A marine bacterial enzymatic cascade degrades the algal polysaccharide ulvan

Reisky, Lukas; Préchoux, Aurélie; Zühlke, Marie-Katherin; Bäumgen, Marcus; Robb, C.S.; Gerlach, N.; Roret, Thomas; Stanetty, Christian; Larocque, Robert; Michel, Gurvan; Song, Tao; Markert, Stephanie; Unfried, Frank; Mihovilovic, Marko D.; Trautwein-Schult, Anke; Becher, Dörte; Schweder, Thomas; Bornscheuer, Uwe T.; Hehemann, Jan‐Hendrik

doi:10.1038/s41589-019-0311-9

Cited by 100 publications

(129 citation statements)

References 68 publications

(90 reference statements)

Supporting

Mentioning

125

Contrasting

Order By: Relevance

“…Such interactions show up graphically as hotpink clash spikes inside the green dots of an H-bond. Occasionally, full coordination is seen, as shown in Figure 2a for the positive ion modeled as HOH 606 in the 6hhm sulfatase (Reisky et al 2019), with two clashes to oxygen atoms. That HOH has 6 ligands --3 backbone CO, 2 Thr Oγ, and a water --in closely octahedral geometry.…”

Section: Ii2 New Features: Undowser To Diagnose Non-water Hohsmentioning

confidence: 99%

“…Examples are shown and discussed here below for about a dozen distinct scenarios, to aid user comparison with their own cases. (Reisky 2019), with 6 near-octahedral oxygen ligands. Lenses of green all-atom contact dots show donor-acceptor overlaps, but 2 distances are so short they also have serious clashes (clusters of hotpink spikes).…”

Section: Ii2 New Features: Undowser To Diagnose Non-water Hohsmentioning

confidence: 99%

See 1 more Smart Citation

CaBLAM for chiropraxis in cryoEM, UnDowser to rethink “waters”, and NGL Viewer to recapture online 3D graphics in MolProbity validation

Prisant

Williams

Chen

et al. 2019

Preprint

View full text Add to dashboard Cite

The MolProbity web service provides macromolecular model validation to help correct local errors, for the structural biology community worldwide. Here we highlight new validation features, and also describe how we are fighting back against recent outside changes that degrade or endanger that mission. Sophisticated hacking of the MolProbity server has required continual monitoring and various security measures short of restricting user access. Refinement software now increasingly restrains validation criteria in order to supplement the sparser experimental data at 3-4Å resolutions typical of modern cryoEM. But unfortunately the broad density allows optimization without fixing underlying problems, which means these structures often score much better than they really are. CaBLAM, our first new tool designed for this regime, was described in the previous Tools issue, and here we demonstrate its effectiveness in diagnosing local errors even when other validation outliers have been artificially removed. The deprecation of Java applets now prevents KiNG interactive online display of outliers on the 3D model during a MolProbity run, but that important functionality is now recaptured with a modified version of the Javascript NGL Viewer. Other new changes are more straightforwardly good. We are moving to the Neo4j database (graphical rather than relational), and will soon have cleaner as well as much larger reference datasets. In addition to several minor new features, we have developed a tool called UnDowser that analyzes the properties and context of modeled but clashing HOH "waters" to diagnose what they might actually represent. A dozen distinct scenarios are illustrated and described.

show abstract

Section: Ii2 New Features: Undowser To Diagnose Non-water Hohsmentioning

confidence: 99%

Section: Ii2 New Features: Undowser To Diagnose Non-water Hohsmentioning

confidence: 99%

CaBLAM for chiropraxis in cryoEM, UnDowser to rethink “waters”, and NGL Viewer to recapture online 3D graphics in MolProbity validation

Prisant

Williams

Chen

et al. 2019

Preprint

View full text Add to dashboard Cite

show abstract

“…Monosaccharides are linked via hydroxyl groups in a vast diversity of linkage conformations; in theory, three different hexoses could lead to 128 different disaccharides (Laine, 1994). Oligo-and polysaccharides are often branched or contain sulfate, methyl, or amino groups, adding further structural complexity and frequently requiring "matching" enzymes to remove the sulfate, methyl, or amino groups prior to degradation of the polysaccharide backbone (e.g., Reisky et al, 2019). The structural diversity of carbohydrates thus could be used to link detrital components back to their sources, but only recently has progress been made in analytical techniques to begin to characterize these structures with sufficient resolution.…”

Section: Carbohydratesmentioning

confidence: 99%

Particulate Organic Carbon Deconstructed: Molecular and Chemical Composition of Particulate Organic Carbon in the Ocean

Kharbush

Mooy

et al. 2020

Front. Mar. Sci.

View full text Add to dashboard Cite

The dynamics of the particulate organic carbon (POC) pool in the ocean are central to the marine carbon cycle. POC is the link between surface primary production, the deep ocean, and sediments. The rate at which POC is degraded in the dark ocean can impact atmospheric CO 2 concentration. Therefore, a central focus of marine organic geochemistry studies is to improve our understanding of POC distribution, composition, and cycling. The last few decades have seen improvements in analytical techniques that have greatly expanded what we can measure, both in terms of organic compound structural diversity and isotopic composition, and complementary molecular omics studies. Here we provide a brief overview of the autochthonous, allochthonous, and anthropogenic components comprising POC in the ocean. In addition, we highlight key needs for future research that will enable us to more effectively connect diverse data sources and link the identity and structural diversity of POC to its sources and transformation processes.

show abstract

“…For instance, the marine flavobacterium Zobellia galactanivorans has complex biochemical and regulatory mechanisms for degrading laminarin, alginate, agar and carrageenan (Hehemann et al 2012, Labourel et al 2014, Ficko-Blean et al 2017. Comparable abilities have been described in the flavobacterial genera Formosa agarivorans and Gramella forsetii through diverse PUL (Mann et al 2013, Kabisch et al 2014, Reisky et al 2019. Also Maribacter, the "sister genus" of Zobellia, exhibits hydrolytic activity (Bakunina et al 2012, Zhan et al 2017.…”

Section: Introductionmentioning

confidence: 99%

CAZymes inMaribacter dokdonensis62-1 from the Patagonian shelf: Genomics and physiology compared to related flavobacteria and a co-occurringAlteromonasstrain

Wolter

Mitulla

Kalem

et al. 2020

Preprint

View full text Add to dashboard Cite

Carbohydrate-active enzymes (CAZymes) are an important feature of bacteria in productive marine systems such as continental shelves, where phytoplankton and macroalgae produce diverse polysaccharides. We herein describe Maribacter dokdonensis 62-1, a novel strain of this flavobacterial species, isolated from alginate-supplemented seawater collected at the Patagonian continental shelf. M. dokdonensis 62-1 harbors a diverse array of CAZymes in multiple polysaccharide utilization loci (PUL). Two PUL encoding polysaccharide lyases from families 6, 7, 12 and 17 allow substantial growth with alginate as sole carbon source, with simultaneous utilization of mannuronate and guluronate as demonstrated by HPLC. Furthermore, strain 62-1 harbors a mixed-feature PUL encoding both ulvan- and fucoidan-targeting CAZymes. Core-genome phylogeny and pangenome analysis revealed variable occurrence of these PUL in related Maribacter and Zobellia strains, indicating specialization to certain “polysaccharide niches”. Furthermore, lineage- and strain-specific genomic signatures for exopolysaccharide synthesis possibly mediate distinct strategies for surface attachment and host interaction. The wide detection of CAZyme homologs in algae-derived metagenomes suggests global occurrence in algal holobionts, supported by sharing multiple adaptive features with the hydrolytic model flavobacterium Zobellia galactanivorans. Comparison with Alteromonas sp. 76-1 isolated from the same seawater sample revealed that these co-occurring strains target similar polysaccharides but with different genomic repertoires, coincident with differing growth behavior on alginate that might mediate ecological specialization. Altogether, our study contributes to the perception of Maribacter as versatile flavobacterial polysaccharide degrader, with implications for biogeochemical cycles, niche specialization and bacteria-algae interactions in the oceans.

show abstract

A marine bacterial enzymatic cascade degrades the algal polysaccharide ulvan

Cited by 100 publications

References 68 publications

CaBLAM for chiropraxis in cryoEM, UnDowser to rethink “waters”, and NGL Viewer to recapture online 3D graphics in MolProbity validation

CaBLAM for chiropraxis in cryoEM, UnDowser to rethink “waters”, and NGL Viewer to recapture online 3D graphics in MolProbity validation

Particulate Organic Carbon Deconstructed: Molecular and Chemical Composition of Particulate Organic Carbon in the Ocean

CAZymes inMaribacter dokdonensis62-1 from the Patagonian shelf: Genomics and physiology compared to related flavobacteria and a co-occurringAlteromonasstrain

Contact Info

Product

Resources

About