Citation: | YANG Xin, QIN Lina, JIANG Xianzhang. Analysis of Codon Usage Bias in the Genome of Trichoderma reesei[J]. Science and Technology of Food Industry, 2022, 43(6): 141−149. (in Chinese with English abstract). doi: 10.13386/j.issn1002-0306.2021110338. |
[1] |
KEMURA T. Codon usage and tRNA content in unicellular and multicellular organisms[J]. Molecular Biology and Evolution,1985,2:13−34.
|
[2] |
DAS S, ROYMONDAL U, SAHOO S. Analyzing gene expression from relative codon usage bias in yeast genome: A statistical significance and biological relevance[J]. Gene,2009,443(1-2):121−31. doi: 10.1016/j.gene.2009.04.022
|
[3] |
MORIYAMA E N. Codon usage bias and tRNA Abundance in Drosophila[J]. Journal of Molecular Evolution,1997,45(5):514−523. doi: 10.1007/PL00006256
|
[4] |
DURET L, MOUCHIROUD D. Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, and Arabidopsis[J]. Proceedings of the National Academy of Sciences of the United States of America,1999,96(8):4482−4487. doi: 10.1073/pnas.96.8.4482
|
[5] |
MORIYAMA E. Gene length and codon usage bias in Drosophila melanogaster, Saccharomyces cerevisiae and Escherichia coli[J]. Nucleic Acids Research,1998,26(19):3188.
|
[6] |
GUPTA S K, MAJUMDAR S, BHATTACHARYA T K, et al. Studies on the relationships between the synonymous codon usage and protein secondary structural units[J]. Biochemical and Biophysical Research Communications,2000,269(3):692−696. doi: 10.1006/bbrc.2000.2351
|
[7] |
SHARP P M, BAILES E, GROCOCK R J, et al. Variation in the strength of selected codon usage bias among bacteria[J]. Nucleic Acids Resarch,2005,33(4):1141−1153. doi: 10.1093/nar/gki242
|
[8] |
SHARP P M, TUOHY T M, MOSURSKI K R. Codon usage in yeast: Cluster analysis clearly differentiates highly and lowly expressed genes[J]. Nucleic Acids Resarch,1986,14(13):5125−5143. doi: 10.1093/nar/14.13.5125
|
[9] |
ZHOU T, SUN X, LU Z. Synonymous codon usage in environmental chlamydia UWE25 reflects an evolutional divergence from pathogenic chlamydiae[J]. Gene,2006,368:117−125. doi: 10.1016/j.gene.2005.10.035
|
[10] |
CHIAPELLO H, LISACEK F, CABOCHE M, et al. Codon usage and gene function are related in sequences of Arabidopsis thaliana[J]. Gene,1998,209(1):1−38.
|
[11] |
SHARP P M, ELIZABETH C, HIGGINS D G, et al. Codon usage patterns in Escherichia coli, Bacillus subtilis, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Drosophila melanogaster and Homo sapiens; a review of the considerable within-species diversity[J]. Nucleic Acids Resarch,1988,16(17):8207−8211. doi: 10.1093/nar/16.17.8207
|
[12] |
BISCHOF R H, RAMONI J, SEIBOTH B. Cellulases and beyond: the first 70 years of the enzyme producer Trichoderma reesei[J]. Microbial Cell Factories,2016,15(1):106. doi: 10.1186/s12934-016-0507-6
|
[13] |
ZIELIŃSKA D, SZENTNER K, WAśKIEWICZ A, et al. Production of nanocellulose by enzymatic treatment for application in polymer composites[J]. Materials,2021,14(9):2124. doi: 10.3390/ma14092124
|
[14] |
KUMAR M R, KUMARAN M D, BALASHANMUGAM P. Production of cellulase enzyme by Trichoderma reesei Cefl9 and its application in the production of bio-ethanol[J]. Pakistan Journal of Pharmaceutical Sciences,2014,17(5):735−739.
|
[15] |
PEIL S, BECKERS S J, FISCHER J, et al. Biodegradable, lignin-based encapsulation enables delivery of Trichoderma reesei with programmed enzymatic release against grapevine trunk diseases[J]. Materials Today Bio,2020,7:100061. doi: 10.1016/j.mtbio.2020.100061
|
[16] |
LICHTENBERG J, PEREZ C E, MADSEN K, et al. Safety evaluation of a novel muramidase for feed application[J]. Regulatory Toxicology and Pharmacology,2017,89:57−69. doi: 10.1016/j.yrtph.2017.07.014
|
[17] |
LANDOWSKI C P, HUUSKONEN A, WAHL R, et al. Enabling low cost biopharmaceuticals: a systematic approach to delete proteases from a well-known protein production host Trichoderma reesei[J]. PLoS One,2015,10(8):e0134723. doi: 10.1371/journal.pone.0134723
|
[18] |
SALOHEIMO M, CULLEN D, MARTINEZ D, et al. Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina)[J]. Nature Biotechnology,2008,26(5):553−560. doi: 10.1038/nbt1403
|
[19] |
MICHAEL S. ROSENBERG M S, SUBRAMANIAN S, KUMAR S. Patterns of transitional mutation biases within and among mammalian genomes[J]. Molecular Biology and Evolution,2003,20(6):988−993. doi: 10.1093/molbev/msg113
|
[20] |
SUEOKA N. Directional mutation pressure and neutral molecular evolution[J]. Proceedings of the National Academy of Sciences,1988,85:2653−2657. doi: 10.1073/pnas.85.8.2653
|
[21] |
WRIGHT F. The 'effective number of codons' used in a gene[J]. Gene,1990,87(1):23−29. doi: 10.1016/0378-1119(90)90491-9
|
[22] |
LIU H, RUI H, ZHANG H, et al. Analysis of synonymous codon usage in Zea mays[J]. Molecular Biology Reports,2010,37(2):677−684. doi: 10.1007/s11033-009-9521-7
|
[23] |
SUEOKA N. Near homogeneity of PR2-bias fingerprints in the human genome and their implications in phylogenetic analyses[J]. Journal of Molecular Evolution,2001,53(4-5):469−476. doi: 10.1007/s002390010237
|
[24] |
FUGLSANG A. The 'effective number of codons' revisited[J]. Biochemical and Biophysical Research Communications,2004,317(3):957−964. doi: 10.1016/j.bbrc.2004.03.138
|
[25] |
刘庆坡, 薛庆中. 粳稻叶绿体基因组的密码子用法[J]. 作物学报, 2004, 30(12): 1220-1224.
LIU Q P, XUE Q Z. Codon usage in the chloroplast genome of rice (Oryza sativa L. ssp. japonica)[J]. Acta Agronomica Sinica, 2004, 30(12); 1220-1224.
|
[26] |
ZHANG W J, JIE Z, LI Z F, et al. Comparative analysis of codon usage patterns among mitochondrion, chloroplast and nuclear Genes in Triticum aestivum L[J]. Journal of Integrative Plant Biology,2007,49(2):246−254. doi: 10.1111/j.1744-7909.2007.00404.x
|
[27] |
范三红, 郭蔼光, 单丽伟, 等. 拟南芥基因密码子偏爱性分析[J]. 生物化学与生物物理进展,2003,30(2):221−225. [FAN S H, GUO A G, SHAN L W, et al. Analysis of genetic code preference in Arabidopsis thaliana[J]. Progress in Biochemistry and Biophysics,2003,30(2):221−225. doi: 10.3321/j.issn:1000-3282.2003.02.012
|
[28] |
JENKINS G M, HOLMES E C. The extent of codon usage bias in human RNA viruses and its evolutionary origin[J]. Virus Research,2003,92(1):1−7. doi: 10.1016/S0168-1702(02)00309-X
|
[29] |
SUEOKA N. Translation-coupled violation of Parity Rule 2 in human genes is not the cause of heterogeneity of the DNA G+C content of third codon position[J]. Gene,1999,238(1):53−58. doi: 10.1016/S0378-1119(99)00320-0
|
[30] |
GUSTAFSSON C, GOVINDARAJAN S, MINSHULL J. Codon bias and heterologous protein expression[J]. Trends is Biotechnology,2004,22(7):346−53. doi: 10.1016/j.tibtech.2004.04.006
|
[31] |
CHERRY J R, FIDANSTSEF A L. Directed evolution of industrial enzymes: an update[J]. Current Opinion in Biotechnology,2003,14(4):438−443. doi: 10.1016/S0958-1669(03)00099-5
|
[32] |
VISSER H, JOOSTEN V, PUNT P J, et al. Development of a mature fungal technology and production platform for industrial enzymes based on a Myceliophthora thermophila isolate, previously known as Chrysosporium lucknowense C1[J]. Industrial Biotechnology,2011,7(3):214−223. doi: 10.1089/ind.2011.7.214
|
[33] |
NOVEMBRE J A. Accounting for background nucleotide composition when measuring codon usage bias[J]. Molecular Biology and Evolution,2002(8):1390.
|
[34] |
SUN F F, BAI R, YANG H, et al. Heterologous expression of codon optimized Trichoderma reesei Cel6A in Pichia pastoris[J]. Enzyme and Microbial Technology,2016,92:107−116. doi: 10.1016/j.enzmictec.2016.07.004
|
[35] |
白仁惠, 张云博, 王春迪, 等. 里氏木霉Cel5A基因优化及其在毕赤酵母中的高效表达[J]. 生物工程学报,2016,32(10):1381−1394. [BAI R H, ZHANG Y B, WANG C D, et al. Gene optimization and efficient expression of Trichoderma reesei Cel5A in Pichia pastoris[J]. Chinese Journal of Biotechnology,2016,32(10):1381−1394.
|
[36] |
XIONG Y, WU V W, LUBBE A, et al. A fungal transcription factor essential for starch degradation affects integration of carbon and nitrogen metabolism[J]. PLoS Genetics,2017,13(5):e1006737. doi: 10.1371/journal.pgen.1006737
|
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