dddP Gene Research Articles

A bacterial symbiont in the gill of the marine scallop Argopecten irradians irradians metabolizes dimethylsulfoniopropionate.

Microbial lysis of dimethylsulfoniopropionate (DMSP) is a key step in marine organic sulfur cycling and has been recently demonstrated to play an important role in mediating interactions between bacteria, algae, and zooplankton. To date, microbes that have been found to lyse DMSP are largely confined to free-living and surface-attached bacteria. In this study, we report for the first time that a symbiont (termed "Rhodobiaceae bacterium HWgs001") in the gill of the marine scallop Argopecten irradians irradians can lyse and metabolize DMSP. Analysis of 16S rRNA gene sequences suggested that HWgs001 accounted for up to 93% of the gill microbiota. Microscopic observations suggested that HWgs001 lived within the gill tissue. Unlike symbionts of other bivalves, HWgs001 belongs to Alphaproteobacteria rather than Gammaproteobacteria, and no genes for carbon fixation were identified in its small genome. Moreover, HWgs001 was found to possess a dddP gene, responsible for the lysis of DMSP to acrylate. The enzymatic activity of dddP was confirmed using the heterologous expression, and in situ transcription of the gene in scallop gill tissues was demonstrated using reverse-transcription PCR. Together, these results revealed a taxonomically and functionally unique symbiont, which represents the first-documented DMSP-metabolizing symbiont likely to play significant roles in coastal marine ecosystems.

Responses of biogenic dimethylated sulfur compounds to environmental changes in the northwestern Pacific continental sea

AbstractContinental seas are facing rapid environmental shifts, but how biogenic dimethylated sulfur compounds, including dimethylsulfide (DMS), dimethylsulfoniopropionate (DMSP), and dimethylsulfoxide (DMSO), will respond to these environmental changes remains poorly understood. Here we investigated the effects of nutrient input, ocean acidification, and dust deposition on the phytoplankton community and organic sulfur cycle in the East China Sea. Nutrient input promoted phytoplankton growth and increased the concentrations of DMS, DMSP, and DMSO. With sufficient nutrients, especially nitrate, the dissolved DMSP degradation was inhibited, and the bacterial DMSP‐cleavage pathway (inferred by dddP gene abundance) was enhanced, causing increased DMS production. The sensitivity of phytoplankton biomass and DMS to ocean acidification varied with different initial nutrient levels, demonstrating insensitivity under eutrophic conditions and negative responses under nutrient‐limited conditions. The ocean acidification promoted the dissolved DMSP degradation and bacterial DMSP‐demethylation pathway (inferred by dmdA gene abundance) and weakened the DMS production, causing the decreases of DMS and DMSP. The nutrient from dust deposition (2 mg L−1) was identified as the key factor in enhancing phytoplankton biomass and the organic sulfur compounds concentrations, but trace metals input from dust deposition had no significant effect. This study has identified environmental drivers and suppressors of phytoplankton and biogenic dimethylated sulfur compounds in a changing marine environment, which will enable the effective modeling of future climate change.

Abundance and Diversity of Dimethylsulfoniopropionate Degradation Genes of Roseobacter Group in the Northern South China Sea

Bacterial degradation of dimethylsulfoniopropionate (DMSP) plays a significant role in ecosystem productivity and global climate. In this study, the abundance and diversity of Roseobacter group DMSP degradation genes were explored in spatial scale of the South China Sea (SCS). Quantitative PCR showed that a higher abundance of dmdA (DMSP demethylase) and dddP (DMSP lyase) genes was detected above 75 m than deep water, especially in surface water. A high ratio of dmdA/dddP existed in all sites and increased with water depth, indicating that demethylation was the main degradation pathway in the Roseobacter group. High-throughput sequencing analysis showed that distribution of dmdA gene had a significant layering structure in the northern SCS, and high taxonomic diversity of dmdA gene was observed in near-surface waters (25 and 50 m). DmdA gene in the Roseobacter group, such as Leisingera, Nioella, Roseobacter, Roseovarius, Donghicola, Phaeobacter, and Tateyamaria, had remarkable specificity due to the effect of different sites and water depths. Different ecological strategies of DMSP degradation may be used by members of the bacterial community harboring demethylation genes. In addition, many dmdA sequences were affiliated with unidentified bacteria, indicating that the SCS reserved high diversity of DMSP-degrading bacteria. Canonical correspondence analysis (CCA) suggested that temperature and depth were the most important factors to determine the taxonomic distribution of DMSP degradation genes in the Roseobacter group, as well as their abundance. This study highlighted the understanding of the role of Roseobacter group in DMSP degradation in the tropical ocean.

Distribution of Dimethylsulfoniopropionate Degradation Genes Reflects Strong Water Current Dependencies in the Sanriku Coastal Region in Japan: From Mesocosm to Field Study

Dimethyl sulfide (DMS) is an important component of the global sulfur cycle as it is the most abundant sulfur compound that is emitted via the ocean surface to the atmosphere. Dimethylsulfoniopropionate (DMSP), the precursor of DMS, is mainly produced by phytoplankton and is degraded by marine bacteria. To reveal the role of bacteria in the regulation of DMSP degradation and DMS production, mesocosm and field studies were performed in the Sanriku Coast on the Pacific Ocean in northeast Japan. The responsible bacteria for the transformation of DMSP to DMS and the assimilation of DMSP were monitored, and the genes encoding DMSP lyase (dddD and dddP) and DMSP demethylase (dmdA) were analyzed. The mesocosm study showed that the dmdA subclade D was the dominant DMSP degradation gene in the free-living (FL) and particle-associated (PA) fractions. The dddD gene was found in higher abundance than the dddP gene in all the tested samples. Most importantly, DMS concentration was positively correlated with the abundance of the dddD gene. These results indicated that bacteria possessing dmdA and dddD genes were the major contributors to the DMSP degradation and DMS production, respectively. The genes dmdA subclade D and dddP were abundant in the Tsugaru Warm (TW) Current, while the dmdA subclade C/2 and dddD genes were dominant in the Oyashio (OY) Current. Functional gene network analysis also showed that the DMSP degradation genes were divided into OY and TW Current-related modules, and genes sharing similar functions were clustered in the same module. Our data suggest that environmental fluctuations resulted in habitat filtering and niche partitioning of bacteria possessing DMSP degradation genes. Overall, our findings provide novel insights into the distribution and abundance of DMSP degradation genes in a coastal region with different water current systems.

Diversity of Dimethylsulfoniopropionate Degradation Genes Reveals the Significance of Marine Roseobacter Clade in Sulfur Metabolism in Coastal Areas of Antarctic Maxwell Bay.

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.

Diversity of bacterial dimethylsulfoniopropionate degradation genes in surface seawater of Arctic Kongsfjorden.

Dimethylsulfoniopropionate (DMSP), which is the major source of organic sulfur in the world’s oceans, plays a significant role in the global sulfur cycle. This compound is rapidly degraded by marine bacteria either by cleavage to dimethylsulfide (DMS) or demethylation to 3-methylmercaptopropionate (MMPA). The diversity of genes encoding bacterial demethylation (dmdA) and DMS production (dddL and dddP) were measured in Arctic Kongsfjorden. Both dmdA and dddL genes were detected in all stations along a transect from the outer to the inner fjord, while dddP gene was only found in the outer and middle parts of the fjord. The dmdA gene was completely confined to the Roseobacter clade, while the dddL gene was confined to the genus Sulfitobacter. Although the dddP gene pool was also dominated by homologs from the Roseobacter clade, there were a few dddP genes showing close relationships to both Alphaproteobacter and Gammaproteobacter. The results of this study suggest that the Roseobacter clade may play an important role in DMSP catabolism via both demethylation and cleavage pathways in surface waters of Kongsfjorden during summer.

Structural and molecular basis for the novel catalytic mechanism and evolution of DddP, an abundant peptidase‐like bacterial Dimethylsulfoniopropionate lyase: a new enzyme from an old fold

The microbial cleavage of dimethylsulfoniopropionate (DMSP) generates volatile dimethyl sulfide (DMS) and is an important step in global sulfur and carbon cycles. DddP is a DMSP lyase in marine bacteria, and the deduced dddP gene product is abundant in marine metagenomic data sets. However, DddP belongs to the M24 peptidase family according to sequence alignment. Peptidases hydrolyze C-N bonds, but DddP is deduced to cleave C-S bonds. Mechanisms responsible for this striking functional shift are currently unknown. We determined the structures of DMSP lyase RlDddP (the DddP from Ruegeria lacuscaerulensis ITI_1157) bound to inhibitory 2-(N-morpholino) ethanesulfonic acid or PO4 (3-) and of two mutants of RlDddP bound to acrylate. Based on structural, mutational and biochemical analyses, we characterized a new ion-shift catalytic mechanism of RlDddP for DMSP cleavage. Furthermore, we suggested the structural mechanism leading to the loss of peptidase activity and the subsequent development of DMSP lyase activity in DddP. This study sheds light on the catalytic mechanism and the divergent evolution of DddP, leading to a better understanding of marine bacterial DMSP catabolism and global DMS production.

Pyrosequencing Revealed SAR116 Clade as Dominant dddP-Containing Bacteria in Oligotrophic NW Pacific Ocean

Dimethyl sulfide (DMS) is a climatically active gas released into the atmosphere from oceans. It is produced mainly by bacterial enzymatic cleavage of dimethylsulfoniopropionate (DMSP), and six DMSP lyases have been identified to date. To determine the biogeographical distribution of bacteria relevant to DMS production, we investigated the diversity of dddP—the most abundant DMS-producing gene—in the northwestern Pacific Ocean using newly developed primers and the pyrosequencing method. Consistent with previous studies, the major dddP-containing bacteria in coastal areas were those belonging to the Roseobacter clade. However, genotypes closely related to the SAR116 group were found to represent a large portion of dddP-containing bacteria in the surface waters of the oligotrophic ocean. The addition of DMSP to a culture of the SAR116 strain Candidatus Puniceispirillum marinum IMCC1322 resulted in the production of DMS and upregulated expression of the dddP gene. Considering the large area of oligotrophic water and the wide distribution of the SAR116 group in oceans worldwide, we propose that these bacteria may play an important role in oceanic DMS production and biogeochemical sulfur cycles, especially via bacteria-mediated DMSP degradation.

Phylogenetic diversity of the dddP gene for dimethylsulfoniopropionate-dependent dimethyl sulfide synthesis in mangrove soils

The dddP gene encodes an enzyme that cleaves dimethylsulfoniopropionate (DMSP) into dimethyl sulfide (DMS) plus acrylate and has been identified in various marine bacteria and some fungi. The diversity of dddP genes was investigated by culture-independent PCR-based analysis of metagenomic DNA extracted from 4 mangrove soils in Southern China. A phylogenetic tree of 144 cloned dddP sequences comprised 7 groups, 3 of which also included dddP genes from previously identified Ddd(+) (DMSP-dependent DMS production) bacteria. However, most (69%) of the DddP sequences from the mangroves were in 4 other subgroups that did not include sequences from known bacteria, demonstrating a high level of diversity of this gene in these environments. Each clade contained clones from all of the sample sites, suggesting that different dddP types are widespread in mangroves of different geographical locations. Furthermore, it was found the dddP genotype distribution was remarkably influenced by the soil properties pH, available sulfur, salt, and total nitrogen.

The dddP gene of Roseovarius nubinhibens encodes a novel lyase that cleaves dimethylsulfoniopropionate into acrylate plus dimethyl sulfide

The cloned dddP gene of the marine bacterium Roseovarius nubinhibens allows Escherichia coli to form the volatile dimethyl sulfide (DMS) from dimethylsulfoniopropionate (DMSP), an abundant anti-stress compatible solute made by many marine plankton and macroalgae. Using purified DddP, we show here that this enzyme is a DMSP lyase that cleaves DMSP to DMS plus acrylate. DddP forms a functional homodimeric enzyme, has a pH optimum of 6.0 and was a K(m) of approximately 14 mM for the DMSP substrate. DddP belongs to the M24B family of peptidases, some members of which have metal cofactors. However, the metal chelators EDTA and bipyridyl did not affect DddP activity in vitro and the as-isolated enzyme did not contain metal ions. Thus, DddP resembles those members of the M24B family, such as creatinase, which also act on a non-peptide substrate and have no metal cofactor. Site-directed mutagenesis of the active-site region of DddP completely abolished its activity. Another enzyme, termed DddL, which occurs in other alphaproteobacteria, had also been shown to generate DMS plus acrylate from DMSP. However, DddL and DddP have no sequence similarity to each other, so DddP represents a second, wholly different class of DMSP lyase.

The opportunistic coral pathogen Aspergillus sydowii contains dddP and makes dimethyl sulfide from dimethylsulfoniopropionate

The ascomycete Aspergillus sydowii is associated with a serious epizootic of sea fan corals in the Caribbean. Corals are rich in the compatible solute, dimethylsulfoniopropionate (DMSP), produced by their symbionts, the dinoflagellate Symbiodinium. As other Aspergillus species can catabolize DMSP, liberating dimethyl sulfide (DMS) in the process, we tested A. sydowii strains, obtained from diseased corals and other environments, for this Ddd(+) phenotype. All the strains, irrespective of their geographical or environmental origins, made DMS from DMSP, and all of them contained homologs (>87% identical) of the dddP gene, which encodes an enzyme that releases DMS from DMSP and which occurs in other Ddd(+) fungi and in some marine bacteria. The dddP gene was likely acquired by the Aspergillus fungi by inter-domain horizontal gene transfer from alpha-proteobacteria.

The dddP gene, encoding a novel enzyme that converts dimethylsulfoniopropionate into dimethyl sulfide, is widespread in ocean metagenomes and marine bacteria and also occurs in some Ascomycete fungi

In the article ‘The dddP gene, encoding a novel enzyme that converts dimethylsulfoniopropionate into dimethyl sulfide, is widespread in ocean metagenomes and marine bacteria and also occurs in some Ascomycete fungi’ (Todd et al., 2009), the following errors were published in Table 2, page 6: Table 2 was incorrect and should be: The occurrences of the different polypeptides are now given in terms of their frequencies, to the nearest integer, per 100 000 reads in each of the GOS survey sites. The major effect is that this reduces the apparent predominance of DddP at the Punta Cormorant site. The criteria for the numbers of the DmdA, DddD and DddL polypeptides are as described by Howard and colleagues (2008). We apologize for this error.

The dddP gene, encoding a novel enzyme that converts dimethylsulfoniopropionate into dimethyl sulfide, is widespread in ocean metagenomes and marine bacteria and also occurs in some Ascomycete fungi

The marine alphaproteobacterium Roseovarius nubinhibens ISM can produce the gas dimethyl sulfide (DMS) from dimethylsulfoniopropionate (DMSP), a widespread secondary metabolite that occurs in many phytoplankton. Roseovarius possesses a novel gene, termed dddP, which when cloned, confers on Escherichia coli the ability to produce DMS. The DddP polypeptide is in the large family of M24 metallopeptidases and is wholly different from two other enzymes, DddD and DddL, which were previously shown to generate DMS from dimethylsulfoniopropionate. Close homologues of DddP occur in other alphaproteobacteria and more surprisingly, in some Ascomycete fungi. These were the biotechnologically important Aspergillus oryzae and the plant pathogen, Fusarium graminearum. The dddP gene is abundant in the bacterial metagenomic sequences in the Global Ocean Sampling Expedition. Thus, dddP has several novel features and is widely dispersed, both taxonomically and geographically.

Complete Genome Viral Phylogenies Suggests the Concerted Evolution of Regulatory Cores and Accessory Satellites

We consider the concerted evolution of viral genomes in four families of DNA viruses. Given the high rate of horizontal gene transfer among viruses and their hosts, it is an open question as to how representative particular genes are of the evolutionary history of the complete genome. To address the concerted evolution of viral genes, we compared genomic evolution across four distinct, extant viral families. For all four viral families we constructed DNA-dependent DNA polymerase-based (DdDp) phylogenies and in addition, whole genome sequence, as quantitative descriptions of inter-genome relationships. We found that the history of the polymerase gene was highly predictive of the history of the genome as a whole, which we explain in terms of repeated, co-divergence events of the core DdDp gene accompanied by a number of satellite, accessory genetic loci. We also found that the rate of gene gain in baculovirus and poxviruses proceeds significantly more quickly than the rate of gene loss and that there is convergent acquisition of satellite functions promoting contextual adaptation when distinct viral families infect related hosts. The congruence of the genome and polymerase trees suggests that a large set of viral genes, including polymerase, derive from a phylogenetically conserved core of genes of host origin, secondarily reinforced by gene acquisition from common hosts or co-infecting viruses within the host. A single viral genome can be thought of as a mutualistic network, with the core genes acting as an effective host and the satellite genes as effective symbionts. Larger virus genomes show a greater departure from linkage equilibrium between core and satellites functions.