Comparative analysis of bacterial communities associated with healthy and diseased corals in the Indonesian sea

Coral reef ecosystems are impacted by climate change and human activities, such as increasing coastal development, overfishing, sewage and other pollutant discharge, and consequent eutrophication, which triggers increasing incidents of diseases and deterioration of corals worldwide. In this study, bacterial communities associated with four species of corals: Acropora aspera, Acropora formosa, Cyphastrea sp., and Isopora sp. in the healthy and disease stages with different diseases were compared using tagged 16S rRNA sequencing. In total, 59 bacterial phyla, 190 orders, and 307 genera were assigned in coral metagenomes where Proteobacteria and Firmicutes were predominated followed by Bacteroidetes together with Actinobacteria, Fusobacteria, and Lentisphaerae as minor taxa. Principal Coordinates Analysis (PCoA) showed separated clustering of bacterial diversity in healthy and infected groups for individual coral species. Fusibacter was found as the major bacterial genus across all corals. The lower number of Fusibacter was found in A. aspera infected with white band disease and Isopora sp. with white plaque disease, but marked increases of Vibrio and Acrobacter, respectively, were observed. This was in contrast to A. formosa infected by a black band and Cyphastrea sp. infected by yellow blotch diseases which showed an increasing abundance of Fusibacter but a decrease in WH1-8 bacteria. Overall, infection was shown to result in disturbance in the complexity and structure of the associated bacterial microbiomes which can be relevant to the pathogenicity of the microbes associated with infected corals

Analysis of the interaction between human kidney anion exchanger 1 and kanadaptin using yeast two-hybrid systems

Abstract Kidney anion exchanger adaptor protein (Kanadaptin) is a protein which interacts with the cytoplasmic N-terminal domain of kidney anion exchanger 1 (kAE1) and was first detected in mice using the yeast two-hybrid system and was also found to co-localize with kAE1 in rabbit a-intercalated cells. Impaired trafficking of human kAE1 can result in the kidney disease-distal renal tubular acidosis (dRTA), and defective interaction between human kAE1 and kanadaptin may cause this trafficking impairment and be the basis for dRTA pathogenesis. However, it is unknown whether kAE1 can really interact with kanadaptin in humans. We have thus investigated the interaction between human kAE1 and human kanadaptin by using both Gal4 and LexA yeast two-hybrid systems. It was found that co-expression of Gal4DBD fused to the cytoplasmic N-terminal domain of kAE1 and Gal4AD fused to kanadaptin could not activate the transcription of the ADE2, HIS3 and lacZ reporters in the Gal4 system. A similar result was obtained for the interaction between B42AD fused to the cytoplasmic N-terminal domain of kAE1 and LexA fused to kanadaptin in activation of lacZ transcription in the LexA system. The absence of interaction between the fusion proteins in both yeast two-hybrid systems raises the possibility that kAE1 may not interact with kanadaptin in human cells. Considerably different structures of both kAE1 and kanadaptin in mice and humans may lead to different binding properties of the proteins in these two species

MycoBank gearing up for new horizons.

MycoBank, a registration system for fungi established in 2004 to capture all taxonomic novelties, acts as a coordination hub between repositories such as Index Fungorum and Fungal Names. Since January 2013, registration of fungal names is a mandatory requirement for valid publication under the International Code of Nomenclature for algae, fungi and plants (ICN). This review explains the database innovations that have been implemented over the past few years, and discusses new features such as advanced queries, registration of typification events (MBT numbers for lecto, epi- and neotypes), the multi-lingual database interface, the nomenclature discussion forum, annotation system, and web services with links to third parties. MycoBank has also introduced novel identification services, linking DNA sequence data to numerous related databases to enable intelligent search queries. Although MycoBank fills an important void for taxon registration, challenges for the future remain to improve links between taxonomic names and DNA data, and to also introduce a formal system for naming fungi known from DNA sequence data only. To further improve the quality of MycoBank data, remote access will now allow registered mycologists to act as MycoBank curators, using Citrix software

The global catalogue of microorganisms 10K type strain sequencing project: closing the genomic gaps for the validly published prokaryotic and fungi species

Genomic information is essential for taxonomic, phylogenetic and functional studies to comprehensively decipher the characteristics of microorganisms, to explore microbiomes through metagenomics, and to answer fundamental questions of nature and human life. However, large gaps remain in the available genomic sequencing information published for bacterial and archaeal species, and the gaps are even larger for fungal type strains. The Global Catalogue of Microorganisms (GCM) leads an internationally coordinated effort to sequence type strains and close gaps in the genomic maps of microbes. Hence, the GCM aims to promote research by deep-mining genomic data.This work was supported by the Strategic Priority Research Program of the Chinese Academy of Sciences (grant XDA19050301), the Bureau of International Cooperation of the Chinese Academy of Sciences (grants 153211KYSB20160029 and 153211KYSB20150010), the National Key Research Program of China (grants 2017YFC1201202, 2016YFC1201303, and 2016YFC0901702), the 13th Five-year Informatization Plan of the Chinese Academy of Sciences (grant XXH13506), and the National Science Foundation for Young Scientists of China (grant 31701157).info:eu-repo/semantics/publishedVersio

Depletion in the levels of the release factor eRF1 causes a reduction in the efficiency of translation termination in yeast

In Saccharomyces cerevisiae, translation termination is mediated by a complex of two proteins, eRF1 and eRF3, encoded by the SUP45 and SUP35 genes, respectively, Mutations in the SUP45 gene were selected which enhanced suppression by the weak ochre (UAA) suppressor tRNA(Ser) SUQ5. In each of four such allosuppressor alleles examined, an in-frame ochre (TAA) mutation was present in the SUP45 coding region; therefore each allele encoded both a truncated eRF1 protein and a full-length eRF1 polypeptide containing a serine missense substitution at the premature UAA codon, The full-length eRF1 generated by UAA readthrough was present at sub-wild-type levels, In an suq5(+) (i.e, non-suppressor) background none of the truncated eRF1 polypeptides were able to support cell viability, with the loss of only 27 amino acids from the C-terminus being lethal, The reduced eRF1 levels in these sup45 mutants did not lead to a proportional reduction in the levels of ribosome-bound eRF3, indicating that eRF3 can bind the ribosome independently of eRF1, A serine codon inserted in place of the premature stop codon at codon 46 in the sup45-22 allele did not generate an allosuppressor phenotype, thereby ruling out this 'missense' mutation as the cause of the allosuppressor phenotype, These data indicate that the cellular levels of eRF1 are important for ensuring efficient translation termination in yeast

Expression of the release factor eRF1 (Sup45p) gene of higher eukaryotes in yeast and mammalian tissues

Polypeptide chain termination in eukaryotic cells is mediated in part by the release factor eRF1 (Sup45p). We have isolated and characterised cDNAs encoding this translation factor from Syrian hamster (Mesocricetus auratus) and human (Homo sapiens) Daudi cells. Comparison of the deduced amino acid sequence of these new eRF1 (Sup45p) sequences with those published for Saccharomyces cerevisiae, Arabidopsis thaliana, Xenopus laevis and human indicates a high degree of amino acid identity across a broad evolutionary range of species. Both the 5' and 3' UTRs of the mammalian eRF1 (Sup45p)-encoding cDNAs show an unusually high degree of conservation for non-coding regions. Ln addition, the presence of two different lengths of 3'UTR sequences in the mammalian eRF1 (Sup45p) cDNAs indicated that alternative polyadenylation sites might be used in vivo. Northern blot analysis demonstrated that eRF1 (Sup45p) transcripts of differing length, consistent with the use of alternative polyadenylation sites, were detectable in a wide range of mammalian tissues. The Xenopus, human and Syrian hamster eRF1 (Sup45p) cDNAs were shown to support the viability of a strain of S. cerevisiae carrying an otherwise lethal sup45::HIS3 gene disruption indicating evolutionary conservation of function. However, the yeast strains expressing the heterologous eRF1 (Sup45p) showed a defect in translation termination as defined by an enhancement of nonsense suppressor tRNA activity in vivo. Western blot analysis confirmed that Xenopus eRF1 (Sup45p) was primarily ribosome-associated when expressed in yeast indicating that the ribosome-binding domain of eRF1 (Sup45p) is also conserved

Analysis of the interaction between human kidney anion exchanger 1 and kanadaptin using yeast two-hybrid systems

Kidney anion exchanger adaptor protein (Kanadaptin) is a protein which interacts with the cytoplasmic N-terminal domain of kidney anion exchanger 1 (kAE1) and was first detected in mice using the yeast two-hybrid system and was also found to co-localize with kAE1 in rabbit a-intercalated cells. Impaired trafficking of human kAE1 can result in the kidney disease-distal renal tubular acidosis (dRTA), and defective interaction between human kAE1 and kanadaptin may cause this trafficking impairment and be the basis for dRTA pathogenesis. However, it is unknown whether kAE1 can really interact with kanadaptin in humans. We have thus investigated the interaction between human kAE1 and human kanadaptin by using both Gal4 and LexA yeast two-hybrid systems. It was found that co-expression of Gal4DBD fused to the cytoplasmic N-terminal domain of kAE1 and Gal4AD fused to kanadaptin could not activate the transcription of the ADE2, HIS3 and lacZ reporters in the Gal4 system. A similar result was obtained for the interaction between B42AD fused to the cytoplasmic N-terminal domain of kAE1 and LexA fused to kanadaptin in activation of lacZ transcription in the LexA system. The absence of interaction between the fusion proteins in both yeast two-hybrid systems raises the possibility that kAE1 may not interact with kanadaptin in human cells. Considerably different structures of both kAE1 and kanadaptin in mice and humans may lead to different binding properties of the proteins in these two species