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Genome analysis of mitochondria and chloroplast from red alga dulse and the relation of bioactivity × SDGs
It is found that red algae from northern Japan, such as the low-use red alga Dulse from Hokkaido, are rich in a variety of useful biochemical components. The mitochondrial and chloroplast genome structures of several species of red algae have been determined in order to understand the mechanisms by which these components are produced. Through these studies, we hope to contribute to the development of foods that improve people's health.
Abstract
Red algae are classified more than 7,000 species in the world and have great diversity among seaweeds. The number of species have been increasing by the new classification method by gene marker and genome information. Genome contains seaweed proteins information. Red algae are rich in proteins, especially Nori possesses about 40% protein in dry weight, having great concern for new protein sources. Proteins have a potential not only the source of amino acid but also bioactive peptides. We here determined the complete genome structure of mitochondria and chloroplast from Japanese dulse, which is a new bioresource in Southern Hokkaido and attempted to elucidate of the bioactivity.
Dulse Red alga dulse lives in cold region from Iwate prefecture to Hokkaido prefecture in Japan. Dulse contains high amount of protein like Nori. Red algae have galactan (agar and carrageenan) in their cell wall, but dulse contains xylan as the cell wall.
Functional peptides Angiotensin converting enzyme I (ACE) and dipeptidyl peptidase 4 are the enzymes, which are related to blood pressure and blood sugar. Peptides having specific structure repress rapid increases in blood pressure and blood sugar by the inhibition of enzyme activities.
in silico analysis in silico analysis is performed by using computer not in vivo and in vitro. In this study, ACE inhibitory peptide information was obtained from database and evaluated in the chloroplast proteins in Southern Hokkaido dulse. This information is useful for exploring novel peptides and breeding of high value dulse.
Research purpose In this study, we determined the complete mitochondria and chloroplast genome of Southern Hokkaido dulse and explored peptides related to health functions.
Mitochondria and Chloroplast genome of Southern Hokkaido Dulse
Genome DNA was extracted from dulse leaf, and the complete genomes were determined by next generation sequencer. Chloroplast genome is circular structure composed of 192,409 bp containing 205 protein coding genes. Mitochondrial genome is also circular structure composed of 31,399 bp containing 27 protein coding genes. These accession numbers were deposited in DDBJ (ddbj.nig.ac.jp/) as chloroplast: AB807662 and mitochondria: AP019296.
Functional peptides in chloroplast genome
Photosynthesis is essential for the growth of seaweed. Chloroplasts have many proteins involved in photosynthesis. The composition of amino acids in dulse was very similar to that of chloroplast proteins (Table 1). Therefore, peptide information that inhibits ACE was obtained from the database and compared with the chloroplast genome proteins (Table 2). This study is focusing on tripeptides, revealing that many peptides are found in photosynthesis (PS) and metabolism (Meta). The data would be more accurate by calculating the amount of each component.
Genetic Classification of Southern Hokkaido Dulse
Phylogenetic tree Phylogenetic tree was constructed by maximum likelihood method using successive mitochondrial gene (cox1) and chloroplast genes (psbA and rbcL). Red and blue box shows Southern Hokkaido dulse and Atlantic dulse, respectively. Chloroplast genomes were similar between them, however, these species were genetically separated in this tree.
Mitochondrial genome structures There are two different between Southern Hokkaido dulse and Atlantic dulse. One is intron size in ribosomal RNA large subunit. The other is the direction of two genes (orf43 and orf44) were opposite.
The amount of protein in Southern Hokkaido dulse contains about 40% of dry weight, which is higher than the Atlantic dulse and Palmaria mollis (Devaleraea mollis). We need to investigate in future studies whether the difference from growth condition or genetics.
Future plan
Dulse chloroplast proteins contain many peptides that inhibit ACE. It is necessary to investigate the cooking methods (peptide production by protease) for bioavailability.
Find novel peptides by in silico and in vitro studies. Red algae mitochondria and chloroplast genomes are close. Therefore, the novel peptides will be also found in other red algae, leading to a comprehensive understanding of the health functionality of red algae.
- Southern Hokkaido dulse may contain more protein than overseas. Therefore, it is expected to clarify the reason for a new protein source.