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Article ; Online: The Evolution of Rag Gene Enhancers and Transcription Factor E and Id Proteins in the Adaptive Immune System

Genki Yoshikawa / Kazuko Miyazaki / Hiroyuki Ogata / Masaki Miyazaki

International Journal of Molecular Sciences, Vol 22, Iss 5888, p

2021 Volume 5888

Abstract: Adaptive immunity relies on the V(D)J DNA recombination of immunoglobulin ( Ig ) and T cell receptor ( TCR ) genes, which enables the recognition of highly diverse antigens and the elicitation of antigen-specific immune responses. This process is ... ...

Abstract	Adaptive immunity relies on the V(D)J DNA recombination of immunoglobulin ( Ig ) and T cell receptor ( TCR ) genes, which enables the recognition of highly diverse antigens and the elicitation of antigen-specific immune responses. This process is mediated by recombination-activating gene (Rag) 1 and Rag2 (Rag1/2), whose expression is strictly controlled in a cell type-specific manner; the expression of Rag1/2 genes represents a hallmark of lymphoid lineage commitment. Although Rag genes are known to be evolutionally conserved among jawed vertebrates, how Rag genes are regulated by lineage-specific transcription factors (TFs) and how their regulatory system evolved among vertebrates have not been fully elucidated. Here, we reviewed the current body of knowledge concerning the cis-regulatory elements (CREs) of Rag genes and the evolution of the basic helix-loop-helix TF E protein regulating Rag gene CREs, as well as the evolution of the antagonist of this protein, the Id protein. This may help to understand how the adaptive immune system develops along with the evolution of responsible TFs and enhancers.
Keywords	adaptive immune system ; Rag1/2 gene enhancers ; E protein ; Id protein ; bHLH transcription factors ; T and B cell development ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
Subject code	570
Language	English
Publishing date	2021-05-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Ecological Structuring of Temperate Bacteriophages in the Inflammatory Bowel Disease-Affected Gut

Hiroki Nishiyama / Hisashi Endo / Romain Blanc-Mathieu / Hiroyuki Ogata

Microorganisms, Vol 8, Iss 1663, p

2020 Volume 1663

Abstract: The aim of this study was to elucidate the ecological structure of the human gut temperate bacteriophage community and its role in inflammatory bowel disease (IBD). Temperate bacteriophages make up a large proportion of the human gut microbiota and are ... ...

Abstract	The aim of this study was to elucidate the ecological structure of the human gut temperate bacteriophage community and its role in inflammatory bowel disease (IBD). Temperate bacteriophages make up a large proportion of the human gut microbiota and are likely to play a role in IBD pathogenesis. However, many of these bacteriophages await characterization in reference databases. Therefore, we conducted a large-scale reconstruction of temperate bacteriophage and bacterial genomes from the whole-metagenome sequence data generated by the IBD Multi’omics Database project. By associating phages with their hosts via genome comparisons, we found that temperate bacteriophages infect a phylogenetically wide range of bacteria. The majority of variance in bacteriophage community composition was explained by variation among individuals, but differences in the abundance of temperate bacteriophages were identified between IBD and non-IBD patients. Of note, in active ulcerative colitis patients, temperate bacteriophages infecting Bacteroides uniformis and Bacteroides thetaiotaomicron —two species experimentally proven to be beneficial to gut homeostasis—were over-represented, whereas their hosts were under-represented in comparison with non-IBD patients. Supporting the mounting evidence that gut viral community plays a vital role in IBD, our results show potential association between temperate bacteriophages and IBD pathogenesis.
Keywords	temperate bacteriophage ; inflammatory bowel disease ; ulcerative colitis ; Crohn’s disease ; gut microbiota ; Biology (General) ; QH301-705.5
Subject code	610
Language	English
Publishing date	2020-10-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Contrasting biogeography and diversity patterns between diatoms and haptophytes in the central Pacific Ocean

Hisashi Endo / Hiroyuki Ogata / Koji Suzuki

Scientific Reports, Vol 8, Iss 1, Pp 1-

2018 Volume 13

Abstract: Abstract Diatoms and haptophytes are two major phytoplankton groups, playing pivotal roles in global biogeochemical cycles and marine ecosystems. In general, diatoms have higher growth rates than haptophytes, whereas haptophytes tend to have higher ... ...

Abstract	Abstract Diatoms and haptophytes are two major phytoplankton groups, playing pivotal roles in global biogeochemical cycles and marine ecosystems. In general, diatoms have higher growth rates than haptophytes, whereas haptophytes tend to have higher nutrient uptake affinity. However, precise linkages between their ecological traits and geographical distributions remain poorly understood. Herein, we examined the basin-scale variability of the abundance and taxonomic composition of these two phytoplankton groups across 35 sites in the Pacific Ocean using DNA metabarcoding. The diatom community was generally dominated by a few genera at each sample site, whereas the haptophyte community consisted of a large number of genera in most of the sites. The coexistence of various haptophyte genera might be achieved by diversification of their ecophysiological traits such as mixotrophy. On the other hand, the diatom community might experience greater inter-genus competition due to the rapid uptake of nutrients. Our data further supports the notion that their distinct ecological strategies underlie the emergence of contrasting diversity patterns of these phytoplankton groups in the central Pacific at a basin scale.
Keywords	Medicine ; R ; Science ; Q
Subject code	551
Language	English
Publishing date	2018-07-01T00:00:00Z
Publisher	Nature Publishing Group
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Genomic adaptation of giant viruses in polar oceans

Lingjie Meng / Tom O. Delmont / Morgan Gaïa / Eric Pelletier / Antonio Fernàndez-Guerra / Samuel Chaffron / Russell Y. Neches / Junyi Wu / Hiroto Kaneko / Hisashi Endo / Hiroyuki Ogata

Nature Communications, Vol 14, Iss 1, Pp 1-

2023 Volume 12

Abstract: Abstract Despite being perennially frigid, polar oceans form an ecosystem hosting high and unique biodiversity. Various organisms show different adaptive strategies in this habitat, but how viruses adapt to this environment is largely unknown. Viruses of ...

Abstract	Abstract Despite being perennially frigid, polar oceans form an ecosystem hosting high and unique biodiversity. Various organisms show different adaptive strategies in this habitat, but how viruses adapt to this environment is largely unknown. Viruses of phyla Nucleocytoviricota and Mirusviricota are groups of eukaryote-infecting large and giant DNA viruses with genomes encoding a variety of functions. Here, by leveraging the Global Ocean Eukaryotic Viral database, we investigate the biogeography and functional repertoire of these viruses at a global scale. We first confirm the existence of an ecological barrier that clearly separates polar and nonpolar viral communities, and then demonstrate that temperature drives dramatic changes in the virus–host network at the polar–nonpolar boundary. Ancestral niche reconstruction suggests that adaptation of these viruses to polar conditions has occurred repeatedly over the course of evolution, with polar-adapted viruses in the modern ocean being scattered across their phylogeny. Numerous viral genes are specifically associated with polar adaptation, although most of their homologues are not identified as polar-adaptive genes in eukaryotes. These results suggest that giant viruses adapt to cold environments by changing their functional repertoire, and this viral evolutionary strategy is distinct from the polar adaptation strategy of their hosts.
Keywords	Science ; Q
Subject code	551
Language	English
Publishing date	2023-10-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Genome analysis of Parmales, the sister group of diatoms, reveals the evolutionary specialization of diatoms from phago-mixotrophs to photoautotrophs

Hiroki Ban / Shinya Sato / Shinya Yoshikawa / Kazumasa Yamada / Yoji Nakamura / Mutsuo Ichinomiya / Naoki Sato / Romain Blanc-Mathieu / Hisashi Endo / Akira Kuwata / Hiroyuki Ogata

Communications Biology, Vol 6, Iss 1, Pp 1-

2023 Volume 14

Abstract: Abstract The order Parmales (class Bolidophyceae) is a minor group of pico-sized eukaryotic marine phytoplankton that contains species with cells surrounded by silica plates. Previous studies revealed that Parmales is a member of ochrophytes and sister ... ...

Abstract	Abstract The order Parmales (class Bolidophyceae) is a minor group of pico-sized eukaryotic marine phytoplankton that contains species with cells surrounded by silica plates. Previous studies revealed that Parmales is a member of ochrophytes and sister to diatoms (phylum Bacillariophyta), the most successful phytoplankton group in the modern ocean. Therefore, parmalean genomes can serve as a reference to elucidate both the evolutionary events that differentiated these two lineages and the genomic basis for the ecological success of diatoms vs. the more cryptic lifestyle of parmaleans. Here, we compare the genomes of eight parmaleans and five diatoms to explore their physiological and evolutionary differences. Parmaleans are predicted to be phago-mixotrophs. By contrast, diatoms have lost genes related to phagocytosis, indicating the ecological specialization from phago-mixotrophy to photoautotrophy in their early evolution. Furthermore, diatoms show significant enrichment in gene sets involved in nutrient uptake and metabolism, including iron and silica, in comparison with parmaleans. Overall, our results suggest a strong evolutionary link between the loss of phago-mixotrophy and specialization to a silicified photoautotrophic life stage early in diatom evolution after diverging from the Parmales lineage.
Keywords	Biology (General) ; QH301-705.5
Language	English
Publishing date	2023-07-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: DNA repair genes in the Megavirales pangenome

Blanc-Mathieu, Romain / Hiroyuki Ogata

Current opinion in microbiology. 2016 June, v. 31

2016

Abstract: The order ‘Megavirales’ represents a group of eukaryotic viruses with a large genome encoding a few hundred up to two thousand five hundred genes. Several members of Megavirales possess genes involved in major DNA repair pathways. Some of these genes ... ...

Abstract	The order ‘Megavirales’ represents a group of eukaryotic viruses with a large genome encoding a few hundred up to two thousand five hundred genes. Several members of Megavirales possess genes involved in major DNA repair pathways. Some of these genes were likely inherited from an ancient virus world and some others were derived from the genomes of their hosts. Here we examine molecular phylogenies of key DNA repair enzymes in light of recent hypotheses on the origin of Megavirales, and propose that the last common ancestors of the individual families of the order Megavirales already possessed DNA repair functions to achieve and maintain a moderately large genome and that this repair capacity gradually increased, in a family-dependent manner, during their recent evolution.
Keywords	ancestry ; DNA repair ; enzymes ; genes ; hosts ; inheritance (genetics) ; phylogeny ; viruses
Language	English
Dates of publication	2016-06
Size	p. 94-100.
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	1418474-6
ISSN	1879-0364 ; 1369-5274
ISSN (online)	1879-0364
ISSN	1369-5274
DOI	10.1016/j.mib.2016.03.011
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Xanthomonas citri jumbo phage XacN1 exhibits a wide host range and high complement of tRNA genes

Genki Yoshikawa / Ahmed Askora / Romain Blanc-Mathieu / Takeru Kawasaki / Yanze Li / Miyako Nakano / Hiroyuki Ogata / Takashi Yamada

Scientific Reports, Vol 8, Iss 1, Pp 1-

2018 Volume 10

Abstract: Abstract Xanthomonas virus (phage) XacN1 is a novel jumbo myovirus infecting Xanthomonas citri, the causative agent of Asian citrus canker. Its linear 384,670 bp double-stranded DNA genome encodes 592 proteins and presents the longest (66 kbp) direct ... ...

Abstract	Abstract Xanthomonas virus (phage) XacN1 is a novel jumbo myovirus infecting Xanthomonas citri, the causative agent of Asian citrus canker. Its linear 384,670 bp double-stranded DNA genome encodes 592 proteins and presents the longest (66 kbp) direct terminal repeats (DTRs) among sequenced viral genomes. The DTRs harbor 56 tRNA genes, which correspond to all 20 amino acids and represent the largest number of tRNA genes reported in a viral genome. Codon usage analysis revealed a propensity for the phage encoded tRNAs to target codons that are highly used by the phage but less frequently by its host. The existence of these tRNA genes and seven additional translation-related genes as well as a chaperonin gene found in the XacN1 genome suggests a relative independence of phage replication on host molecular machinery, leading to a prediction of a wide host range for this jumbo phage. We confirmed the prediction by showing a wider host range of XacN1 than other X. citri phages in an infection test against a panel of host strains. Phylogenetic analyses revealed a clade of phages composed of XacN1 and ten other jumbo phages, indicating an evolutionary stable large genome size for this group of phages.
Keywords	Medicine ; R ; Science ; Q
Subject code	572
Language	English
Publishing date	2018-03-01T00:00:00Z
Publisher	Nature Publishing Group
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Supplementation of pancreatic digestive enzymes alters the composition of intestinal microbiota in mice

Nishiyama, Hiroki / Hiroyuki Ogata / Masatoshi Kudo / Susumu Goto / Tomohiro Watanabe / Tomoyuki Nagai / Toshiharu Sakurai / Yoshihisa Okazaki / Yoshinao Azuma

Biochemical and biophysical research communications. 2018 Jan. 01, v. 495, no. 1

2018

Abstract: Although pancreatic enzyme replacement therapy (PERT) is effective in the alleviation of pancreatic exocrine insufficiency (PEI)-related symptoms in patients with chronic pancreatitis, its mechanism of action is poorly understood. Recent studies suggest ... ...

Abstract	Although pancreatic enzyme replacement therapy (PERT) is effective in the alleviation of pancreatic exocrine insufficiency (PEI)-related symptoms in patients with chronic pancreatitis, its mechanism of action is poorly understood. Recent studies suggest that the intestinal microbiota is associated with the pathogenesis of chronic pancreatitis. Therefore, we hypothesized that PERT exerts its effect by modifying the intestinal microbiota in addition to its presumed role in promoting fat and protein absorption. To explore the mechanism of action of PERT, we analyzed the intestinal microbiotas of two groups of mice treated with either pancrelipase or tap water by using 16S rRNA amplicon sequencing. The results revealed that the bacterial compositions of the pancrelipase-treated mice were significantly different from those of the control samples. Akkermansia muciniphila, a key beneficial bacterium in the intestinal tract, showed a higher relative abundance in the pancrelipase-treated samples than in the control samples. Lactobacillus reuteri, a widely used probiotic bacterium known to relieve intestinal inflammation, also showed a higher relative abundance in the pancrelipase-treated samples. These results suggested that PERT induces the colonization of beneficial bacteria, thereby contributing to the attenuation of PEI-associated symptoms in addition to improvement of the nutritional state.
Keywords	absorption ; digestive enzymes ; inflammation ; intestinal microorganisms ; intestines ; Lactobacillus reuteri ; mechanism of action ; mice ; nutritional status ; pancreatitis ; pathogenesis ; patients ; probiotics ; ribosomal RNA ; tap water ; therapeutics
Language	English
Dates of publication	2018-0101
Size	p. 273-279.
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	205723-2
ISSN	0006-291X ; 0006-291X
ISSN (online)	0006-291X
ISSN	0006-291X
DOI	10.1016/j.bbrc.2017.10.130
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Mucosal microbiota and gene expression are associated with long-term remission after discontinuation of adalimumab in ulcerative colitis

Toshiharu Sakurai / Hiroki Nishiyama / Kazuko Sakai / Marco A. De Velasco / Tomoyuki Nagai / Yoriaki Komeda / Hiroshi Kashida / Akiyoshi Okada / Isao Kawai / Kazuto Nishio / Hiroyuki Ogata / Masatoshi Kudo

Scientific Reports, Vol 10, Iss 1, Pp 1-

2020 Volume 12

Abstract: Abstract Given that sustained remission is the ultimate treatment goal in the management of patients with ulcerative colitis (UC), the decision to stop anti-tumor necrosis factor (anti-TNF) treatment in UC patients is difficult. The aim of this study was ...

Abstract	Abstract Given that sustained remission is the ultimate treatment goal in the management of patients with ulcerative colitis (UC), the decision to stop anti-tumor necrosis factor (anti-TNF) treatment in UC patients is difficult. The aim of this study was to evaluate mucosal microbiota and gene expression profiles associated with long-term remission after discontinuation of anti-TNF therapy. In nine UC patients who received anti-TNF therapy for 6 months, microbiota isolated from uninflamed mucosae and gene expression in inflamed and uninflamed mucosae were investigated at week 0 and at week 24. At treatment initiation, Fusobacterium sp. and Veillonella dispar were over-represented in the relapse group compared with the non-relapse group. After treatment, Dorea sp. and Lachnospira sp. were over-represented in the non-relapse group. In the relapse group only, a significant shift in gut bacterial community composition was found between week 0 and week 24. Gene expression of ALIX (PDCD6IP) and SLC9A3 was significantly higher in the non-relapse group than in the relapse group. Lastly, we used machine learning methods to identify relevant gene signatures associated with sustained remission. Statistical analyses of microbiota and expression profiles revealed differences between UC patients who did or did not keep remission after the discontinuation of TNF inhibitors. Trial registration: UMIN000020785: Evaluation of adalimumab therapy in mesalazine-resistant or -intolerant ulcerative colitis; an observational study (EARLY study).
Keywords	Medicine ; R ; Science ; Q
Subject code	616
Language	English
Publishing date	2020-11-01T00:00:00Z
Publisher	Nature Publishing Group
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: An Optimized Metabarcoding Method for Mimiviridae

Florian Prodinger / Hisashi Endo / Yasuhiro Gotoh / Yanze Li / Daichi Morimoto / Kimiho Omae / Kento Tominaga / Romain Blanc-Mathieu / Yoshihito Takano / Tetsuya Hayashi / Keizo Nagasaki / Takashi Yoshida / Hiroyuki Ogata

Microorganisms, Vol 8, Iss 506, p

2020 Volume 506

Abstract: Mimiviridae is a group of viruses with large genomes and virions. Ecological relevance of Mimiviridae in marine environments has been increasingly recognized through the discoveries of novel isolates and metagenomic studies. To facilitate ecological ... ...

Abstract	Mimiviridae is a group of viruses with large genomes and virions. Ecological relevance of Mimiviridae in marine environments has been increasingly recognized through the discoveries of novel isolates and metagenomic studies. To facilitate ecological profiling of Mimiviridae , we previously proposed a meta-barcoding approach based on 82 degenerate primer pairs (i.e., MEGAPRIMER) targeting the DNA polymerase gene of Mimiviridae . The method detected a larger number of operational taxonomic units (OTUs) in environmental samples than previous methods. However, it required large quantities of DNA and was laborious due to the use of individual primer pairs. Here, we examined coastal seawater samples using varying PCR conditions and purification protocols to streamline the MEGAPRIMER method. Mixing primer pairs in “cocktails” reduced the required amount of environmental DNA by 90%, while reproducing the results obtained by the original protocol. We compared the results obtained by the meta-barcoding approach with quantifications using qPCR for selected OTUs. This revealed possible amplification biases among different OTUs, but the frequency profiles for individual OTUs across multiple samples were similar to those obtained by qPCR. We anticipate that the newly developed MEGAPRIMER protocols will be useful for ecological investigation of Mimiviridae in a larger set of environmental samples.
Keywords	‘Megaviridae’ ; Mimiviridae ; DNA polymerase ; MEGAPRIMER ; primer cocktail ; Biology (General) ; QH301-705.5
Subject code	500
Language	English
Publishing date	2020-04-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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