Engineering broad-spectrum digestion of polyuronides from an exolytic polysaccharide lyase

MacDonald, Logan C.; Weiler, Elizabeth B.; Berger, Bryan W.

doi:10.1186/s13068-016-0455-8

Cited by 17 publications

(12 citation statements)

References 48 publications

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“…The specificity and the mode of action of the alginate lyases were carefully determined using alginate substrates with known, controlled structures (poly-M, poly-G or poly-MG chains). The results were in agreement with the previous enzymology and crystallography studies carried out on other recombinant enzymes 26 , 31 – 35 . One report indicates that the expression of the marine strain Gramella forsetti PL17 enzyme is upregulated when alginate is added to the culture medium 18 , supporting substrate specificity towards alginate.…”

Section: Discussionsupporting

confidence: 92%

“…The eight proteins selected from the PL17_2 clade all displayed alginate lyase activity (Table 1 ), as reported for other members of this clade based on digestion experiments conducted with either raw alginate substrates or on isolated poly-M or poly-G block fractions prepared by chemical treatment 26 , 31 – 35 . The substrate specificity of the enzymes was determined using at least two independent production of enzymes by measuring the velocity of degradation using poly-M, poly-G and poly-MG substrates (Fig.…”

Section: Resultsmentioning

confidence: 86%

“…MJ-3 Poly-M * n.d. Poly-MG/Poly-G n.d. OalY1, OalY2 33 Halomonas sp. Poly-M * Δ (Exo) Alg17c 26 Saccharophagus degradans 2–40 Oligo-alginates Δ (Exo) AlgL 34 Stenotrophomas maltophilia KJ-2 Poly-M * , Oligo-alginates n.d. Smlt2602 35 Stenotrophomonas maltophilia K279a Poly-M * Δ (Exo) OalB 51 Vibrio splendidus 12B01 Poly-MG * n.d. OalC 51 Vibrio splendidus 12B01 Poly-M n.d. OalS17 52 Shewanella sp.Kz7 Poly-M n.d. * The substrates used to characterize the enzyme specificities were alginate or enriched poly-M or poly-G fractions obtained by acid hydrolysis. ** Δ: 4-deoxy-L-erythro-5-hexoseulose uronic acid The table summarizes the substrate specificities, end products and mode of action (endo-, exo-) of the polysaccharide lyases investigated.…”

Section: Resultsmentioning

confidence: 99%

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Ancient acquisition of “alginate utilization loci” by human gut microbiota

Mathieu

Touvrey-Loiodice

Poulet

et al. 2018

Sci Rep

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In bacteria from the phylum Bacteroidetes, the genes coding for enzymes involved in polysaccharide degradation are often colocalized and coregulated in so-called “polysaccharide utilization loci” (PULs). PULs dedicated to the degradation of marine polysaccharides (e.g. laminaran, ulvan, alginate and porphyran) have been characterized in marine bacteria. Interestingly, the gut microbiome of Japanese individuals acquired, by lateral transfer from marine bacteria, the genes involved in the breakdown of porphyran, the cell wall polysaccharide of the red seaweed used in maki. Sequence similarity analyses predict that the human gut microbiome also encodes enzymes for the degradation of alginate, the main cell wall polysaccharide of brown algae. We undertook the functional characterization of diverse polysaccharide lyases from family PL17, frequently found in marine bacteria as well as those of human gut bacteria. We demonstrate here that this family is polyspecific. Our phylogenetic analysis of family PL17 reveals that all alginate lyases, which have all the same specificity and mode of action, cluster together in a very distinct subfamily. The alginate lyases found in human gut bacteria group together in a single clade which is rooted deeply in the PL17 tree. These enzymes were found in PULs containing PL6 enzymes, which also clustered together in the phylogenetic tree of PL6. Together, biochemical and bioinformatics analyses suggest that acquisition of this system appears ancient and, because only traces of two successful transfers were detected upon inspection of PL6 and PL17 families, the pace of acquisition of marine polysaccharide degradation system is probably very slow.

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Section: Discussionsupporting

confidence: 92%

Section: Resultsmentioning

confidence: 86%

Section: Resultsmentioning

confidence: 99%

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Ancient acquisition of “alginate utilization loci” by human gut microbiota

Mathieu

Touvrey-Loiodice

Poulet

et al. 2018

Sci Rep

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“…Therefore, the PLs of the Thalassotalea spp. could be used as highly active and specific enzymes for energy and chemical production via glycan saccharification [ 79 ]. Taken together, these enzymes for polysaccharide degradation of the Thalassotalea spp.…”

Section: Resultsmentioning

confidence: 99%

Genomics Reveals the Metabolic Potential and Functions in the Redistribution of Dissolved Organic Matter in Marine Environments of the Genus Thalassotalea

et al. 2020

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Members of the bacterial genus Thalassotalea have been isolated recently from various marine environments, including marine invertebrates. A metagenomic study of the Deepwater Horizon oil plume has identified genes involved in aromatic hydrocarbon degradation in the Thalassotalea genome, shedding light on its potential role in the degradation of crude oils. However, the genomic traits of the genus are not well-characterized, despite the ability of the species to degrade complex natural compounds, such as agar, gelatin, chitin, or starch. Here, we obtained a complete genome of a new member of the genus, designated PS06, isolated from marine sediments containing dead marine benthic macroalgae. Unexpectedly, strain PS06 was unable to grow using most carbohydrates as sole carbon sources, which is consistent with the finding of few ABC transporters in the PS06 genome. A comparative analysis of 12 Thalassotalea genomes provided insights into their metabolic potential (e.g., microaerobic respiration and carbohydrate utilization) and evolutionary stability [including a low abundance of clustered regularly interspaced short palindromic repeats (CRISPR) loci and prophages]. The diversity and frequency of genes encoding extracellular enzymes for carbohydrate metabolism in the 12 genomes suggest that members of Thalassotalea contribute to nutrient cycling by the redistribution of dissolved organic matter in marine environments. Our study improves our understanding of the ecological and genomic properties of the genus Thalassotalea.

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“…The abundance of Bacillus in Lake Xuanwu (China) is increased from the outbreak to the decline of a Microcystis bloom, and Bacillus dominates the bacterial community at the decline of the bloom (Zheng et al 2008). Stenotrophomonas maltophilia and Bacillus are able to produce polysaccharide lyases (MacDonald et al 2016;Ochiai et al 2007). The colony size of Microcystis in Lake Taihu decreases at the decline of the bloom .…”

Section: Discussionmentioning

confidence: 99%

Effects of the cultivable bacteria attached toMicrocystiscolonies on the colony size and growth ofMicrocystis

Zhang

Jia

et al. 2019

Journal of Freshwater Ecology

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The interactions between bacteria and algae may play a significant part in the formation and development of algal blooms. The bloom-forming cyanobacterium Microcystis occurs mainly as colonial form in natural waters, and thus it is necessary to study the interaction between bacteria and colonial Microcystis. This paper aimed to investigate effects of the cultivable bacteria attached to Microcystis colonies on the colony size and growth of colonial Microcystis aeruginosa. Eleven bacterial strains were isolated from M. aeruginosa colonies collected from Lake Taihu. Among these bacteria, seven bacterial isolates significantly influenced the colony size of M. aeruginosa, and four bacterial isolates significantly influenced the growth rate of M. aeruginosa. Four isolates, related to the Exiguobacterium, Delftia, Bacillus and Stenotrophomonas, significantly decreased the colony size of M. aeruginosa by 36-51%, and two isolates, assigned to the Chryseobacterium and Pseudomonas chengduensis, significantly increased the M. aeruginosa colony size by 89% and 63%, respectively, while these isolates had no effect on the cyanobacterial growth rate. Two isolates, belonged to the Rheinheimera and Pseudomonas, significantly decreased the growth rate of M. aeruginosa by 47% and 36%, respectively, and one bacterial strain related to Aeromonas increased the cyanobacterial growth rate by 22%, while these isolates had no effect on the cyanobacterial colony size. One isolate belonged to Sphingomonas was found to significantly increase the colony size of M. aeruginosa by 80% and significantly decrease the growth rate of M. aeruginosa by 21%. PCR-denaturing gradient gel electrophoresis (PCR-DGGE) analysis showed that all of the bacterial isolates were able to colonize M. aeruginosa colonies. Our data suggested that the bacteria attached to Microcystis colonies might influence the cyanobacterial colony size and growth, and thus influence the formation and development of Microcystis blooms. ARTICLE HISTORY

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Engineering broad-spectrum digestion of polyuronides from an exolytic polysaccharide lyase

Cited by 17 publications

References 48 publications

Ancient acquisition of “alginate utilization loci” by human gut microbiota

Ancient acquisition of “alginate utilization loci” by human gut microbiota

Genomics Reveals the Metabolic Potential and Functions in the Redistribution of Dissolved Organic Matter in Marine Environments of the Genus Thalassotalea

Effects of the cultivable bacteria attached toMicrocystiscolonies on the colony size and growth ofMicrocystis

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