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All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Mo than meets the eye: genomic insights into molybdoenzyme diversity of Seleniivibrio woodruffii strain S4T

Abstract Seleniivibrio woodruffii strain S4T is an obligate anaerobe belonging to the phylum Deferribacterota. It was isolated for its ability to respire selenate and was also found to respire arsenate. The high-quality draft genome of this bacterium is 2.9 Mbp, has a G+C content of 48%, 2762 predicted genes of which 2709 are protein-coding, and 53 RNA genes. An analysis of the genome focusing on the genes encoding for molybdenum-containing enzymes (molybdoenzymes) uncovered a remarkable number of genes encoding for members of the dimethylsulfoxide reductase family of proteins (DMSOR), including putative reductases for selenate and arsenate respiration, as well as genes for nitrogen fixation. Respiratory molybdoenzymes catalyze redox reactions that transfer electrons to a variety of substrates that can act as terminal electron acceptors for energy generation. Seleniivibrio woodruffii strain S4T also has essential genes for molybdate transporters and the biosynthesis of the molybdopterin guanine dinucleotide cofactors characteristic of the active centers of DMSORs. Phylogenetic analysis revealed candidate respiratory DMSORs spanning nine subfamilies encoded within the genome. Our analysis revealed the untapped potential of this interesting microorganism and expanded our knowledge of molybdoenzyme co-occurrence.

Louie, Tiffany S.↗
DOE OSTI2023

Seasonal activities of the phyllosphere microbiome of perennial crops

Understanding the interactions between plants and microorganisms can inform microbiome management to enhance crop productivity and resilience to stress. Here, we apply a genome-centric approach to identify ecologically important leaf microbiome members on replicated plots of field-grown switchgrass and miscanthus, and to quantify their activities over two growing seasons for switchgrass. We use metagenome and metatranscriptome sequencing and curate 40 medium- and high-quality metagenome-assembled-genomes (MAGs). We find that classes represented by these MAGs (Actinomycetia, Alpha- and Gamma- Proteobacteria, and Bacteroidota) are active in the late season, and upregulate transcripts for short-chain dehydrogenase, molybdopterin oxidoreductase, and polyketide cyclase. Stress-associated pathways are expressed for most MAGs, suggesting engagement with the host environment. We also detect seasonally activated biosynthetic pathways for terpenes and various non-ribosomal peptide pathways that are poorly annotated. Our findings support that leaf-associated bacterial populations are seasonally dynamic and responsive to host cues.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

ShadeLab/PAPER_Howe_2023_switchgrass_MetaT

The raw data (metagenomes and metatranscriptomes) for this study are available in the Joint Genomes Institute Genome Portal (https://genome.jgi.doe.gov/portal/ Project ID 503249) with projects designated by year and product type. The MAG genomes analyzed in this paper are available on NCBI, as bioproject PRJNA800073. Plants and microorganisms form beneficial associations. Understanding plant-microbe interactions will inform microbiome management to enhance crop productivity and resilience to stress. Here, we apply a genome-centric approach to identify ecologically important leaf microbiome members on field-grown switchgrass and miscanthus and to quantify their activities for switchgrass over two growing seasons. We integrate metagenome and metatranscriptome sequencing from 192 leaf samples collected over representative time points in crop phenology. We curated 40 medium- and high-quality metagenome-assembled-genomes (MAGs) and focused analysis on seasonal transcript recruitment to them. Classes represented by these focal MAGs (Actinomycetia, Alpha- and Gamma- Proteobacteria, and Bacteroidota) were active and had increases in transcripts for short-chain dehydrogenase, molybdopterin oxidoreductase, and polyketide cyclase in the late season. The majority of MAGs had activated stress-associated pathways, including trehalose metabolism, indole acetic acid degradation, betaine biosynthesis, and reactive oxygen species degradation, suggesting direct engagement with the host environment. We also detected seasonally activated biosynthetic pathways for terpenes (carotenoids and isoprenoids) and for various non-ribosomal peptide pathways that were poorly annotated. Overall, this study overcame laboratory and bioinformatic challenges associated with field-based leaf metatranscriptome analysis to inform both general and likely specialized activities of these phyllosphere populations. These activities collectively support that leaf-associated bacterial populations are seasonally dynamic, responsive to host cues, and interactively engage in feedback with the plant. This analysis represented quality filtering of metagenomes and metatranscriptomes (data-preparation folder), metagenome assemblies (metagenome-assembly folder) and metagenome-assembled genome binning, curation, refinement, annotation (mag-evaluation folder). Abundances of sequencing libraries were calculated based on reads mapped (mapping folder). Additionallly, analysis of our annotated results are also included (analysis folder).

Howe, Adina↗
DOE OSTI2022

Iodate Reduction by Shewanella oneidensis Requires Genes Encoding an Extracellular Dimethylsulfoxide Reductase

Microbial iodate (IO 3 – ) reduction is a major component of the iodine biogeochemical reaction network in anaerobic marine basins and radioactive iodine-contaminated subsurface environments. Alternative iodine remediation technologies include microbial reduction of IO 3 – to iodide (I – ) and microbial methylation of I – to volatile gases. The metal reduction pathway is required for anaerobic IO 3 – respiration by the gammaproteobacterium Shewanella oneidensis . However, the terminal IO 3 – reductase and additional enzymes involved in the S. oneidensis IO 3 – electron transport chain have not yet been identified. In this study, gene deletion mutants deficient in four extracellular electron conduits (EECs; Δ mtrA , Δ mtrA -Δ mtrDEF , Δ mtrA -Δ dmsEF , Δ mtr A-ΔSO4360) and DMSO reductase (Δ dmsB ) of S. oneidensis were constructed and examined for anaerobic IO 3 – reduction activity with either 20 mM lactate or formate as an electron donor. IO 3 – reduction rate experiments were conducted under anaerobic conditions in defined minimal medium amended with 250 μM IO 3 – as anaerobic electron acceptor. Only the Δ mtrA mutant displayed a severe deficiency in IO 3 – reduction activity with lactate as the electron donor, which suggested that the EEC-associated decaheme cytochrome was required for lactate-dependent IO 3 – reduction. The Δ mtrA -Δ dmsEF triple mutant displayed a severe deficiency in IO 3 – reduction activity with formate as the electron donor, whereas Δ mtrA -Δ mtrDEF and Δ mtr A-ΔSO4360 retained moderate IO 3 – reduction activity, which suggested that the EEC-associated dimethylsulfoxide (DMSO) reductase membrane-spanning protein DmsE, but not MtrA, was required for formate-dependent IO 3 – reduction. Furthermore, gene deletion mutant Δ dmsB (deficient in the extracellular terminal DMSO reductase protein DmsB) and wild-type cells grown with tungsten replacing molybdenum (a required co-factor for DmsA catalytic activity) in defined growth medium were unable to reduce IO 3 – with either lactate or formate as the electron donor, which indicated that the DmsAB complex functions as an extracellular IO 3 – terminal reductase for both electron donors. Results of this study provide complementary genetic and phenotypic evidence that the extracellular DMSO reductase complex DmsAB of S. oneidensis displays broad substrate specificity and reduces IO 3 – as an alternate terminal electron acceptor.

, Shewanella oneidensis↗
DOE OSTI2023

Advancing Our Understanding of Pyranopterin-Dithiolene Contributions to Moco Enzyme Catalysis

The pyranopterin dithiolene ligand is remarkable in terms of its geometric and electronic structure and is uniquely found in mononuclear molybdenum and tungsten enzymes. The pyranopterin dithiolene is found coordinated to the metal ion, deeply buried within the protein, and non-covalently attached to the protein via an extensive hydrogen bonding network that is enzyme-specific. However, the function of pyranopterin dithiolene in enzymatic catalysis has been difficult to determine. This focused account aims to provide an overview of what has been learned from the study of pyranopterin dithiolene model complexes of molybdenum and how these results relate to the enzyme systems. This work begins with a summary of what is known about the pyranopterin dithiolene ligand in the enzymes. We then introduce the development of inorganic small molecule complexes that model aspects of a coordinated pyranopterin dithiolene and discuss the results of detailed physical studies of the models by electronic absorption, resonance Raman, X-ray absorption and NMR spectroscopies, cyclic voltammetry, X-ray crystallography, and chemical reactivity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗