Diversity of GH51 α-L-arabinofuranosidase homolog sequences from subantarctic intertidal sediments

Dionisi, Hebe M.; Lozada, Mariana; Campos, Eleonora

doi:10.1007/s11756-023-01382-x

Cited by 4 publications

(6 citation statements)

References 130 publications

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“…The high degree of novelty within planctomycetotal CAZyomes is in line with a previous study analysing a large group of β-galactosidase homologues from planctomycetotal genomes, which highlighted the presence of multiple, poorly characterised CAZymes, almost exclusively present in the PVC superphylum and some Bacteroidota [ 67 ]. Another recent study described the diversity of α-l-arabinofuranosidase homologues (GH51) from subantarctic intertidal sediments in different bacteria including Planctomycetota [ 68 ]. Similarly, further investigation of unclassified CAZymes, and CAZymes with a low sequence homology to known proteins, shall, in the future, allow the discovery of novel CAZyme functionalities as highlighted in the past by Naumoff and Dedysh [ 69 ].…”

Section: Resultsmentioning

confidence: 99%

Comparative genomic analysis of Planctomycetota potential for polysaccharide degradation identifies biotechnologically relevant microbes

Klimek,

Herold,

Calusinska

2024

BMC Genomics

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Background Members of the Planctomycetota phylum harbour an outstanding potential for carbohydrate degradation given the abundance and diversity of carbohydrate-active enzymes (CAZymes) encoded in their genomes. However, mainly members of the Planctomycetia class have been characterised up to now, and little is known about the degrading capacities of the other Planctomycetota. Here, we present a comprehensive comparative analysis of all available planctomycetotal genome representatives and detail encoded carbohydrolytic potential across phylogenetic groups and different habitats. Results Our in-depth characterisation of the available planctomycetotal genomic resources increases our knowledge of the carbohydrolytic capacities of Planctomycetota. We show that this single phylum encompasses a wide variety of the currently known CAZyme diversity assigned to glycoside hydrolase families and that many members encode a versatile enzymatic machinery towards complex carbohydrate degradation, including lignocellulose. We highlight members of the Isosphaerales, Pirellulales, Sedimentisphaerales and Tepidisphaerales orders as having the highest encoded hydrolytic potential of the Planctomycetota. Furthermore, members of a yet uncultivated group affiliated to the Phycisphaerales order could represent an interesting source of novel lytic polysaccharide monooxygenases to boost lignocellulose degradation. Surprisingly, many Planctomycetota from anaerobic digestion reactors encode CAZymes targeting algal polysaccharides – this opens new perspectives for algal biomass valorisation in biogas processes. Conclusions Our study provides a new perspective on planctomycetotal carbohydrolytic potential, highlighting distinct phylogenetic groups which could provide a wealth of diverse, potentially novel CAZymes of industrial interest.

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Section: Resultsmentioning

confidence: 99%

Comparative genomic analysis of Planctomycetota potential for polysaccharide degradation identifies biotechnologically relevant microbes

Klimek,

Herold,

Calusinska

2024

BMC Genomics

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Section: Discussionmentioning

confidence: 99%

“…Sequences homologous to members of the GH107 family assigned to the Planctomycetota phylum were identified in the two analyzed intertidal sediment metagenomes [35,36]. In particular, these sequences were abundant in the OR07 metagenomic dataset, which was generated by shotgun sequencing of fosmid DNA purified from a metagenomic library of intertidal sediments [36]. Conversely, the MM dataset was generated from a kelp-enriched community that presented a decreased abundance of members of Planctomycetota when compared to the sampled sediments [35], which could explain the lower abundance of putative GH107 sequences from Planctomycetota in this dataset.…”

Section: Discussionmentioning

confidence: 99%

“…Two metagenomic datasets from intertidal sediments of Ushuaia Bay (54 • 48 S, 68 • 17 W) were used for mining GH107 homolog sequences. More information about the sampling site and the experimental approach used for each metagenome dataset have been previously published [35,36]. Briefly, the OR07 dataset, containing 682,972 protein-coding sequences (CDSs), was generated by shotgun sequencing of a fosmid metagenomic library built from Ushuaia Bay intertidal sediments, and gene prediction was performed using MetaGeneMark v. 1 [37].…”

Section: Intertidal Sediment Metagenomic Datasetsmentioning

confidence: 99%

“…Sequences homologous to members of the GH107 family were identified in two metagenomic datasets from intertidal sediments of a subantarctic environment, named MM [35] and OR07 [36] (see details in Section 2). The two tools used for the annotation, dbCAN2 and CUPP [43,44], produced similar results (Table S1).…”

Section: Diversity Of Gh107 Homolog Sequences In Intertidal Sediment ...mentioning

confidence: 99%

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Fucanases Related to the GH107 Family from Members of the PVC Superphylum

Gonzalez,

Ponce,

Lozada

et al. 2024

JMSE

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The glycoside hydrolase 107 (GH107) family includes fucanase enzymes from only two bacterial phyla, Bacteroidota and Pseudomonadota. The goal of this work was to explore the diversity of putative fucanase enzymes related to this family in organisms of the PVC superphylum (Planctomycetota, Verrucomicrobiota, Chlamydiota), in order to expand our knowledge of the fucoidan-degrading potential in this ecologically and biotechnologically relevant group. Using hidden Markov model- and peptide-based annotation tools, 26 GH107 homolog sequences were identified in metagenome and genome datasets. The sequences formed two distinct clusters in a phylogenetic analysis, only one including members of the GH107 family. The endo-acting fucoidan degrading activity was confirmed in an enzyme included in the most divergent cluster. The fucanase, which probably originated in an uncultured planctomycete from the sampled subantarctic sediments, was cloned and expressed in Escherichia coli. The enzyme catalyzed the rapid hydrolysis of internal glycosidic bonds of fucoidan from Macrocystis pyrifera, a macroalgae species abundant at the site. It was active in a wide range of temperatures (5–45 °C), salinities (9.5–861 mM NaCl), and pH values (4.5–9), mainly producing sulfated α-(1,3)-linked fuco-oligosaccharides of various lengths. The PVC superphylum represents a promising source of fucanase enzymes with various biotechnological applications.

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Microbial α-L-arabinofuranosidases: diversity, properties, and biotechnological applications

Long,

Lin,

Wang

et al. 2024

World J Microbiol Biotechnol

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Diversity of GH51 α-L-arabinofuranosidase homolog sequences from subantarctic intertidal sediments

Cited by 4 publications

References 130 publications

Comparative genomic analysis of Planctomycetota potential for polysaccharide degradation identifies biotechnologically relevant microbes

Comparative genomic analysis of Planctomycetota potential for polysaccharide degradation identifies biotechnologically relevant microbes

Fucanases Related to the GH107 Family from Members of the PVC Superphylum

Microbial α-L-arabinofuranosidases: diversity, properties, and biotechnological applications

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