Bacterial genomes: what they teach us about cellulose degradation

Figures & data

Figure 1.  Structural organization of cellulose from individual molecules to crystal, microfibrils, plant cell walls and finally whole plants.

Reproduced from [106].

Figure 2.  Shotgun cloning strategy for isolating cellulases from a genome.

DNA is prepared, sheared, ligated into a vector, screened for positive colonies, and then the protein is expressed and characterized.

Figure 3.  Potential mechanism of cellulose hydrolysis by Cellvibrio japonicus.

(A) A GH45 decrystallization of cellulose; (B) nicking of decrystallized cellulose; and (C) degradation of nicked chains.

CBM: Carbohydrate binding modules; GH: Glycosyl hydrolase.

Figure 4.  Potential mechanism for decrystallization and cellulose hydrolysis by Clostridium thermocellum.

Figure 5.  Potential mechanism for decrystallization and cellulose hydrolysis by Fibrobacter succinogenes, Cytophaga hutchinsonii and Sorangium cellulosum.

(A) Binding of cellulose to outer membrane; (B) abstraction of a single cellulose chain; (C) translocation of chain through outer membrane pore; and (D) cleavage of chain in periplasm and transport of oligosaccharides through inner membrane. Based on alginate transport and utilization model [85].

Table 1.  Potential cellulases of Gram-positive organisms.

Organism	GH5	GH6	GH9	GH12	GH48	With CBM	Desc.
Soluble cellulases only – aerobic Gram-positives
Sfla	4	2	1	2	1	6/10	Supplementary Table A
Sacte	3	1	1	1	1	6/7	Supplementary Table B
Acel	2	2	2	2	1	7/8	Supplementary Table C
Celfi	3	3	5	0	1	10/12	Supplementary Table D
Cfla	3	3	5	0	1	11/12	Supplementary Table E
Celgi	2	4	2	0	1	6/9	Supplementary Table F
Soluble cellulases only – anaerobic Gram-positives
Csac	6		2	0	1	6/9	Supplementary Table G
Calkro	6		2	0	3	10/12	Supplementary Table H

Acel: Acidothermus cellulolyticus 11B ATCC 43068™; Calkro: Caldicellulosiruptor kronotskyensis 2002; CBM: Carbohydrate binding modules; Celfi: Cellulomonas fimi ATCC 484™; Celgi: Cellulomonas gilvus ATCC 13127™; Cfla: Cellulomonas flavigena DSM 20109™; Csac: Caldicellulosiruptor saccharolyticus DSM 8903™; Desc.: Detailed description of potential cellulase genes inSupplementary Material; GH: Glycoside hydrolases; Sacte: Streptomyces sp. SirexAA-E; Sfla: Streptomyces flavogriseus ATCC 33331™.

Table 2.  Cellulases of Clostridiaceae.

Organism	GH5	GH6	GH8	GH9	GH12	GH48	With CBM	Desc.
Cellulosomal Gram-positives
Cphy	3		1	1	1	1	3/7	Supplementary Table I
Cthe	9		1	16	0	2	16/28	Supplementary Table J
Clocel	14		1	12	0	1	19/27	Supplementary Table K
Rumal	13		1	8	0	1	15/23	Supplementary Table L

CBM: Carbohydrate binding modules; Clocel: Clostridium cellulovorans 743B; Cphy: Clostridium phytofermentans ISDg; Cthe: Clostridium thermocellum ATCC 27405™; Desc.: Detailed description of individual cellulase genes; GH: Glycoside hydrolases; Rumal: Ruminococcus albus 7.

Table 3.  Cellulases of Gram-negative organisms.

Organism	GH5	GH6	GH8	GH9	GH12	GH45	GH51	With CBM	Desc.
Aerobic Gram-negatives
CHU	5		6	7	0	0	0	0/18	Supplementary Table P
Anaerobic Gram-negatives
Fisuc	12		6	9	0	4	1	2/33	Supplementary Table N
Sce	9	1	3	2	1	0	0	0/16	Supplementary Table O

CBM: Carbohydrate binding modules; CHU: Cytophaga hutchinsonii ATCC 33406™; Desc.: Detailed description of individual cellulase genes in Supplementary Material; Fisuc: Fibrobacter succinogenes subsp. succinogenes S85; GH: Glycoside hydrolases; Sce: Sorangium cellulosum ‘So ce 56’.

US Department of Energy. Genomic science program. http://genomicscience.energy.gov

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Hashimoto W, He J, Wada Y et al. Proteomics-based identification of outer-membrane proteins responsible for import of macromolecules in Sphingomonas sp. A1: alginate-binding flagellin on the cell surface. Biochemistry44,13783–13794 (2005).

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