> <p>Conclusions</p> <p>These <it>GH </it>genes were expressed in Pichia pastoris and/or Saccharomyces cerevisiae for functional characterization. At least five novel cellulases displayed cellulytic activity for glucose production. One β-glucosidase (W5-16143) and one exocellulase (W5-CAT26) showed strong activities and could potentially be developed into commercial enzymes.</p> |
| first_indexed | 2024-04-13T18:41:54Z |
| format | Article |
| id | doaj.art-c394d86fecdc4bc0889d144621a49b49 |
| institution | Directory Open Access Journal |
| issn | 1754-6834 |
| language | English |
| last_indexed | 2024-04-13T18:41:54Z |
| publishDate | 2011-08-01 |
| publisher | BMC |
| record_format | Article |
| series | Biotechnology for Biofuels |
| spelling | doaj.art-c394d86fecdc4bc0889d144621a49b492022-12-22T02:34:42ZengBMCBiotechnology for Biofuels1754-68342011-08-01412410.1186/1754-6834-4-24Functional characterization of cellulases identified from the cow rumen fungus <b><it>Neocallimastix patriciarum </it></b>W5 by transcriptomic and secretomic analysesWang Tzi-YuanChen Hsin-LiangLu Mei-Yeh JChen Yo-ChiaSung Huang-MoMao Chi-TangCho Hsing-YiKe Huei-MienHwa Teh-YangRuan Sz-KaiHung Kuo-YenChen Chih-KuanLi Jeng-YiWu Yueh-ChinChen Yu-HsiangChou Shao-PeiTsai Ya-WenChu Te-ChinShih Chun-Chieh ALi Wen-HsiungShih Ming-Che<p>Abstract</p> <p>Background</p> <p><it>Neocallimastix patriciarum</it> is one of the common anaerobic fungi in the digestive tracts of ruminants that can actively digest cellulosic materials, and its cellulases have great potential for hydrolyzing cellulosic feedstocks. Due to the difficulty in culture and lack of a genome database, it is not easy to gain a global understanding of the glycosyl hydrolases (<it>GHs</it>) produced by this anaerobic fungus.</p> <p>Results</p> <p>We have developed an efficient platform that uses a combination of transcriptomic and proteomic approaches to <it>N. patriciarum </it>to accelerate gene identification, enzyme classification and application in rice straw degradation. By conducting complementary studies of transcriptome (Roche 454 GS and Illumina GA IIx) and secretome (ESI-Trap LC-MS/MS), we identified 219 putative <it>GH </it>contigs and classified them into 25 <it>GH</it> families. The secretome analysis identified four major enzymes involved in rice straw degradation: β-glucosidase, endo-1,4-β-xylanase, xylanase B and Cel48A exoglucanase. From the sequences of assembled contigs, we cloned 19 putative cellulase genes, including the <it>GH1</it>, <it>GH3</it>, <it>GH5</it>, <it>GH6</it>, <it>GH9</it>, <it>GH18</it>, <it>GH43 </it>and <it>GH48 </it>gene families, which were highly expressed in <it>N. patriciarum </it>cultures grown on different feedstocks.</p> <p>Conclusions</p> <p>These <it>GH </it>genes were expressed in Pichia pastoris and/or Saccharomyces cerevisiae for functional characterization. At least five novel cellulases displayed cellulytic activity for glucose production. One β-glucosidase (W5-16143) and one exocellulase (W5-CAT26) showed strong activities and could potentially be developed into commercial enzymes.</p>http://www.biotechnologyforbiofuels.com/content/4/1/24anaerobic fungibiomassrice strawsugarcanenapiergrass<it>GH</it>next-generation sequencing |
| spellingShingle | Wang Tzi-Yuan Chen Hsin-Liang Lu Mei-Yeh J Chen Yo-Chia Sung Huang-Mo Mao Chi-Tang Cho Hsing-Yi Ke Huei-Mien Hwa Teh-Yang Ruan Sz-Kai Hung Kuo-Yen Chen Chih-Kuan Li Jeng-Yi Wu Yueh-Chin Chen Yu-Hsiang Chou Shao-Pei Tsai Ya-Wen Chu Te-Chin Shih Chun-Chieh A Li Wen-Hsiung Shih Ming-Che Functional characterization of cellulases identified from the cow rumen fungus <b><it>Neocallimastix patriciarum </it></b>W5 by transcriptomic and secretomic analyses Biotechnology for Biofuels anaerobic fungi biomass rice straw sugarcane napiergrass <it>GH</it> next-generation sequencing |
| title | Functional characterization of cellulases identified from the cow rumen fungus <b><it>Neocallimastix patriciarum </it></b>W5 by transcriptomic and secretomic analyses |
| title_full | Functional characterization of cellulases identified from the cow rumen fungus <b><it>Neocallimastix patriciarum </it></b>W5 by transcriptomic and secretomic analyses |
| title_fullStr | Functional characterization of cellulases identified from the cow rumen fungus <b><it>Neocallimastix patriciarum </it></b>W5 by transcriptomic and secretomic analyses |
| title_full_unstemmed | Functional characterization of cellulases identified from the cow rumen fungus <b><it>Neocallimastix patriciarum </it></b>W5 by transcriptomic and secretomic analyses |
| title_short | Functional characterization of cellulases identified from the cow rumen fungus <b><it>Neocallimastix patriciarum </it></b>W5 by transcriptomic and secretomic analyses |
| title_sort | functional characterization of cellulases identified from the cow rumen fungus b it neocallimastix patriciarum it b w5 by transcriptomic and secretomic analyses |
| topic | anaerobic fungi biomass rice straw sugarcane napiergrass <it>GH</it> next-generation sequencing |
| url | http://www.biotechnologyforbiofuels.com/content/4/1/24 |
| work_keys_str_mv | AT wangtziyuan functionalcharacterizationofcellulasesidentifiedfromthecowrumenfungusbitneocallimastixpatriciarumitbw5bytranscriptomicandsecretomicanalyses AT chenhsinliang functionalcharacterizationofcellulasesidentifiedfromthecowrumenfungusbitneocallimastixpatriciarumitbw5bytranscriptomicandsecretomicanalyses AT lumeiyehj functionalcharacterizationofcellulasesidentifiedfromthecowrumenfungusbitneocallimastixpatriciarumitbw5bytranscriptomicandsecretomicanalyses AT chenyochia functionalcharacterizationofcellulasesidentifiedfromthecowrumenfungusbitneocallimastixpatriciarumitbw5bytranscriptomicandsecretomicanalyses AT sunghuangmo functionalcharacterizationofcellulasesidentifiedfromthecowrumenfungusbitneocallimastixpatriciarumitbw5bytranscriptomicandsecretomicanalyses AT maochitang functionalcharacterizationofcellulasesidentifiedfromthecowrumenfungusbitneocallimastixpatriciarumitbw5bytranscriptomicandsecretomicanalyses AT chohsingyi functionalcharacterizationofcellulasesidentifiedfromthecowrumenfungusbitneocallimastixpatriciarumitbw5bytranscriptomicandsecretomicanalyses AT kehueimien functionalcharacterizationofcellulasesidentifiedfromthecowrumenfungusbitneocallimastixpatriciarumitbw5bytranscriptomicandsecretomicanalyses AT hwatehyang functionalcharacterizationofcellulasesidentifiedfromthecowrumenfungusbitneocallimastixpatriciarumitbw5bytranscriptomicandsecretomicanalyses AT ruanszkai functionalcharacterizationofcellulasesidentifiedfromthecowrumenfungusbitneocallimastixpatriciarumitbw5bytranscriptomicandsecretomicanalyses AT hungkuoyen functionalcharacterizationofcellulasesidentifiedfromthecowrumenfungusbitneocallimastixpatriciarumitbw5bytranscriptomicandsecretomicanalyses AT chenchihkuan functionalcharacterizationofcellulasesidentifiedfromthecowrumenfungusbitneocallimastixpatriciarumitbw5bytranscriptomicandsecretomicanalyses AT lijengyi functionalcharacterizationofcellulasesidentifiedfromthecowrumenfungusbitneocallimastixpatriciarumitbw5bytranscriptomicandsecretomicanalyses AT wuyuehchin functionalcharacterizationofcellulasesidentifiedfromthecowrumenfungusbitneocallimastixpatriciarumitbw5bytranscriptomicandsecretomicanalyses AT chenyuhsiang functionalcharacterizationofcellulasesidentifiedfromthecowrumenfungusbitneocallimastixpatriciarumitbw5bytranscriptomicandsecretomicanalyses AT choushaopei functionalcharacterizationofcellulasesidentifiedfromthecowrumenfungusbitneocallimastixpatriciarumitbw5bytranscriptomicandsecretomicanalyses AT tsaiyawen functionalcharacterizationofcellulasesidentifiedfromthecowrumenfungusbitneocallimastixpatriciarumitbw5bytranscriptomicandsecretomicanalyses AT chutechin functionalcharacterizationofcellulasesidentifiedfromthecowrumenfungusbitneocallimastixpatriciarumitbw5bytranscriptomicandsecretomicanalyses AT shihchunchieha functionalcharacterizationofcellulasesidentifiedfromthecowrumenfungusbitneocallimastixpatriciarumitbw5bytranscriptomicandsecretomicanalyses AT liwenhsiung functionalcharacterizationofcellulasesidentifiedfromthecowrumenfungusbitneocallimastixpatriciarumitbw5bytranscriptomicandsecretomicanalyses AT shihmingche functionalcharacterizationofcellulasesidentifiedfromthecowrumenfungusbitneocallimastixpatriciarumitbw5bytranscriptomicandsecretomicanalyses |