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1.
Nat Commun ; 11(1): 4658, 2020 09 16.
Artigo em Inglês | MEDLINE | ID: mdl-32938931

RESUMO

Dimethylsulfoniopropionate (DMSP) is an important marine osmolyte. Aphotic environments are only recently being considered as potential contributors to global DMSP production. Here, our Mariana Trench study reveals a typical seawater DMSP/dimethylsulfide (DMS) profile, with highest concentrations in the euphotic zone and decreased but consistent levels below. The genetic potential for bacterial DMSP synthesis via the dsyB gene and its transcription is greater in the deep ocean, and is highest in the sediment.s DMSP catabolic potential is present throughout the trench waters, but is less prominent below 8000 m, perhaps indicating a preference to store DMSP in the deep for stress protection. Deep ocean bacterial isolates show enhanced DMSP production under increased hydrostatic pressure. Furthermore, bacterial dsyB mutants are less tolerant of deep ocean pressures than wild-type strains. Thus, we propose a physiological function for DMSP in hydrostatic pressure protection, and that bacteria are key DMSP producers in deep seawater and sediment.


Assuntos
Bactérias/genética , Bactérias/metabolismo , Água do Mar/química , Água do Mar/microbiologia , Compostos de Sulfônio/metabolismo , Bactérias/isolamento & purificação , Clorofila A/análise , Clorofila A/metabolismo , Genes Bacterianos , Sedimentos Geológicos/química , Pressão Hidrostática , Marinobacter/genética , Marinobacter/isolamento & purificação , Marinobacter/metabolismo , Metagenoma , Mutação , Oceanos e Mares , Prochlorococcus/genética , Prochlorococcus/isolamento & purificação , Prochlorococcus/metabolismo , RNA Ribossômico 16S , Sulfetos/análise , Sulfetos/metabolismo , Compostos de Sulfônio/análise , Synechococcus/genética , Synechococcus/isolamento & purificação , Synechococcus/metabolismo
2.
Nat Commun ; 11(1): 1942, 2020 04 23.
Artigo em Inglês | MEDLINE | ID: mdl-32327645

RESUMO

Dimethylsulfoniopropionate (DMSP) is a pivotal compound in marine biogeochemical cycles and a key chemical currency in microbial interactions. Marine bacteria transform DMSP via two competing pathways with considerably different biogeochemical implications: demethylation channels sulfur into the microbial food web, whereas cleavage releases sulfur into the atmosphere. Here, we present single-cell measurements of the expression of these two pathways using engineered fluorescent reporter strains of Ruegeria pomeroyi DSS-3, and find that external DMSP concentration dictates the relative expression of the two pathways. DMSP induces an upregulation of both pathways, but only at high concentrations (>1 µM for demethylation; >35 nM for cleavage), characteristic of microscale hotspots such as the vicinity of phytoplankton cells. Co-incubations between DMSP-producing microalgae and bacteria revealed an increase in cleavage pathway expression close to the microalgae's surface. These results indicate that bacterial utilization of microscale DMSP hotspots is an important determinant of the fate of sulfur in the ocean.


Assuntos
Regulação Bacteriana da Expressão Gênica , Água do Mar/microbiologia , Compostos de Sulfônio/metabolismo , Enxofre/metabolismo , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Proteínas Luminescentes/genética , Proteínas Luminescentes/metabolismo , Redes e Vias Metabólicas/genética , Microalgas/metabolismo , Interações Microbianas , Fitoplâncton/metabolismo , Proteínas Recombinantes de Fusão/genética , Proteínas Recombinantes de Fusão/metabolismo , Rhodobacteraceae/genética , Rhodobacteraceae/metabolismo , Água do Mar/química , Análise de Célula Única , Compostos de Sulfônio/análise , Enxofre/análise , Transcrição Genética
3.
ISME J ; 14(5): 1290-1303, 2020 05.
Artigo em Inglês | MEDLINE | ID: mdl-32055028

RESUMO

Dominant coral-associated Endozoicomonas bacteria species are hypothesized to play a role in the coral sulfur cycle by metabolizing dimethylsulfoniopropionate (DMSP) into dimethylsulfide (DMS); however, no sequenced genome to date harbors genes for this process. In this study, we assembled high-quality (>95% complete) draft genomes of strains of the recently added species Endozoicomonas acroporae (Acr-14T, Acr-1, and Acr-5) isolated from the coral Acropora sp. and performed a comparative genomic analysis on the genus Endozoicomonas. We identified DMSP CoA-transferase/lyase-a dddD gene homolog in all sequenced genomes of E. acroporae strains-and functionally characterized bacteria capable of metabolizing DMSP into DMS via the DddD cleavage pathway using RT-qPCR and gas chromatography (GC). Furthermore, we demonstrated that E. acroporae strains can use DMSP as a carbon source and have genes arranged in an operon-like manner to link DMSP metabolism to the central carbon cycle. This study confirms the role of Endozoicomonas in the coral sulfur cycle.


Assuntos
Antozoários/microbiologia , Gammaproteobacteria/metabolismo , Compostos de Sulfônio/metabolismo , Animais , Bactérias/genética , Liases de Carbono-Enxofre , Gammaproteobacteria/genética , Genômica , Sulfetos , Enxofre/metabolismo
4.
Microb Ecol ; 79(1): 12-20, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31144003

RESUMO

The coastal zone has distinguishable but tightly connected ecosystems from rivers to the ocean and globally contributes to nutrient cycling including phytoplankton-derived organic matter. Particularly, bacterial contributions to phytoplankton-derived dimethylsulfoniopropionate (DMSP) degradation have been recently evaluated by using advanced sequencing technologies to understand their role in the marine microbial food web. Here, we surveyed the bacterial diversity and community composition under seasonal water mixing in the bay of Gwangyang (GW), a semi-enclosed estuary at the southern tip of the Korea Peninsula. We detected phylogenetic dissimilarities among season-specific habitats in GW and their specific bacterial taxa. Additionally, bacterial contribution to degradation of phytoplankton-derived DMSP from estuarine to coastal waters at euphotic depths in GW was investigated as the presence or absence of DMSP demethylation gene, encoded by dmdA. Among the operational taxonomic units (OTUs) in GW bacterial communities, the most dominant and ubiquitous OTU1 was affiliated with the SAR11 clade (SAR11-OTU). The population dynamics of SAR11-OTU in dmdA-detected GW waters suggest that water mass mixing plays a major role in shaping bacterial communities involved in phytoplankton-derived DMSP demethylation.


Assuntos
Bactérias/metabolismo , Fitoplâncton/metabolismo , Compostos de Sulfônio/metabolismo , Bactérias/classificação , Bactérias/genética , Bactérias/isolamento & purificação , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Biodegradação Ambiental , Estuários , Filogenia , Fitoplâncton/química , República da Coreia , Estações do Ano , Água do Mar/química , Água do Mar/microbiologia
5.
Nat Microbiol ; 4(11): 1815-1825, 2019 11.
Artigo em Inglês | MEDLINE | ID: mdl-31427729

RESUMO

Dimethylsulfoniopropionate (DMSP) and its catabolite dimethyl sulfide (DMS) are key marine nutrients1,2 that have roles in global sulfur cycling2, atmospheric chemistry3, signalling4,5 and, potentially, climate regulation6,7. The production of DMSP was previously thought to be an oxic and photic process that is mainly confined to the surface oceans. However, here we show that DMSP concentrations and/or rates of DMSP and DMS synthesis are higher in surface sediment from, for example, saltmarsh ponds, estuaries and the deep ocean than in the overlying seawater. A quarter of bacterial strains isolated from saltmarsh sediment produced DMSP (up to 73 mM), and we identified several previously unknown producers of DMSP. Most DMSP-producing isolates contained dsyB8, but some alphaproteobacteria, gammaproteobacteria and actinobacteria used a methionine methylation pathway independent of DsyB that was previously only associated with higher plants. These bacteria contained a methionine methyltransferase gene (mmtN)-a marker for bacterial synthesis of DMSP through this pathway. DMSP-producing bacteria and their dsyB and/or mmtN transcripts were present in all of the tested seawater samples and Tara Oceans bacterioplankton datasets, but were much more abundant in marine surface sediment. Approximately 1 × 108 bacteria g-1 of surface marine sediment are predicted to produce DMSP, and their contribution to this process should be included in future models of global DMSP production. We propose that coastal and marine sediments, which cover a large part of the Earth's surface, are environments with high levels of DMSP and DMS productivity, and that bacteria are important producers of DMSP and DMS within these environments.


Assuntos
Bactérias/classificação , Redes Reguladoras de Genes , Sedimentos Geológicos/microbiologia , Compostos de Sulfônio/metabolismo , Bactérias/genética , Bactérias/isolamento & purificação , Bactérias/metabolismo , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Perfilação da Expressão Gênica , Regulação Bacteriana da Expressão Gênica , Metionina/metabolismo , Metiltransferases/genética , Metiltransferases/metabolismo , Filogenia , Água do Mar/microbiologia , Análise de Sequência de RNA
6.
Sci China Life Sci ; 62(10): 1296-1319, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31231779

RESUMO

Dimethyl sulfide (DMS) is the most abundant form of volatile sulfur in Earth's oceans, and is mainly produced by the enzymatic clevage of dimethylsulfoniopropionate (DMSP). DMS and DMSP play important roles in driving the global sulfur cycle and may affect climate. DMSP is proposed to serve as an osmolyte, a grazing deterrent, a signaling molecule, an antioxidant, a cryoprotectant and/or as a sink for excess sulfur. It was long believed that only marine eukaryotes such as phytoplankton produce DMSP. However, we recently discovered that marine heterotrophic bacteria can also produce DMSP, making them a potentially important source of DMSP. At present, one prokaryotic and two eukaryotic DMSP synthesis enzymes have been identified. Marine heterotrophic bacteria are likely the major degraders of DMSP, using two known pathways: demethylation and cleavage. Many phytoplankton and some fungi can also cleave DMSP. So far seven different prokaryotic and one eukaryotic DMSP lyases have been identified. This review describes the global distribution pattern of DMSP and DMS, the known genes for biosynthesis and cleavage of DMSP, and the physiological and ecological functions of these important organosulfur molecules, which will improve understanding of the mechanisms of DMSP and DMS production and their roles in the environment.


Assuntos
Sulfetos/química , Compostos de Sulfônio/química , Enxofre/química , Bactérias/genética , Bactérias/metabolismo , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Biodegradação Ambiental , Liases de Carbono-Enxofre , Fungos/genética , Fungos/metabolismo , Genes Bacterianos , Oceanos e Mares , Filogenia , Fitoplâncton/genética , Fitoplâncton/metabolismo , Sulfetos/metabolismo , Compostos de Sulfônio/metabolismo , Enxofre/metabolismo
7.
J Microbiol ; 57(8): 676-687, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31201724

RESUMO

Strain IMCC1322 was isolated from a surface water sample from the East Sea of Korea. Based on 16S rRNA analysis, IMCC1322 was found to belong to the OCS28 sub-clade of SAR116. The cells appeared as short vibrioids in logarithmic-phase culture, and elongated spirals during incubation with mitomycin or in aged culture. Growth characteristics of strain IMCC1322 were further evaluated based on genomic information; proteorhodopsin (PR), carbon monoxide dehydrogenase, and dimethylsulfoniopropionate (DMSP)-utilizing enzymes. IMCC1322 PR was characterized as a functional retinylidene protein that acts as a light-driven proton pump in the cytoplasmic membrane. However, the PR-dependent phototrophic potential of strain IMCC1322 was only observed under CO-inhibited and nutrient-limited culture conditions. A DMSP-enhanced growth response was observed in addition to cultures grown on C1 compounds like methanol, formate, and methane sulfonate. Strain IMCC1322 cultivation analysis revealed biogeochemical processes characteristic of the SAR116 group, a dominant member of the microbial community in euphotic regions of the ocean. The polyphasic taxonomy of strain IMCC1322 is given as Candidatus Puniceispirillum marinum, and was confirmed by chemotaxonomic tests, in addition to 16S rRNA phylogeny and cultivation analyses.


Assuntos
Alphaproteobacteria , RNA Ribossômico 16S/genética , Rodopsinas Microbianas , Água do Mar/microbiologia , Alphaproteobacteria/classificação , Alphaproteobacteria/genética , Alphaproteobacteria/crescimento & desenvolvimento , Alphaproteobacteria/isolamento & purificação , Técnicas de Tipagem Bacteriana/métodos , DNA Bacteriano/genética , República da Coreia , Rodopsinas Microbianas/química , Rodopsinas Microbianas/metabolismo , Compostos de Sulfônio/metabolismo , Sequenciamento Completo do Genoma/métodos
8.
Curr Microbiol ; 76(9): 967-974, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31134298

RESUMO

Dimethylsulfoniopropionate (DMSP) is an organic sulfur compound that occurs in large amounts in oceans around the world, and it plays an important role in the global sulfur cycle. DMSP released into seawater can be rapidly catabolized by bacteria via two pathways, namely, demethylation or cleavage pathway. Members of the Roseobacter clade frequently possess enzymes involved in the DMSP demethylation or cleavage pathway. We tried to measure the diversity of genes encoding DMSP demethylase (dmdA) and DMSP lyases (dddD, dddL, and dddP) in bacteria in the surface seawater of Ardley Cove and Great Wall Cove in Antarctic Maxwell Bay using DMSP degradation gene clone library analysis. Although we did not detect sequences related to the dddD or dddL gene, both bacterial dmdA and dddP genes found in the two coves were completely confined to the Roseobacter clade, which indicated that this clade plays a significant role in DMSP catabolism in the coastal seawaters of Maxwell Bay. In addition, compared with bacterial DMSP degradation genes in Arctic coastal seawater, our results suggest that both bipolar and endemic bacterial DMSP degradation genes exist in polar marine environments. The findings of this study improve our knowledge of the distribution of DMSP degradation genes in polar marine ecosystems.


Assuntos
Baías/microbiologia , Roseobacter/metabolismo , Água do Mar/microbiologia , Compostos de Sulfônio/metabolismo , Enxofre/metabolismo , Regiões Antárticas , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Biodiversidade , Liases de Carbono-Enxofre/genética , Liases de Carbono-Enxofre/metabolismo , Filogenia , Roseobacter/classificação , Roseobacter/genética , Roseobacter/isolamento & purificação
9.
Biochemistry ; 58(16): 2152-2159, 2019 04 23.
Artigo em Inglês | MEDLINE | ID: mdl-30810306

RESUMO

The N-methyltransferase TylM1 from Streptomyces fradiae catalyzes the final step in the biosynthesis of the deoxyamino sugar mycaminose, a substituent of the antibiotic tylosin. The high-resolution crystal structure of TylM1 bound to the methyl donor S-adenosylmethionine (AdoMet) illustrates a network of carbon-oxygen (CH···O) hydrogen bonds between the substrate's sulfonium cation and residues within the active site. These interactions include hydrogen bonds between the methyl and methylene groups of the AdoMet sulfonium cation and the hydroxyl groups of Tyr14 and Ser120 in the enzyme. To examine the functions of these interactions, we generated Tyr14 to phenylalanine (Y14F) and Ser120 to alanine (S120A) mutations to selectively ablate the CH···O hydrogen bonding to AdoMet. The TylM1 S120A mutant exhibited a modest decrease in its catalytic efficiency relative to that of the wild type (WT) enzyme, whereas the Y14F mutation resulted in an approximately 30-fold decrease in catalytic efficiency. In contrast, site-specific substitution of Tyr14 by the noncanonical amino acid p-aminophenylalanine partially restored activity comparable to that of the WT enzyme. Correlatively, quantum mechanical calculations of the activation barrier energies of WT TylM1 and the Tyr14 mutants suggest that substitutions that abrogate hydrogen bonding with the AdoMet methyl group impair methyl transfer. Together, these results offer insights into roles of CH···O hydrogen bonding in modulating the catalytic efficiency of TylM1.


Assuntos
Proteínas de Bactérias/química , Ligação de Hidrogênio , Metiltransferases/química , S-Adenosilmetionina/química , Compostos de Sulfônio/química , Amino Açúcares/química , Amino Açúcares/metabolismo , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Biocatálise , Carbono/química , Carbono/metabolismo , Cristalografia por Raios X , Glucosamina/análogos & derivados , Glucosamina/química , Glucosamina/metabolismo , Cinética , Metiltransferases/genética , Metiltransferases/metabolismo , Mutação , Oxigênio/química , Oxigênio/metabolismo , Ligação Proteica , Domínios Proteicos , S-Adenosilmetionina/metabolismo , Streptomyces/enzimologia , Streptomyces/genética , Especificidade por Substrato , Compostos de Sulfônio/metabolismo
10.
Appl Environ Microbiol ; 85(8)2019 04 15.
Artigo em Inglês | MEDLINE | ID: mdl-30770407

RESUMO

The osmolyte dimethylsulfoniopropionate (DMSP) is produced in petagram quantities in marine environments and has important roles in global sulfur and carbon cycling. Many marine microorganisms catabolize DMSP via DMSP lyases, generating the climate-active gas dimethyl sulfide (DMS). DMS oxidation products participate in forming cloud condensation nuclei and, thus, may influence weather and climate. SAR11 bacteria are the most abundant marine heterotrophic bacteria; many of them contain the DMSP lyase DddK, and their dddK transcripts are relatively abundant in seawater. In a recently described catalytic mechanism for DddK, Tyr64 is predicted to act as the catalytic base initiating the ß-elimination reaction of DMSP. Tyr64 was proposed to be deprotonated by coordination to the metal cofactor or its neighboring His96. To further probe this mechanism, we purified and characterized the DddK protein from Pelagibacter ubique strain HTCC1062 and determined the crystal structures of wild-type DddK and its Y64A and Y122A mutants (bearing a change of Y to A at position 64 or 122, respectively), where the Y122A mutant is complexed with DMSP. The structural and mutational analyses largely support the catalytic role of Tyr64, but not the method of its deprotonation. Our data indicate that an active water molecule in the active site of DddK plays an important role in the deprotonation of Tyr64 and that this is far more likely than coordination to the metal or His96. Sequence alignment and phylogenetic analysis suggest that the proposed catalytic mechanism of DddK has universal significance. Our results provide new mechanistic insights into DddK and enrich our understanding of DMS generation by SAR11 bacteria.IMPORTANCE The climate-active gas dimethyl sulfide (DMS) plays an important role in global sulfur cycling and atmospheric chemistry. DMS is mainly produced through the bacterial cleavage of marine dimethylsulfoniopropionate (DMSP). When released into the atmosphere from the oceans, DMS can be photochemically oxidized into DMSO or sulfate aerosols, which form cloud condensation nuclei that influence the reflectivity of clouds and, thereby, global temperature. SAR11 bacteria are the most abundant marine heterotrophic bacteria, and many of them contain DMSP lyase DddK to cleave DMSP, generating DMS. In this study, based on structural analyses and mutational assays, we revealed the catalytic mechanism of DddK, which has universal significance in SAR11 bacteria. This study provides new insights into the catalytic mechanism of DddK, leading to a better understanding of how SAR11 bacteria generate DMS.


Assuntos
Liases de Carbono-Enxofre/química , Liases de Carbono-Enxofre/metabolismo , Domínio Catalítico , Compostos de Sulfônio/química , Compostos de Sulfônio/metabolismo , Água/química , Alphaproteobacteria/genética , Alphaproteobacteria/metabolismo , Sequência de Aminoácidos , Bactérias/genética , Bactérias/metabolismo , Liases de Carbono-Enxofre/genética , Escherichia coli/genética , Regulação Bacteriana da Expressão Gênica , Modelos Moleculares , Oceanos e Mares , Filogenia , Mutação Puntual , Conformação Proteica , Água do Mar/microbiologia , Alinhamento de Sequência , Sulfetos , Enxofre/metabolismo
11.
Appl Environ Microbiol ; 85(7)2019 04 01.
Artigo em Inglês | MEDLINE | ID: mdl-30709822

RESUMO

Labrenzia aggregata LZB033 (Rhodobacteraceae), which produces dimethylsulfoniopropionate (DMSP) and reduces nitrate to nitrogen, was isolated from seawater of the East China Sea. Its genome encodes a large number of transcriptional regulators which may be important for its adaptation to diverse marine environments. The alternative σ54 factor (RpoN) is a central regulator of many bacteria, regulating the transcription of multiple genes and controlling important cellular functions. However, the exact role of RpoN in Labrenzia spp. is unknown. In this study, an in-frame rpoN deletion mutant was constructed in LZB033, and the function of RpoN was determined. To systematically identify RpoN-controlled genes, we performed a detailed analysis of gene expression differences between the wild-type strain and the ΔrpoN mutant using RNA sequencing. The expression of 175 genes was shown to be controlled by RpoN. Subsequent phenotypic assays showed that the ΔrpoN mutant was attenuated in flagellar biosynthesis and swimming motility, utilized up to 13 carbon substrates differently, lacked the ability to assimilate malic acid, and displayed markedly decreased biofilm formation. In addition, stress response assays showed that the ΔrpoN mutant was impaired in the ability to survive under different challenge conditions, including osmotic stress, oxidative stress, temperature changes, and acid stress. Moreover, both the DMSP synthesis and catabolism rates of LZB033 decreased after rpoN was knocked out. Our work provides essential insight into the regulatory function of RpoN, revealing that RpoN is a key determinant for LZB033 flagellar formation, motility, biofilm formation, and environmental fitness, as well as DMSP production and degradation.IMPORTANCE This study established an in-frame gene deletion method in the alphaproteobacterium Labrenzia aggregata LZB033 and generated an rpoN gene mutant. A comparison of the transcriptomes and phenotypic characteristics between the mutant and wild-type strains confirmed the role of RpoN in L. aggregata LZB033 flagellar formation, motility, biofilm formation, and carbon usage. Most importantly, RpoN is a key factor for survival under different environmental challenge conditions. Furthermore, the ability to synthesize and metabolize dimethylsulfoniopropionate (DMSP) was related to RpoN. These features revealed RpoN to be an important regulator of stress resistance and survival for L. aggregata LZB033 in marine environments.


Assuntos
Adaptação Fisiológica/fisiologia , Biofilmes/crescimento & desenvolvimento , Flagelos/metabolismo , RNA Polimerase Sigma 54/genética , RNA Polimerase Sigma 54/metabolismo , Rhodobacteraceae/genética , Rhodobacteraceae/metabolismo , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , China , Regulação Bacteriana da Expressão Gênica , Técnicas de Inativação de Genes , Pressão Osmótica , Estresse Oxidativo , RNA Bacteriano/isolamento & purificação , Rhodobacteraceae/citologia , Rhodobacteraceae/crescimento & desenvolvimento , Análise de Sequência de RNA , Compostos de Sulfônio/metabolismo , Temperatura , Transcriptoma
12.
ISME J ; 13(6): 1506-1519, 2019 06.
Artigo em Inglês | MEDLINE | ID: mdl-30742057

RESUMO

Prochlorococcus and SAR11 are among the smallest and most abundant organisms on Earth. With a combined global population of about 2.7 × 1028 cells, they numerically dominate bacterioplankton communities in oligotrophic ocean gyres and yet they have never been grown together in vitro. Here we describe co-cultures of Prochlorococcus and SAR11 isolates representing both high- and low-light adapted clades. We examined: (1) the influence of Prochlorococcus on the growth of SAR11 and vice-versa, (2) whether Prochlorococcus can meet specific nutrient requirements of SAR11, and (3) how co-culture dynamics vary when Prochlorococcus is grown with SAR11 compared with sympatric copiotrophic bacteria. SAR11 grew 15-70% faster in co-culture with Prochlorococcus, while the growth of the latter was unaffected. When Prochlorococcus populations entered stationary phase, this commensal relationship rapidly became amensal, as SAR11 abundances decreased dramatically. In parallel experiments with copiotrophic bacteria; however, the heterotrophic partner increased in abundance as Prochlorococcus densities leveled off. The presence of Prochlorococcus was able to meet SAR11's central requirement for organic carbon, but not reduced sulfur. Prochlorococcus strain MIT9313, but not MED4, could meet the unique glycine requirement of SAR11, which could be due to the production and release of glycine betaine by MIT9313, as supported by comparative genomic evidence. Our findings also suggest, but do not confirm, that Prochlorococcus MIT9313 may compete with SAR11 for the uptake of 3-dimethylsulfoniopropionate (DMSP). To give our results an ecological context, we assessed the relative contribution of Prochlorococcus and SAR11 genome equivalents to those of identifiable bacteria and archaea in over 800 marine metagenomes. At many locations, more than half of the identifiable genome equivalents in the euphotic zone belonged to Prochlorococcus and SAR11 - highlighting the biogeochemical potential of these two groups.


Assuntos
Alphaproteobacteria/crescimento & desenvolvimento , Prochlorococcus/crescimento & desenvolvimento , Alphaproteobacteria/genética , Alphaproteobacteria/metabolismo , Técnicas de Cocultura , Processos Heterotróficos , Prochlorococcus/genética , Prochlorococcus/metabolismo , Água do Mar/microbiologia , Compostos de Sulfônio/metabolismo
13.
Environ Microbiol ; 21(5): 1687-1701, 2019 05.
Artigo em Inglês | MEDLINE | ID: mdl-30761723

RESUMO

Dimethylsulfoniopropionate (DMSP) is an abundant organic sulfur metabolite produced by many phytoplankton species and degraded by bacteria via two distinct pathways with climate-relevant implications. We assessed the diversity and abundance of bacteria possessing these pathways in the context of phytoplankton community composition over a 3-week time period spanning September-October, 2014 in Monterey Bay, CA. The dmdA gene from the DMSP demethylation pathway dominated the DMSP gene pool and was harboured mostly by members of the alphaproteobacterial SAR11 clade and secondarily by the Roseobacter group, particularly during the second half of the study. Novel members of the DMSP-degrading community emerged from dmdA sequences recovered from metagenome assemblies and single-cell sequencing, including largely uncharacterized gammaproteobacteria and alphaproteobacteria taxa. In the DMSP cleavage pathway, the SAR11 gene dddK was the most abundant early in the study, but was supplanted by dddP over time. SAR11 members, especially those harbouring genes for both DMSP degradation pathways, had a strong positive relationship with the abundance of dinoflagellates, and DMSP-degrading gammaproteobacteria co-occurred with haptophytes. This in situ study of the drivers of DMSP fate in a coastal ecosystem demonstrates for the first time correlations between specific groups of bacterial DMSP degraders and phytoplankton taxa.


Assuntos
Alphaproteobacteria/genética , Proteínas de Bactérias/genética , Gammaproteobacteria/genética , Alphaproteobacteria/isolamento & purificação , Alphaproteobacteria/metabolismo , Proteínas de Bactérias/metabolismo , Gammaproteobacteria/isolamento & purificação , Gammaproteobacteria/metabolismo , Genoma Bacteriano , Metagenoma , Filogenia , Roseobacter/genética , Roseobacter/isolamento & purificação , Roseobacter/metabolismo , Água do Mar/microbiologia , Compostos de Sulfônio/metabolismo , Enxofre/metabolismo
14.
Mol Microbiol ; 111(4): 1057-1073, 2019 04.
Artigo em Inglês | MEDLINE | ID: mdl-30677184

RESUMO

The vast majority of oceanic dimethylsulfoniopropionate (DMSP) is thought to be catabolized by bacteria via the DMSP demethylation pathway. This pathway contains four enzymes termed DmdA, DmdB, DmdC and DmdD/AcuH, which together catabolize DMSP to acetylaldehyde and methanethiol as carbon and sulfur sources respectively. While molecular mechanisms for DmdA and DmdD have been proposed, little is known of the catalytic mechanisms of DmdB and DmdC, which are central to this pathway. Here, we undertake physiological, structural and biochemical analyses to elucidate the catalytic mechanisms of DmdB and DmdC. DmdB, a 3-methylmercaptopropionate (MMPA)-coenzyme A (CoA) ligase, undergoes two sequential conformational changes to catalyze the ligation of MMPA and CoA. DmdC, a MMPA-CoA dehydrogenase, catalyzes the dehydrogenation of MMPA-CoA to generate MTA-CoA with Glu435 as the catalytic base. Sequence alignment suggests that the proposed catalytic mechanisms of DmdB and DmdC are likely widely adopted by bacteria using the DMSP demethylation pathway. Analysis of the substrate affinities of involved enzymes indicates that Roseobacters kinetically regulate the DMSP demethylation pathway to ensure DMSP functioning and catabolism in their cells. Altogether, this study sheds novel lights on the catalytic and regulative mechanisms of bacterial DMSP demethylation, leading to a better understanding of bacterial DMSP catabolism.


Assuntos
Proteínas de Bactérias/metabolismo , Desmetilação , Propionatos/metabolismo , Roseobacter/enzimologia , Compostos de Sulfônio/metabolismo , Coenzima A/metabolismo , Coenzima A Ligases/metabolismo , Cinética , Oceanos e Mares , Oxirredutases/metabolismo , Roseobacter/genética , Enxofre/metabolismo
15.
ISME J ; 13(5): 1183-1197, 2019 05.
Artigo em Inglês | MEDLINE | ID: mdl-30643200

RESUMO

Dimethylsulfoniopropionate (DMSP) is produced mainly by phytoplankton and bacteria. It is relatively abundant and ubiquitous in the marine environment, where bacterioplankton make use of it readily as both carbon and sulfur sources. In one transformation pathway, part of the molecule becomes dimethylsulfide (DMS), which escapes into the atmosphere and plays an important role in the sulfur exchange between oceans and atmosphere. Through its other dominant catabolic pathway, bacteria are able to use it as sulfur source. During the past few years, a number of genes involved in its transformation have been characterized. Identifying genes in taxonomic groups not amenable to conventional methods of cultivation is challenging. Indeed, functional annotation of genes in environmental studies is not straightforward, considering that particular taxa are not well represented in the available sequence databases. Furthermore, many genes belong to families of paralogs with similar sequences but perhaps different functions. In this study, we develop in silico approaches to infer protein function of an environmentally important gene (dmdA) that carries out the first step in the sulfur assimilation from DMSP. The method combines a set of tools to annotate a targeted gene in genome databases and metagenome assemblies. The method will be useful to identify genes that carry out key biochemical processes in the environment.


Assuntos
Bactérias/metabolismo , Genes Bacterianos , Metagenoma , Plâncton/metabolismo , Água do Mar/microbiologia , Compostos de Sulfônio/metabolismo , Bactérias/genética , Simulação por Computador , Anotação de Sequência Molecular , Oceanos e Mares , Fitoplâncton/metabolismo , Alinhamento de Sequência , Enxofre/metabolismo
16.
Sci Adv ; 4(10): eaau5716, 2018 10.
Artigo em Inglês | MEDLINE | ID: mdl-30397652

RESUMO

Emiliania huxleyi is a bloom-forming microalga that affects the global sulfur cycle by producing large amounts of dimethylsulfoniopropionate (DMSP) and its volatile metabolic product dimethyl sulfide. Top-down regulation of E. huxleyi blooms has been attributed to viruses and grazers; however, the possible involvement of algicidal bacteria in bloom demise has remained elusive. We demonstrate that a Roseobacter strain, Sulfitobacter D7, that we isolated from a North Atlantic E. huxleyi bloom, exhibited algicidal effects against E. huxleyi upon coculturing. Both the alga and the bacterium were found to co-occur during a natural E. huxleyi bloom, therefore establishing this host-pathogen system as an attractive, ecologically relevant model for studying algal-bacterial interactions in the oceans. During interaction, Sulfitobacter D7 consumed and metabolized algal DMSP to produce high amounts of methanethiol, an alternative product of DMSP catabolism. We revealed a unique strain-specific response, in which E. huxleyi strains that exuded higher amounts of DMSP were more susceptible to Sulfitobacter D7 infection. Intriguingly, exogenous application of DMSP enhanced bacterial virulence and induced susceptibility in an algal strain typically resistant to the bacterial pathogen. This enhanced virulence was highly specific to DMSP compared to addition of propionate and glycerol which had no effect on bacterial virulence. We propose a novel function for DMSP, in addition to its central role in mutualistic interactions among marine organisms, as a mediator of bacterial virulence that may regulate E. huxleyi blooms.


Assuntos
Bactérias/patogenicidade , Fitoplâncton/crescimento & desenvolvimento , Fitoplâncton/metabolismo , Água do Mar/microbiologia , Compostos de Sulfônio/metabolismo , Proteínas de Algas/metabolismo , Filogenia , Fitoplâncton/microbiologia , Virulência
17.
Nature ; 563(7731): 412-415, 2018 11.
Artigo em Inglês | MEDLINE | ID: mdl-30429546

RESUMO

Algae produce massive amounts of dimethylsulfoniopropionate (DMSP), which fuel the organosulfur cycle1,2. On a global scale, several petagrams of this sulfur species are produced annually, thereby driving fundamental processes and the marine food web1. An important DMSP transformation product is dimethylsulfide, which can be either emitted to the atmosphere3,4 or oxidized to dimethylsulfoxide (DMSO) and other products5. Here we report the discovery of a structurally unusual metabolite, dimethylsulfoxonium propionate (DMSOP), that is synthesized by several DMSP-producing microalgae and marine bacteria. As with DMSP, DMSOP is a low-molecular-weight zwitterionic metabolite that carries both a positively and a negatively charged functional group. Isotope labelling studies demonstrate that DMSOP is produced from DMSP, and is readily metabolized to DMSO by marine bacteria. DMSOP was found in near nanomolar amounts in field samples and in algal culture media, and thus represents-to our knowledge-a previously undescribed biogenic source for DMSO in the marine environment. The estimated annual oceanic production of oxidized sulfur from this pathway is in the teragram range, similar to the calculated dimethylsulfide flux to the atmosphere3. This sulfoxonium metabolite is therefore a key metabolite of a previously undescribed pathway in the marine sulfur cycle. These findings highlight the importance of DMSOP in the marine organosulfur cycle.


Assuntos
Organismos Aquáticos/metabolismo , Bactérias/metabolismo , Microalgas/metabolismo , Compostos de Enxofre/metabolismo , Bactérias/crescimento & desenvolvimento , Dimetil Sulfóxido/metabolismo , Marcação por Isótopo , Microalgas/crescimento & desenvolvimento , Oxirredução , Fitoplâncton/citologia , Fitoplâncton/metabolismo , Sulfetos/metabolismo , Compostos de Sulfônio/metabolismo , Compostos de Enxofre/química
18.
Nature ; 562(7728): 563-568, 2018 10.
Artigo em Inglês | MEDLINE | ID: mdl-30323287

RESUMO

Nature has a remarkable ability to carry out site-selective post-translational modification of proteins, therefore enabling a marked increase in their functional diversity1. Inspired by this, chemical tools have been developed for the synthetic manipulation of protein structure and function, and have become essential to the continued advancement of chemical biology, molecular biology and medicine. However, the number of chemical transformations that are suitable for effective protein functionalization is limited, because the stringent demands inherent to biological systems preclude the applicability of many potential processes2. These chemical transformations often need to be selective at a single site on a protein, proceed with very fast reaction rates, operate under biologically ambient conditions and should provide homogeneous products with near-perfect conversion2-7. Although many bioconjugation methods exist at cysteine, lysine and tyrosine, a method targeting a less-explored amino acid would considerably expand the protein functionalization toolbox. Here we report the development of a multifaceted approach to protein functionalization based on chemoselective labelling at methionine residues. By exploiting the electrophilic reactivity of a bespoke hypervalent iodine reagent, the S-Me group in the side chain of methionine can be targeted. The bioconjugation reaction is fast, selective, operates at low-micromolar concentrations and is complementary to existing bioconjugation strategies. Moreover, it produces a protein conjugate that is itself a high-energy intermediate with reactive properties and can serve as a platform for the development of secondary, visible-light-mediated bioorthogonal protein functionalization processes. The merger of these approaches provides a versatile platform for the development of distinct transformations that deliver information-rich protein conjugates directly from the native biomacromolecules.


Assuntos
Metionina/química , Metionina/metabolismo , Proteínas/química , Proteínas/metabolismo , Iodo/química , Substâncias Macromoleculares/química , Processamento de Proteína Pós-Traducional , Compostos de Sulfônio/química , Compostos de Sulfônio/metabolismo
19.
Bioessays ; 40(10): e1800107, 2018 10.
Artigo em Inglês | MEDLINE | ID: mdl-30151860

RESUMO

The acoel worm Symsagittifera roscoffensis, an early offshoot of the Bilateria and the only well-studied marine acoel that lives in a photosymbiotic relationship, exhibits a centralized nervous system, brain regeneration, and a wide repertoire of complex behaviors such as circatidal rhythmicity, photo/geotaxis, and social interactions. While this animal can be collected by the thousands and is studied historically, significant progress is made over the last decade to develop it as an emerging marine model. The authors here present the feasibility of culturing it in the laboratory and describe the progress made on different areas, including genomic and tissue architectures, highlighting the associated challenges. In light of these developments, and on the ability to access abundant synchronized embryos, the authors put forward S. roscoffensis as a marine system to revisit questions in the areas of photosymbiosis, regeneration, chronobiology, and the study of complex behaviors from a molecular and evolutionary perspective.


Assuntos
Encéfalo/fisiologia , Platelmintos/fisiologia , Regeneração/fisiologia , Animais , Organismos Aquáticos , Comportamento Animal , Encéfalo/citologia , Fenômenos Cronobiológicos , Ritmo Circadiano/genética , Microalgas/fisiologia , Microbiota/fisiologia , Compostos de Sulfônio/metabolismo , Simbiose , Células-Tronco Totipotentes/fisiologia
20.
Methods Enzymol ; 605: 269-289, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-29909827

RESUMO

Dimethyl sulfide (DMS) is released at rates of >107 tons annually and plays a key role in the oceanic sulfur cycle and ecology. Marine bacteria, algae, and possibly other organisms release DMS via cleavage of dimethylsulfoniopropionate (DMSP). DMSP lyases have been identified in various organisms, including bacteria, coral, and algae, thus comprising a range of gene families putatively assigned as DMSP lyases. Metagenomics may therefore provide insight regarding the presence of DMSP lyases in various marine environments, thereby promoting a better understanding of global DMS emission. However, gene counts, and even mRNA levels, do not necessarily reflect the level of DMSP cleavage activity in a given environmental sample, especially because some of the families assigned as DMSP lyases may merely exhibit promiscuous lyase activity. Here, we describe a range of biochemical profiling methods that can assign an observed DMSP lysis activity to a specific gene family. These methods include selective inhibitors and DMSP substrate analogues. Combined with genomics and metagenomics, biochemical profiling may enable a more reliable identification of the origins of DMS release in specific organisms and in crude environmental samples.


Assuntos
Organismos Aquáticos/metabolismo , Liases de Carbono-Enxofre/análise , Monitoramento Ambiental/métodos , Ensaios Enzimáticos/métodos , Organismos Aquáticos/genética , Liases de Carbono-Enxofre/antagonistas & inibidores , Liases de Carbono-Enxofre/genética , Liases de Carbono-Enxofre/metabolismo , Clima , Metagenômica/métodos , Sulfetos/análise , Sulfetos/metabolismo , Compostos de Sulfônio/metabolismo
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