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PlantCAZyme
Cite: NAR/gkaa742 2020

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 General Information

Literature Information

PUL ID

PUL0405

PubMed

30116038, ISME J. 2019 Jan;13(1):92-103. doi: 10.1038/s41396-018-0252-4. Epub 2018 Aug 16.

Characterization method

RNA-Seq

Genomic accession number

CABDWQ010000001.1

Nucelotide position range

4433602-4444984

Substrate

pectin

Loci

ALT831_03876-ALT831_03879

Species

Alteromonas macleodii/28108

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- ALT831_03876 VTO45596.1 0 - 744 (+) CABDWQ010000001.1:4433602-4434346 -
- ALT831_03877 VTO45597.1 743 - 2066 (+) CABDWQ010000001.1:4434345-4435668 -
- ALT831_03878 VTO45598.1 2213 - 5147 (+) CABDWQ010000001.1:4435815-4438749 -
- ALT831_03879 VTO45599.1 5245 - 11383 (+) CABDWQ010000001.1:4438847-4444985 -

Cluster number

0

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 744 (+) TF: DBD-Pfam|TrmB No
- 744 - 2066 (+) CAZyme: PL1|PL1_2 No
- 2214 - 5147 (+) CDS No
- 5246 - 11383 (+) CAZyme: PL1_5|CE8 No

PUL ID

PUL0405

PubMed

30116038, ISME J. 2019 Jan;13(1):92-103. doi: 10.1038/s41396-018-0252-4. Epub 2018 Aug 16.

Title

Biphasic cellular adaptations and ecological implications of Alteromonas macleodii degrading a mixture of algal polysaccharides.

Author

Koch H, Durwald A, Schweder T, Noriega-Ortega B, Vidal-Melgosa S, Hehemann JH, Dittmar T, Freese HM, Becher D, Simon M, Wietz M

Abstract

Algal polysaccharides are an important bacterial nutrient source and central component of marine food webs. However, cellular and ecological aspects concerning the bacterial degradation of polysaccharide mixtures, as presumably abundant in natural habitats, are poorly understood. Here, we contextualize marine polysaccharide mixtures and their bacterial utilization in several ways using the model bacterium Alteromonas macleodii 83-1, which can degrade multiple algal polysaccharides and contributes to polysaccharide degradation in the oceans. Transcriptomic, proteomic and exometabolomic profiling revealed cellular adaptations of A. macleodii 83-1 when degrading a mix of laminarin, alginate and pectin. Strain 83-1 exhibited substrate prioritization driven by catabolite repression, with initial laminarin utilization followed by simultaneous alginate/pectin utilization. This biphasic phenotype coincided with pronounced shifts in gene expression, protein abundance and metabolite secretion, mainly involving CAZymes/polysaccharide utilization loci but also other functional traits. Distinct temporal changes in exometabolome composition, including the alginate/pectin-specific secretion of pyrroloquinoline quinone, suggest that substrate-dependent adaptations influence chemical interactions within the community. The ecological relevance of cellular adaptations was underlined by molecular evidence that common marine macroalgae, in particular Saccharina and Fucus, release mixtures of alginate and pectin-like rhamnogalacturonan. Moreover, CAZyme microdiversity and the genomic predisposition towards polysaccharide mixtures among Alteromonas spp. suggest polysaccharide-related traits as an ecophysiological factor, potentially relating to distinct 'carbohydrate utilization types' with different ecological strategies. Considering the substantial primary productivity of algae on global scales, these insights contribute to the understanding of bacteria-algae interactions and the remineralization of chemically diverse polysaccharide pools, a key step in marine carbon cycling.