The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled insight... more The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled insights into the ecology and evolution of environmental and host-associated microbiomes. Here we applied this approach to >10,000 metagenomes collected from diverse habitats covering all of Earth’s continents and oceans, including metagenomes from human and animal hosts, engineered environments, and natural and agricultural soils, to capture extant microbial, metabolic and functional potential. This comprehensive catalog includes 52,515 metagenome-assembled genomes representing 12,556 novel candidate species-level operational taxonomic units spanning 135 phyla. The catalog expands the known phylogenetic diversity of bacteria and archaea by 44% and is broadly available for streamlined comparative analyses, interactive exploration, metabolic modeling and bulk download. We demonstrate the utility of this collection for understanding secondary-metabolite biosynthetic potential and for resolving...
Numerous investigations of bacterial communities using sequence analysis of environmental DNA hav... more Numerous investigations of bacterial communities using sequence analysis of environmental DNA have revealed extensive diversity of microbial taxa in an array of different environmental habitats. Community analysis based solely on DNA, however, does not reveal whether the detected community members are actively contributing to community functioning, or whether they are dormant or remnants of dead cells. This dilemma is of particular concern when analyzing microbial community structure of sites with a high degree of deposited matter, such as marine sediments. For example, the Baltic Sea’s deepest point, the Landsort Deep, consists of anoxic sediments with a large deposition of allochthonous organic matter from the highly stratified 460 m water column above. Our previous metagenomics results indicated the presence of potential obligately aerobic and phototrophic microorganisms in the Landsort Deep sediment. To further elucidate which taxa may contribute to ecosystem function at this si...
Benthic ecosystems have come under intense pressure, due to eutrophication-driven oxygen decline ... more Benthic ecosystems have come under intense pressure, due to eutrophication-driven oxygen decline and industrial metal contamination. One of the most toxic metals is Cadmium (Cd), which is lethal to many aquatic organisms already at low concentrations. Denitrification by facultative anaerobic microorganisms is an essential process to transform, but also to remove, excess nitrate in eutrophied systems. Cd has been shown to decrease denitrification and sequester free sulfide, which is available when oxygen is scarce and generally inhibits complete denitrification (i.e. N 2 O to N 2). In polluted sediments, an interaction between oxygen and Cd may influence denitrification and this relationship has not been studied. For example, in the Baltic Sea some sediments are double exposed to both Cd and hypoxia. In this study, we examined how the double exposure of Cd and fluctuations in oxygen affects denitrification in Baltic Sea sediment. Results show that oxygen largely regulated N 2 O and N 2 production after 21 days of exposure to Cd (ranging from 0 to 500 μg/L, 5 different treatments, measured by the isotope pairing technique (IPT)). In the high Cd treatment (500 μg/L) the variation in N 2 production increased compared to the other treatments. Increases in N 2 production are suggested to be an effect of 1) enhanced nitrification that increases NO 3 − availability thus stimulating denitrification, and 2) Cd successfully sequestrating sulfide (yielding CdS), which allows for full denitrification to N 2. The in situ field sediment contained initially high Cd concentrations in the pore water (∼10 μg/L) and microbial communities might already have been adapted to metal stress, making the effect of low Cd levels negligible. Here we show that high levels of cadmium pollution might increase N 2 production and influence nitrogen cycling in marine sediments. −), 2) NO 2 − to nitric oxide (NO), 3) NO to nitrous oxide (N 2 O), and finally 4) N 2 O to nitrogen gas (N 2) (Devol, 2015). The enzymes nitrite reductase (nir i.e. NO 2 − to NO) and
Our growing awareness of the microbial world's importance and diversity contrasts starkly wit... more Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete ...
The goal of this work was to identify sequences encoding monooxygenase biocatalysts with novel fe... more The goal of this work was to identify sequences encoding monooxygenase biocatalysts with novel features by in silico mining an assembled metagenomic dataset of polar and subpolar marine sediments. The targeted enzyme sequences were Baeyer-Villiger and bacterial cytochrome P450 monooxygenases (CYP153). These enzymes have wide-ranging applications, from the synthesis of steroids, antibiotics, mycotoxins and pheromones to the synthesis of monomers for polymerization and anticancer precursors, due to their extraordinary enantio-, regio-, and chemo- selectivity that are valuable features for organic synthesis. Phylogenetic analyses were used to select the most divergent sequences affiliated to these enzyme families among the 264 putative monooxygenases recovered from the ~14 million protein-coding sequences in the assembled metagenome dataset. Three-dimensional structure modeling and docking analysis suggested features useful in biotechnological applications in five metagenomic sequences...
In this work, we analyzed the community structure and metabolic potential of sediment microbial c... more In this work, we analyzed the community structure and metabolic potential of sediment microbial communities in high-latitude coastal environments subjected to low to moderate levels of chronic pollution. Subtidal sediments from four low-energy inlets located in polar and subpolar regions from both Hemispheres were analyzed using large-scale 16S rRNA gene and metagenomic sequencing. Communities showed high diversity (Shannon's index 6.8 to 10.2), with distinct phylogenetic structures (<40% shared taxa at the Phylum level among regions) but similar metabolic potential in terms of sequences assigned to KOs. Environmental factors (mainly salinity, temperature, and in less extent organic pollution) were drivers of both phylogenetic and functional traits. Bacterial taxa correlating with hydrocarbon pollution included families of anaerobic or facultative anaerobic lifestyle, such as Desulfuromonadaceae, Geobacteraceae, and Rhodocyclaceae. In accordance, biomarker genes for anaerobic...
Information in this manuscript is the first study on microbial rhodopsins present in coastal mari... more Information in this manuscript is the first study on microbial rhodopsins present in coastal marine sediments. Also it reported a previously undescribed allopatric cladism for the viral rhodopsins sequences.
Baltic Sea deep water and sediments hold one of the largest anthropogenically induced hypoxic are... more Baltic Sea deep water and sediments hold one of the largest anthropogenically induced hypoxic areas in the world. High nutrient input and low water exchange result in eutrophication and oxygen depletion below the halocline. As a consequence at Landsort Deep, the deepest point of the Baltic Sea, anoxia in the sediments has been a persistent condition over the past decades. Given that microbial communities are drivers of essential ecosystem functions we investigated the microbial community metabolisms and functions of oxygen depleted Landsort Deep sediments by metatranscriptomics. Results show substantial expression of genes involved in protein metabolism demonstrating that the Landsort Deep sediment microbial community is active. Identified expressed gene suites of metabolic pathways with importance for carbon transformation including fermentation, dissimilatory sulphate reduction and methanogenesis were identified. The presence of transcripts for these metabolic processes suggests a...
Mitochondrial biogenesis requires a coordinated expression of both the nuclear and the organellar... more Mitochondrial biogenesis requires a coordinated expression of both the nuclear and the organellar genomes and specific intracellular protein trafficking, processing and assembly machinery. Most mitochondrial proteins are synthesised as precursor proteins containing an N-terminal extension which functions as a targeting signal, which is proteolytically cleaved off after import into mitochondria. We review our present knowledge on components and mechanisms involved in the mitochondrial protein import process in plants. This encompasses properties of targeting peptides, sorting of precursor proteins between mitochondria and chloroplasts, signal recognition, mechanism of translocation across the mitochondrial membranes and the role of cytosolic and organellar molecular chaperones in this process. The mitochondrial protein processing in plants is catalysed by the mitochondrial processing peptidase (MPP), which in contrast to other sources, is integrated into the bc1 complex of the respir...
The mitochondrial processing peptidase (MPP) in lower eucaryots and mammals is a matrix enzyme, w... more The mitochondrial processing peptidase (MPP) in lower eucaryots and mammals is a matrix enzyme, whereas MPP in plants constitutes an integral part of the bc1 complex of the respiratory chain. The isolated spinach leaf bc1 complex catalyzes cleavage of the precursor of Nicotiana plumbaginifolia F1 beta subunit of the ATP synthase, resulting in a production of mature protein and a presequence that consists of 54 amino acids. A synthetic peptide derived from the C-terminal part of the presequence, containing 17 amino acids with a helical structural element, p-F1 beta(38-54), was an efficient inhibitor of the processing, whereas a peptide derived from the N-terminal part of the presequence, p-F1 beta(1-18), was much less effective. ATIII, a helical peptide derived from antithrombin III, was not recognized by MPP. Synthetic peptides corresponding to 4, 6, and 11 amino acids of the C terminus of the presequence, p-F1 beta(51-54), p-F1 beta(49-54), and p-F1 beta(44-54) were almost complete...
The plant mitochondrial processing peptidase (MPP) that catalyses the cleavage of the presequence... more The plant mitochondrial processing peptidase (MPP) that catalyses the cleavage of the presequences from precursor proteins during or after protein import is a membrane-bound enzyme that constitutes an integral part of the be, complex of the respiratory chain. In contrast, MPP from mammals is soluble in the matrix space and does not form part of the respiratory chain. In the present study, we have compared the substrate specificity of the isolated spinach leaf bc,lMPP with rat liver MPP using synthetic signal peptides and different mitochondrial precursor proteins. Inhibition studies of processing with synthetic peptides showed a similar inhibition pattern for plant and rat MPP activity. A peptide derived from the presequence of rat liver mitochondrial aldehyde dehydrogenase (ALDH) was a potent inhibitor of the spinach and rat MPP. Two nonprocessed signal peptides, rhodanese and linker-deleted ALDH (a form of ALDH that lacks the RGP linker connecting two helices in the presequence) had lower inhibitory effects towards each protease. The signal peptide from thiolase, another nonprocessed protein, had little inhibitory effect on MPP. Peptides derived from presequence of the plant Nicotiana plunzbaginifolia FIB also showed a similar inhibitory pattern with rat MPP as with spinach MPP processing. In-vitro synthesised precursors of plant N. plunzbaginifolia F,P and rat liver ALDH were cleaved to mature form by both spinach and rat MPP. However, the efficiency of processing was higher with the homologous precursor. Linker-deleted ALDH, rhodanese, and thiolase were not processed by the mammalian or plant MPP. However, both forms of MPP cleaved a mutated form of rhodanese that possesses a typical MPP cleavage motif, RXY S. Addition of the same cleavage motif to thiolase did not result in processing by either MPP. These results show that similar higher-order structural elements upstream from the cleavage site are important for processing by both the membrane-bound plant and the soluble mammalian MPP. Keywords: mitochondrial processing peptidase : signal peptide : protein processing; protein import; cytochrome bc, complex. Kuclear-encoded mitochondrial proteins are translated on cytosolic polyribosomes as precursor proteins. Most of the precursor proteins carry an N-terminal extension, the presequence or signal sequence, that contains information for mitochondrial targeting and sorting. Import of the precursor proteins into the mitochondria is usually accompanied by proteolytic removal of the presequence [l-31 resulting in the production of mature proteins. This step is catalysed by the mitochondrial processing peptidase (MPP) [4-91. MPP, a metal-dependent endopeptidase consisting of two structurally related subunits, a-MPP and b-MPP, forms a heterodimeric complex [lo, 111, in which both subunits are essential Correspondrrzce to E.
The current study assessed the occurrence of the Vibrio cholerae serogroups O1 and O139 in enviro... more The current study assessed the occurrence of the Vibrio cholerae serogroups O1 and O139 in environmental samples along salinity gradients in three selected estuaries of Tanzania both through culture independent methods and by cultured bacteria. Occurrence of V. cholerae was determined by PCR targeting the V. cholerae outer membrane protein gene ompW. Furthermore, the presence of toxigenic strains and serogroups O1 and O139 was determined using multiplex PCR with specific primers targeting the cholera toxin gene subunit A, ctxA, and serotype specific primers, O1-rfb and O139-rfb, respectively. Results showed that V. cholerae occurred in approximately 10% (n = 185) of both the environmental samples and isolated bacteria. Eight of the bacteria isolates (n = 43) were confirmed as serogroup O1 while one belonged to serogroup O139, the first reported identification of this epidemic strain in East African coastal waters. All samples identified as serogroup O1 or O139 and a number of non-O1/O139 strains were ctxA positive. This study provides in situ evidence of the presence of pathogenic V. cholerae O1 and O139 and a number of V. cholerae non-O1/O139 that carry the cholera toxin gene in estuaries along the coast of Tanzania.
Psychrophiles: from Biodiversity to Biotechnology, 2008
... Genomes Revealed Sara Sjöling(*ü) and Don A. Cowan ... Metagenomics is therefore the applicat... more ... Genomes Revealed Sara Sjöling(*ü) and Don A. Cowan ... Metagenomics is therefore the application of modern genomic tools used to analyze Sara Sjöling School of Life Sciences, University College Södertörn, 14189 Huddinge, Sweden e-mail: [email protected] ...
ABSTRACT Brown macroalgae are considered an attractive option as sustainable feedstock for the pr... more ABSTRACT Brown macroalgae are considered an attractive option as sustainable feedstock for the production of biofuels and commodity chemicals due to their high carbohydrate content (such as alginates), and the absence of hemicellulose and lignin. Microbial communities from cold coastal environments represent promising sources of novel alginate-depolymerizing enzymes, as brown algae constitute a large primary biomass in these environments. We used a nested sampling strategy to obtain coastal sediment samples from four high-latitude regions (Svalbard Archipelago, Norway; Baltic Sea, Sweden; Ushuaia Bay, Argentina and Potter Cove, Antarctic Peninsula). Metagenomes were sequenced using 23 lanes of Illumina HiSeq™ 1500, and were annotated at the IMG/M pipeline. The complete assembled metagenome dataset contains 5.6 Gb and 1.4 x 107 protein coding genes. We mined this dataset with the goal of identifying alginate lyase homologs using both blastp searches and assigned product names. We retrieved 2,705 sequences ≥ 100 amino acids in length, 75% of them belonging to the samples from polar regions. Most sequences were classified as belonging to PL17 (30.4%), PL7 (28%) or PL6 (22%) families (CAZy database), and 13% of them were too distant to reference sequences and could not be classified. Phylogenetic analysis of full length sequences and gene order conservation for long scaffolds show moderate relatedness to sequences from isolated bacteria. This study revealed a large diversity of alginate lyase sequences from marine yet-to-be cultured microorganisms, which could aid in the engineering of microorganisms for biorefineries.
This report summarizes the events of the 1(st) International Functional Metagenomics Workshop. Th... more This report summarizes the events of the 1(st) International Functional Metagenomics Workshop. The workshop was held on May 7 and 8, 2012, in St. Jacobs, Ontario, Canada and was focused on building an international functional metagenomics community, exploring strategic research areas, and identifying opportunities for future collaboration and funding. The workshop was initiated by researchers at the University of Waterloo with support from the Ontario Genomics Institute (OGI), Natural Sciences and Engineering Research Council of Canada (NSERC) and the University of Waterloo.
Proteins function at distinct sites in the cell, yet most are primarily synthesized in the cytoso... more Proteins function at distinct sites in the cell, yet most are primarily synthesized in the cytosol and must therefore be transported intracellularly to their final destination. Mitochondrial targeting peptides are localized at the N-terminus of the precursor proteins and most are cleaved off after import into mitochondria. Cleavage is catalysed by the general mitochondrial processing peptidase, which, in plants, is integrated into the bc 1 complex of the respiratory chain. This peptidase recognizes the cleavage sites of nearly 1000 precursor proteins that have no sequence similarity. Fig. 1. Conserved domains within plant mitochondrial presequences. The sequences were aligned with Clustal W. An asterisk marks identical amino acid residues. Abbreviations: F 1 , F 1  subunit of the ATP synthase; FeS, Rieske-FeS protein; Hsp60, heat shock protein of 60 kDa. Numerals show the number of amino acid residues.
Soil teems with microbial genetic information that can be exploited for biotechnological innovati... more Soil teems with microbial genetic information that can be exploited for biotechnological innovation. Because only a fraction of the soil microbiota is cultivable, our ability to unlock this genetic complement has been hampered. Recently developed molecular tools, which make it possible to utilize genomic DNA from soil, can bypass cultivation and provide information on the collective soil metagenome with the aim to explore genes that encode functions of key interest to biotechnology. The metagenome of disease-suppressive soils is of particular interest given the expected prevalence of antibiotic biosynthetic clusters. However, owing to the complexity of soil microbial communities, deciphering this key genetic information is challenging. Here, we examine crucial issues and challenges that so far have hindered the metagenomic exploration of soil by drawing on experience from a trans-European project on disease-suppressive soils denoted METACONTROL.
Determinants for the recognition of a mitochondrial presequence by the mitochondrial processing p... more Determinants for the recognition of a mitochondrial presequence by the mitochondrial processing peptidase (MPP) have been investigated using mutagenesis and bioinformatics approaches. All plant mitochondrial presequences with a cleavage site that was con®rmed by experimental studies can be grouped into three classes. Two major classes contain an arginine residue at position ±2 or ±3, and the third class does not have any conserved arginines. Sequence logos revealed loosely conserved cleavage motifs for the ®rst two classes but no signi®cant amino acid conservation for the third class. Investigation of processing determinants for a class III precursor, Nicotiana plumbaginifolia F 1 b precursor of ATP synthase (pF 1 b), was performed using a series of pF 1 b presequence mutants and mutant presequence peptides derived from the C-terminal portion of the presequence. Replacement of ±2 Gln by Arg inhibited processing, whereas replacement of either the most proximally located ±5 Arg or ±15 Arg by Leu had only a low inhibitory effect. The C-terminal portion of the pF 1 b presequence forms a helix± turn±helix structure. Mutations disturbing or prolonging the helical element upstream of the cleavage site inhibited processing signi®cantly. Structural models of potato MPP and the C-terminal pF 1 b presequence peptide were built by homology modelling and empirical conformational energy search methods, respectively. Molecular docking of the pF 1 b presequence peptide to the MPP model suggested binding of the peptide to the negatively charged binding cleft formed by the a-MPP and b-MPP subunits in close proximity to the H 111 XXE 114 H 115 X (116±190) E 191 proteolytic active site on b-MPP. Our results show for the ®rst time that the amino acid at the ±2 position, even if not an arginine, as well as structural properties of the C-terminal portion of the presequence are important determinants for the processing of a class III precursor by MPP.
The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled insight... more The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled insights into the ecology and evolution of environmental and host-associated microbiomes. Here we applied this approach to >10,000 metagenomes collected from diverse habitats covering all of Earth’s continents and oceans, including metagenomes from human and animal hosts, engineered environments, and natural and agricultural soils, to capture extant microbial, metabolic and functional potential. This comprehensive catalog includes 52,515 metagenome-assembled genomes representing 12,556 novel candidate species-level operational taxonomic units spanning 135 phyla. The catalog expands the known phylogenetic diversity of bacteria and archaea by 44% and is broadly available for streamlined comparative analyses, interactive exploration, metabolic modeling and bulk download. We demonstrate the utility of this collection for understanding secondary-metabolite biosynthetic potential and for resolving...
Numerous investigations of bacterial communities using sequence analysis of environmental DNA hav... more Numerous investigations of bacterial communities using sequence analysis of environmental DNA have revealed extensive diversity of microbial taxa in an array of different environmental habitats. Community analysis based solely on DNA, however, does not reveal whether the detected community members are actively contributing to community functioning, or whether they are dormant or remnants of dead cells. This dilemma is of particular concern when analyzing microbial community structure of sites with a high degree of deposited matter, such as marine sediments. For example, the Baltic Sea’s deepest point, the Landsort Deep, consists of anoxic sediments with a large deposition of allochthonous organic matter from the highly stratified 460 m water column above. Our previous metagenomics results indicated the presence of potential obligately aerobic and phototrophic microorganisms in the Landsort Deep sediment. To further elucidate which taxa may contribute to ecosystem function at this si...
Benthic ecosystems have come under intense pressure, due to eutrophication-driven oxygen decline ... more Benthic ecosystems have come under intense pressure, due to eutrophication-driven oxygen decline and industrial metal contamination. One of the most toxic metals is Cadmium (Cd), which is lethal to many aquatic organisms already at low concentrations. Denitrification by facultative anaerobic microorganisms is an essential process to transform, but also to remove, excess nitrate in eutrophied systems. Cd has been shown to decrease denitrification and sequester free sulfide, which is available when oxygen is scarce and generally inhibits complete denitrification (i.e. N 2 O to N 2). In polluted sediments, an interaction between oxygen and Cd may influence denitrification and this relationship has not been studied. For example, in the Baltic Sea some sediments are double exposed to both Cd and hypoxia. In this study, we examined how the double exposure of Cd and fluctuations in oxygen affects denitrification in Baltic Sea sediment. Results show that oxygen largely regulated N 2 O and N 2 production after 21 days of exposure to Cd (ranging from 0 to 500 μg/L, 5 different treatments, measured by the isotope pairing technique (IPT)). In the high Cd treatment (500 μg/L) the variation in N 2 production increased compared to the other treatments. Increases in N 2 production are suggested to be an effect of 1) enhanced nitrification that increases NO 3 − availability thus stimulating denitrification, and 2) Cd successfully sequestrating sulfide (yielding CdS), which allows for full denitrification to N 2. The in situ field sediment contained initially high Cd concentrations in the pore water (∼10 μg/L) and microbial communities might already have been adapted to metal stress, making the effect of low Cd levels negligible. Here we show that high levels of cadmium pollution might increase N 2 production and influence nitrogen cycling in marine sediments. −), 2) NO 2 − to nitric oxide (NO), 3) NO to nitrous oxide (N 2 O), and finally 4) N 2 O to nitrogen gas (N 2) (Devol, 2015). The enzymes nitrite reductase (nir i.e. NO 2 − to NO) and
Our growing awareness of the microbial world's importance and diversity contrasts starkly wit... more Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete ...
The goal of this work was to identify sequences encoding monooxygenase biocatalysts with novel fe... more The goal of this work was to identify sequences encoding monooxygenase biocatalysts with novel features by in silico mining an assembled metagenomic dataset of polar and subpolar marine sediments. The targeted enzyme sequences were Baeyer-Villiger and bacterial cytochrome P450 monooxygenases (CYP153). These enzymes have wide-ranging applications, from the synthesis of steroids, antibiotics, mycotoxins and pheromones to the synthesis of monomers for polymerization and anticancer precursors, due to their extraordinary enantio-, regio-, and chemo- selectivity that are valuable features for organic synthesis. Phylogenetic analyses were used to select the most divergent sequences affiliated to these enzyme families among the 264 putative monooxygenases recovered from the ~14 million protein-coding sequences in the assembled metagenome dataset. Three-dimensional structure modeling and docking analysis suggested features useful in biotechnological applications in five metagenomic sequences...
In this work, we analyzed the community structure and metabolic potential of sediment microbial c... more In this work, we analyzed the community structure and metabolic potential of sediment microbial communities in high-latitude coastal environments subjected to low to moderate levels of chronic pollution. Subtidal sediments from four low-energy inlets located in polar and subpolar regions from both Hemispheres were analyzed using large-scale 16S rRNA gene and metagenomic sequencing. Communities showed high diversity (Shannon's index 6.8 to 10.2), with distinct phylogenetic structures (<40% shared taxa at the Phylum level among regions) but similar metabolic potential in terms of sequences assigned to KOs. Environmental factors (mainly salinity, temperature, and in less extent organic pollution) were drivers of both phylogenetic and functional traits. Bacterial taxa correlating with hydrocarbon pollution included families of anaerobic or facultative anaerobic lifestyle, such as Desulfuromonadaceae, Geobacteraceae, and Rhodocyclaceae. In accordance, biomarker genes for anaerobic...
Information in this manuscript is the first study on microbial rhodopsins present in coastal mari... more Information in this manuscript is the first study on microbial rhodopsins present in coastal marine sediments. Also it reported a previously undescribed allopatric cladism for the viral rhodopsins sequences.
Baltic Sea deep water and sediments hold one of the largest anthropogenically induced hypoxic are... more Baltic Sea deep water and sediments hold one of the largest anthropogenically induced hypoxic areas in the world. High nutrient input and low water exchange result in eutrophication and oxygen depletion below the halocline. As a consequence at Landsort Deep, the deepest point of the Baltic Sea, anoxia in the sediments has been a persistent condition over the past decades. Given that microbial communities are drivers of essential ecosystem functions we investigated the microbial community metabolisms and functions of oxygen depleted Landsort Deep sediments by metatranscriptomics. Results show substantial expression of genes involved in protein metabolism demonstrating that the Landsort Deep sediment microbial community is active. Identified expressed gene suites of metabolic pathways with importance for carbon transformation including fermentation, dissimilatory sulphate reduction and methanogenesis were identified. The presence of transcripts for these metabolic processes suggests a...
Mitochondrial biogenesis requires a coordinated expression of both the nuclear and the organellar... more Mitochondrial biogenesis requires a coordinated expression of both the nuclear and the organellar genomes and specific intracellular protein trafficking, processing and assembly machinery. Most mitochondrial proteins are synthesised as precursor proteins containing an N-terminal extension which functions as a targeting signal, which is proteolytically cleaved off after import into mitochondria. We review our present knowledge on components and mechanisms involved in the mitochondrial protein import process in plants. This encompasses properties of targeting peptides, sorting of precursor proteins between mitochondria and chloroplasts, signal recognition, mechanism of translocation across the mitochondrial membranes and the role of cytosolic and organellar molecular chaperones in this process. The mitochondrial protein processing in plants is catalysed by the mitochondrial processing peptidase (MPP), which in contrast to other sources, is integrated into the bc1 complex of the respir...
The mitochondrial processing peptidase (MPP) in lower eucaryots and mammals is a matrix enzyme, w... more The mitochondrial processing peptidase (MPP) in lower eucaryots and mammals is a matrix enzyme, whereas MPP in plants constitutes an integral part of the bc1 complex of the respiratory chain. The isolated spinach leaf bc1 complex catalyzes cleavage of the precursor of Nicotiana plumbaginifolia F1 beta subunit of the ATP synthase, resulting in a production of mature protein and a presequence that consists of 54 amino acids. A synthetic peptide derived from the C-terminal part of the presequence, containing 17 amino acids with a helical structural element, p-F1 beta(38-54), was an efficient inhibitor of the processing, whereas a peptide derived from the N-terminal part of the presequence, p-F1 beta(1-18), was much less effective. ATIII, a helical peptide derived from antithrombin III, was not recognized by MPP. Synthetic peptides corresponding to 4, 6, and 11 amino acids of the C terminus of the presequence, p-F1 beta(51-54), p-F1 beta(49-54), and p-F1 beta(44-54) were almost complete...
The plant mitochondrial processing peptidase (MPP) that catalyses the cleavage of the presequence... more The plant mitochondrial processing peptidase (MPP) that catalyses the cleavage of the presequences from precursor proteins during or after protein import is a membrane-bound enzyme that constitutes an integral part of the be, complex of the respiratory chain. In contrast, MPP from mammals is soluble in the matrix space and does not form part of the respiratory chain. In the present study, we have compared the substrate specificity of the isolated spinach leaf bc,lMPP with rat liver MPP using synthetic signal peptides and different mitochondrial precursor proteins. Inhibition studies of processing with synthetic peptides showed a similar inhibition pattern for plant and rat MPP activity. A peptide derived from the presequence of rat liver mitochondrial aldehyde dehydrogenase (ALDH) was a potent inhibitor of the spinach and rat MPP. Two nonprocessed signal peptides, rhodanese and linker-deleted ALDH (a form of ALDH that lacks the RGP linker connecting two helices in the presequence) had lower inhibitory effects towards each protease. The signal peptide from thiolase, another nonprocessed protein, had little inhibitory effect on MPP. Peptides derived from presequence of the plant Nicotiana plunzbaginifolia FIB also showed a similar inhibitory pattern with rat MPP as with spinach MPP processing. In-vitro synthesised precursors of plant N. plunzbaginifolia F,P and rat liver ALDH were cleaved to mature form by both spinach and rat MPP. However, the efficiency of processing was higher with the homologous precursor. Linker-deleted ALDH, rhodanese, and thiolase were not processed by the mammalian or plant MPP. However, both forms of MPP cleaved a mutated form of rhodanese that possesses a typical MPP cleavage motif, RXY S. Addition of the same cleavage motif to thiolase did not result in processing by either MPP. These results show that similar higher-order structural elements upstream from the cleavage site are important for processing by both the membrane-bound plant and the soluble mammalian MPP. Keywords: mitochondrial processing peptidase : signal peptide : protein processing; protein import; cytochrome bc, complex. Kuclear-encoded mitochondrial proteins are translated on cytosolic polyribosomes as precursor proteins. Most of the precursor proteins carry an N-terminal extension, the presequence or signal sequence, that contains information for mitochondrial targeting and sorting. Import of the precursor proteins into the mitochondria is usually accompanied by proteolytic removal of the presequence [l-31 resulting in the production of mature proteins. This step is catalysed by the mitochondrial processing peptidase (MPP) [4-91. MPP, a metal-dependent endopeptidase consisting of two structurally related subunits, a-MPP and b-MPP, forms a heterodimeric complex [lo, 111, in which both subunits are essential Correspondrrzce to E.
The current study assessed the occurrence of the Vibrio cholerae serogroups O1 and O139 in enviro... more The current study assessed the occurrence of the Vibrio cholerae serogroups O1 and O139 in environmental samples along salinity gradients in three selected estuaries of Tanzania both through culture independent methods and by cultured bacteria. Occurrence of V. cholerae was determined by PCR targeting the V. cholerae outer membrane protein gene ompW. Furthermore, the presence of toxigenic strains and serogroups O1 and O139 was determined using multiplex PCR with specific primers targeting the cholera toxin gene subunit A, ctxA, and serotype specific primers, O1-rfb and O139-rfb, respectively. Results showed that V. cholerae occurred in approximately 10% (n = 185) of both the environmental samples and isolated bacteria. Eight of the bacteria isolates (n = 43) were confirmed as serogroup O1 while one belonged to serogroup O139, the first reported identification of this epidemic strain in East African coastal waters. All samples identified as serogroup O1 or O139 and a number of non-O1/O139 strains were ctxA positive. This study provides in situ evidence of the presence of pathogenic V. cholerae O1 and O139 and a number of V. cholerae non-O1/O139 that carry the cholera toxin gene in estuaries along the coast of Tanzania.
Psychrophiles: from Biodiversity to Biotechnology, 2008
... Genomes Revealed Sara Sjöling(*ü) and Don A. Cowan ... Metagenomics is therefore the applicat... more ... Genomes Revealed Sara Sjöling(*ü) and Don A. Cowan ... Metagenomics is therefore the application of modern genomic tools used to analyze Sara Sjöling School of Life Sciences, University College Södertörn, 14189 Huddinge, Sweden e-mail: [email protected] ...
ABSTRACT Brown macroalgae are considered an attractive option as sustainable feedstock for the pr... more ABSTRACT Brown macroalgae are considered an attractive option as sustainable feedstock for the production of biofuels and commodity chemicals due to their high carbohydrate content (such as alginates), and the absence of hemicellulose and lignin. Microbial communities from cold coastal environments represent promising sources of novel alginate-depolymerizing enzymes, as brown algae constitute a large primary biomass in these environments. We used a nested sampling strategy to obtain coastal sediment samples from four high-latitude regions (Svalbard Archipelago, Norway; Baltic Sea, Sweden; Ushuaia Bay, Argentina and Potter Cove, Antarctic Peninsula). Metagenomes were sequenced using 23 lanes of Illumina HiSeq™ 1500, and were annotated at the IMG/M pipeline. The complete assembled metagenome dataset contains 5.6 Gb and 1.4 x 107 protein coding genes. We mined this dataset with the goal of identifying alginate lyase homologs using both blastp searches and assigned product names. We retrieved 2,705 sequences ≥ 100 amino acids in length, 75% of them belonging to the samples from polar regions. Most sequences were classified as belonging to PL17 (30.4%), PL7 (28%) or PL6 (22%) families (CAZy database), and 13% of them were too distant to reference sequences and could not be classified. Phylogenetic analysis of full length sequences and gene order conservation for long scaffolds show moderate relatedness to sequences from isolated bacteria. This study revealed a large diversity of alginate lyase sequences from marine yet-to-be cultured microorganisms, which could aid in the engineering of microorganisms for biorefineries.
This report summarizes the events of the 1(st) International Functional Metagenomics Workshop. Th... more This report summarizes the events of the 1(st) International Functional Metagenomics Workshop. The workshop was held on May 7 and 8, 2012, in St. Jacobs, Ontario, Canada and was focused on building an international functional metagenomics community, exploring strategic research areas, and identifying opportunities for future collaboration and funding. The workshop was initiated by researchers at the University of Waterloo with support from the Ontario Genomics Institute (OGI), Natural Sciences and Engineering Research Council of Canada (NSERC) and the University of Waterloo.
Proteins function at distinct sites in the cell, yet most are primarily synthesized in the cytoso... more Proteins function at distinct sites in the cell, yet most are primarily synthesized in the cytosol and must therefore be transported intracellularly to their final destination. Mitochondrial targeting peptides are localized at the N-terminus of the precursor proteins and most are cleaved off after import into mitochondria. Cleavage is catalysed by the general mitochondrial processing peptidase, which, in plants, is integrated into the bc 1 complex of the respiratory chain. This peptidase recognizes the cleavage sites of nearly 1000 precursor proteins that have no sequence similarity. Fig. 1. Conserved domains within plant mitochondrial presequences. The sequences were aligned with Clustal W. An asterisk marks identical amino acid residues. Abbreviations: F 1 , F 1  subunit of the ATP synthase; FeS, Rieske-FeS protein; Hsp60, heat shock protein of 60 kDa. Numerals show the number of amino acid residues.
Soil teems with microbial genetic information that can be exploited for biotechnological innovati... more Soil teems with microbial genetic information that can be exploited for biotechnological innovation. Because only a fraction of the soil microbiota is cultivable, our ability to unlock this genetic complement has been hampered. Recently developed molecular tools, which make it possible to utilize genomic DNA from soil, can bypass cultivation and provide information on the collective soil metagenome with the aim to explore genes that encode functions of key interest to biotechnology. The metagenome of disease-suppressive soils is of particular interest given the expected prevalence of antibiotic biosynthetic clusters. However, owing to the complexity of soil microbial communities, deciphering this key genetic information is challenging. Here, we examine crucial issues and challenges that so far have hindered the metagenomic exploration of soil by drawing on experience from a trans-European project on disease-suppressive soils denoted METACONTROL.
Determinants for the recognition of a mitochondrial presequence by the mitochondrial processing p... more Determinants for the recognition of a mitochondrial presequence by the mitochondrial processing peptidase (MPP) have been investigated using mutagenesis and bioinformatics approaches. All plant mitochondrial presequences with a cleavage site that was con®rmed by experimental studies can be grouped into three classes. Two major classes contain an arginine residue at position ±2 or ±3, and the third class does not have any conserved arginines. Sequence logos revealed loosely conserved cleavage motifs for the ®rst two classes but no signi®cant amino acid conservation for the third class. Investigation of processing determinants for a class III precursor, Nicotiana plumbaginifolia F 1 b precursor of ATP synthase (pF 1 b), was performed using a series of pF 1 b presequence mutants and mutant presequence peptides derived from the C-terminal portion of the presequence. Replacement of ±2 Gln by Arg inhibited processing, whereas replacement of either the most proximally located ±5 Arg or ±15 Arg by Leu had only a low inhibitory effect. The C-terminal portion of the pF 1 b presequence forms a helix± turn±helix structure. Mutations disturbing or prolonging the helical element upstream of the cleavage site inhibited processing signi®cantly. Structural models of potato MPP and the C-terminal pF 1 b presequence peptide were built by homology modelling and empirical conformational energy search methods, respectively. Molecular docking of the pF 1 b presequence peptide to the MPP model suggested binding of the peptide to the negatively charged binding cleft formed by the a-MPP and b-MPP subunits in close proximity to the H 111 XXE 114 H 115 X (116±190) E 191 proteolytic active site on b-MPP. Our results show for the ®rst time that the amino acid at the ±2 position, even if not an arginine, as well as structural properties of the C-terminal portion of the presequence are important determinants for the processing of a class III precursor by MPP.
Uploads
Papers by Sara Sjöling