Archaeal histones
A subpopulation of archaea possesses histones, which are similar to eukaryotic histones H3 and H4. However, archaeal histones are smaller than H3 and H4, and are not post-translationally modified. Archaeal histones are more diverse in amino acid sequences than eukaryotic histones. Nishida and Oshima (2017) showed that distribution of archaeal histones is associated with genomic guanine-cytosine content (GC content). Thus, archaeal histones have evolved concomitantly with their genomic GC content.
Archiascomycetes
Nishida and Sugiyama (1994) proposed archiascomycetes as the earliest ascomycetous lineage. Introductory Mycology 4th edition (Alexopoulos, Mims, and Blackwell 1996) included a chapter on archiascomycetes. At present, the archiascomycetes consists of the genera Archaeorhizomyces, Neolecta, Pneumocystis, Protomyces, Saitoella, Schizosaccharomyces, and Taphrina.
Bacterial cell enlargement and microinjection into the cell
Generally, cell wall inhibits enlargement of bacteria. Protoplasts and spheroplasts are generated by lysing the cell wall (peptidoglycan layer) of Gram-positive (G+) and Gram-negative (G-) bacteria, respectively. Bacterial protoplasts and spheroplasts can enlarge under suitable conditions. The cell size should be more than 15 μm in diameter for microinjection. In our studies, the spheroplasts of Deinococcus grandis, Erythrobacter litoralis, Lelliottia amnigena, and Rhodospirullum rubrum enlarged in the Marine Broth including penicillin. In addition, the Enterococcus faecalis protoplasts enlarged. During the growth of those spheroplasts/protoplasts, although cell division was not observed, DNA replication and vacuoles were observed. Nishida (2020) summarized the factors that influence bacterial cell enlargement. Takahashi et al. (2020) succeeded in generating cells of Enterococcus faecalis (G+) and Lelliottia amnigena (G-) suitable for microinjection by adjusting the metal salt composition in the medium. In addition, Takahashi and Nishida (2022) enlarged cells of E. faecalis for microinjection of heterogeneous genomic DNAs into the cytoplasm. YouTube: microinjection of calligraphy ink into a bacterial cell
Genome comparison
Nishida et al. (2011) showed the phylogenetic position of Dictyoglomus, inferred form whole-genome comparison. There are three major strategies of whole-genome comparison; comparison of orthologous sequences, comparison of gene content, and comparison of genome signature. In the orthologous sequences comparison, only mutational sites are used. Thus, evolutionary factors are considered in that comparison. In the gene content comparison, only gene gain and loss information are used. Thus, ecological (environmental) factors are considered in that comparison. In contrast, it is uncertain how evolutionary and/or ecological factors affect the result in the genome signature comparison.
Histone and nucleosome
Genomic base composition (guanine-cytosine content, GC content) is maintained by GC content-dependent DNA-binding proteins. Histone is one of GC content-dependent DNA-binding proteins, which maintains eukaryotic genomic GC content. Eukaryotic genomic DNA is packaged with histone proteins to form chromatin. The most fundamental repeating unit of chromatin is the nucleosome. Nucleosomes consist of an octamer of histones, around which genomic DNA is wrapped. GC and AT rich sequences, respectively, favor and disfavor core nucleosomes, although some variations of preferred sequences exist between species. Nishida et al. (2006) showed that nucleosome depletion occurs in the vicinity of the transcription start site in human cells. Genome-wide nucleosome mapping revealed that nucleosome-free regions are pervasive in gene promoters. Nucleosome positioning plays an important role in gene expression as well as genomic DNA maintenance. Nucleosomes downstream from the nucleosome-depleted region are well positioned, with positioning decaying with increasing distance into protein coding region.
Histone genes
Histone is one of the most conserved proteins among eukaryotes, which is a GC content-dependent DNA-binding protein. Although animals and plants lack intron in their replication-dependent histone genes, some fungi have introns. Basidiomycetes and filamentous ascomycetes have introns in their histone genes. A common ancestor of ascomycetes and basidiomycetes might have a few introns in the histone genes. Yun and Nishida (2011) suggested that during the fungal evolution, archiascomycetes and ascomycetous yeasts had lost the introns on histone genes; basidiomycetes and filamentous ascomycetes had acquired other introns independently.
Lysine biosynthesis
It has been recognized that fungi and some of protists biosynthesize lysine through the α-aminoadipate and that archaea, bacteria, and plants biosynthesize lysine through the diaminopimelate. However, it was discovered that the bacterium Thermus thermophilus biosynthesizes lysine via the AAA pathway. Nishida et al. (1999) showed that Thermus AAA pathway is not identical to eukaryotic one, which is distributed to the archaeon Pyrococcus. This lysine biosynthesis led a light on the evolution of amino acid biosynthesis.
Mixia osmundae
Mixia osmundae had belonged to the ascomycetes until 1995. Nishida et al. (1995) showed that Mixia osmundae is a member of the basidiomycetes, based on its 18S rDNA sequence and morphological characters. Mixia osmundae was described as a basidiomycetous yeast in The Yeasts 5th edition, a taxonomic study. Nishida et al. (2012) identified and reported 13,393,708 nucleotides and 6,726 protein-coding genes of Mixia osmundae.
Sake production and kuratsuki bacteria
Sake production maintains a critical position in traditional Japanese cultures. In the sake production process, the two eukaryotic microorganisms, koji mold and sake yeast are used. Koji mold Aspergillus oryzae converts starch of rice to sugar, but sake yeast Saccharomyces cerevisiae cannot digest the starch. Sake yeast converts the sugar to ethanol, but koji mold cannot produce ethanol. Sake yeast produces not only ethanol but also other chemical compounds that affect the flavor and taste of sake. Sake yeast interacts with other microorganisms during the sake production process. As is known as far, kuratsuki yeasts and kuratsuki lactic acid bacteria have existed in sake breweries. The Japanese words "kura" and "tsuki" correspond to "sake brewery" and "inhabiting", respectively. Terasaki et al. (2021) reported kuratsuki Kocuria, which was isolated from Narimasa Sake Brewery. Kocuria belongs to actinomycetes, which is not lactic acid bacteria. Kanamoto et al. (2021) reported kuratsuki Bacillus, which was isolated from Shiraki-Tsunesuke Sake Brewery. Nishida (2024) summarized the interaction between sake yeast and kuratsuki bacteria. TOYOWebStyle [in Japanese]: our research concept for kuratsuki bacteria in sake making