Draft genome sequences of Arthrobacter sp. AZCC_0090 and Mycobacterium sp. AZCC_0083 isolated from oligotrophic subsurface forest soil in the Santa Catalina mountains of Southern Arizona.

Here, we present the genomes of two soil actinobacteria: Arthrobacter sp. strain AZCC_0090 and Mycobacterium sp. strain AZCC_0083, isolated from oligotrophic subsurface soils in Southern Arizona, USA.

Geothermobacter hydrogeniphilus sp. nov., a mesophilic, iron(III)-reducing bacterium from seafloor/subseafloor environments in the Pacific Ocean, and emended description of the genus Geothermobacter.

A novel mesophilic, anaerobic, mixotrophic bacterium, with designated strains EPR-MT and HR-1, was isolated from a semi-extinct hydrothermal vent at the East Pacific Rise and from an Fe-mat at Lo'ihi Seamount, respectively. The cells were Gram-negative, pleomorphic rods of about 2.0 µm in length and 0.5 µm in width. Strain EPR-MT grew between 25 and 45 °C (optimum, 37.5-40 °C), 10 and 50 g l-1 NaCl (optimum, 15-20 g l-1) and pH 5.5 and 8.6 (optimum, pH 6.4). Strain HR-1 grew between 20 and 45 °C (optimum, 37.5-40 °C), 10 and 50 g l-1 NaCl (optimum, 15-25 g l-1) and pH 5.5 and 8.6 (optimum, pH 6.4). Shortest generation times with H2 as the primary electron donor, CO2 as the carbon source and ferric citrate as terminal electron acceptor were 6.7 and 5.5 h for EPR-MT and HR-1, respectively. Fe(OH)3, MnO2, AsO4 3-, SO4 2-, SeO4 2-, S2O3 2-, S0 and NO3 - were also used as terminal electron acceptors. Acetate, yeast extract, formate, lactate, tryptone and Casamino acids also served as both electron donors and carbon sources. G+C content of the genomic DNA was 59.4 mol% for strain EPR-MT and 59.2 mol% for strain HR-1. Phylogenetic and phylogenomic analyses indicated that both strains were closely related to each other and to Geothermobacter ehrlichii, within the class δ-Proteobacteria (now within the class Desulfuromonadia). Based on phylogenetic and phylogenomic analyses in addition to physiological and biochemical characteristics, both strains were found to represent a novel species within the genus Geothermobacter, for which the name Geothermobacter hydrogeniphilus sp. nov. is proposed. Geothermobacter hydrogeniphilus is represented by type strain EPR-MT (=JCM 32109T=KCTC 15831T=ATCC TSD-173T) and strain HR-1 (=JCM 32110=KCTC 15832).

Spatiotemporal Control of Acetyl-CoA Metabolism in Chromatin Regulation.

The epigenome is sensitive to the availability of metabolites that serve as substrates of chromatin-modifying enzymes. Links between acetyl-CoA metabolism, histone acetylation, and gene regulation have been documented, although how specificity in gene regulation is achieved by a metabolite has been challenging to answer. Recent studies suggest that acetyl-CoA metabolism is tightly regulated both spatially and temporally to elicit responses to nutrient availability and signaling cues. Here we discuss evidence that acetyl-CoA production is differentially regulated in the nucleus and cytosol of mammalian cells. Recent findings indicate that acetyl-CoA availability for site-specific histone acetylation is influenced through post-translational modification of acetyl-CoA-producing enzymes, as well as through dynamic regulation of the nuclear localization and chromatin recruitment of these enzymes.

Nuclear Acetyl-CoA Production by ACLY Promotes Homologous Recombination.

While maintaining the integrity of the genome and sustaining bioenergetics are both fundamental functions of the cell, potential crosstalk between metabolic and DNA repair pathways is poorly understood. Since histone acetylation plays important roles in DNA repair and is sensitive to the availability of acetyl coenzyme A (acetyl-CoA), we investigated a role for metabolic regulation of histone acetylation during the DNA damage response. In this study, we report that nuclear ATP-citrate lyase (ACLY) is phosphorylated at S455 downstream of ataxia telangiectasia mutated (ATM) and AKT following DNA damage. ACLY facilitates histone acetylation at double-strand break (DSB) sites, impairing 53BP1 localization and enabling BRCA1 recruitment and DNA repair by homologous recombination. ACLY phosphorylation and nuclear localization are necessary for its role in promoting BRCA1 recruitment. Upon PARP inhibition, ACLY silencing promotes genomic instability and cell death. Thus, the spatial and temporal control of acetyl-CoA production by ACLY participates in the mechanism of DNA repair pathway choice.