Because CGCFinder predicted no CGC for this PUL, the gene cluster depicted below contains dbCAN2 and CGC signature predictions for all genes in the PUL, instead of a predicted CGC.


PUL ID

PUL0605

PubMed

33101261, Front Microbiol. 2020 Sep 25;11:588099. doi: 10.3389/fmicb.2020.588099. eCollection 2020.
21029047, Biochem J. 2011 Jan 1;433(1):107-17. doi: 10.1042/BJ20101186.

Characterization method

RT-PCR, gene deletion mutant and growth assay

Genomic accession number

CP025268.1

Nucelotide position range

3564821-3574189

Substrate

glycogen

Loci

CXP41_18685-CXP41_18705

Species

Escherichia coli/562

Degradation or Biosynthesis

biosynthesis

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- CXP41_18685 AUG18131.1 0 - 2448 (-) CP025268.1:3564821-3567269 -
- CXP41_18690 AUG18132.1 2466 - 3900 (-) CP025268.1:3567287-3568721 -
glgC CXP41_18695 AUG18133.1 3899 - 5195 (-) CP025268.1:3568720-3570016 -
- CXP41_18700 AUG18134.1 5212 - 7186 (-) CP025268.1:3570033-3572007 -
- CXP41_18705 AUG18135.1 7182 - 9369 (-) CP025268.1:3572003-3574190 -

Cluster number

0

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 2448 (-) CAZyme: GT35 No
- 2467 - 3900 (-) CAZyme: GT5 No
- 3900 - 5195 (-) CDS No
- 5213 - 7186 (-) CAZyme: GH13|GH13_11|CBM48|GH77 No
- 7183 - 9369 (-) CAZyme: GH13|GH13_9|CBM48 No

PUL ID

PUL0605

PubMed

33101261, Front Microbiol. 2020 Sep 25;11:588099. doi: 10.3389/fmicb.2020.588099. eCollection 2020.

Title

Glycogen Metabolism Impairment via Single Gene Mutation in the glgBXCAP Operon Alters the Survival Rate of Escherichia coli Under Various Environmental Stresses.

Author

Wang M, Liu Q, Kang X, Zhu Z, Yang H, Xi X, Zhang X, Du Y, Guo M, Tang D, Wang L

Abstract

Glycogen is a highly branched polysaccharide that is widely present in all life domains. It has been identified in many bacterial species and functions as an important energy storage compound. In addition, it plays important roles in bacterial transmission, pathogenicity, and environmental viability. There are five essential enzymes (coding genes) directly involved in bacterial glycogen metabolism, which forms a single operon glgBXCAP with a suboperonic promoter in glgC gene in Escherichia coli. Currently, there is no comparative study of how the disruptions of the five glycogen metabolism genes influence bacterial phenotypes, such as growth rate, biofilm formation, and environmental survival, etc. In this study, we systematically and comparatively studied five E. coli single-gene mutants (DeltaglgC, DeltaglgA, DeltaglgB, DeltaglgP, DeltaglgX) in terms of glycogen metabolism and explored their phenotype changes with a focus on environmental stress endurance, such as nutrient deprivation, low temperature, desiccation, and oxidation, etc. Biofilm formation in wild-type and mutant strains was also compared. E. coli wild-type stores the highest glycogen content after around 20-h culture while disruption of degradation genes (glgP, glgX) leads to continuous accumulation of glycogen. However, glycogen primary structure was abnormally changed in DeltaglgP and DeltaglgX. Meanwhile, increased accumulation of glycogen facilitates the growth of E. coli mutants but reduces glucose consumption in liquid culture and vice versa. Glycogen metabolism disruption also significantly and consistently increases biofilm formation in all the mutants. As for environmental stress endurance, glycogen over-accumulating mutants have enhanced starvation viability and reduced desiccation viability while all mutants showed decreased survival rate at low temperature. No consistent results were found for oxidative stress resistance in terms of glycogen metabolism disruptions, though DeltaglgA shows highest resistance toward oxidation with unknown mechanisms. In sum, single gene disruptions in glgBXCAP operon significantly influence bacterial growth and glucose consumption during culture. Accumulation and structure of intracellular glycogen were also significantly altered. In addition, we observed significant changes in E. coli environmental viabilities due to the deletions of certain genes in the operon. Further investigations shall be focused on the molecular mechanisms behind these phenotype changes.

PubMed

21029047, Biochem J. 2011 Jan 1;433(1):107-17. doi: 10.1042/BJ20101186.

Title

Escherichia coli glycogen genes are organized in a single glgBXCAP transcriptional unit possessing an alternative suboperonic promoter within glgC that directs glgAP expression.

Author

Montero M, Almagro G, Eydallin G, Viale AM, Munoz FJ, Bahaji A, Li J, Rahimpour M, Baroja-Fernandez E, Pozueta-Romero J

Abstract

Although it is generally accepted that Escherichia coli glycogen genes are organized in two tandemly arranged, differentially regulated glgBX and glgCAP operons, RT (reverse transcriptase)-PCR analyses carried out in the present study showed that E. coli cells possess transcripts comprising the five glgBXCAP genes. glg::lacZY expression analyses in cells lacking the region immediately upstream of the glgB gene revealed an almost total abolishment of glgB, glgX and glgC expression, but only a 50-60% reduction of the wild-type glgA and glgP expression levels. Furthermore, similar analyses showed that glgA and glgP expression was almost totally abolished in cells lacking glgA upstream sequences, including glgC, glgB and the asd-glgB intergenic region upstream of glgB. These results indicate that E. coli glgBXCAP genes are organized in a single transcriptional unit controlled by promoter sequences occurring upstream of glgB, and that an alternative suboperonic promoter is located within glgC, driving expression of the glgA and glgP genes. Computer searches for consensus promoters, and analyses of glgB::lacZY and glgA::lacZY expression in cells containing deletions of glgB and glgA upstream sequences identified regions directing glgBXCAP and glgAP expression. 5' RACE (rapid amplification of cDNA ends) analyses located a glgBXCAP transcription start site 155 bp upstream of the glgB initiation codon, and a glgAP transcription start site 359 bp upstream of the glgA initiation codon. Finally, glg::lacZY expression analyses on cells lacking the relA or phoP regulatory genes indicated that both the glgBXCAP operon and the suboperonic promoter driving glgAP expression form part of both the RelA and PhoP-PhoQ regulons.