Wild-type Aspergillus oryzae RIB40 contains two copies of the AO090005001597 gene. We previously constructed A. oryzae RIB40 strain, RKuAF8B, with multiple chromosomal deletions, in which the AO090005001597 copy number was found to be increased significantly. Sequence analysis indicated that AO090005001597 is part of a putative 6,000-bp retrotransposable element, flanked by two long terminal repeats (LTRs) of 669 bp, with characteristics of retroviruses and retrotransposons, and thus designated AoLTR (A. oryzae LTR-retrotransposable element). AoLTR comprised putative reverse transcriptase, RNase H, and integrase domains. The deduced amino acid sequence alignment of AoLTR showed 94% overall identity with AFLAV, an A. flavus Tf1/sushi retrotransposon. Quantitative real-time RT-PCR showed that AoLTR gene expression was significantly increased in the RKuAF8B, in accordance with the increased copy number. Inverse PCR indicated that the full-length retrotransposable element was randomly integrated into multiple genomic locations. However, no obvious phenotypic changes were associated with the increased AoLTR gene copy number.
We sequenced the genomic DNA and the transcribed RNA of the ascomycetous budding yeast Saitoella complicata, which belongs to the earliest lineage (Taphrinomycotina) of ascomycetes. We found 3 protein-coding regions similar to Clr6 of Schizosaccharomyces (a member of Taphrinomycotina). Clr6 has a structure similar to that of Rpd3 and Hos2 of Saccharomyces. These proteins belong to the class 1 histone deacetylase (HDAC) family. The phylogenetic tree showed that the Clr6, Hos2, and Rpd3 lineages are separated in fungal HDACs. Basidiomycetes have 3 proteins belonging to the Clr6, Hos2, and Rpd3 lineages. On the other hand, whereas ascomycetes except for Schizosaccharomyces have the Hos2 and Rpd3 homologs, and lack the Clr6 homolog, Schizosaccharomyces has the Clr6 and Hos2 homologs, and lacks the Rpd3 homolog. Interestingly, Pneumocystis and Saitoella have 3 proteins belonging to the Clr6, Hos2, and Rpd3 lineages. Thus, these fungi are the first ascomycete found to possess all 3 types. Our findings indicated that Taphrinomycotina has conserved the Clr6 protein, suggesting that the ancestor of Dikarya (ascomycetes and basidiomycetes) had 3 proteins belonging to the Clr6, Hos2, and Rpd3 lineages. During ascomycete evolution, Pezizomycotina and Saccharomycotina appear to have lost their Clr6 homologs and Schizosaccharomyces to have lost its Rpd3 homolog.
Eleven strains of poly(L-lactide) (PLLA)-degrading thermophilic bacteria were isolated from forest soils and selected based on clear zone formation on an emulsified PLLA agar plate at 50°C. Among the isolates, strain LP175 showed the highest PLLA-degrading ability. It was closely related to Laceyella sacchari, with 99.9% similarity based on the 16S rRNA gene sequence. The PLLA-degrading enzyme produced by the strain was purified to homogeneity by 48.1% yield and specific activity of 328 U·mg-protein-1 with a 15.3-fold purity increase. The purified enzyme was strongly active against specific substrates such as casein and gelatin and weakly active against Suc-(Ala)3-pNA. Optimum enzyme activity was exhibited at a temperature of 60°C with thermal stability up to 50°C and a pH of 9.0 with pH stability in a range of 8.5-10.5. Molecular weight of the enzyme was approximately 28.0 kDa, as determined by gel filtration and SDS-PAGE. The inhibitors phenylmethylsulfonyl fluoride (PMSF), ethylenediaminetetraacetate (EDTA), and ethylene glycol-bis(2-aminoethylether)-N,N,N′,N′-tetraacetic acid (EGTA) strongly inhibited enzyme activity, but the activity was not inhibited by 1 mM 1,10-phenanthroline (1,10-phen). The N-terminal amino acid sequences had 100% homology with thermostable serine protease (thermitase) from Thermoactinomyces vulgaris. The results obtained suggest that the PLLA-degrading enzyme produced by L. sacchari strain LP175 is serine protease.
A Gram-positive, facultative-anaerobic, rod-shaped and endospore-forming bacterium designated as strain J30-4T was isolated from peat-soil collected in Russia. 16S rRNA gene sequence analysis revealed that strain belongs to the genus Paenibacillus, closely related to Paenibacillus terrigena A35T (98.1%) and Paenibacillus harenae B519T (95.5%). Chemotaxonomic analysis revealed that strain J30-4T possessed menaquinone MK-7 as predominant quinone and diphosphatidylglycerol, phosphatidylglycerol, phosphatidyl-ethanolamine, phosphatidyl-N-methylethanolamine and several unknown lipids were detected in the polar lipid profile. The cell wall peptidoglycan was of the A1γ type (meso-diaminopimelic acid). The major fatty acids were anteiso-C15:0 and iso-C16:0. The DNA G+C content of J30-4T was 55.5 mol%. Based on phenotypic, chemotaxonomic and phylogenetic data presented in this study, strain J30-4T (= KEMC 7302-014T = JCM 18166T) is indicative of a new Paenibacillus species, for which the name Paenibacillus humi sp. nov., is proposed.
A Gram-negative, facultatively anaerobic, pale-red-pigmented, non-motile, rod-shaped strain designated HG677T was isolated from a sediment sample collected at Nagasuka Fishery Harbor in Miyagi Prefecture, Japan. Phylogenetic analyses based on the 16S rRNA gene sequence revealed that the novel isolate was affiliated with the phylum Bacteroidetes and that it showed highest sequence similarity (97.2%) to Sunxiuqiniaelliptica DQHS4T. The hybridization values for DNA-DNA relatedness between the strains of HG677T and Sunxiuqiniaelliptica DQHS4T were lower than 70%, which is accepted as the phylogenetic definition of a novel species. The DNA G+C content of strain HG677T was 47.5 mol%; MK-7 was the major menaquinone; and the presence of iso-C15：0 and iso-C17：0 3-OH as the major cellular fatty acids supported the identification of the novel isolate as a member of the genus Sunxiuqinia. A complex polar lipid profile was present consisting of phosphatidylethanolamine, unidentified phospholipids, an unidentified aminolipid and four unidentified lipids. From the distinct phylogenetic position and combination of genotypic and phenotypic characteristics, the strain is considered to represent a novel species for which the name Sunxiuqiniarutila sp. nov. is proposed. The type strain of Sunxiuqiniarutila is HG677T (= KCTC 32434T = NBRC 109919T).
A Gram-negative, strictly aerobic, reddish-pink-pigmented, non-motile, rod-shaped strain designated A6F-52T was isolated from a lake sediment sample. Preliminary analysis based on the 16S rRNA gene sequence revealed that the novel isolate could be affiliated with the family Catalimonadaceae of the phylum Bacteroidetes and that it showed highest sequence similarity (97.2%) to Catalinimonas alkaloidigena CNU-914T. The level of DNA-DNA relatedness between strains A6F-52T and Catalinimonas alkaloidigena CNU-914T was less than 70%, which is accepted as the phylogenetic definition of a species. The DNA G+C content of strain A6F-52T was 44.4 mol%; MK-7 was the major menaquinone; and the presence of iso-C15：0, C16：1 ω5C and iso-C17：0 3-OH as the major cellular fatty acids supported the identification of the novel isolate as a member of the genus Catalinimonas. A complex polar lipid profile was present consisting of phosphatidylethanolamine, an unidentified phospholipid, and an unidentified lipid. From the distinct phylogenetic position and combination of genotypic and phenotypic characteristics, the strain is considered to represent a novel species for which the name Catalinimonas niigatensis sp. nov. is proposed. The type strain of Catalinimonas niigatensis is A6F-52T (= KCTC 32474T = NBRC 109829T).
A novel bacterial strain belonging to the genus Roseomonas was isolated from the trunk surface of a mono maple (Acer mono) tree growing in the Shirakami Mountains. The strain, designated R-1T, was Gram-negative, non-motile, and oval-rod, and formed reddish colonies on agar plates, as has previously been described for Roseomonas species. Although motility was not observed, cells were peritrichously flagellated. Strain R-1T preferred organic acids over carbohydrates as growth substrates. The major cellular fatty acid was C18:1 ω7c (48.79%). Ubiquinone-10 was the major respiratory quinone. Strain R-1T demonstrated the highest 16S rRNA gene sequence similarity with Roseomonas pecuniae N75T (96.9%). Phylogenetic analysis based on 16S rRNA gene sequences confirmed that strain R-1T was a member of the genus Roseomonas and formed a cluster with R. pecuniae N75T. DNA-DNA hybridization between strain R-1T and R. pecuniae N75T yielded 21.7% relatedness. On the basis of its phenotypic, phylogenetic, and chemotaxonomic characteristics, strain R-1T represents a novel species within the genus Roseomonas, for which the name Roseomonas aceris sp. nov. has been proposed. The type strain is R-1T (NBRC 109410T = DSM 26554 T).
Small regulatory RNAs (sRNAs) are conserved among a wide range of bacteria. They modulate the translational efficiency of target mRNAs through base-pairing with the help of RNA chaperone Hfq. The present study identified a novel sRNA, Esr41 (enterohemorrhagic Escherichia coli O157 small RNA #41), from an intergenic region of an enterohemorrhagic E. coli (EHEC) O157:H7 Sakai-specific sequence that is not present in the nonpathogenic E. coli K-12. Esr41 was detected as an RNA molecule approximately 70 nucleotides long with a 3′ GC-rich palindrome sequence followed by a long poly(U), which is a characteristic of rho-independent terminators and is also a structural feature required for the action of Hfq. EHEC O157 harboring a multicopy plasmid carrying the esr41 gene increased cell motility and the expression of fliC, a gene encoding a major flagellar component. These results indicate that Esr41 stimulates fliC expression in EHEC O157. Furthermore, the increase in cell motility induced by Esr41 was also observed in the E. coli K-12, suggesting that target genes controlled by Esr41 are present in both EHEC O157 and K-12.