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PlantCAZyme
Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0564

PubMed

18996345, Cell Host Microbe. 2008 Nov 13;4(5):447-57. doi: 10.1016/j.chom.2008.09.007.
22205877, PLoS Biol. 2011 Dec;9(12):e1001221. doi: 10.1371/journal.pbio.1001221. Epub 2011 Dec 20.

Characterization method

microarray,qPCR

Genomic accession number

AE015928.1

Nucelotide position range

5441391-5517337

Substrate

rhamnogalacturonan

Loci

BT4145-BT4183

Species

Bacteroides thetaiotaomicron/818

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- BT_4145 AAO79250.1 0 - 2775 (-) AE015928.1:5441391-5444166 -
- BT_4146 AAO79251.1 2774 - 4178 (-) AE015928.1:5444165-5445569 -
- BT_4147 AAO79252.1 4267 - 4858 (-) AE015928.1:5445658-5446249 -
- BT_4148 AAO79253.1 4808 - 5024 (-) AE015928.1:5446199-5446415 -
- BT_4149 AAO79254.1 5269 - 6328 (-) AE015928.1:5446660-5447719 -
- BT_4150 AAO79255.1 6352 - 7591 (-) AE015928.1:5447743-5448982 -
- BT_4151 AAO79256.1 7608 - 10485 (-) AE015928.1:5448999-5451876 -
- BT_4152 AAO79257.1 10748 - 13709 (+) AE015928.1:5452139-5455100 -
- BT_4153 AAO79258.1 13752 - 15051 (+) AE015928.1:5455143-5456442 -
- BT_4154 AAO79259.1 15063 - 16032 (+) AE015928.1:5456454-5457423 -
- BT_4155 AAO79260.1 16098 - 17445 (+) AE015928.1:5457489-5458836 -
- BT_4156 AAO79261.1 17569 - 20455 (-) AE015928.1:5458960-5461846 -
- BT_4157 AAO79262.1 20479 - 22300 (-) AE015928.1:5461870-5463691 -
- BT_4158 AAO79263.1 22306 - 22999 (+) AE015928.1:5463697-5464390 -
- BT_4159 AAO79264.1 23269 - 24901 (+) AE015928.1:5464660-5466292 -
- BT_4160 AAO79265.1 24929 - 27026 (+) AE015928.1:5466320-5468417 -
- BT_4161 AAO79266.1 27164 - 27767 (-) AE015928.1:5468555-5469158 -
- BT_4162 AAO79267.1 28179 - 30258 (+) AE015928.1:5469570-5471649 -
- BT_4163 AAO79268.1 30897 - 33150 (+) AE015928.1:5472288-5474541 -
- BT_4164 AAO79269.1 33168 - 36435 (+) AE015928.1:5474559-5477826 -
- BT_4165 AAO79270.1 36474 - 38034 (+) AE015928.1:5477865-5479425 -
- BT_4166 AAO79271.1 38042 - 39788 (+) AE015928.1:5479433-5481179 -
- BT_4167 AAO79272.1 39793 - 41536 (+) AE015928.1:5481184-5482927 -
- BT_4168 AAO79273.1 41552 - 44705 (+) AE015928.1:5482943-5486096 -
- BT_4169 AAO79274.1 44710 - 46462 (+) AE015928.1:5486101-5487853 -
- BT_4170 AAO79275.1 46494 - 48102 (+) AE015928.1:5487885-5489493 -
- BT_4171 AAO79276.1 48123 - 48777 (+) AE015928.1:5489514-5490168 -
- BT_4172 AAO79277.1 49029 - 52326 (+) AE015928.1:5490420-5493717 -
- BT_4173 AAO79278.1 52404 - 53979 (-) AE015928.1:5493795-5495370 -
- BT_4174 AAO79279.1 54039 - 55200 (-) AE015928.1:5495430-5496591 -
- BT_4175 AAO79280.1 55466 - 57308 (+) AE015928.1:5496857-5498699 -
- BT_4176 AAO79281.1 57311 - 58709 (+) AE015928.1:5498702-5500100 -
- BT_4177 AAO79282.1 58739 - 59054 (+) AE015928.1:5500130-5500445 -
- BT_4178 AAO79283.1 59196 - 63498 (+) AE015928.1:5500587-5504889 -
- BT_4179 AAO79284.1 63807 - 65433 (+) AE015928.1:5505198-5506824 -
- BT_4180 AAO79285.1 65480 - 66284 (+) AE015928.1:5506871-5507675 -
- BT_4181 AAO79286.1 66936 - 69906 (-) AE015928.1:5508327-5511297 -
- BT_4182 AAO79287.1 69993 - 74289 (-) AE015928.1:5511384-5515680 -
- BT_4183 AAO79288.1 74633 - 75947 (+) AE015928.1:5516024-5517338 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 2775 (-) CAZyme: GH106 Yes
- 2775 - 4178 (-) CAZyme: GH28 Yes
- 4268 - 4858 (-) other Yes
- 4809 - 5024 (-) other Yes
- 5270 - 6328 (-) CAZyme: GH28 Yes
- 6353 - 7591 (-) CAZyme: CE12 Yes
- 7609 - 10485 (-) CAZyme: GH2 Yes
- 10749 - 13709 (+) CAZyme: GH43|GH43_18|GH42 Yes
- 13753 - 15051 (+) CAZyme: GH28 Yes
- 15064 - 16032 (+) CAZyme: CE4|CE0 Yes
- 16099 - 17445 (+) CAZyme: GH28 Yes
- 17570 - 20455 (-) CAZyme: GH2 Yes
- 20480 - 22300 (-) CAZyme: GH27|CBM35 Yes
- 22307 - 22999 (+) other Yes
- 23270 - 24901 (+) other Yes
- 24930 - 27026 (+) CAZyme: GH35 Yes
- 27165 - 27767 (-) other Yes
- 28180 - 30258 (+) other Yes
- 30898 - 33150 (+) other Yes
- 33169 - 36435 (+) TC: gnl|TC-DB|Q45780|1.B.14.6.1 Yes
- 36475 - 38034 (+) TC: gnl|TC-DB|Q5LEN2|8.A.46.1.4 Yes
- 38043 - 39788 (+) other Yes
- 39794 - 41536 (+) other Yes
- 41553 - 44705 (+) TC: gnl|TC-DB|Q93TH9|1.B.14.6.2 Yes
- 44711 - 46462 (+) other Yes
- 46495 - 48102 (+) CAZyme: PL9|PL9_1 Yes
- 48124 - 48777 (+) other Yes
- 49030 - 52326 (+) CAZyme: PL26 Yes
- 52405 - 53979 (-) CAZyme: CE12 Yes
- 54040 - 55200 (-) CAZyme: GH105 Yes
- 55467 - 57308 (+) CAZyme: PL11|PL11_1 Yes
- 57312 - 58709 (+) CAZyme: GH105 Yes
- 58740 - 59054 (+) other Yes
- 59197 - 63498 (+) TF: DBD-Pfam|HTH_AraC,DBD-Pfam|HTH_AraC,DBD-SUPERFAMILY|0036286 Yes
- 63808 - 65433 (+) CAZyme: CE4|CE0 Yes
- 65481 - 66284 (+) CAZyme: CE6 Yes
- 66937 - 69906 (-) CAZyme: GH2 Yes
- 69994 - 74289 (-) TF: DBD-Pfam|HTH_AraC,DBD-SUPERFAMILY|0035607 Yes
- 74634 - 75947 (+) CAZyme: PL9_1 Yes

PUL ID

PUL0564

PubMed

18996345, Cell Host Microbe. 2008 Nov 13;4(5):447-57. doi: 10.1016/j.chom.2008.09.007.

Title

Mucosal glycan foraging enhances fitness and transmission of a saccharolytic human gut bacterial symbiont.

Author

Martens EC, Chiang HC, Gordon JI

Abstract

The distal human gut is a microbial bioreactor that digests complex carbohydrates. The strategies evolved by gut microbes to sense and process diverse glycans have important implications for the assembly and operation of this ecosystem. The human gut-derived bacterium Bacteroides thetaiotaomicron forages on both host and dietary glycans. Its ability to target these substrates resides in 88 polysaccharide utilization loci (PULs), encompassing 18% of its genome. Whole genome transcriptional profiling and genetic tests were used to define the mechanisms underlying host glycan foraging in vivo and in vitro. PULs that target all major classes of host glycans were identified. However, mucin O-glycans are the principal host substrate foraged in vivo. Simultaneous deletion of five genes encoding ECF-sigma transcription factors, which activate mucin O-glycan utilization, produces defects in bacterial persistence in the gut and in mother-to-offspring transmission. Thus, PUL-mediated glycan catabolism is an important component in gut colonization and may impact microbiota ecology.

PubMed

22205877, PLoS Biol. 2011 Dec;9(12):e1001221. doi: 10.1371/journal.pbio.1001221. Epub 2011 Dec 20.

Title

Recognition and degradation of plant cell wall polysaccharides by two human gut symbionts.

Author

Martens EC, Lowe EC, Chiang H, Pudlo NA, Wu M, McNulty NP, Abbott DW, Henrissat B, Gilbert HJ, Bolam DN, Gordon JI

Abstract

Symbiotic bacteria inhabiting the human gut have evolved under intense pressure to utilize complex carbohydrates, primarily plant cell wall glycans in our diets. These polysaccharides are not digested by human enzymes, but are processed to absorbable short chain fatty acids by gut bacteria. The Bacteroidetes, one of two dominant bacterial phyla in the adult gut, possess broad glycan-degrading abilities. These species use a series of membrane protein complexes, termed Sus-like systems, for catabolism of many complex carbohydrates. However, the role of these systems in degrading the chemically diverse repertoire of plant cell wall glycans remains unknown. Here we show that two closely related human gut Bacteroides, B. thetaiotaomicron and B. ovatus, are capable of utilizing nearly all of the major plant and host glycans, including rhamnogalacturonan II, a highly complex polymer thought to be recalcitrant to microbial degradation. Transcriptional profiling and gene inactivation experiments revealed the identity and specificity of the polysaccharide utilization loci (PULs) that encode individual Sus-like systems that target various plant polysaccharides. Comparative genomic analysis indicated that B. ovatus possesses several unique PULs that enable degradation of hemicellulosic polysaccharides, a phenotype absent from B. thetaiotaomicron. In contrast, the B. thetaiotaomicron genome has been shaped by increased numbers of PULs involved in metabolism of host mucin O-glycans, a phenotype that is undetectable in B. ovatus. Binding studies of the purified sensor domains of PUL-associated hybrid two-component systems in conjunction with transcriptional analyses demonstrate that complex oligosaccharides provide the regulatory cues that induce PUL activation and that each PUL is highly specific for a defined cell wall polymer. These results provide a view of how these species have diverged into different carbohydrate niches by evolving genes that target unique suites of available polysaccharides, a theme that likely applies to disparate bacteria from the gut and other habitats.