TABLE 3.
Cellulase and xylanase genes in F. succinogenes and F. intestinalis identified by reverse and forward SSH using genomic DNA from F. intestinalis and F. succinogenes, respectively, as the drivers
| FSU gene identification no. | Protein encoded by genea | Prior protein nameb (reference[s]) | F. succinogenes gene(s) showing similarity to an F. intestinalis genec | Gene unique to F. succinogenesd | F. intestinalis gene showing similarity to F. succinogenes genee | Non-Fibrobacter organism showing highest BLAST match scoref |
|---|---|---|---|---|---|---|
| 2622 | Cel16A | RSGB_633 | Bacillus circulans | |||
| 1893 | Cel45A | RSGB_423 | Cellvibrio japonicus | |||
| 1894 | Cel45B | RSGB_424 | Cellvibrio japonicus | |||
| 1947 | Cel45C | + | Cellvibrio japonicus | |||
| 0382 | Cel51A | CelF (22, 24) | RSGB_074 | + | Alicyclobacillus acidocaldarius | |
| 1685 | Cel5A | RSGB_380 | Cytophaga hutchinsonii | |||
| 2070 | Cel5C | CedA (13) | RSGB_476, RSGB_477 | Unidentified bacterium | ||
| 2290 | Cel5E | Cel5Kg | Saccharophagus degradans | |||
| 2534 | Cel5F | RSGB_612 | + | Orpinomyces joyonii | ||
| 2772 | Cel5G | Cel-3 (25) | RSGB_666, RSGB_667 | + | Cytophaga hutchinsonii | |
| 2914 | Cel5H | + | Orpinomyces joyonii | |||
| 1346 | Cel5K | CelG (14) | RSGB_289 | Saccharophagus degradans | ||
| 2866 | Cel74A | RSGB_694 | + | Cytophaga hutchinsonii | ||
| 1680 | Cel8A | + | Cytophaga hutchinsonii | |||
| 2303 | Cel8B | RSGB_549 | Cytophaga hutchinsonii | |||
| 3149 | Cel8C | RSGB_771 | + | Cytophaga hutchinsonii | ||
| 2013 | Cel9A | RSGB_459 | Xanthomonas axonopodis | |||
| 2361 | Cel9B | CelE (21, 32) | RSGB_564 | + | Pseudomonas sp. | |
| 2362 | Cel9C | CelDg (21) | Cytophaga hutchinsonii | |||
| 2558 | Cel9D | RSGB_618 | Vibrio parahaemolyticus | |||
| 2912 | Cel9E | RSGB_704,705 | Cytophaga hutchinsonii | |||
| 0134 | Cel9F | RSGB_018 | + | Bacillus pumilus | ||
| 0451 | Cel9G | EGBg (6) | Cytophaga hutchinsonii | |||
| 0809 | Cel9H | RSGB_149 | + | Clostridium cellulovorans | ||
| 0810 | Cel9I | RSGB_150, RSGB_151 | + | Acetivibrio cellulolyticus | ||
| 0257 | Cel10A | ClCBase (12) | RSGB_042 | Cytophaga hutchinsonii | ||
| 0226 | Lic16C | LicA (37) | + | Cytophaga hutchinsonii | ||
| 2181 | Man26B | RSGB_513 | + | Clostridium thermocellum | ||
| 1165 | Man26C | RSGB_231 | Piromyces sp. | |||
| 1166 | Man5B | RSGB_231 | Saccharophagus degradans | |||
| 2292 | Xyn10A | XynD (15) | RSGB_541 | Saccharophagus degradans | ||
| 2293 | Xyn10B | XynEg (15) | Cytophaga hutchinsonii | |||
| 2294 | Xyn10C | XynB (15) | RSGB_542 | Saccharophagus degradans | ||
| 2851 | Xyn10D | RSGB_686, RSGB_687 | Cytophaga hutchinsonii | |||
| 1195 | Xyn10F | RSGB_237 | + | Thermotoga neapolitana | ||
| 0777 | Xyn11C | XynCg (31) | Piromyces sp. | |||
| 2265 | Xyn30A | RSGB_532, RSGB_533 | Cytophaga hutchinsonii | |||
| 0206 | Xyn30B | RSGB_032 | Clostridium thermocellum | |||
| 1373 | Xyn39A | RSGB_298 | Clostridium acetobutylicum | |||
| 2263 | Xyn43B | RSGB_530 | Clostridium thermocellum | |||
| 2264 | Xyn43C | RSGB_531 | + | Clostridium thermocellum | ||
| 2520 | Xyn43G | RSGB_606 | Bacteroides thetaiotaomicron | |||
| 2622 | Xyn43J | + | Clostridium thermocellum | |||
| 0651 | Xyn8B | RSGB_123 | Cytophaga hutchinsonii | |||
| 0889 | Xyn8C | RSGB_172 | Cytophaga hutchinsonii |
The names of the genes as per the genome of F. succinogenes S85.
Previous names of the genes and references are provided where applicable.
Cellulase and xylanase genes identified in this study with F. succinogenes S85 as tester and F. intestinalis DR7 as driver that hybridized to DIG-labeled F. intestinalis genomic DNA under low-stringency conditions (hybridization at 37°C) but not under high-stringency conditions (hybridization at 60°C) in dot-Southern hybridization experiments. These genes are likely to be present in F. intestinalis but show low DNA sequence similarity to their counterparts in F. succinogenes. The clone names of the genes identified are shown.
Data are the same as described for column 4 in footnote c except that these genes did not hybridize to an F. intestinalis genomic DNA probe in either high- or low-stringency Southern blotting analysis, indicating they were absent from the genome of F. intestinalis DR7.
Cellulase and xylanase genes identified in F. intestinalis in the forward SSH experiment with F. intestinalis DR7 as tester and F. succinogenes S85 as driver (33). Although they had low similarity at the DNA sequence level, the amino acid sequences were quite similar to their counterparts in F. succinogenes.
The amino acid sequences encoded were used for BLAST searches of the NCBI nonredundant amino acid database; the non-Fibrobacter-genus organisms containing a glycoside hydrolase with the highest match score are listed.
These genes were not identified in either of the SSH experiments. However, they are included to give a complete list of the cellulase and xylanase genes reported to date.