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Seaweed Biorefinery and Related Technologies
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Seaweed Biorefinery and Related Technologies

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Natural Products Chemistry".

Deadline for manuscript submissions: closed (1 April 2022) | Viewed by 9841

Special Issue Editors

Dr. Toshiyuki Shibata

E-Mail Website
Guest Editor
1. Major of Life Sciences, Graduate School of Bioresources, Mie University, 1577 Kurimamachiya-cho, Tsu, Mie 514-8507, Japan
2. Seaweed Biorefinery Research Center, Mie University, 1577 Kurimamachiya-cho, Tsu, Mie 514-8507, Japan
Interests: bioactive substances; chromatography; polyphenols; phlorotannins; rare sugar; seaweed
Dr. Tetsushi Mori

E-Mail Website
Guest Editor
Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Japan
Interests: enzyme/microbe screening techniques; microbial diversity; seaweed degrading microbes; depolymerizing enzymes; metabolic pathways; genetic variance

Special Issue Information

Dear Colleagues,

In order to build a sustainable society, it is necessary to establish "biorefinery technologies" that convert raw materials from petroleum or renewable resources such as biomass, for the production of fuel and a variety of chemical products. Biorefinery is a technical approach that produces fuels and chemicals by fermenting monosaccharides obtained by decomposing polysaccharides from biomass with microorganisms. Seaweed is an unused plant resource, with the exception of several species. Thus, seaweed is attracting attention as an alternative raw material to replace food biomass, cellulosic biomass, and microalgae. In order to establish highly efficient, robust and applicable "seaweed biorefinery technologies", it is necessary to accumulate basic findings based on the following fields: marine bacteria with the activity of decomposing seaweed polysaccharides, seaweed polysaccharide-degrading enzymes (e.g., alginate lyases, ulvan lyases, etc.), physiologically active substances derived from seaweed (e.g., phlorotannins, sterols, fatty acids, and pigment composition), component analysis of seaweed, and seaweed physiology. Therefore, original articles, short communications and review articles covering all areas of research on "seaweed biorefinery" are welcome for submission to this Special Issue of Molecules.

Dr. Toshiyuki Shibata
Dr. Tetsushi Mori
Guest Editors

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Keywords

  • biofuel
  • biorefinery
  • marine bacteria
  • seaweed
  • seaweed polysaccharide degrading enzyme
  • synthetic biology
  • physiologically active substance

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Published Papers (4 papers)

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Research

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14 pages, 3889 KiB  
Article
Cell-Penetrating Peptide–Peptide Nucleic Acid Conjugates as a Tool for Protein Functional Elucidation in the Native Bacterium
by Yasuhito Yokoi, Yugo Kawabuchi, Abdullah Adham Zulmajdi, Reiji Tanaka, Toshiyuki Shibata, Takahiro Muraoka and Tetsushi Mori
Molecules 2022, 27(24), 8944; https://doi.org/10.3390/molecules27248944 - 15 Dec 2022
Cited by 5 | Viewed by 2381
Abstract
Approximately 30% or more of the total proteins annotated from sequenced bacteria genomes are annotated as hypothetical or uncharacterized proteins. However, elucidation on the function of these proteins is hindered by the lack of simple and rapid screening methods, particularly with novel or [...] Read more.
Approximately 30% or more of the total proteins annotated from sequenced bacteria genomes are annotated as hypothetical or uncharacterized proteins. However, elucidation on the function of these proteins is hindered by the lack of simple and rapid screening methods, particularly with novel or hard-to-transform bacteria. In this report, we employed cell-penetrating peptide (CPP) –peptide nucleotide acid (PNA) conjugates to elucidate the function of such uncharacterized proteins in vivo within the native bacterium. Paenibacillus, a hard-to-transform bacterial genus, was used as a model. Two hypothetical genes showing amino acid sequence similarity to ι-carrageenases, termed cgiA and cgiB, were identified from the draft genome of Paenibacillus sp. strain YYML68, and CPP–PNA probes targeting the mRNA of the acyl carrier protein gene, acpP, and the two ι-carrageenase candidate genes were synthesized. Upon direct incubation of CPP–PNA targeting the mRNA of the acpP gene, we successfully observed growth inhibition of strain YYML68 in a concentration-dependent manner. Similarly, both the function of the candidate ι-carrageenases were also inhibited using our CPP–PNA probes allowing for the confirmation and characterization of these hypothetical proteins. In summary, we believe that CPP–PNA conjugates can serve as a simple and efficient alternative approach to characterize proteins in the native bacterium. Full article
(This article belongs to the Special Issue Seaweed Biorefinery and Related Technologies)
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12 pages, 2044 KiB  
Article
Isolation, Diversity and Characterization of Ulvan-Degrading Bacteria Isolated from Marine Environments
by Reiji Tanaka, Yu Kurishiba, Hideo Miyake and Toshiyuki Shibata
Molecules 2022, 27(11), 3420; https://doi.org/10.3390/molecules27113420 - 25 May 2022
Cited by 3 | Viewed by 2336
Abstract
In this study, we aimed to isolate bacteria capable of degrading the polysaccharide ulvan from the green algae Ulva sp. (Chlorophyta, Ulvales, Ulvaceae) in marine environments. We isolated 13 ulvan-degrading bacteria and observed high diversity at the genus level. Further, the genera Paraglaciecola [...] Read more.
In this study, we aimed to isolate bacteria capable of degrading the polysaccharide ulvan from the green algae Ulva sp. (Chlorophyta, Ulvales, Ulvaceae) in marine environments. We isolated 13 ulvan-degrading bacteria and observed high diversity at the genus level. Further, the genera Paraglaciecola, Vibrio, Echinicola, and Algibacter, which can degrade ulvan, were successfully isolated for the first time from marine environments. Among the 13 isolates, only one isolate (Echinicola sp.) showed the ability not only to produce externally expressed ulvan lyase, but also to be periplasmic or on the cell surface. From the results of the full-genome analysis, lyase was presumed to be a member of the PL25 (BNR4) family of ulvan lyases, and the bacterium also contained the sequence for glycoside hydrolase (GH43, GH78 and GH88), which is characteristic of other ulvan-degrading bacteria. Notably, this bacterium has a unique ulvan lyase gene not previously reported. Full article
(This article belongs to the Special Issue Seaweed Biorefinery and Related Technologies)
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9 pages, 1954 KiB  
Article
Production of 4-Deoxy-L-erythro-5-Hexoseulose Uronic Acid Using Two Free and Immobilized Alginate Lyases from Falsirhodobacter sp. Alg1
by Yuzuki Tanaka, Yoshihiro Murase, Toshiyuki Shibata, Reiji Tanaka, Tetsushi Mori and Hideo Miyake
Molecules 2022, 27(10), 3308; https://doi.org/10.3390/molecules27103308 - 21 May 2022
Cited by 2 | Viewed by 2042
Abstract
Falsirhodobacter sp. alg1 expresses two alginate lyases, AlyFRA and AlyFRB, to produce the linear monosaccharide 4-deoxy-L-erythro-5-hexoseulose uronic acid (DEH) from alginate, metabolizing it to pyruvate. In this study, we prepared recombinant AlyFRA and AlyFRB and their immobilized enzymes and investigated DEH [...] Read more.
Falsirhodobacter sp. alg1 expresses two alginate lyases, AlyFRA and AlyFRB, to produce the linear monosaccharide 4-deoxy-L-erythro-5-hexoseulose uronic acid (DEH) from alginate, metabolizing it to pyruvate. In this study, we prepared recombinant AlyFRA and AlyFRB and their immobilized enzymes and investigated DEH production. Purified AlyFRA and AlyFRB reacted with sodium alginate and yielded approximately 96.8% DEH. Immobilized AlyFRA and AlyFRB were prepared using each crude enzyme solution and κ-carrageenan, and immobilized enzyme reuse in batch reactions and DEH yield were examined. Thus, DEH was produced in a relatively high yield of 79.6%, even after the immobilized enzyme was reused seven times. This method can produce DEH efficiently and at a low cost and can be used to mass produce the next generation of biofuels using brown algae. Full article
(This article belongs to the Special Issue Seaweed Biorefinery and Related Technologies)
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Review

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14 pages, 3190 KiB  
Review
4-Deoxy-l-erythro-5-hexoseulose Uronate (DEH) and DEH Reductase: Key Molecule and Enzyme for the Metabolism and Utilization of Alginate
by Shigeyuki Kawai and Wataru Hashimoto
Molecules 2022, 27(2), 338; https://doi.org/10.3390/molecules27020338 - 6 Jan 2022
Cited by 6 | Viewed by 2386
Abstract
4-Deoxy-l-erythro-5-hexoseulose uronate (DEH), DEH reductase, and alginate lyase have key roles in the metabolism of alginate, a promising carbon source in brown macroalgae for biorefinery. In contrast to the widely reviewed alginate lyase, DEH and DEH reductase have not [...] Read more.
4-Deoxy-l-erythro-5-hexoseulose uronate (DEH), DEH reductase, and alginate lyase have key roles in the metabolism of alginate, a promising carbon source in brown macroalgae for biorefinery. In contrast to the widely reviewed alginate lyase, DEH and DEH reductase have not been previously reviewed. Here, we summarize the current understanding of DEH and DEH reductase, with emphasis on (i) the non-enzymatic and enzymatic formation and structure of DEH and its reactivity to specific amino groups, (ii) the molecular identification, classification, function, and structure, as well as the structural determinants for coenzyme specificity of DEH reductase, and (iii) the significance of DEH for biorefinery. Improved understanding of this and related fields should lead to the practical utilization of alginate for biorefinery. Full article
(This article belongs to the Special Issue Seaweed Biorefinery and Related Technologies)
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