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| ==Dimethylsulfoniopropionate: Role in the ocean== | |||
| ==The bacterial flagellar motor switch== | |||
| Billions of tonnes of of DMSP are produced annually by ], ]s, plants, and ] bacteria.<ref>{{cite journal |doi = 10.1126/science.aaf7796}}</ref><ref name=Zhang2019>{{cite journal |doi = 10.1007/s11427-018-9524-y}}</ref> In these organisms, DMSP functions as an important marine ], and is thought to act as a ], predator deterrent, and ].<ref name=Sunda2002>{{cite journal |doi = 10.1016/S1385-1101(00)00023-X}}</ref><ref name=Kiene2000>{{cite journal |doi = 10.1016/S1385-1101(00)00023-X}}</ref><ref name=Strom2003>{{cite journal |doi = 10.4319/lo.2003.48.1.0230}}</ref> DMSP is synthesized from ] via three distinct synthesis pathways.<ref name=Sunda2002 /><ref name=Kiene2000 /><ref name=Strom2003 /> involving bacteria,<ref>{{cite journal |doi = 10.1002/ange.201814662}}</ref><ref name=Williams2019> | |||
| ] Material was copied from this source, which is available under a .</ref>}}]] | |||
| {{cite journal |doi = 10.1038/s41564-019-0527-1}}</ref>algae genes, and the ] '']''.<ref>{{cite journal |doi = 10.1038/nmicrobiol.2017.9}}</ref><ref name=Curson2018>{{cite journal |doi = 10.1038/s41564-018-0119-5}}</ref><ref>{{cite journal |doi = 10.1016/j.abb.2018.03.019}}</ref> Recent studies suggest bacteria are likely important DMSP producers in coastal sediments, which have far higher DMSP-standing stocks than surface seawater samples where phytoplankton likely drive DMSP production.<ref name=Curson2018 /><ref name=Williams2019 /><ref name=Zheng2020 /> | |||
| DMSP is released into the environment through grazing and virus-induced ], and provides key sources of carbon, ] and energy for microbial communities.<ref name=Curson2011>{{cite journal |doi = 10.1038/nrmicro2653}}</ref><ref>{{cite journal |doi = 10.1126/science.aac5661}}</ref>. Many bacteria and phytoplankton ] DMSP via diverse DMSP ] enzymes to generate the climate-active volatile ] (DMS).<ref name=Zhang2019 /><ref name=Curson2011 /> DMS is an ]{{hsp}}<ref>{{cite journal |doi = 10.4319/lo.2006.51.4.1925}}</ref><ref>{{cite journal |doi = 10.1242/jeb.015412}}</ref> and the largest biogenic source of atmospheric sulfur, with roles in ] and, potentially, climate regulation.<ref>{{cite journal |doi = 10.1038/326655a0}}</ref><ref>{{cite journal |doi = 10.1126/science.1135370}}</ref><ref name=Zheng2020 /> | |||
| Four landmarks in understanding the bacterial flagellar motor switch are shown in the diagram on the right... | |||
| Seawater DMSP concentrations in the ] (above 200 m) vary from 1 to 100 ]s in the ] ocean<ref>{{cite journal |doi = 10.1029/JD095iD12p20607}}</ref><ref>{{cite journal |doi = 10.1128/AEM.03873-14}}</ref><ref name=Galí2015>{{cite journal |doi = 10.1016/j.rse.2015.10.012}}</ref><ref>{{cite journal |doi = 10.5194/bg-15-2449-2018}}</ref><ref>{{cite journal |doi = 10.1016/S0967-0637(98)00048-X}}</ref> to ] levels in ]s,<ref>{{cite journal |doi = 10.1016/S1385-1101(98)00024-0}}</ref><ref>{{cite journal |doi = 10.1016/j.scitotenv.2017.11.359}}</ref> and are generally highest in ]s.<ref name=Galí2015 /> Marine ] seawaters (below 200 m) have lower DMSP levels (~1.0–3.3 nM) in comparison,<ref>{{cite journal |doi = 10.1016/j.marchem.2018.01.009}}</ref> but represent a much larger global volume. There are few analyses of DMSP in ] and seawater,<ref name=Zhang2019 /> and none investigating bacterial DMSP production and cycling. Recently, a 4500 m deep ] ] sample was shown to have far higher DMSP concentrations than in surface water samples,<ref name=Williams2019 /> highlighting the need for further surveys of deep ocean organosulfur cycling.<ref name=Zheng2020 /> | |||
| (A) Conceptualization: (i) The switch complex was proposed based on phenotypic characterization of mot, che and fla alleles and their suppressor mutations in swarm plate assays. Its interactions with chemotaxis components and Mot proteins were also identified. {a} Schematic of a swarm plate—the native (WT) strain forms a swarm with chemotactic rings. Strains carrying mot mutations (Mot-) do not swarm while those with che mutations (Che-) have reduced swarms. Suppressor mutations yield pseudo-revertant strain (PR) with partially restored swarming. {b} Color codes are followed in subsequent Figures for the switch complex components (FliG (green), FliM (gold), FliN (cyan)), the CheY protein (salmon) and the MS-ring scaffold (orange) (adapted from Yamaguchi et al., 1986<ref>{{cite journal |doi = 10.1128/jb.168.3.1172-1179.1986|title = Genetic evidence for a switching and energy-transducing complex in the flagellar motor of Salmonella typhimurium|year = 1986|last1 = Yamaguchi|first1 = S.|last2 = Aizawa|first2 = S.|last3 = Kihara|first3 = M.|last4 = Isomura|first4 = M.|last5 = Jones|first5 = C. J.|last6 = MacNab|first6 = R. M.|journal = Journal of Bacteriology|volume = 168|issue = 3|pages = 1172–1179|pmid = 3536867|pmc = 213619}}</ref>). (ii) Gene sequencing identified the mutations. The fliM gene (N–C terminal residue numbers) predominantly contained the che lesions, clustered into distinct CW (green) and CCW (magenta) regions. Arrows mark mot lesions (adapted from Irikura et al., 1993<ref>{{cite journal |doi = 10.1128/jb.174.3.793-806.1992|title = Molecular analysis of the flagellar switch protein FliM of Salmonella typhimurium|year = 1992|last1 = Sockett|first1 = H.|last2 = Yamaguchi|first2 = S.|last3 = Kihara|first3 = M.|last4 = Irikura|first4 = V. M.|last5 = MacNab|first5 = R. M.|journal = Journal of Bacteriology|volume = 174|issue = 3|pages = 793–806|pmid = 1732214|pmc = 206156}}</ref>).<ref name=Khan2020 /> | |||
| <gallery mode=packed style=float:left heights=320px> | |||
| (B) Structural identification: (i) An extended cytoplasmic structure contiguous with the basal body MS-ring (yellow arrow) was isolated using gentler protocols and subsequently established as the switch complex by immuno-EM and biochemistry (from Khan et al., 1992).<ref>{{cite journal |doi = 10.1073/pnas.89.13.5956|title = The cytoplasmic component of the bacterial flagellar motor|year = 1992|last1 = Khan|first1 = I. H.|last2 = Reese|first2 = T. S.|last3 = Khan|first3 = S.|journal = Proceedings of the National Academy of Sciences|volume = 89|issue = 13|pages = 5956–5960|pmid = 1631080|pmc = 402117|bibcode = 1992PNAS...89.5956K}}</ref> (ii) Assembly of switch complex by overproduction of plasmid-encoded components allowed biochemical characterization culminating in the determination of the C ring subunit stoichiometry (n = 33–34) (from Young et al., 2003<ref>{{cite journal |doi = 10.1016/S0006-3495(03)74877-2|title = Variable Symmetry in Salmonella typhimurium Flagellar Motors|year = 2003|last1 = Young|first1 = Howard S.|last2 = Dang|first2 = Hongyue|last3 = Lai|first3 = Yimin|last4 = Derosier|first4 = David J.|last5 = Khan|first5 = Shahid|journal = Biophysical Journal|volume = 84|issue = 1|pages = 571–577|pmid = 12524310|pmc = 1302638|bibcode = 2003BpJ....84..571Y}}</ref>). (iii) Single-particle analysis resolved FliG domain substructure (yellow arrows) from differences in central sections from wild-type (WT) and ∆FliFFliG (∆) 3D basal-body reconstructions (from Thomas et al., 2001, with permission<ref>{{cite journal |doi = 10.1128/JB.183.21.6404-6412.2001|title = Structures of Bacterial Flagellar Motors from Two FliF-FliG Gene Fusion Mutants|year = 2001|last1 = Thomas|first1 = Dennis|last2 = Morgan|first2 = David Gene|last3 = Derosier|first3 = David J.|journal = Journal of Bacteriology|volume = 183|issue = 21|pages = 6404–6412|pmid = 11591685|pmc = 100136}}</ref>).<ref name=Khan2020 /> | |||
| File:Ocean surface.webp| DMSP made in the oceans gets readily converted into a gas called ] (DMS), which is the largest natural source of sulfur entering the atmosphere. In the air, DMS is converted to ] and other by-products that can act as ], which, as the name suggests, are involved in ]. In this way, DMS can influence weather and climate, so it is often referred to as ‘climate-active’ gas.<ref> '']'', 28 May 2021. Material was copied from this source, which is available under a .</ref> | |||
| File:Cycling of DMSP throughout the water column.webp| {{center|'''Cycling of DMSP in the water column'''{{hsp}}<ref name=Zheng2020>{{cite journal |doi = 10.1038/s41467-020-18434-4}} ] Material was copied from this source, which is available under a .</ref><br /><small>DMSP and DMS produced in the surface water is labeled blue<br />Deep-ocean DMSP and DMS is yellow<br />Sedimentary DMSP is labeled brown</small>}} | |||
| </gallery> | |||
| {{clear}} | |||
| (C) Motor function and mechanism: (i) Temporally resolved measurement of filament rotation, as a sinusoidal variation of laser dark-field spot intensity, characterized aberrant phenotypes in switch complex mutant strains. Panels (top to bottom) show slow rotation (S), pausing (P) and reversal (R) episodes (reproduced from Kudo et al., 1990, with permission<ref>{{cite journal |doi = 10.1038/346677a0|title = Abrupt changes in flagellar rotation observed by laser dark-field microscopy|year = 1990|last1 = Kudo|first1 = Seishi|last2 = Magariyama|first2 = Yukio|last3 = Aizawa|first3 = Shin-Ichi|journal = Nature|volume = 346|issue = 6285|pages = 677–680|pmid = 2200968|bibcode = 1990Natur.346..677K|s2cid = 30579886}}</ref>). (ii) The first atomic structure of a switch component (FliGc Lloyd et al., 1999<ref>{{cite journal |doi = 10.1038/22794|title = Structure of the C-terminal domain of FliG, a component of the rotor in the bacterial flagellar motor|year = 1999|last1 = Lloyd|first1 = Scott A.|last2 = Whitby|first2 = Frank G.|last3 = Blair|first3 = David F.|last4 = Hill|first4 = Christopher P.|journal = Nature|volume = 400|issue = 6743|pages = 472–475|pmid = 10440379|bibcode = 1999Natur.400..472L|s2cid = 4367420}}</ref>) followed by the FliGMC structure localized much of the mutant library then available ((mot lesions (black); CW lesions (red); CCW lesions (yellow); CW or CCW, depending on the residue substitution, orange; and motB suppressors (purple)) to generate chemically explicit ideas for motor reversal (PDB: 1lkv (modified from Brown et al., 2002<ref>{{cite journal |doi = 10.1093/emboj/cdf332|title = Crystal structure of the middle and C-terminal domains of the flagellar rotor protein FliG|year = 2002|last1 = Brown|first1 = P. N.|last2 = Hill|first2 = C. P.|last3 = Blair|first3 = D. F.|journal = The EMBO Journal|volume = 21|issue = 13|pages = 3225–3234|pmid = 12093724|pmc = 126082}}</ref>).<ref name=Khan2020 /> | |||
| As illustrated in the diagram above on the right, ] are the major contributors to DMSP production in the photic zone, whereas in aphotic zones where no sunlight penetrates heterotrophic bacteria likely contribute significantly to DMSP production. DMSP produced in the surface waters can sink to lower levels. Sedimentary DMSP levels are two to three orders of magnitude higher, per equivalent mass, than in the seawater, and are also most likely produced by bacteria. The relative abundance of DMSP catabolic genes was lowest in the deepest water and sediment samples, and DMSP can play a role in protecting bacteria against increased hydrostatic pressure in such deep waters and sediment.<ref name=Zheng2020 /> | |||
| (D) Switch chemotactic signal transduction: (i) {1}—Determination of switch “ultra-sensitivity” (Hill coefficient, H = 10.3) by simultaneous measurement of the CW bias of beads on flagellar stubs (red) and concentration of a fluorescent GFP-CheY fusion (green) locked in the active state (*) in engineered strains (reproduced from Cluzel et al., 2000, with permission<ref>{{cite journal |doi = 10.1126/science.287.5458.1652|title = An Ultrasensitive Bacterial Motor Revealed by Monitoring Signaling Proteins in Single Cells|year = 2000|last1 = Cluzel|first1 = P.|last2 = Surette|first2 = Michael|last3 = Leibler|first3 = Stanislas|journal = Science|volume = 287|issue = 5458|pages = 1652–1655|pmid = 10698740|bibcode = 2000Sci...287.1652C}}</ref>). {2}—Plots show non-cooperative binding of acetate-activated CheY to overproduced C rings , Sagi et al., 2003,<ref>{{cite journal |doi = 10.1074/jbc.M303201200|title = Binding of the Chemotaxis Response Regulator CheY to the Isolated, Intact Switch Complex of the Bacterial Flagellar Motor|year = 2003|last1 = Sagi|first1 = Yael|last2 = Khan|first2 = Shahid|last3 = Eisenbach|first3 = Michael|journal = Journal of Biological Chemistry|volume = 278|issue = 28|pages = 25867–25871|pmid = 12736245|s2cid = 6721145}}</ref> compared to the in-vivo change in CW bias. (ii) The atomic structure of beryllium-fluoride (BeF3 (black))-activated CheY (salmon) bound to the FliM N-terminal peptide (yellow) initiated structure guided mutagenesis to explain the switch ultra-sensitivity. Aromatic residue (W58, Y106 (orange)) motions were early diagnostics for activation. Magnesium ion (red) (PDB: 1f4v (modified from Lee et al., 2001<ref>{{cite journal |doi = 10.1038/nsb0901-789|year = 2001|last1 = Lee|first1 = Jae Young|last2 = Kwak|first2 = Jae Eun|last3 = Moon|first3 = Jinho|last4 = Eom|first4 = Soo Hyun|last5 = Liong|first5 = Elaine C.|last6 = Pedelacq|first6 = Jean-Denis|last7 = Berendzen|first7 = Joel|last8 = Suh|first8 = Se Won|title = Crystal structure and functional analysis of the SurE protein identify a novel phosphatase family|journal = Nature Structural Biology|volume = 8|issue = 9|pages = 789–794|pmid = 11524683|s2cid = 25643004}}</ref>).<ref name=Khan2020 /> | |||
| ; references | |||
| {{reflist}} | |||
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RESOURCES AND WORKING DRAFTS ONLY
Dimethylsulfoniopropionate: Role in the ocean
Billions of tonnes of of DMSP are produced annually by marine algae, corals, plants, and heterotrophic bacteria. In these organisms, DMSP functions as an important marine osmolyte, and is thought to act as a cryoprotectant, predator deterrent, and antioxidant. DMSP is synthesized from methionine via three distinct synthesis pathways. involving bacteria,algae genes, and the diatom Thalassiosira pseudonana. Recent studies suggest bacteria are likely important DMSP producers in coastal sediments, which have far higher DMSP-standing stocks than surface seawater samples where phytoplankton likely drive DMSP production.
DMSP is released into the environment through grazing and virus-induced lysis, and provides key sources of carbon, reduced sulfur and energy for microbial communities.. Many bacteria and phytoplankton catabolize DMSP via diverse DMSP lyase enzymes to generate the climate-active volatile dimethylsulfide (DMS). DMS is an infochemical and the largest biogenic source of atmospheric sulfur, with roles in cloud formation and, potentially, climate regulation.
Seawater DMSP concentrations in the photic zone (above 200 m) vary from 1 to 100 nanomolars in the oligotrophic ocean to micromolar levels in phytoplankton blooms, and are generally highest in chlorophyll maximum layers. Marine aphotic seawaters (below 200 m) have lower DMSP levels (~1.0–3.3 nM) in comparison, but represent a much larger global volume. There are few analyses of DMSP in deep ocean sediment and seawater, and none investigating bacterial DMSP production and cycling. Recently, a 4500 m deep Mariana Trench sediment sample was shown to have far higher DMSP concentrations than in surface water samples, highlighting the need for further surveys of deep ocean organosulfur cycling.
-
DMSP made in the oceans gets readily converted into a gas called dimethyl sulfide (DMS), which is the largest natural source of sulfur entering the atmosphere. In the air, DMS is converted to sulfate and other by-products that can act as cloud condensation nuclei, which, as the name suggests, are involved in cloud formation. In this way, DMS can influence weather and climate, so it is often referred to as ‘climate-active’ gas.
-
Cycling of DMSP in the water column
DMSP and DMS produced in the surface water is labeled blue
Deep-ocean DMSP and DMS is yellow
Sedimentary DMSP is labeled brown
.jpg)
As illustrated in the diagram above on the right, phytoplankton are the major contributors to DMSP production in the photic zone, whereas in aphotic zones where no sunlight penetrates heterotrophic bacteria likely contribute significantly to DMSP production. DMSP produced in the surface waters can sink to lower levels. Sedimentary DMSP levels are two to three orders of magnitude higher, per equivalent mass, than in the seawater, and are also most likely produced by bacteria. The relative abundance of DMSP catabolic genes was lowest in the deepest water and sediment samples, and DMSP can play a role in protecting bacteria against increased hydrostatic pressure in such deep waters and sediment.
- . doi:10.1126/science.aaf7796.
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{{cite journal}}: Cite journal requires|journal=(help); Missing or empty|title=(help) - From ocean to atmosphere eLife, 28 May 2021. Material was copied from this source, which is available under a Creative Commons Attribution 4.0 International License.
