Engineering new metabolic capabilities in bacteria: Lessons from recombinant cellulolytic strategies

Trends in Biotechnology

Volumn 30, Issue 2, 2012, Pages 111-119

  Mazzoli, Roberto ^a   Lamberti, Cristina ^a   Pessione, Enrica ^a  

^a UNIVERSITY OF TURIN   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

BIOREFINERIES; CELLULOSE WASTES; CONSOLIDATED BIOPROCESSING; EXTRACELLULAR PROTEINS; HEMICELLULASES; HETEROLOGOUS EXPRESSION; KEY FEATURE; METABOLIC CAPABILITIES; METABOLIC ENGINEERING; MOLECULAR TOOLS; MULTISTEP PROCESS; PRODUCT YIELDS; RECOMBINANT MICROORGANISM; SECRETED PROTEIN; SINGLE-STEP;

BIOCONVERSION; BIOMASS; FERMENTATION; METABOLISM; REFINING;

MICROORGANISMS;

CELLULASE; CELLULOSE; CELLULOSOME; MESSENGER RNA; POLYGALACTURONASE; XYLAN ENDO 1,3 BETA XYLOSIDASE;

BACILLUS SUBTILIS; BACTERIAL GENE; BACTERIAL METABOLISM; BIODEGRADATION; CELL SURFACE; CLOSTRIDIUM CELLULOLYTICUM; CLOSTRIDIUM THERMOCELLUM; CYTOLYSIS; ENZYME SPECIFICITY; ESCHERICHIA COLI; GENE EXPRESSION; HETEROLOGOUS EXPRESSION; LACTOBACILLUS ACIDOPHILUS; METABOLIC ENGINEERING; MICROBIAL BIOMASS; MOLECULAR MECHANICS; NONHUMAN; OPERON; PRIORITY JOURNAL; PROCESSING; PROMOTER REGION; PROTEIN SECRETION; REVIEW; RNA STABILITY; ZYMOMONAS MOBILIS;

BACTERIA; CELLULOSE; HYDROLYSIS; METABOLIC ENGINEERING; METABOLIC NETWORKS AND PATHWAYS;

BIOMASS; FERMENTATION; METABOLISM; MICROORGANISMS; REFINING;

BACTERIA (MICROORGANISMS);

EID: 84856081234     PISSN: 01677799     EISSN: 18793096     Source Type: Journal    
DOI: 10.1016/j.tibtech.2011.08.003     Document Type: Review

References (76)

1. Octave S., Thomas D. Biorefinery: toward an industrial metabolism. Biochimie 2009, 91:659-964.
2. Fitzpatrick M., et al. A biorefinery processing perspective: treatment of lignocellulosic materials for the production of value-added products. Bioresour. Technol. 2010, 101:8915-8922.
3. Tan T., et al. Current development of biorefinery in China. Biotechnol. Adv. 2010, 28:543-555.
4. Lynd L.R., et al. Consolidated bioprocessing of cellulosic biomass: an update. Curr. Opin. Biotechnol. 2005, 16:577-583.
5. Adrio J.L., Demain A.L. Recombinant organisms for production of industrial products. Bioeng. Bugs 2010, 1:116-131.
6. La Grange D.C., et al. Engineering cellulolytic ability into bioprocessing organisms. Appl. Microbiol. Biotechnol. 2010, 87:1195-1208.
7. Adsul M.G., et al. Development of biocatalysts for production of commodity chemicals from lignocellulosic biomass. Bioresour. Technol. 2011, 102:4304-4312.
8. Maki M., et al. The prospects of cellulase-producing bacteria for the bioconversion of lignocellulosic biomass. Int. J. Biol. Sci. 2009, 5:500-516.
9. Elkins J.G., et al. Engineered microbial systems for enhanced conversion of lignocellulosic biomass. Curr. Opin. Biotechnol. 2010, 21:657-662.
10. Moraïs S., et al. Cellulase-xylanase synergy in designer cellulosomes for enhanced degradation of a complex cellulosic substrate. MBio 2010, 1:e00285-e310.
11. Dressaire C., et al. Transcriptome and proteome exploration to model translation efficiency and protein stability in Lactococcus lactis. PLoS Comput. Biol. 2009, 5:e1000606.
12. Picard F., et al. Examination of post-transcriptional regulations in prokaryotes by integrative biology. C. R. Biol. 2009, 332:958-973.
13. Fredrick K., Ibba M. How the sequence of a gene can tune its translation. Cell 2010, 141:227-229.
14. Tyo K.E., et al. Toward design-based engineering of industrial microbes. Curr. Opin. Microbiol. 2010, 13:255-262.
15. Lynd L.R. Microbial cellulose utilization: fundamentals and biotechnology. Microbiol. Mol. Biol. Rev. 2002, 66:506-577.
16. Bayer E.A., et al. From cellulosomes to cellulosomics. Chem. Rec. 2008, 8:364-377.
17. Doi R.H. Cellulases of mesophilic microorganisms: cellulosome and noncellulosome producers. Ann. N. Y. Acad. Sci. 2008, 1125:267-279.
18. Dashtban M., et al. Fungal bioconversion of lignocellulosic residues; opportunities & perspectives. Int. J. Biol. Sci. 2009, 5:578-595.
19. Rincon M.T., et al. Abundance and diversity of dockerin-containing proteins in the fiber-degrading rumen bacterium, Ruminococcus flavefaciens FD-1. PLoS ONE 2010, 5:e12476.
20. Maamar H., et al. Transcriptional analysis of the cip-cel gene cluster from Clostridium cellulolyticum. J. Bacteriol. 2006, 188:2614-2624.
21. Newcomb M., et al. Co-transcription of the celC gene cluster in Clostridium thermocellum. Appl. Microbiol. Biotechnol. 2011, 90:625-634.
22. Nataf Y., et al. Clostridium thermocellum cellulosomal genes are regulated by extracytoplasmic polysaccharides via alternative sigma factors. Proc. Natl. Acad. Sci. U.S.A. 2010, 107:18646-18651.
23. De Mey M., et al. Promoter knock-in: a novel rational method for the fine tuning of genes. BMC Biotechnol. 2010, 10:26.
24. Arai T., et al. Synthesis of Clostridium cellulovorans minicellulosomes by intercellular complementation. Proc. Natl. Acad. Sci. U.S.A. 2007, 104:1456-1460.
25. Linger J.G., et al. Heterologous expression and extracellular secretion of cellulolytic enzymes by Zymomonas mobilis. Appl. Environ. Microbiol. 2010, 76:6360-6369.
26. Okano K., et al. D-lactic acid production from cellooligosaccharides and β-glucan using L-LDH gene-deficient and endoglucanase-secreting Lactobacillus plantarum. Appl. Microbiol. Biotechnol. 2010, 85:643-650.
27. Tsai S.L., et al. Surface display of a functional minicellulosome by intracellular complementation using a synthetic yeast consortium and its application to cellulose hydrolysis and ethanol production. Appl. Environ. Microbiol. 2010, 76:7514-7520.
28. Wieczorek A.S., Martin V.J. Engineering the cell surface display of cohesins for assembly of cellulosome-inspired enzyme complexes on Lactococcus lactis. Microb. Cell Fact. 2010, 9:69.
29. Mingardon F., et al. The issue of secretion in heterologous expression of Clostridium cellulolyticum cellulase-encoding genes in Clostridium acetobutylicum ATCC 824. Appl. Environ. Microbiol. 2011, 77:2831-2838.
30. Mingardon F., et al. Heterologous production, assembly, and secretion of a minicellulosome by Clostridium acetobutylicum ATCC 824. Appl. Environ. Microbiol. 2005, 71:1215-1222.
31. Jeon E., et al. Cellulosic alcoholic fermentation using recombinant Saccharomyces cerevisiae engineered for the production of Clostridium cellulovorans endoglucanase and Saccharomycopsis fibuligera β-glucosidase. FEMS Microbiol. Lett. 2009, 301:130-136.
32. Ozkose E., et al. Expression of fungal cellulase gene in Lactococcus lactis to construct novel recombinant silage inoculants. Folia Microbiol. (Praha) 2009, 54:335-342.
33. Wen F., et al. Yeast surface display of trifunctional minicellulosomes for simultaneous saccharification and fermentation of cellulose to ethanol. Appl. Environ. Microbiol. 2010, 76:1251-1260.
34. Lu T.K., et al. Next-generation synthetic gene networks. Nat. Biotechnol. 2009, 27:1139-1150.
35. Narita J., et al. Improvement of protein production in lactic acid bacteria using 5'-untranslated leader sequence of slpA from Lactobacillus acidophilus. Improvement in protein production using UTLS. Appl. Microbiol. Biotechnol. 2006, 73:366-373.
36. Yeh C.M., et al. Extracellular expression of a functional recombinant Ganoderma lucidium immunomodulatory protein by Bacillus subtilis and Lactococcus lactis. Appl. Environ. Microbiol. 2008, 74:1039-1049.
37. Daguer J.P., et al. Increasing the stability of sacB transcript improves levansucrase production in Bacillus subtilis. Lett. Appl. Microbiol. 2005, 41:221-226.
38. Komarova A.V., et al. AU-rich sequences within 5' untranslated leaders enhance translation and stabilize mRNA in Escherichia coli. J. Bacteriol. 2005, 187:1344-1349.
39. Lightfield J., et al. Across bacterial phyla, distantly-related genomes with similar genomic GC content have similar patterns of amino acid usage. PLoS ONE 2011, 6:e17677.
40. Talarico L.A., et al. Construction and expression of an ethanol production operon in Gram-positive bacteria. Microbiology 2005, 151:4023-4031.
41. Talarico L.A., et al. Production of the Gram-positive Sarcina ventriculi pyruvate decarboxylase in Escherichia coli. Microbiology 2001, 147:2425-2435.
42. Raj K.C., et al. Cloning and characterization of the Zymobacter palmae pyruvate decarboxylase (pdc): comparison to bacterial homologues. Appl. Environ. Microbiol. 2002, 68:2869-2876.
43. Du Plessis L., et al. Exploring improved endoglucanase expression in Saccharomyces cerevisiae strains. Appl. Microbiol. Biotechnol. 2010, 86:1503-1511.
44. Angov E., et al. Adjustment of codon usage frequencies by codon harmonization improves protein expression and folding. Methods Mol. Biol. 2011, 705:1-13.
45. Camps M. Modulation of ColE1-like plasmid replication for recombinant gene expression. Recent Pat. DNA Gene Seq. 2010, 4:58-73.
46. Cho H.Y., et al. Production of minicellulosomes from Clostridium cellulovorans in Bacillus subtilis WB800. Appl. Environ. Microbiol. 2004, 70:5704-5707.
47. Blouzard J.C., et al. Modulation of cellulosome composition in Clostridium cellulolyticum: adaptation to the polysaccharide environment revealed by proteomic and carbohydrate-active enzyme analyses. Proteomics 2010, 10:541-554.
48. Cho W., et al. Cellulosomic profiling produced by Clostridium cellulovorans during growth on different carbon sources explored by the cohesin marker. J. Biotechnol. 2010, 145:233-239.
49. Lochner A., et al. Label-free quantitative proteomics distinguish the secreted cellulolytic systems of Caldicellulosiruptor bescii and Caldicellulosiruptor obsidiansis. Appl. Environ. Microbiol. 2011, 77:4042-4054.
50. Vanfossen A.L., et al. Glycoside hydrolase inventory drives plant polysaccharide deconstruction by the extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus. Biotechnol. Bioeng. 2011, 108:1559-1569.
51. Mingardon F., et al. Exploration of new geometries in cellulosome-like chimeras. Appl. Environ. Microbiol. 2007, 73:7138-7149.
52. Wilson D.B. Cellulases and biofuels. Curr. Opin. Biotechnol. 2009, 20:295-299.
53. Bayer E.A., et al. The potential of cellulases and cellulosomes for cellulosic waste management. Curr. Opin. Biotechnol. 2007, 18:237-245.
54. Sabathé F., Soucaille P. Characterization of the CipA scaffolding protein and in vivo production of a minicellulosome in Clostridium acetobutylicum. J. Bacteriol. 2003, 185:1092-1096.
55. Perret S., et al. Production of heterologous and chimeric scaffoldins by Clostridium acetobutylicum ATCC 824. J. Bacteriol. 2004, 186:253-257.
56. Morello E., et al. Lactococcus lactis, an efficient cell factory for recombinant protein production and secretion. J. Mol. Microbiol. Biotechnol. 2008, 14:48-58.
57. Zweers J.C., et al. Towards the development of Bacillus subtilis as a cell factory for membrane proteins and protein complexes. Microb. Cell Fact. 2008, 7:10.
58. Jong W.S., et al. Extracellular production of recombinant proteins using bacterial autotransporters. Curr. Opin. Biotechnol. 2010, 21:646-652.
59. Desvaux M., et al. Secretion and subcellular localizations of bacterial proteins: a semantic awareness issue. Trends Microbiol. 2009, 17:139-145.
60. Pohl S., Harwood C.R. Heterologous protein secretion by Bacillus species from the cradle to the grave. Adv. Appl. Microbiol. 2010, 73:1-25.
61. Chanal A., et al. Scaffoldin modules can serve as " cargo" domains to promote the secretion of heterologous cellulosomal cellulases by Clostridium acetobutylicum. Appl. Environ. Microbiol. 2011, 77:6277-6280.
62. Bomble Y.J., et al. Modeling the self-assembly of the cellulosome enzyme complex. J. Biol. Chem. 2011, 286:5614-5623.
63. Jose J., Meyer F. The autodisplay story, from discovery to biotechnical and biomedical applications. Microbiol. Mol. Biol. Rev. 2007, 71:600-619.
64. Desvaux M., et al. Protein cell surface display in Gram-positive bacteria: from single protein to macromolecular protein structure. FEMS Microbiol. Lett. 2006, 256:1-15.
65. Lilly M., et al. Heterologous expression of a Clostridium minicellulosome in Saccharomyces cerevisiae. FEMS Yeast Res. 2009, 9:1236-1249.
66. Anderson T.D., et al. Assembly of minicellulosomes on the surface of Bacillus subtilis. Appl. Environ. Microbiol. 2011, 77:4849-4858.
67. Okano K., et al. System using tandem repeats of the cA peptidoglycan-binding domain from Lactococcus lactis for display of both N- and C-terminal fusions on cell surfaces of lactic acid bacteria. Appl. Environ. Microbiol. 2008, 74:1117-1123.
68. Xu Q., et al. The cellulosome system of Acetivibrio cellulolyticus includes a novel type of adaptor protein and a cell surface anchoring protein. J. Bacteriol. 2003, 185:4548-4557.
69. Xu Q., et al. Architecture of the Bacteroides cellulosolvens cellulosome: description of a cell surface-anchoring scaffoldin and a family 48 cellulase. J. Bacteriol. 2004, 186:968-977.
70. Demain A.L., et al. Cellulase, clostridia, and ethanol. Microbiol. Mol. Biol. Rev. 2005, 69:124-154.
71. Weimer P.J., et al. Studies of the extracellular glycocalyx of the anaerobic cellulolytic bacterium Ruminococcus albus. Appl. Environ. Microbiol. 2006, 72:7559-7566.
72. Desvaux M. Unravelling carbon metabolism in anaerobic cellulolytic bacteria. Biotechnol. Prog. 2006, 22:1229-1238.
73. Meynial Salles I., et al. Evolution of a Saccharomyces cerevisiae metabolic pathway in Escherichia coli. Metab. Eng. 2007, 9:152-159.
74. Wilson D.B. Microbial diversity of cellulose hydrolysis. Curr. Opin. Microbiol. 2011, 14:259-263.
75. Harwood C.R., Cranenburgh R. Bacillus protein secretion: an unfolding story. Trends Microbiol. 2008, 16:73-79.
76. Hendrickx A.P., et al. Architects at the bacterial surface - sortases and the assembly of pili with isopeptide bonds. Nat. Rev. Microbiol. 2011, 9:166-176.