Nucleocytoplasmic large DNA viruses (NCLDVs) are ubiquitous in marine environments and infect diverse eukaryotes. However, little is known about their biogeography and ecology in the ocean. By leveraging the Tara Oceans pole-to-pole metagenomic data set, we investigated the distribution of NCLDVs across size fractions, depths and biomes, as well as their associations with eukaryotic communities. Our analyses revealed a heterogeneous distribution of NCLDVs across oceans, with an elevated uniqueness in polar biomes. The community structures of NCLDV families were correlated with specific eukaryotic lineages including many photosynthetic groups.NCDLV communities were generally distinct between surface and mesopelagic zones, but at some locations, they exhibited a high similarity between the two depths. This vertical similarity was correlated to surface phytoplankton biomass but not to physical mixing processes, suggesting the potential role of vertical export in structuring mesopelagic NCLDV communities. These results underscore the importance of the coupling between NCLDVs and eukaryotes in biogeochemical processes in the ocean.

GMrepo (data repository for Gut Microbiota) is a database of curated and consistently annotated human gut metagenomes. Its main purpose is to facilitate the reusability and accessibility of the rapidly growing human metagenomic data. This is achieved by consistently annotating the microbial contents of collected samples using state-of-art toolsets and by manual curation of the meta-data of the corresponding human hosts. GMrepo organizes the collected samples according to their associated phenotypes and includes all possible related meta-data such as age, sex, country, body-mass-index (BMI) and recent antibiotics usage. To make relevant information easier to access, GMrepo is equipped with a graphical query builder, enabling users to make customized, complex and biologically relevant queries. For example, to find (1) samples from healthy individuals of 18 to 25 years old with BMIs between 18.5 and 24.9, or (2) projects that are related to colorectal neoplasms, with each containing >100 samples and both patients and healthy controls. Precomputed species/genus relative abundances, prevalence within and across phenotypes, and pairwise co-occurrence information are all available at the website and accessible through programmable interfaces. So far, GMrepo contains 58 903 human gut samples/runs (including 17 618 metagenomes and 41 285 amplicons) from 253 projects concerning 92 phenotypes. GMrepo is freely available at: https://gmrepo.humangut.info.

We previously reported that sirtuin 2 (SIRT2), a mammalian member of the NAD+-dependent protein deacetylases, participates in mitotic regulation, specifically, in efficient mitotic cell death caused by the spindle checkpoint. Here, we describe a novel function of SIRT2 that is different from mitotic regulation. SIRT2 down-regulation using siRNA caused apoptosis in cancer cell lines such as HeLa cells, but not in normal cells. The apoptosis was caused by p53 accumulation, which is mediated by p38 MAPK activation-dependent degradation of p300 and the subsequent MDM2 degradation. Sirtuin inhibitors are emerging as antitumor drugs, and this function has been ascribed to the inhibition of SIRT1, the most well-characterized sirtuin that deacetylases p53 to promote cell survival and also binds to other proteins in response to genotoxic stress. This study suggests that SIRT2 can be a novel molecular target for cancer therapy and provides a molecular basis for the efficacy of SIRT2 for future cancer therapy.

The RING finger protein family plays a crucial role in plant growth and development and in response to biotic and abiotic stresses. However, no detailed information concerning this family is available for apple (Malus × domestica L. Borkh) due to the limited information on whole genome sequences. In this study, 688 RING domains in 663 predicted proteins were identified in apple. Based on the spacing between metal ligands or substitutions at one or more of the metal ligand positions, nine RING types were identified: RING-H2, RING-HC, RING-C2, RING-v, RING-D, RING-S/T, RING-G, RING-mH2, and RING-mHC, in which the first seven types were described previously in Arabidopsis, while the latter two were newly identified in apple. Proteins containing RING finger motifs were further classified into 57 groups according to the different known or unknown domains outside the RING domains. A total of 643 retrieved proteins appear to be distributed over all 17 linkage groups with different densities. Microarray and expressed sequence tag data revealed that only a few of these RING finger proteins may be involved in fruit development. As a first step towards genome-wide analyses of the RING-containing genes in apple, our results provide valuable information for understanding the classification and putative functions of the RING finger gene family in higher plants.

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.