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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0404

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

2755697-2777573

Substrate

pectin

Loci

ALT831_02415-ALT831_02432

Species

Alteromonas macleodii/28108

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- ALT831_02415 VTO44167.1 0 - 1230 (-) CABDWQ010000001.1:2755697-2756927 -
- ALT831_02416 VTO44168.1 1408 - 2167 (+) CABDWQ010000001.1:2757105-2757864 -
- ALT831_02417 VTO44169.1 2189 - 3053 (+) CABDWQ010000001.1:2757886-2758750 -
- ALT831_02418 VTO44170.1 3083 - 4067 (+) CABDWQ010000001.1:2758780-2759764 -
- ALT831_02419 VTO44171.1 4069 - 4555 (+) CABDWQ010000001.1:2759766-2760252 -
- ALT831_02420 VTO44172.1 4554 - 5850 (+) CABDWQ010000001.1:2760251-2761547 -
- ALT831_02421 VTO44173.1 5996 - 7013 (+) CABDWQ010000001.1:2761693-2762710 -
- ALT831_02422 VTO44174.1 7222 - 8713 (+) CABDWQ010000001.1:2762919-2764410 -
- ALT831_02423 VTO44175.1 8724 - 10140 (+) CABDWQ010000001.1:2764421-2765837 -
- ALT831_02424 VTO44176.1 10142 - 11684 (+) CABDWQ010000001.1:2765839-2767381 -
- ALT831_02425 VTO44177.1 11683 - 12322 (+) CABDWQ010000001.1:2767380-2768019 -
- ALT831_02426 VTO44178.1 12318 - 13290 (+) CABDWQ010000001.1:2768015-2768987 -
- ALT831_02427 VTO44179.1 13435 - 14371 (-) CABDWQ010000001.1:2769132-2770068 -
- ALT831_02428 VTO44180.1 14436 - 14715 (+) CABDWQ010000001.1:2770133-2770412 -
- ALT831_02429 VTO44181.1 14574 - 17274 (-) CABDWQ010000001.1:2770271-2772971 -
- ALT831_02430 VTO44182.1 17955 - 19161 (+) CABDWQ010000001.1:2773652-2774858 -
- ALT831_02431 VTO44183.1 19191 - 20661 (+) CABDWQ010000001.1:2774888-2776358 -
- ALT831_02432 VTO44184.1 20674 - 21877 (+) CABDWQ010000001.1:2776371-2777574 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 1230 (-) CDS No
- 1409 - 2167 (+) CDS No
- 2190 - 3053 (+) CDS No
- 3084 - 4067 (+) TC: gnl|TC-DB|P43020|2.A.56.1.5 Yes
- 4070 - 4555 (+) TC: gnl|TC-DB|Q8ZKR9|2.A.56.1.5 Yes
- 4555 - 5850 (+) TC: gnl|TC-DB|Q8ZKS0|2.A.56.1.5 Yes
- 5997 - 7013 (+) TF: DBD-Pfam|LacI,DBD-SUPERFAMILY|0036955 Yes
- 7223 - 8713 (+) other Yes
- 8725 - 10140 (+) other Yes
- 10143 - 11684 (+) other Yes
- 11684 - 12322 (+) other Yes
- 12319 - 13290 (+) STP: STP|PfkB Yes
- 13436 - 14371 (-) CAZyme: CE12 Yes
- 14437 - 14715 (+) other Yes
- 14575 - 17274 (-) TC: gnl|TC-DB|Q9AAZ6|1.B.14.12.2 Yes
- 17956 - 19161 (+) CAZyme: GH105 Yes
- 19192 - 20661 (+) CAZyme: GH28 Yes
- 20675 - 21877 (+) CAZyme: CE8 Yes

PUL ID

PUL0404

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.