Toward the development of a molecular toolkit for the microbial remediation of per-and polyfluoroalkyl substances

In the paper

“However, the aldehyde product was not observed in these reactions, which is necessary to confirm the desulfonation of 6:2 FTSA by SsuD/SsuE in strain RHA1.”

What the sources say

• Disputed

  In Results, under “Effects of carbon and sulfur sources,” the paper reports sulfite production in the SsuD/SsuE assays and explicitly says this confirmed desulfonation of 6:2 FTSA. It does not say that observing an aldehyde is necessary for confirmation. A separate Results section, “A proposed biotransformation pathway,” says the study’s method could not detect the proposed downstream aldehyde, 6:2 FTAL; no page numbers are available in our copy. (LLM, conf=0.85)

  Checked by a reasoning model — may be wrong.

  cites [73] Yang SH, Shi Y, Strynar M, Chu KH. 2022. Desulfonation and defluorination of 6: 2 fluorotelomer sulfonic acid (6: 2 FTSA) by Rhodococcus jostii RHA1: carbon and sulfur sources, enzymes, and pathways. J Hazard Mater 423: 127052. doi: 10.1016/j.jhazmat.2021.127052 34523492 PMC8823295 sourceExperimental — accuracy not yet measured

In the paper

“2-Fluoroacid dehalogenases (often referred to as fluoroacetate dehalogenases) exhibit enzymatic defluorinase activity and often possess activity against other haloalkanoic acids, such as chloroacetate, albeit often with lower efficacy than with fluoroacetate (54–56).”

What the sources say

• Partly supported

  The Abstract and the Drug-resistancy section report that Moraxella halidohydrolase 1 acts on both fluoroacetate and chloroacetate, supporting the defluorination and cross-substrate activity. The Discussion says enzymes from two Pseudomonas strains favored fluoroacetate over other haloacetates, but our copy does not establish that lower activity against chloroacetate is generally common or that it applies to the Moraxella enzyme. (LLM, conf=0.84)

  cites [54] Kawasaki H, Tone N, Tonomura K. 1981. Plasmid-determined dehalogenation of haloacetates in Moraxella species. Agric Biol Chem 45: 29– 34. doi: 10.1271/bbb1961.45.29 sourceExperimental — accuracy not yet measured
• ?Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  cites [55] Kawasaki H, Miyoshi K, Tonomura K. 1981. Purification, crystallization and properties of haloacetate halidohydrolase from Pseudomonas species. Agric Biol Chem 45: 543– 544. doi: 10.1271/bbb1961.45.543
• ?Not checked — no full text of the sourcecites [56] Kurihara T, Yamauchi T, Ichiyama S, Takahata H, Esaki N. 2003. Purification, characterization, and gene cloning of a novel fluoroacetate dehalogenase from Burkholderia sp. FA1. J Mol Catal B: Enzym 23: 347– 355. doi: 10.1016/S1381-1177(03)00098-5 source

In the paper

“PFAS have been widely employed in numerous industrial and consumer applications since the 1950s due to their exceptional physicochemical properties, including hydrophobicity, lipophobicity, and thermal stability (2–4).”

What the sources say

• Supported

  The Introduction states that PFASs have been widely used in industrial and commercial applications since 1950. It also attributes the useful properties of PFAS-containing surfactants and polymers to the perfluoroalkyl moiety’s chemical and thermal stability, hydrophobicity, and lipophobicity, and gives consumer-product examples. (LLM, conf=0.94)

  cites [2] Buck RC, Franklin J, Berger U, Conder JM, Cousins IT, de Voogt P, Jensen AA, Kannan K, Mabury SA, van Leeuwen SPJ. 2011. Perfluoroalkyl and polyfluoroalkyl substances in the environment: terminology, classification, and origins. Integr Environ Assess Manag 7: 513– 541. doi: 10.1002/ieam.258 21793199 PMC3214619 source
• Supported

  The Introduction (page not provided) says PFAS have been produced since the 1940s and used in a broad range of consumer products and industrial applications. It also identifies hydrophobicity, oleophobicity, stability, and performance across wide temperature ranges as reasons for their use. The paper gives an earlier starting date than the claim’s 1950s, but supports the claim’s account of longstanding, widespread use. (LLM, conf=0.90)

  cites [3] Glüge J, Scheringer M, Cousins IT, DeWitt JC, Goldenman G, Herzke D, Lohmann R, Ng CA, Trier X, Wang Z. 2020. An overview of the uses of per- and polyfluoroalkyl substances (PFAS). Environ Sci Process Impacts 22: 2345– 2373. doi: 10.1039/d0em00291g 33125022 PMC7784712 source
• Supported

  The Conclusion states that PFAS’ particular properties have led to a wide variety of consumer and industrial applications since at least the 1950s. The Textiles section describes water and oil repellency, and the Medical uses section describes a fluorinated coating that increases thermal stability, hydrophobicity, and oleophobicity. (LLM, conf=0.93)

  cites [4] Gaines LGT. 2023. Historical and current usage of per- and polyfluoroalkyl substances (PFAS): a literature review. Am J Ind Med 66: 353– 378. doi: 10.1002/ajim.23362 35614869 source

In the paper

“Consequently, both wildlife and humans are subject to exposure to PFAS contamination (19–24).”

What the sources say

• Partly supported

  The Introduction and Discussion describe human PFAS exposure through contaminated drinking water, and the Results report PFAS in participants’ serum. The Introduction discusses bioaccumulation in organisms and PFAS elimination in animals, but it does not specifically establish exposure of wildlife to PFAS contamination. (LLM, conf=0.82)

  cites [19] Pitter G, Da Re F, Canova C, Barbieri G, Zare Jeddi M, Daprà F, Manea F, Zolin R, Bettega AM, Stopazzolo G, Vittorii S, Zambelli L, Martuzzi M, Mantoan D, Russo F. 2020. Serum levels of perfluoroalkyl substances (PFAS) in adolescents and young adults exposed to contaminated drinking water in the Veneto region, Italy: a cross-sectional study based on a health surveillance program. Environ Health Perspect 128: 27007. doi: 10.1289/EHP5337 32068468 PMC7064325 sourceExperimental — accuracy not yet measured
• ?Not checked — no full text of the sourcecites [20] Domingo JL, Nadal M. 2019. Human exposure to per-and polyfluoroalkyl substances (PFAS) through drinking water: a review of the recent scientific literature. Environ Res 177: 108648. doi: 10.1016/j.envres.2019.108648 31421451 source
• ?Not checked — no full text of the sourcecites [21] Sörengård M, Bergström S, McCleaf P, Wiberg K, Ahrens L. 2022. Long-distance transport of per-and polyfluoroalkyl substances (PFAS) in a Swedish drinking water aquifer. Environ Pollut 311: 119981. doi: 10.1016/j.envpol.2022.119981 35988673 source
• ?Not checked — no full text of the sourcecites [22] Lee K, Alava JJ, Cottrell P, Cottrell L, Grace R, Zysk I, Raverty S. 2023. Emerging contaminants and new POPs (PFAS and HBCDD) in endangered southern resident and bigg’s (transient) killer whales (Orcinus orca): in utero maternal transfer and pollution management implications. Environ Sci Technol 57: 360– 374. doi: 10.1021/acs.est.2c04126 36512803 source
• Partly supported

  The Introduction (page not available) identifies facemasks as a potential source of human PFAS exposure, and the PFAS Exposure Estimation methods model that exposure. The Landfill and Wastewater Environment Implications section estimates PFAS release to leachate and wastewater, but does not address wildlife exposure; that part of the claim is unsupported by our copy. (LLM, conf=0.84)

  cites [23] Muensterman DJ, Cahuas L, Titaley IA, Schmokel C, De la Cruz FB, Barlaz MA, Carignan CC, Peaslee GF, Field JA. 2022. Per- and polyfluoroalkyl substances (PFAS) in facemasks: potential source of human exposure to PFAS with implications for disposal to landfills. Environ Sci Technol Lett 9: 320– 326. doi: 10.1021/acs.estlett.2c00019 37599856 PMC10438898 sourceExperimental — accuracy not yet measured
• Supported

  The paper’s wildlife occurrence section reports elevated PFAS exposures across numerous animal groups. Its section on communities near contaminated sites reports human exposure through contaminated drinking water. Together, these passages support the claim that both wildlife and humans are exposed to PFAS contamination. (LLM, conf=0.94)

  cites [24] De Silva AO, Armitage JM, Bruton TA, Dassuncao C, Heiger-Bernays W, Hu XC, Kärrman A, Kelly B, Ng C, Robuck A, Sun M, Webster TF, Sunderland EM. 2021. PFAS exposure pathways for humans and wildlife: a synthesis of current knowledge and key gaps in understanding. Environ Toxicol Chem 40: 631– 657. doi: 10.1002/etc.4935 33201517 PMC7906948 source

In the paper

“Numerous epidemiological and mechanistic investigations have implied a connection between exposure to PFAS and a wide range of diseases, such as altered immune function, adverse reproductive effects, liver and kidney damage, obesity, and cancers (25–31).”

What the sources say

• Partly supported

  The Conclusions (page not available) report epidemiological and mechanistic evidence that PFAS exposure alters immune function. The paper focuses on immunotoxicity; the passages reviewed do not support the full attributed list of adverse reproductive effects, liver and kidney damage, obesity, and cancers. (LLM, conf=0.88)

  cites [25] Ehrlich V, Bil W, Vandebriel R, Granum B, Luijten M, Lindeman B, Grandjean P, Kaiser A-M, Hauzenberger I, Hartmann C, Gundacker C, Uhl M. 2023. Consideration of pathways for immunotoxicity of per-and polyfluoroalkyl substances (PFAS). Environ Health 22: 19. doi: 10.1186/s12940-022-00958-5 36814257 PMC9944481 sourceExperimental — accuracy not yet measured
• Supported

  The review’s Immune function and Reproductive and developmental outcomes sections link PFAS exposure to immune suppression and adverse reproductive outcomes. Its Liver disease and cancer, Kidney disease, uric acid, and kidney cancer, and Obesity sections report evidence of the other listed associations, while noting uncertainty and mixed findings for some outcomes. The citing sentence’s cautious wording, “implied a connection,” reflects those qualifications; page numbers were not available in our copy. (LLM, conf=0.92)

  cites [26] Fenton SE, Ducatman A, Boobis A, DeWitt JC, Lau C, Ng C, Smith JS, Roberts SM. 2021. Per‐and polyfluoroalkyl substance toxicity and human health review: current state of knowledge and strategies for informing future research. Environ Toxicol Chem 40: 606– 630. doi: 10.1002/etc.4890 33017053 PMC7906952 source
• Partly supported

  The sections on female reproductive tract disease and the breast (page unavailable) report associations between PFAS exposure and adverse reproductive outcomes and some cancers. The paper also discusses metabolic effects, but the passages found do not support the specific claims about altered immune function, liver or kidney damage, or obesity. (LLM, conf=0.86)

  cites [27] Rickard BP, Rizvi I, Fenton SE. 2022. Per- and poly-fluoroalkyl substances (PFAS) and female reproductive outcomes: PFAS elimination, endocrine-mediated effects, and disease. Toxicology 465: 153031. doi: 10.1016/j.tox.2021.153031 34774661 PMC8743032 sourceExperimental — accuracy not yet measured
• Partly supported

  The Introduction describes PFAS as immunotoxic and hepatotoxic and discusses epidemiological associations with liver enzymes and experimental effects on immune function and liver cells. The Discussion addresses altered adipokines and obesity-related disease, but not a clear PFAS–obesity association. The passages reviewed do not establish the claimed links to adverse reproductive effects, kidney damage, or cancers. (LLM, conf=0.86)

  cites [28] Bassler J, Ducatman A, Elliott M, Wen S, Wahlang B, Barnett J, Cave MC. 2019. Environmental perfluoroalkyl acid exposures are associated with liver disease characterized by apoptosis and altered serum adipocytokines. Environ Pollut 247: 1055– 1063. doi: 10.1016/j.envpol.2019.01.064 30823334 PMC6404528 sourceExperimental — accuracy not yet measured
• ?Not checked — no full text of the sourcecites [29] Geiger SD, Yao P, Vaughn MG, Qian Z. 2021. PFAS exposure and overweight/obesity among children in a nationally representative sample. Chemosphere 268: 128852. doi: 10.1016/j.chemosphere.2020.128852 33223205 source
• Partly supported

  Section 3.3 reports epidemiological associations between PFAS exposure and kidney cancer, along with studies of renal injury mechanisms; it also mentions emerging evidence concerning other cancers. The passages do not establish the claimed links to adverse reproductive effects, obesity, or liver damage, and altered immune function appears only in a reference title. Section 3.2 also notes conflicting evidence on chronic kidney disease. (LLM, conf=0.87)

  cites [30] Zhang X, Flaws JA, Spinella MJ, Irudayaraj J. 2022. The relationship between typical environmental endocrine disruptors and kidney disease. Toxics 11: 32. doi: 10.3390/toxics11010032 36668758 PMC9863798 sourceExperimental — accuracy not yet measured
• Partly supported

  The Introduction links PFAS exposure to several cancers, section 2.1 describes liver toxicity and metabolic effects, and section 2.2 reports adverse reproductive effects. The cited paper does not establish the other listed connections—altered immune function, non-cancer kidney damage, or obesity. Its discussion of kidney cancer is not evidence of kidney damage generally. (LLM, conf=0.85)

  cites [31] Boyd RI, Ahmad S, Singh R, Fazal Z, Prins GS, Madak Erdogan Z, Irudayaraj J, Spinella MJ. 2022. Toward a mechanistic understanding of poly-and perfluoroalkylated substances and cancer. Cancers (Basel) 14: 2919. doi: 10.3390/cancers14122919 35740585 PMC9220899 sourceExperimental — accuracy not yet measured

In the paper

“Due to the extensive use and consequent discharge, PFAS have been identified in a range of environmental contexts, such as drinking water (7, 8), surface and groundwater (9, 10), soils (11, 12), wastewater (13, 14), landfills (15), remote areas (far from any local point sources, e.g., Arctic environment) (16, 17), and agricultural plants (18).”

What the sources say

• Supported

  The cited paper is offered for the surface- and groundwater portion of the sentence, not the entire list of environmental contexts. Its Introduction discusses PFAS transport in both surface water and groundwater, and its Conclusions report measured PFAS contamination in groundwater. (LLM, conf=0.91)

  cites [7] Mussabek D, Söderman A, Imura T, Persson KM, Nakagawa K, Ahrens L, Berndtsson R. 2022. PFAS in the drinking water source: analysis of the contamination levels, origin and emission rates. Water 15: 137. doi: 10.3390/w15010137 source
• Supported

  This source is cited for the drinking-water example (references 7 and 8), not for every environment listed in the sentence. The Background reports PFAS detection in drinking water, including in China. (LLM, conf=0.94)

  cites [8] Liu L, Qu Y, Huang J, Weber R. 2021. Per-and polyfluoroalkyl substances (PFASs) in Chinese drinking water: risk assessment and geographical distribution. Environ Sci Eur 33: 6. doi: 10.1186/s12302-020-00425-3 source
• Supported

  The citation is attached to “surface and groundwater,” not the sentence’s entire list of environmental contexts. The Conclusion reports the widespread presence of PFAS in both surface water and groundwater. (LLM, conf=0.93)

  cites [9] Johnson GR, Brusseau ML, Carroll KC, Tick GR, Duncan CM. 2022. Global distributions, source-type dependencies, and concentration ranges of per-and polyfluoroalkyl substances in groundwater. Sci Total Environ 841: 156602. doi: 10.1016/j.scitotenv.2022.156602 35690215 PMC9653090 source
• ?Not checked — no full text of the sourcecites [10] Sims JL, Stroski KM, Kim S, Killeen G, Ehalt R, Simcik MF, Brooks BW. 2022. Global occurrence and probabilistic environmental health hazard assessment of per-and polyfluoroalkyl substances (PFASs) in groundwater and surface waters. Sci Total Environ 816: 151535. doi: 10.1016/j.scitotenv.2021.151535 34762945 source
• Supported

  This source is cited alongside the sentence’s claim about soils, not the full list of environmental contexts. The Abstract reports PFAS in soil at almost every site tested, including remote regions, and the Results (section 3.2) report measurable levels across varied soil-sampling locations. (LLM, conf=0.94)

  cites [11] Brusseau ML, Anderson RH, Guo B. 2020. PFAS concentrations in soils: background levels versus contaminated sites. Sci Total Environ 740: 140017. doi: 10.1016/j.scitotenv.2020.140017 32927568 PMC7654437 source
• ?Not checked — no full text of the sourcecites [12] Zhu Q, Qian J, Huang S, Li Q, Guo L, Zeng J, Zhang W, Cao X, Yang J. 2022. Occurrence, distribution, and input pathways of per- and polyfluoroalkyl substances in soils near different sources in Shanghai. Environ Pollut 308: 119620. doi: 10.1016/j.envpol.2022.119620 35709920 source

In the paper

“However, of the 4,730 PFAS with CAS registry numbers, only 256 are considered commercially relevant (5, 6).”

What the sources say

• ?Could not verify

  The Introduction (Background; page unavailable) discusses PFAS in commerce, and the Results (page unavailable) give counts under different PFAS definitions. Neither reports 4,730 PFAS with CAS registry numbers or identifies 256 as commercially relevant. Searches for both numbers and commercial relevance found no passage establishing the claimed comparison. (LLM, conf=0.72)

  cites [5] Williams AJ, Gaines LGT, Grulke CM, Lowe CN, Sinclair GFB, Samano V, Thillainadarajah I, Meyer B, Patlewicz G, Richard AM. 2022. Assembly and curation of lists of per- and polyfluoroalkyl substances (PFAS) to support environmental science research. Front Environ Sci 10: 1– 13. doi: 10.3389/fenvs.2022.850019 PMC9350880 35936994 sourceExperimental — accuracy not yet measured
• Supported

  The Materials and Methods section identifies the list as 4,730 PFAS-related CAS numbers. The Summary and Conclusions section states that the study identified 256 of those substances as commercially relevant, based on input from three major global producers. (LLM, conf=0.94)

  cites [6] Buck RC, Korzeniowski SH, Laganis E, Adamsky F. 2021. Identification and classification of commercially relevant per- and poly-fluoroalkyl substances (PFAS). Integr Environ Assess Manag 17: 1045– 1055. doi: 10.1002/ieam.4450 33991049 PMC9292543 source

In the paper

“Furthermore, the crystallographic findings reveal that both FA1 and RPA1163 are homodimer proteins, belonging to α/β hydrolase superfamily (67, 68).”

What the sources say

• Partly supported

  The Results and Discussion section, “Overall Structure of RPA1163” (page unavailable), explicitly describes RPA1163 as a homodimer with an α/β hydrolase fold. It compares RPA1163 with a Burkholderia FAcD, but does not identify that enzyme as FA1 or state that FA1 is homodimeric. The FA1 portion therefore remains unsupported by this source. (LLM, conf=0.86)

  cites [67] Chan PWY, Yakunin AF, Edwards EA, Pai EF. 2011. Mapping the reaction coordinates of enzymatic defluorination. J Am Chem Soc 133: 7461– 7468. doi: 10.1021/ja200277d 21510690 PMC3101105 sourceExperimental — accuracy not yet measured
• ?Not checked — no full text of the sourcecites [68] Jitsumori K, Omi R, Kurihara T, Kurata A, Mihara H, Miyahara I, Hirotsu K, Esaki N. 2009. X-Ray crystallographic and mutational studies of fluoroacetate dehalogenase from Burkholderia sp. strain FA1. J Bacteriol 191: 2630– 2637. doi: 10.1128/JB.01654-08 19218394 PMC2668400 source

In the paper

“Reductive dehalogenation of organochlorides, bromides, and iodides has been demonstrated in biochemical and microbiological studies (86).”

What the sources say

• Partly supported

  Section 2.3 (Substrate Range and Specificity; page unavailable) reports characterized reductive dehalogenases acting on chlorinated and brominated organic compounds, supporting those parts of the claim. The copy does not report reductive dehalogenation of organoiodides; the iodide-cobalamin signal mentioned in Figure 5 does not establish that reaction. (LLM, conf=0.85)

  cites [86] Fincker M, Spormann AM. 2017. Biochemistry of catabolic reductive dehalogenation. Annu Rev Biochem 86: 357– 386. doi: 10.1146/annurev-biochem-061516-044829 28654328 sourceExperimental — accuracy not yet measured

In the paper

“One line of evidence against the feasibility of reductive defluorination of PFAS is that the redox midpoint potential of organofluorides may be too low to yield energy when used as terminal electron acceptors for biologically relevant electron donors (46).”

What the sources say

• Supported

  The PERSPECTIVE section says that the reduction potential of many polyfluorinated compounds is negative, making them unable to serve as final electron acceptors. It contrasts this with reductive dechlorination, whose sufficiently positive potential can support ATP-generating electron transport. This supports the cited sentence’s proposed energetic obstacle to reductive defluorination. (LLM, conf=0.92)

  cites [46] Wackett LP. 2021. Why is the biodegradation of polyfluorinated compounds so rare? mSphere 6: e0072121. doi: 10.1128/mSphere.00721-21 34643420 PMC8513679 source

In the paper

“Laccases catalyze the oxidation of various substrates via a single-electron transfer, involving a chemical mediator.”

What the sources say

• Partly supported

  The Laccase section describes oxidation of various substrates through single-electron reactions. The Laccase–mediator system section says chemical mediators can extend the range of substrates, but also describes laccase oxidizing some substrates directly. Thus, the source does not support implying that a chemical mediator is involved in every such reaction; page numbers are not provided in our copy. (LLM, conf=0.84)

  cites [145] Gu Y, Yuan L, Jia L, Xue P, Yao H. 2021. Recent developments of a co-immobilized laccase–mediator system: a review. RSC Adv 11: 29498– 29506. doi: 10.1039/d1ra05104k 35479547 PMC9040808 sourceExperimental — accuracy not yet measured
• Partly supported

  Section 2.2 describes laccases oxidizing various substrates through electron transfer and explains that mediator compounds enable indirect oxidation of substrates laccases cannot oxidize directly. It does not say a chemical mediator is involved in oxidation generally; laccases can oxidize other substrates directly. The paper describes four-electron reduction of oxygen alongside the electron-transfer step. (LLM, conf=0.88)

  cites [146] Rodríguez-Delgado MM, Alemán-Nava GS, Rodríguez-Delgado JM, Dieck-Assad G, Martínez-Chapa SO, Barceló D, Parra R. 2015. Laccase-based biosensors for detection of phenolic compounds. Trends Analyt Chem 74: 21– 45. doi: 10.1016/j.trac.2015.05.008 sourceExperimental — accuracy not yet measured

In the paper

“Specifically, they oxidize suitable redox mediators through a single-electron transfer mediated by the copper site, forming a free radical cation.”

What the sources say

• Supported

  The Laccase section says that laccase oxidizes a redox substrate by single-electron transfer mediated by T1 copper, forming a free-radical cation. The Laccase–mediator system section states that laccase oxidizes mediators. Together, these passages support the paraphrase. (LLM, conf=0.91)

  cites [145] Gu Y, Yuan L, Jia L, Xue P, Yao H. 2021. Recent developments of a co-immobilized laccase–mediator system: a review. RSC Adv 11: 29498– 29506. doi: 10.1039/d1ra05104k 35479547 PMC9040808 source
• Partly supported

  Section 2.2 describes electron transfer at the T1 copper site and says laccase–mediator compounds act as intermediate substrates for laccase. It does not say that oxidation of a mediator forms a free radical cation, so that product is unsupported by our copy. No page number is available for the passage. (LLM, conf=0.85)

  cites [146] Rodríguez-Delgado MM, Alemán-Nava GS, Rodríguez-Delgado JM, Dieck-Assad G, Martínez-Chapa SO, Barceló D, Parra R. 2015. Laccase-based biosensors for detection of phenolic compounds. Trends Analyt Chem 74: 21– 45. doi: 10.1016/j.trac.2015.05.008 sourceExperimental — accuracy not yet measured

In the paper

“In addition to following a similar catalytic cycle (e.g., HRP or LiP), MnP uses Mn2+ ions as electron donors, wherein these ions are oxidized to Mn3+ ions using H2O2.”

What the sources say

• ?Not checked — no full text of the sourcecites [134] Morsi R, Bilal M, Iqbal HMN, Ashraf SS. 2020. Laccases and peroxidases: the smart, greener and futuristic biocatalytic tools to mitigate recalcitrant emerging pollutants. Sci Total Environ 714: 136572. doi: 10.1016/j.scitotenv.2020.136572 31986384 source
• Supported

  The Peroxidases (EC 1.11.1.x) section states that MnP oxidizes Mn2+ to Mn3+ using H2O2. It also describes a catalytic cycle shared by peroxidases, including LiP. (LLM, conf=0.94)

  cites [141] Khan MF, Hof C, Niemcová P, Murphy CD. 2023. Recent advances in fungal xenobiotic metabolism: enzymes and applications. World J Microbiol Biotechnol 39: 296. doi: 10.1007/s11274-023-03737-7 37658215 PMC10474215 source

In the paper

“When coupled to a reporter system, the fluoride riboswitch has also been shown to have utility as a sensitive and biocompatible fluoride sensor that can be used in living bacteria or in wholly in vitro systems (170, 173).”

What the sources say

• Partly supported

  The indexed paper (section labeled Abstract; no page supplied) reports fluoride-responsive lacZ reporter constructs operating in living B. subtilis and E. coli. It also reports in vitro fluoride-binding assays, but does not show a reporter-coupled sensor operating wholly in vitro or establish the claimed biocompatibility. (LLM, conf=0.86)

  cites [170] Baker JL, Sudarsan N, Weinberg Z, Roth A, Stockbridge RB, Breaker RR. 2012. Widespread genetic switches and toxicity resistance proteins for fluoride. Science 335: 233– 235. doi: 10.1126/science.1215063 22194412 PMC4140402 sourceExperimental — accuracy not yet measured
• Supported

  The Introduction describes a biocompatible fluoride sensor made by coupling the crcB riboswitch aptamer to a fluorescent RNA reporter. The paper reports fluoride detection with purified RNA in vitro (Figure 2) and monitoring defluorinase activity from living bacterial cells (Section 2.4). It does not claim FluorMango is as sensitive as amplified methods for detecting trace fluoride, but the citing sentence makes no such comparison. (LLM, conf=0.87)

  cites [173] Husser C, Vuilleumier S, Ryckelynck M. 2023. FluorMango, an RNA-based fluorogenic biosensor for the direct and specific detection of fluoride. Small 19: e2205232. doi: 10.1002/smll.202205232 36436882 source

In the paper

“TauD is an Fe (II) and α-ketoglutarate-dependent dioxygenase, with activity with a range of sulfonates (e.g., butanesulfonate and pentanesulfonate), but a preference for taurine (153, 157).”

What the sources say

• ?Not checked — no full text of the sourcecites [153] van der Ploeg JR, Eichhorn E, Leisinger T. 2001. Sulfonate-sulfur metabolism and its regulation in Escherichia coli. Arch Microbiol 176: 1– 8. doi: 10.1007/s002030100298 11479697 source
• Supported

  The enzyme-characterization results report that TauD activity depends on Fe(II) and that taurine desulfonation is coupled to α-ketoglutarate oxidation. Table II lists activity with butanesulfonic and pentanesulfonic acids, while showing a lower Km and higher Vmax for taurine than for either; this supports the stated preference. Page numbers are unavailable in our copy. (LLM, conf=0.94)

  cites [157] Eichhorn E, van der Ploeg JR, Kertesz MA, Leisinger T. 1997. Characterization of α-ketoglutarate-dependent taurine dioxygenase from Escherichia coli. J Biol Chem 272: 23031– 23036. doi: 10.1074/jbc.272.37.23031 9287300 source

In the paper

“TauD catalyzes the oxygen-dependent desulfonation of taurine into sulfite and aminoacetaldehyde, with the unstable intermediate 1-hydroxyaminoethanesulfonate presumed as an intermediate (157) (Fig. 5).”

What the sources say

• Partly supported

  The Desulfonation of Taurine section reports oxygen-dependent sulfite release and proposes that a hydroxylated product decomposes to aminoacetaldehyde and sulfite. It names the putative product **1-hydroxy-2-aminoethanesulfonic acid**, not the claimed 1-hydroxyaminoethanesulfonate. The paper also calls aminoacetaldehyde, rather than the proposed intermediate, unstable. (LLM, conf=0.87)

  cites [157] Eichhorn E, van der Ploeg JR, Kertesz MA, Leisinger T. 1997. Characterization of α-ketoglutarate-dependent taurine dioxygenase from Escherichia coli. J Biol Chem 272: 23031– 23036. doi: 10.1074/jbc.272.37.23031 9287300 sourceExperimental — accuracy not yet measured

In the paper

“In general, PFAS uptake by plants occurs through root uptake and foliar uptake, with the former widely regarded as the primary pathway (181, 183, 184) and the latter potentially for semi-volatile PFAA precursors and their degradation products (such as FTOHs) (180, 183).”

What the sources say

• ?Not checked — no full text of the sourcecites [181] Lesmeister L, Lange FT, Breuer J, Biegel-Engler A, Giese E, Scheurer M. 2021. Extending the knowledge about PFAS bioaccumulation factors for agricultural plants – A review. Sci Total Environ 766: 142640. doi: 10.1016/j.scitotenv.2020.142640 33077210 source
• ?Not checked — no full text of the sourcecites [183] Li J, Sun J, Li P. 2022. Exposure routes, bioaccumulation and toxic effects of per- and polyfluoroalkyl substances (PFASs) on plants: a critical review. Environ Int 158: 106891. doi: 10.1016/j.envint.2021.106891 34592655 source
• Partly supported

  Split into 2 atoms — 0 confirmed, 1 partially supported, 0 disputed, 0 misattributed, 1 unverifiable. Expand the claim to see per-atom verdicts.

  cites [184] Mei W, Sun H, Song M, Jiang L, Li Y, Lu W, Ying G-G, Luo C, Zhang G. 2021. Per- and polyfluoroalkyl substances (PFASs) in the soil–plant system: sorption, root uptake, and translocation. Environ Int 156: 106642. doi: 10.1016/j.envint.2021.106642 34004449 sourceExperimental — accuracy not yet measured

In the paper

“For example, haloacid dehalogenase H-2 (H-2) (Uniprot ID: Q01399), isolated and purified from D. acidovorans B (formerly Moraxella sp. B), can dehalogenate chloroacetate, bromoacetate, and iodoacetate, and has some catalytic activity on 2,2-dichloroacetate and 2-chloropropionate (54, 65).”

What the sources say

• Not checked yet

  Checked before — its earlier verdict is held back until a new check runs.

  cites [54] Kawasaki H, Tone N, Tonomura K. 1981. Plasmid-determined dehalogenation of haloacetates in Moraxella species. Agric Biol Chem 45: 29– 34. doi: 10.1271/bbb1961.45.29 source
• ?Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  cites [65] Kawasaki H, Tone N, Tonomura K. 1981. Purification and properties of haloacetate halidohydrolase specified by plasmid from Moraxella sp. strain B. Agric Biol Chem 45: 35– 42. doi: 10.1271/bbb1961.45.35

In the paper

“Second, polyfluorinated products are not known in nature, and only a few naturally occurring monofluorinated compounds have been observed (44, 45).”

What the sources say

• ?Not checked — no full text of the sourcecites [44] O’Hagan D, Deng H. 2015. Enzymatic fluorination and biotechnological developments of the fluorinase. Chem Rev 115: 634– 649. doi: 10.1021/cr500209t 25253234 source
• ?Not checked — no full text of the sourcecites [45] Zhao C, Li P, Deng Z, Ou H-Y, McGlinchey RP, O’Hagan D. 2012. Insights into fluorometabolite biosynthesis in Streptomyces cattleya DSM46488 through genome sequence and knockout mutants. Bioorg Chem 44: 1– 7. doi: 10.1016/j.bioorg.2012.06.002 22858315 source

In the paper

“Biodegradation using microbes or cell-free enzymes has been demonstrated to be technically effective for a range of contaminants, including herbicides (33), insecticides (34, 35), fungicides (36–38), and industrial solvents (39, 40).”

What the sources say

• Not checked yetcites [33] Esquirol L, Peat TS, Sugrue E, Balotra S, Rottet S, Warden AC, Wilding M, Hartley CJ, Jackson CJ, Newman J, Scott C. 2020. Chapter four - bacterial catabolism of s-triazine herbicides: biochemistry, evolution and application. Adv Microb Physiol 76: 129– 186. doi: 10.1016/bs.ampbs.2020.01.004 32408946
• ?Not checked — no full text of the sourcecites [34] Scott C, Begley C, Taylor MJ, Pandey G, Momiroski V, French N, Brearley C, Kotsonis SE, Selleck MJ, Carino FA, Bajet CM, Clarke C, Oakeshott JG, Russell RJ. 2011. Free-enzyme bioremediation of pesticides, p 155– 174. In Goh KS, Bret BL, Potter TL, Gan J (ed), Pesticide mitigation strategies for surface water quality. Vol. 1075. American Chemical Society. source
• Not checked yet

  Checked before — its earlier verdict is held back until a new check runs.

  cites [35] Lal R, Pandey G, Sharma P, Kumari K, Malhotra S, Pandey R, Raina V, Kohler H-PE, Holliger C, Jackson C, Oakeshott JG. 2010. Biochemistry of microbial degradation of hexachlorocyclohexane and prospects for bioremediation. Microbiol Mol Biol Rev 74: 58– 80. doi: 10.1128/MMBR.00029-09 20197499 PMC2832351 source
• ?Not checked — no full text of the sourcecites [36] Singh S, Singh N, Kumar V, Datta S, Wani AB, Singh D, Singh K, Singh J. 2016. Toxicity, monitoring and biodegradation of the fungicide carbendazim. Environ Chem Lett 14: 317– 329. doi: 10.1007/s10311-016-0566-2 source
• ?Not checked — no full text of the sourcecites [37] Clinton B, Warden AC, Haboury S, Easton CJ, Kotsonis S, Taylor MC, Oakeshott JG, Russell RJ, Scott C. 2011. Bacterial degradation of strobilurin fungicides: a role for a promiscuous methyl esterase activity of the subtilisin proteases? Biocatal Biotransformation 29: 119– 129. doi: 10.3109/10242422.2011.578740 source
• Not checked yet

  Checked before — its earlier verdict is held back until a new check runs.

  cites [38] Pandey G, Dorrian SJ, Russell RJ, Brearley C, Kotsonis S, Oakeshott JG. 2010. Cloning and biochemical characterization of a novel carbendazim (Methyl-1H-benzimidazol-2-ylcarbamate)-hydrolyzing esterase from the newly isolated Nocardioides sp. strain SG-4G and its potential for use in enzymatic bioremediation. Appl Environ Microbiol 76: 2940– 2945. doi: 10.1128/AEM.02990-09 20228105 PMC2863442 source

In the paper

“Fluoroacetate is a natural organofluoride compound that is toxic to mammals and produced by actinomycetes, such as Streptomyces cattleya (57), and acts as a defense molecule in some plants (58, 59).”

What the sources say

• ?Not checked — no full text of the sourcecites [57] Murphy CD, Schaffrath C, O’Hagan D. 2003. Fluorinated natural products: the biosynthesis of fluoroacetate and 4-fluorothreonine in Streptomyces cattleya. Chemosphere 52: 455– 461. doi: 10.1016/S0045-6535(03)00191-7 12738270 source
• ?Not checked — no full text of the sourcecites [58] Baron ML, Bothroyd CM, Rogers GI, Staffa A, Rae ID. 1987. Detection and measurement of fluoroacetate in plant extracts by 19FNMR. Phytochemistry 26: 2293– 2295. doi: 10.1016/S0031-9422(00)84704-4 source
• ?Not checked — no full text of the sourcecites [59] O’Hagan D, B. Harper D. 1999. Fluorine-containing natural products. J Fluor Chemi 100: 127– 133. doi: 10.1016/S0022-1139(99)00201-8 source

In the paper

“The FA1 shared a sequence identity of 61% with H-1 (56) and 42% with RPA1163 (67).”

What the sources say

• ?Not checked — no full text of the sourcecites [56] Kurihara T, Yamauchi T, Ichiyama S, Takahata H, Esaki N. 2003. Purification, characterization, and gene cloning of a novel fluoroacetate dehalogenase from Burkholderia sp. FA1. J Mol Catal B: Enzym 23: 347– 355. doi: 10.1016/S1381-1177(03)00098-5 source
• Not checked yetcites [67] Chan PWY, Yakunin AF, Edwards EA, Pai EF. 2011. Mapping the reaction coordinates of enzymatic defluorination. J Am Chem Soc 133: 7461– 7468. doi: 10.1021/ja200277d 21510690 PMC3101105 source

In the paper

“The biodegradation of naturally occurring and synthetic organochlorides has been investigated and documented extensively (41, 42).”

What the sources say

• Not checked yet

  Checked before — its earlier verdict is held back until a new check runs.

  cites [41] Atashgahi S, Liebensteiner MG, Janssen DB, Smidt H, Stams AJM, Sipkema D. 2018. Microbial synthesis and transformation of inorganic and organic chlorine compounds. Front Microbiol 9: 3079. doi: 10.3389/fmicb.2018.03079 30619161 PMC6299022 source
• Not checked yetcites [42] Nagata Y, Tabata M, Ohtsubo Y, Tsuda M. 2016. Biodegradation of organochlorine pesticides, p 5.1.2-1–5.1.2-30. In Yates MV, Nakatsu CH, Miller RV, Pillai SD (ed), Manual of environmental microbiology. American Societ for Microbiology.

In the paper

“Haloacid dehalogenases are a class of hydrolases that specialize in hydrolytic cleavage of carbon-halide bonds (51).”

What the sources say

• Not checked yetcites [51] Shukla E, Bendre AD, Gaikwad SM. 2022. Hydrolases: the most diverse class of enzymes. In Haider S, Haider A, Catalá A (ed), Hydrolases. IntechOpen, London.

In the paper

“This suggests that until the recent introduction of anthropogenic organofluorides, there was no strong selection pressure for the catabolism of these compounds, the exception being for highly toxic natural organofluorides such as fluoroacetate.”

In the paper

“In particular, Trp150 plays a crucial role specifically in the defluorination of fluoroacetate, while its involvement is not necessary for the dechlorination of chloroacetate.”

What the sources say

• ?Not checked — no full text of the sourcecites [68] Jitsumori K, Omi R, Kurihara T, Kurata A, Mihara H, Miyahara I, Hirotsu K, Esaki N. 2009. X-Ray crystallographic and mutational studies of fluoroacetate dehalogenase from Burkholderia sp. strain FA1. J Bacteriol 191: 2630– 2637. doi: 10.1128/JB.01654-08 19218394 PMC2668400 source
• ?Not checked — no full text of the sourcecites [78] Kamachi T, Nakayama T, Shitamichi O, Jitsumori K, Kurihara T, Esaki N, Yoshizawa K. 2009. The catalytic mechanism of fluoroacetate dehalogenase: a computational exploration of biological dehalogenation. Chemistry 15: 7394– 7403. doi: 10.1002/chem.200801813 19551770 source

In the paper

“Similarly, the crystal structure of fluoroacetate dehalogenase RPA1163 revealed the presence of a catalytic triad (Asp110-His280-Asp134; RPA1163 numbering) and an active site composition that is identical to that of FA1 and confirming the functional roles of His155, Trp156, and Tyr219 residues in stabilization of the leaving fluoride (67).”

What the sources say

• Not checked yetcites [67] Chan PWY, Yakunin AF, Edwards EA, Pai EF. 2011. Mapping the reaction coordinates of enzymatic defluorination. J Am Chem Soc 133: 7461– 7468. doi: 10.1021/ja200277d 21510690 PMC3101105 source

In the paper

“Cytochromes P450 (P450s or CYPs) are a widely distributed superfamily of enzymes found in all three domains of life (Archaea, Eubacteria, and Eukaryotes).”

In the paper

“Specifically, the strain RHA1, cultivated with 6:2 FTOH in the absence of CuSO4 (which inhibits L-2-haloacid dehalogenases), exhibited a substantially higher fluoride release compared to samples containing the inhibitor, consistent with the involvement of an L-2-haloacid dehalogenase.”

What the sources say

• Not checked yetcites [73] Yang SH, Shi Y, Strynar M, Chu KH. 2022. Desulfonation and defluorination of 6: 2 fluorotelomer sulfonic acid (6: 2 FTSA) by Rhodococcus jostii RHA1: carbon and sulfur sources, enzymes, and pathways. J Hazard Mater 423: 127052. doi: 10.1016/j.jhazmat.2021.127052 34523492 PMC8823295 source

In the paper

“Moreover, several studies have now demonstrated abiotic reductive defluorination of branched and unsaturated PFAS (e.g., br-PFOS and br-PFHxS) in vitamin B12-Ti(III) citrate catalytic system (94, 95) and vitamin B12-nanoscale zerovalent zinc system (96), suggesting that cobalamin-dependent respiratory reductive dehalogenases could have a role in the defluorination of organofluorides.”

What the sources say

• ?Not checked — no full text of the sourcecites [94] Ochoa-Herrera V, Sierra-Alvarez R, Somogyi A, Jacobsen NE, Wysocki VH, Field JA. 2008. Reductive defluorination of perfluorooctane sulfonate. Environ Sci Technol 42: 3260– 3264. doi: 10.1021/es702842q 18522103 source
• ?Not checked — no full text of the sourcecites [95] Liu J, Van Hoomissen DJ, Liu T, Maizel A, Huo X, Fernández SR, Ren C, Xiao X, Fang Y, Schaefer CE, Higgins CP, Vyas S, Strathmann TJ. 2018. Reductive defluorination of branched per-and polyfluoroalkyl substances with cobalt complex catalysts. Environ Sci Technol Lett 5: 289– 294. doi: 10.1021/acs.estlett.8b00122 source
• ?Not checked — no full text of the sourcecites [96] Park S, de Perre C, Lee LS. 2017. Alternate reductants with VB12 to transform C8 and C6 perfluoroalkyl sulfonates: limitations and insights into isomer-specific transformation rates, products and pathways. Environ Sci Technol 51: 13869– 13877. doi: 10.1021/acs.est.7b03744 29129060 source

In the paper

“The catabolic reductive dehalogenases are cytoplasmic and more oxygen tolerant than their respiratory counterparts (86, 89–91).”

What the sources say

• Not checked yet

  Checked before — its earlier verdict is held back until a new check runs.

  cites [86] Fincker M, Spormann AM. 2017. Biochemistry of catabolic reductive dehalogenation. Annu Rev Biochem 86: 357– 386. doi: 10.1146/annurev-biochem-061516-044829 28654328 source
• ?Not checked — no full text of the sourcecites [89] Jugder BE, Ertan H, Lee M, Manefield M, Marquis CP. 2015. Reductive dehalogenases come of age in biological destruction of organohalides. Trends Biotechnol 33: 595– 610. doi: 10.1016/j.tibtech.2015.07.004 26409778 source
• Not checked yet

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  cites [90] Lohner ST, Spormann AM. 2013. Identification of a reductive tetrachloroethene dehalogenase in Shewanella sediminis. Philos Trans R Soc Lond B Biol Sci 368: 20120326. doi: 10.1098/rstb.2012.0326 23479755 PMC3638466 source
• Not checked yet

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  cites [91] Halliwell T, Fisher K, Payne KAP, Rigby SEJ, Leys D. 2020. Catabolic reductive dehalogenase substrate complex structures underpin rational repurposing of substrate scope. Microorganisms 8: 1344. doi: 10.3390/microorganisms8091344 32887524 PMC7565698 source

In the paper

“However, these results proved difficult to reproduce in methanogenic samples from different environments (100), and the microorganisms and enzymes responsible for reductive defluorination were not identified in the original studies.”

What the sources say

• ?Not checked — no full text of the sourcecites [100] Emptage M, Tabinowski J, Odom JM. 1997. Effect of fluoroacetates on methanogenesis in samples from selected methanogenic environments. Environ Sci Technol 31: 732– 734. doi: 10.1021/es9603822 source

In the paper

“P450 2E1 from human livers exhibited oxidative defluorination activity on fluorinated inhalation anesthetics (e.g., sevoflurane, isoflurane, and methoxyflurane), resulting in the generation of toxic metabolic intermediates (116, 117).”

What the sources say

• Not checked yet

  Checked before — its earlier verdict is held back until a new check runs.

  cites [116] Kharasch ED, Thummel KE. 1993. Identification of cytochrome P450 2E1 as the predominant enzyme catalyzing human liver microsomal defluorination of sevoflurane, isoflurane, and methoxyflurane. Anesthesiology 79: 795– 807. doi: 10.1097/00000542-199310000-00023 8214760 source
• ?Not checked — no full text of the sourcecites [117] Njoku D, Laster MJ, Gong DH, Eger EI, Reed GF, Martin JL. 1997. Biotransformation of halothane, enflurane, isoflurane, and desflurane to trifluoroacetylated liver proteins: association between protein acylation and hepatic injury. Anesth Analg 84: 173– 178. doi: 10.1097/00000539-199701000-00031 8989020 source

In the paper

“and so while this demonstrates that the corrinoid cofactor may be able to catalyze the reduction of organofluorides, there is still doubt that sufficiently low potential biological electron donors are available for this catalysis to be physiologically relevant.”

What the sources say

• ?Not checked — no full text of the sourcecites [97] Uppal R, Incarvito CD, Lakshmi KV, Valentine AM. 2006. Aqueous spectroscopy and redox properties of carboxylate-bound titanium. Inorg Chem 45: 1795– 1804. doi: 10.1021/ic051714j 16471996 source

In the paper

“Furthermore, P450BM3-F87G, a mutant form of P450BM3 from Bacillus megaterium, catalyzed the oxidative defluorination of 4-fluorophenol to benzoquinone that was further reduced to hydroquinone through the NADPH P450-reductase (118) (Fig. 4).”

What the sources say

• Not checked yet

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  cites [118] Harkey A, Kim H-J, Kandagatla S, Raner GM. 2012. Defluorination of 4-fluorophenol by cytochrome P450(BM₃)-F87G: activation by long chain fatty aldehydes. Biotechnol Lett 34: 1725– 1731. doi: 10.1007/s10529-012-0957-9 22639088 source

In the paper

“Structures for both respiratory and catabolic reductive dehalogenases have been obtained, which share several similarities, including the presence of cobalamin and two [4Fe-4S] clusters in the active site (Fig. 3) (92).”

What the sources say

• Not checked yet

  Checked before — its earlier verdict is held back until a new check runs.

  cites [92] Kunze C, Bommer M, Hagen WR, Uksa M, Dobbek H, Schubert T, Diekert G. 2017. Cobamide-mediated enzymatic reductive dehalogenation via long-range electron transfer. Nat Commun 8: 15858. doi: 10.1038/ncomms15858 28671181 PMC5500849 source

In the paper

“The crystal structures of DAR3835 and NOS0089 resemble that of RPA1163, featuring conserved catalytic triads (Asp-His-Asp) and substrate-binding residues engaged in coordinating both the substrate fluorine and carboxylate groups.”

What the sources say

• Not checked yetcites [74] Khusnutdinova AN, Batyrova KA, Brown G, Fedorchuk T, Chai YS, Skarina T, Flick R, Petit AP, Savchenko A, Stogios P, Yakunin AF. 2023. Structural insights into hydrolytic defluorination of difluoroacetate by microbial fluoroacetate dehalogenases. FEBS J 290: 4966– 4983. doi: 10.1111/febs.16903 37437000 source

In the paper

“In terms of PFAS defluorination, P450 from strain RHA1 was implicated in the defluorination of 6:2 FTOH (73); it exhibited a significantly higher rate of release of fluoride when cultivated with 6:2 FTOH in the absence of P450 inhibitors (1-aminobenzotriazole and allylthiourea) than when those inhibitors were present.”

What the sources say

• Not checked yetcites [73] Yang SH, Shi Y, Strynar M, Chu KH. 2022. Desulfonation and defluorination of 6: 2 fluorotelomer sulfonic acid (6: 2 FTSA) by Rhodococcus jostii RHA1: carbon and sulfur sources, enzymes, and pathways. J Hazard Mater 423: 127052. doi: 10.1016/j.jhazmat.2021.127052 34523492 PMC8823295 source

In the paper

“However, it should be noted that the redox midpoint potential for Ti(III) citrate is lower than −800 mV (97), which is considerably lower than physiologically relevant electron donors”

What the sources say

• ?Not checked — no full text of the sourcecites [97] Uppal R, Incarvito CD, Lakshmi KV, Valentine AM. 2006. Aqueous spectroscopy and redox properties of carboxylate-bound titanium. Inorg Chem 45: 1795– 1804. doi: 10.1021/ic051714j 16471996 source

In the paper

“However, there is no direct evidence for reductive defluorination and relatively few reports in which this enzymatic activity has been inferred from indirect evidence; as such, the feasibility of this defluorination mechanism remains unproven and contested.”

In the paper

“Subsequently, the gene (rha1_ro00230) encoding RJO0230 was successfully cloned and expressed in Rhodococcus opacus PD631 (strain PD631), which then gained defluorination activity against 6:2 FTOH as evidenced by the detection of elevated fluoride levels (73).”

What the sources say

• Not checked yetcites [73] Yang SH, Shi Y, Strynar M, Chu KH. 2022. Desulfonation and defluorination of 6: 2 fluorotelomer sulfonic acid (6: 2 FTSA) by Rhodococcus jostii RHA1: carbon and sulfur sources, enzymes, and pathways. J Hazard Mater 423: 127052. doi: 10.1016/j.jhazmat.2021.127052 34523492 PMC8823295 source

In the paper

“The oxygen-sensitive respiratory reductive dehalogenases use these substrates as terminal electron acceptors and are exported into the periplasm via a twin-arginine transport signal, where they form a complex with a membrane anchor protein (86–88).”

What the sources say

• Not checked yet

  Checked before — its earlier verdict is held back until a new check runs.

  cites [86] Fincker M, Spormann AM. 2017. Biochemistry of catabolic reductive dehalogenation. Annu Rev Biochem 86: 357– 386. doi: 10.1146/annurev-biochem-061516-044829 28654328 source
• ?Not checked — no full text of the sourcecites [87] Hug LA, Maphosa F, Leys D, Löffler FE, Smidt H, Edwards EA, Adrian L. 2013. Overview of organohalide-respiring bacteria and a proposal for a classification system for reductive dehalogenases. Philos Trans R Soc Lond B Biol Sci 368: 20120322. doi: 10.1098/rstb.2012.0322 23479752 PMC3638463 source
• ?Not checked — no full text of the sourcecites [88] Müller JA, Rosner BM, Von Abendroth G, Meshulam-Simon G, McCarty PL, Spormann AM. 2004. Molecular identification of the catabolic vinyl chloride reductase from Dehalococcoides sp. strain VS and its environmental distribution. Appl Environ Microbiol 70: 4880– 4888. doi: 10.1128/AEM.70.8.4880-4888.2004 15294827 PMC492378 source

In the paper

“Subsequently, the gene responsible for encoding the responsible P450 was successfully cloned and expressed in strain PD631, which then gained defluorination activity on 6:2 FTOH.”

What the sources say

• Not checked yetcites [73] Yang SH, Shi Y, Strynar M, Chu KH. 2022. Desulfonation and defluorination of 6: 2 fluorotelomer sulfonic acid (6: 2 FTSA) by Rhodococcus jostii RHA1: carbon and sulfur sources, enzymes, and pathways. J Hazard Mater 423: 127052. doi: 10.1016/j.jhazmat.2021.127052 34523492 PMC8823295 source

In the paper

“After over a decade, an anaerobic strain [named MFA1, formally Cloacibacillus porcorum strain MFA1 (101)] belonging to Synergistetes phylum was shown to defluorinate MFA but not TFA (102).”

What the sources say

• ?Not checked — no full text of the sourcecites [102] Davis CK, Webb RI, Sly LI, Denman SE, McSweeney CS. 2012. Isolation and survey of novel fluoroacetate-degrading bacteria belonging to the phylum Synergistetes. FEMS Microbiol Ecol 80: 671– 684. doi: 10.1111/j.1574-6941.2012.01338.x 22372434 source

In the paper

“Furthermore, Yue et al. (70) showed that RPA1163 facilitated the defluorination of difluoroacetate to glyoxylate, leading to a change in the rate-determining step for difluoroacetate degradation to C-F bond activation.”

What the sources say

• ?Not checked — no full text of the sourcecites [70] Yue Y, Fan J, Xin G, Huang Q, Wang JB, Li Y, Zhang Q, Wang W. 2021. Comprehensive understanding of fluoroacetate dehalogenase-catalyzed degradation of fluorocarboxylic acids: a QM/MM approach. Environ Sci Technol 55: 9817– 9825. doi: 10.1021/acs.est.0c08811 34080849 source

In the paper

“Laccases, primarily obtained from bacteria, fungi, plants, and insects, constitute a subgroup within the enzyme family of multi-copper oxidases (143).”

What the sources say

• Not checked yet

  Checked before — its earlier verdict is held back until a new check runs.

  cites [143] Arregui L, Ayala M, Gómez-Gil X, Gutiérrez-Soto G, Hernández-Luna CE, Herrera de Los Santos M, Levin L, Rojo-Domínguez A, Romero-Martínez D, Saparrat MCN, Trujillo-Roldán MA, Valdez-Cruz NA. 2019. Laccases: structure, function, and potential application in water bioremediation. Microb Cell Fact 18: 200. doi: 10.1186/s12934-019-1248-0 31727078 PMC6854816 source

In the paper

“Although these enzymes exhibit varying specificity toward oxidizable substrates, they follow a shared catalytic cycle. Upon interaction with an H2O2 molecule, enzymatic reactions proceed via a sequence of three successive redox steps.”

What the sources say

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  Checked before — its earlier verdict is held back until a new check runs.

  cites [135] Battistuzzi G, Bellei M, Bortolotti CA, Sola M. 2010. Redox properties of heme peroxidases. Arch Biochem Biophys 500: 21– 36. doi: 10.1016/j.abb.2010.03.002 20211593 source

In the paper

“This radical cation formed by mediator oxidation diffuses from the enzyme-active site and non-specifically oxidizes reduced compounds in the local environment.”

What the sources say

• Not checked yet

  Checked before — its earlier verdict is held back until a new check runs.

  cites [145] Gu Y, Yuan L, Jia L, Xue P, Yao H. 2021. Recent developments of a co-immobilized laccase–mediator system: a review. RSC Adv 11: 29498– 29506. doi: 10.1039/d1ra05104k 35479547 PMC9040808 source
• Not checked yet

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  cites [146] Rodríguez-Delgado MM, Alemán-Nava GS, Rodríguez-Delgado JM, Dieck-Assad G, Martínez-Chapa SO, Barceló D, Parra R. 2015. Laccase-based biosensors for detection of phenolic compounds. Trends Analyt Chem 74: 21– 45. doi: 10.1016/j.trac.2015.05.008 source

In the paper

“Both LiP and MnP can oxidize a wide range of environmental pollutants such as phenolic and non-phenolic compounds, dyes, and xenobiotics (134, 139, 142).”

What the sources say

• ?Not checked — no full text of the sourcecites [134] Morsi R, Bilal M, Iqbal HMN, Ashraf SS. 2020. Laccases and peroxidases: the smart, greener and futuristic biocatalytic tools to mitigate recalcitrant emerging pollutants. Sci Total Environ 714: 136572. doi: 10.1016/j.scitotenv.2020.136572 31986384 source
• Not checked yet

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  cites [139] Bilal M, Adeel M, Rasheed T, Zhao Y, Iqbal HMN. 2019. Emerging contaminants of high concern and their enzyme-assisted biodegradation – A review. Environ Int 124: 336– 353. doi: 10.1016/j.envint.2019.01.011 30660847 source
• ?Not checked — no full text of the sourcecites [142] Singh AK, Bilal M, Iqbal HMN, Raj A. 2021. Lignin peroxidase in focus for catalytic elimination of contaminants — A critical review on recent progress and perspectives. Int J Biol Macromol 177: 58– 82. doi: 10.1016/j.ijbiomac.2021.02.032 33577817 source

In the paper

“Peroxidases, heme-containing enzymes, are ubiquitously distributed across fungi, bacteria, plants, and animals.”

In the paper

“Consequently, peroxidases play a crucial role in catalyzing the biodegradation of diverse contaminants, including pesticides, phenolic pollutants, textile dyes, polycyclic aromatic hydrocarbons, and polychlorinated biphenyls [reviewed by Bilal et al. (137) and Sellami et al. (138)].”

What the sources say

• ?Not checked — no full text of the sourcecites [137] Bilal M, Rasheed T, Iqbal HMN, Yan Y. 2018. Peroxidases-assisted removal of environmentally-related hazardous pollutants with reference to the reaction mechanisms of industrial dyes. Sci Total Environ 644: 1– 13. doi: 10.1016/j.scitotenv.2018.06.274 29980079 source
• ?Not checked — no full text of the sourcecites [138] Sellami K, Couvert A, Nasrallah N, Maachi R, Abouseoud M, Amrane A. 2022. Peroxidase enzymes as green catalysts for bioremediation and biotechnological applications: a review. Sci Total Environ 806: 150500. doi: 10.1016/j.scitotenv.2021.150500 34852426 source

In the paper

“Accompanied by PFOA degradation, fluoride ions (less than 1%) and various short-chain fluorinated compounds were identified via ion chromatography and gas chromatography-mass spectrometry, respectively.”

What the sources say

• ?Not checked — no full text of the sourcecites [140] Colosi LM, Pinto RA, Huang Q, Weber WJJ. 2009. Peroxidase-mediated degradation of perfluorooctanoic acid. Environ Toxicol Chem 28: 264– 271. doi: 10.1897/08-282.1 18808217 source

In the paper

“Like the peroxidases, extracellular laccases are used by saprophytes in the decomposition of complex biological polymers, such as polysaccharides and lignin (136).”

What the sources say

• Not checked yet

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  cites [136] Janusz G, Pawlik A, Sulej J, Swiderska-Burek U, Jarosz-Wilkolazka A, Paszczynski A. 2017. Lignin degradation: microorganisms, enzymes involved, genomes analysis and evolution. FEMS Microbiol Rev 41: 941– 962. doi: 10.1093/femsre/fux049 29088355 PMC5812493 source

In the paper

“Correspondingly, the LiP activity exhibited a progressive increase over time, whereas the MnP activity remained stable between days 7 and 14, followed by an upsurge on day 28.”

What the sources say

• ?Not checked — no full text of the sourcecites [122] Merino N, Wang N, Gao Y, Wang M, Mahendra S. 2023. Roles of various enzymes in the biotransformation of 6:2 fluorotelomer alcohol (6:2 FTOH) by a white-rot fungus. J Hazard Mater 450: 131007. doi: 10.1016/j.jhazmat.2023.131007 36871371 source

In the paper

“These observations suggest that both enzymes may have contributed to the biotransformation of 5:3 FTCA or were positively influenced by 5:3 FTCA and its metabolites.”

What the sources say

• ?Not checked — no full text of the sourcecites [122] Merino N, Wang N, Gao Y, Wang M, Mahendra S. 2023. Roles of various enzymes in the biotransformation of 6:2 fluorotelomer alcohol (6:2 FTOH) by a white-rot fungus. J Hazard Mater 450: 131007. doi: 10.1016/j.jhazmat.2023.131007 36871371 source

In the paper

“By employing hydrogen peroxide (H2O2) or organic hydroperoxides as co-substrates, these enzymes facilitate oxidative reactions involving numerous inorganic and organic substrates (134, 135).”

What the sources say

• ?Not checked — no full text of the sourcecites [134] Morsi R, Bilal M, Iqbal HMN, Ashraf SS. 2020. Laccases and peroxidases: the smart, greener and futuristic biocatalytic tools to mitigate recalcitrant emerging pollutants. Sci Total Environ 714: 136572. doi: 10.1016/j.scitotenv.2020.136572 31986384 source
• Not checked yet

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  cites [135] Battistuzzi G, Bellei M, Bortolotti CA, Sola M. 2010. Redox properties of heme peroxidases. Arch Biochem Biophys 500: 21– 36. doi: 10.1016/j.abb.2010.03.002 20211593 source

In the paper

“Examples of such mediators include 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) and 1-hydroxybenzotriazole (HBT) (144, 145).”

What the sources say

• ?Not checked — no full text of the sourcecites [144] Bhardwaj P, Kaur N, Selvaraj M, Ghramh HA, Al-Shehri BM, Singh G, Arya SK, Bhatt K, Ghotekar S, Mani R, Chang SW, Ravindran B, Awasthi MK. 2022. Laccase-assisted degradation of emerging recalcitrant compounds – A review. Bioresour Technol 364: 128031. doi: 10.1016/j.biortech.2022.128031 36167178 source
• Not checked yet

  Checked before — its earlier verdict is held back until a new check runs.

  cites [145] Gu Y, Yuan L, Jia L, Xue P, Yao H. 2021. Recent developments of a co-immobilized laccase–mediator system: a review. RSC Adv 11: 29498– 29506. doi: 10.1039/d1ra05104k 35479547 PMC9040808 source

In the paper

“Fluoride ions were detected, and the concentration revealed 28% defluorination of PFOA.”

What the sources say

• ?Not checked — no full text of the sourcecites [147] Luo Q, Lu J, Zhang H, Wang Z, Feng M, Chiang S-YD, Woodward D, Huang Q. 2015. Laccase-catalyzed degradation of perfluorooctanoic acid. Environ Sci Technol Lett 2: 198– 203. doi: 10.1021/acs.estlett.5b00119 source

In the paper

“Within their active sites, these enzymes harbor four copper atoms, categorized into three types: single “blue” copper (type 1, T1), single “non-blue” copper (type 2, T2), and a copper-copper pair (type 3, T3) (143, 144).”

What the sources say

• Not checked yet

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  cites [143] Arregui L, Ayala M, Gómez-Gil X, Gutiérrez-Soto G, Hernández-Luna CE, Herrera de Los Santos M, Levin L, Rojo-Domínguez A, Romero-Martínez D, Saparrat MCN, Trujillo-Roldán MA, Valdez-Cruz NA. 2019. Laccases: structure, function, and potential application in water bioremediation. Microb Cell Fact 18: 200. doi: 10.1186/s12934-019-1248-0 31727078 PMC6854816 source
• ?Not checked — no full text of the sourcecites [144] Bhardwaj P, Kaur N, Selvaraj M, Ghramh HA, Al-Shehri BM, Singh G, Arya SK, Bhatt K, Ghotekar S, Mani R, Chang SW, Ravindran B, Awasthi MK. 2022. Laccase-assisted degradation of emerging recalcitrant compounds – A review. Bioresour Technol 364: 128031. doi: 10.1016/j.biortech.2022.128031 36167178 source

In the paper

“Based on the structural similarity shared between n-alkanes and FTOHs, it was postulated that alkane-degrading enzymes, particularly butane and alkane monooxygenases, may possess the ability to degrade FTOHs as well (133).”

What the sources say

• ?Not checked — no full text of the sourcecites [133] Kim MH, Wang N, McDonald T, Chu KH. 2012. Biodefluorination and biotransformation of fluorotelomer alcohols by two alkane-degrading Pseudomonas strains. Biotechnol Bioeng 109: 3041– 3048. doi: 10.1002/bit.24561 22614340 source

In the paper

“Subsequently, an internal electron is transferred from the reduced T1 to the T2 and T3 copper sites, where the bound O2 molecule undergoes activation and reduction to water in the T2/T3 trinuclear domain (145, 146).”

What the sources say

• Not checked yet

  Checked before — its earlier verdict is held back until a new check runs.

  cites [145] Gu Y, Yuan L, Jia L, Xue P, Yao H. 2021. Recent developments of a co-immobilized laccase–mediator system: a review. RSC Adv 11: 29498– 29506. doi: 10.1039/d1ra05104k 35479547 PMC9040808 source
• Not checked yet

  Checked before — its earlier verdict is held back until a new check runs.

  cites [146] Rodríguez-Delgado MM, Alemán-Nava GS, Rodríguez-Delgado JM, Dieck-Assad G, Martínez-Chapa SO, Barceló D, Parra R. 2015. Laccase-based biosensors for detection of phenolic compounds. Trends Analyt Chem 74: 21– 45. doi: 10.1016/j.trac.2015.05.008 source

In the paper

“This renders them extensively applicable in the oxidative removal of various pollutants, such as herbicides, synthetic dyes, and pharmaceuticals (134, 143, 144).”

What the sources say

• ?Not checked — no full text of the sourcecites [134] Morsi R, Bilal M, Iqbal HMN, Ashraf SS. 2020. Laccases and peroxidases: the smart, greener and futuristic biocatalytic tools to mitigate recalcitrant emerging pollutants. Sci Total Environ 714: 136572. doi: 10.1016/j.scitotenv.2020.136572 31986384 source
• Not checked yet

  Checked before — its earlier verdict is held back until a new check runs.

  cites [143] Arregui L, Ayala M, Gómez-Gil X, Gutiérrez-Soto G, Hernández-Luna CE, Herrera de Los Santos M, Levin L, Rojo-Domínguez A, Romero-Martínez D, Saparrat MCN, Trujillo-Roldán MA, Valdez-Cruz NA. 2019. Laccases: structure, function, and potential application in water bioremediation. Microb Cell Fact 18: 200. doi: 10.1186/s12934-019-1248-0 31727078 PMC6854816 source
• ?Not checked — no full text of the sourcecites [144] Bhardwaj P, Kaur N, Selvaraj M, Ghramh HA, Al-Shehri BM, Singh G, Arya SK, Bhatt K, Ghotekar S, Mani R, Chang SW, Ravindran B, Awasthi MK. 2022. Laccase-assisted degradation of emerging recalcitrant compounds – A review. Bioresour Technol 364: 128031. doi: 10.1016/j.biortech.2022.128031 36167178 source

In the paper

“Laccases exhibit the capability to oxidize a wide range of phenolic and non-phenolic compounds and employ O2 as an electron acceptor (four-electron reduction of oxygen), yielding water as a by-product (143).”

What the sources say

• Not checked yet

  Checked before — its earlier verdict is held back until a new check runs.

  cites [143] Arregui L, Ayala M, Gómez-Gil X, Gutiérrez-Soto G, Hernández-Luna CE, Herrera de Los Santos M, Levin L, Rojo-Domínguez A, Romero-Martínez D, Saparrat MCN, Trujillo-Roldán MA, Valdez-Cruz NA. 2019. Laccases: structure, function, and potential application in water bioremediation. Microb Cell Fact 18: 200. doi: 10.1186/s12934-019-1248-0 31727078 PMC6854816 source

In the paper

“Many peroxidases are excreted into the environment to catalyze the decomposition of complex organic polymers, such as cellulose and lignin, by saprotrophic organisms (136).”

What the sources say

• Not checked yet

  Checked before — its earlier verdict is held back until a new check runs.

  cites [136] Janusz G, Pawlik A, Sulej J, Swiderska-Burek U, Jarosz-Wilkolazka A, Paszczynski A. 2017. Lignin degradation: microorganisms, enzymes involved, genomes analysis and evolution. FEMS Microbiol Rev 41: 941– 962. doi: 10.1093/femsre/fux049 29088355 PMC5812493 source

In the paper

“As an integral membrane-bound diiron ω-hydroxylase, alkane monooxygenase from Pseudomonas putida Gpo1 (formerly known as Pseudomonas oleovorans) can selectively introduce O2 into the unreactive terminal methyl group of C5–C12 linear alkanes, generating primary alcohols (131, 132).”

What the sources say

• Not checked yet

  Checked before — its earlier verdict is held back until a new check runs.

  cites [131] Tsai YF, Luo WI, Chang JL, Chang CW, Chuang HC, Ramu R, Wei GT, Zen JM, Yu SSF. 2017. Electrochemical hydroxylation of C3–C12 n-alkanes by recombinant alkane hydroxylase (AlkB) and rubredoxin-2 (AlkG) from Pseudomonas putida GPo1. Sci Rep 7: 8369. doi: 10.1038/s41598-017-08610-w 28827709 PMC5566439 source
• Not checked yet

  Checked before — its earlier verdict is held back until a new check runs.

  cites [132] Shanklin J, Achim C, Schmidt H, Fox BG, Münck E. 1997. Mössbauer studies of alkane ω-hydroxylase: evidence for a diiron cluster in an integral-membrane enzyme. Proc Natl Acad Sci U S A 94: 2981– 2986. doi: 10.1073/pnas.94.7.2981 9096332 PMC20308 source

In the paper

“Notably, Cu2+ and Fe3+ can complex with PFOA, thereby enhancing PFOA degradation and increasing the HBT radical efficacy.”

What the sources say

• ?Not checked — no full text of the sourcecites [148] Luo Q, Wang Z, Feng M, Chiang D, Woodward D, Liang S, Lu J, Huang Q. 2017. Factors controlling the rate of perfluorooctanoic acid degradation in laccase-mediator systems: the impact of metal ions. Environ Pollut 224: 649– 657. doi: 10.1016/j.envpol.2017.02.050 28262377 source

In the paper

“Hence, in addition to its application in the degradation of phenol-containing wastewater, HRP has also been extensively employed for the transformation/degradation of dyes, pesticides, pharmaceuticals, and various hazardous contaminants (137, 138).”

What the sources say

• ?Not checked — no full text of the sourcecites [137] Bilal M, Rasheed T, Iqbal HMN, Yan Y. 2018. Peroxidases-assisted removal of environmentally-related hazardous pollutants with reference to the reaction mechanisms of industrial dyes. Sci Total Environ 644: 1– 13. doi: 10.1016/j.scitotenv.2018.06.274 29980079 source
• ?Not checked — no full text of the sourcecites [138] Sellami K, Couvert A, Nasrallah N, Maachi R, Abouseoud M, Amrane A. 2022. Peroxidase enzymes as green catalysts for bioremediation and biotechnological applications: a review. Sci Total Environ 806: 150500. doi: 10.1016/j.scitotenv.2021.150500 34852426 source

In the paper

“This oxidative transformation is a crucial step contributing to lignin degradation and activation of the ligninolytic system (134, 141).”

What the sources say

• ?Not checked — no full text of the sourcecites [134] Morsi R, Bilal M, Iqbal HMN, Ashraf SS. 2020. Laccases and peroxidases: the smart, greener and futuristic biocatalytic tools to mitigate recalcitrant emerging pollutants. Sci Total Environ 714: 136572. doi: 10.1016/j.scitotenv.2020.136572 31986384 source
• Not checked yet

  Checked before — its earlier verdict is held back until a new check runs.

  cites [141] Khan MF, Hof C, Niemcová P, Murphy CD. 2023. Recent advances in fungal xenobiotic metabolism: enzymes and applications. World J Microbiol Biotechnol 39: 296. doi: 10.1007/s11274-023-03737-7 37658215 PMC10474215 source

In the paper

“Moreover, proteins in plant roots have been identified in various studies as factors influencing the processes of PFAS uptake and accumulation (179, 185, 186).”

What the sources say

• Not checked yetcites [179] Costello MCS, Lee LS. 2020. Sources, fate, and plant uptake in agricultural systems of per- and polyfluoroalkyl substances. Curr Pollution Rep. doi: 10.1007/s40726-020-00168-y
• ?Not checked — no full text of the sourcecites [185] Mayakaduwage S, Ekanayake A, Kurwadkar S, Rajapaksha AU, Vithanage M. 2022. Phytoremediation prospects of per- and polyfluoroalkyl substances: a review. Environ Res 212: 113311. doi: 10.1016/j.envres.2022.113311 35460639 source
• ?Not checked — no full text of the sourcecites [186] Adu O, Ma X, Sharma VK. 2023. Bioavailability, phytotoxicity and plant uptake of per-and polyfluoroalkyl substances (PFAS): a review. J Hazard Mater 447: 130805. doi: 10.1016/j.jhazmat.2023.130805 36669401 source

In the paper

“This enzyme consists of two components, NtaA and NtaB (165).”

What the sources say

• ?Not checked — no full text of the sourcecites [165] Xu Y, Mortimer MW, Fisher TS, Kahn ML, Brockman FJ, Xun L. 1997. Cloning, sequencing, and analysis of a gene cluster from Chelatobacter heintzii ATCC 29600 encoding nitrilotriacetate monooxygenase and NADH: flavin mononucleotide oxidoreductase. J Bacteriol 179: 1112– 1116. doi: 10.1128/jb.179.4.1112-1116.1997 9023192 PMC178806 source

In the paper

“Meanwhile, the latter, a flavin reductase, utilizes NADH to reduce FMN to FMNH2, a requisite cofactor in the oxidization step by NtaA (165).”

What the sources say

• ?Not checked — no full text of the sourcecites [165] Xu Y, Mortimer MW, Fisher TS, Kahn ML, Brockman FJ, Xun L. 1997. Cloning, sequencing, and analysis of a gene cluster from Chelatobacter heintzii ATCC 29600 encoding nitrilotriacetate monooxygenase and NADH: flavin mononucleotide oxidoreductase. J Bacteriol 179: 1112– 1116. doi: 10.1128/jb.179.4.1112-1116.1997 9023192 PMC178806 source

In the paper

“Consistent with their metabolic function, the Tau and Ssu proteins demonstrate a lower-than-average content of sulfur-containing amino acid residues (151, 153–155).”

What the sources say

• Not checked yet

  Checked before — its earlier verdict is held back until a new check runs.

  cites [151] Kertesz MA. 2000. Riding the sulfur cycle–metabolism of sulfonates and sulfate esters in Gram-negative bacteria. FEMS Microbiol Rev 24: 135– 175. doi: 10.1016/S0168-6445(99)00033-9 10717312 source
• ?Not checked — no full text of the sourcecites [153] van der Ploeg JR, Eichhorn E, Leisinger T. 2001. Sulfonate-sulfur metabolism and its regulation in Escherichia coli. Arch Microbiol 176: 1– 8. doi: 10.1007/s002030100298 11479697 source
• ?Not checked — no full text of the sourcecites [154] Eichhorn E, Davey CA, Sargent DF, Leisinger T, Richmond TJ. 2002. Crystal structure of Escherichia coli alkanesulfonate monooxygenase SsuD. J Mol Biol 324: 457– 468. doi: 10.1016/s0022-2836(02)01069-0 12445781 source
• ?Not checked — no full text of the sourcecites [155] Scott C, Hilton ME, Coppin CW, Russell RJ, Oakeshott JG, Sutherland TD. 2007. A global response to sulfur starvation in Pseudomonas putida and its relationship to the expression of low-sulfur-content proteins. FEMS Microbiol Lett 267: 184– 193. doi: 10.1111/j.1574-6968.2006.00575.x 17187657 source

In the paper

“SsuD is an alkanesulfonate monooxygenase belonging to a two-component system that catalyzes the desulfonation of organosulfonates to sulfite and the corresponding aldehyde (153, 154, 158) (Fig. 5).”

What the sources say

• ?Not checked — no full text of the sourcecites [153] van der Ploeg JR, Eichhorn E, Leisinger T. 2001. Sulfonate-sulfur metabolism and its regulation in Escherichia coli. Arch Microbiol 176: 1– 8. doi: 10.1007/s002030100298 11479697 source
• ?Not checked — no full text of the sourcecites [154] Eichhorn E, Davey CA, Sargent DF, Leisinger T, Richmond TJ. 2002. Crystal structure of Escherichia coli alkanesulfonate monooxygenase SsuD. J Mol Biol 324: 457– 468. doi: 10.1016/s0022-2836(02)01069-0 12445781 source
• Not checked yet

  Checked before — its earlier verdict is held back until a new check runs.

  cites [158] Eichhorn E, van der Ploeg JR, Leisinger T. 1999. Characterization of a two-component alkanesulfonate monooxygenase from Escherichia coli. J Biol Chem 274: 26639– 26646. doi: 10.1074/jbc.274.38.26639 10480865 source

In the paper

“Moreover, neither strain is able to grow with PFOS or PFHxS as sole sulfur sources (160, 162).”

What the sources say

• ?Not checked — no full text of the sourcecites [160] Van Hamme JD, Bottos EM, Bilbey NJ, Brewer SE. 2013. Genomic and proteomic characterization of Gordonia sp. NB4-1Y in relation to 6: 2 fluorotelomer sulfonate biodegradation. Microbiology (Reading) 159: 1618– 1628. doi: 10.1099/mic.0.068932-0 23744905 source
• Not checked yetcites [162] Méndez V, Holland S, Bhardwaj S, McDonald J, Khan S, O’Carroll D, Pickford R, Richards S, O’Farrell C, Coleman N, Lee M, Manefield MJ. 2022. Aerobic biotransformation of 6: 2 fluorotelomer sulfonate by Dietzia aurantiaca J3 under sulfur-limiting conditions. Sci Total Environ 829: 154587. doi: 10.1016/j.scitotenv.2022.154587 35306084 source

In the paper

“NTA-Mo belongs to the family of two-component monooxygenases as SsuD/SsuE, functioning as an oxidoreductase for initiating the oxidation of NTA under aerobic conditions (164, 165).”

What the sources say

• Not checked yetcites [164] van Berkel WJH, Kamerbeek NM, Fraaije MW. 2006. Flavoprotein monooxygenases, a diverse class of oxidative biocatalysts. J Biotechnol 124: 670– 689. doi: 10.1016/j.jbiotec.2006.03.044 16712999
• ?Not checked — no full text of the sourcecites [165] Xu Y, Mortimer MW, Fisher TS, Kahn ML, Brockman FJ, Xun L. 1997. Cloning, sequencing, and analysis of a gene cluster from Chelatobacter heintzii ATCC 29600 encoding nitrilotriacetate monooxygenase and NADH: flavin mononucleotide oxidoreductase. J Bacteriol 179: 1112– 1116. doi: 10.1128/jb.179.4.1112-1116.1997 9023192 PMC178806 source

In the paper

“A subclass of bacterial CLC proteins has been described that lack the conserved chloride-binding motif and that were expressed under the control of a fluoride-inducible riboswitch.”

In the paper

“Both operons encode an ABC-type transport system for the uptake of organosulfonates (tauABC and ssuABC) and an oxygenase system for their desulfonation (tauD and ssuDE) (Fig. 5).”

What the sources say

• Not checked yet

  Checked before — its earlier verdict is held back until a new check runs.

  cites [151] Kertesz MA. 2000. Riding the sulfur cycle–metabolism of sulfonates and sulfate esters in Gram-negative bacteria. FEMS Microbiol Rev 24: 135– 175. doi: 10.1016/S0168-6445(99)00033-9 10717312 source

In the paper

“The broader CLC family members are chloride transporters that are found in every domain of life.”

In the paper

“Moreover, expression of CLCF has been demonstrated to confer resistance to fluoride toxicity, supporting the hypothesis that F− efflux is its physiological function (172).”

What the sources say

• Not checked yetcites [172] Stockbridge RB, Lim H-H, Otten R, Williams C, Shane T, Weinberg Z, Miller C. 2012. Fluoride resistance and transport by riboswitch-controlled CLC antiporters. Proc Natl Acad Sci U S A 109: 15289– 15294. doi: 10.1073/pnas.1210896109 22949689 PMC3458365 source

In the paper

“Under sulfur-limiting conditions, certain bacteria express two operons, tau and ssu, to utilize organosulfonates as sulfur sources for growth.”

What the sources say

• Not checked yet

  Checked before — its earlier verdict is held back until a new check runs.

  cites [151] Kertesz MA. 2000. Riding the sulfur cycle–metabolism of sulfonates and sulfate esters in Gram-negative bacteria. FEMS Microbiol Rev 24: 135– 175. doi: 10.1016/S0168-6445(99)00033-9 10717312 source

In the paper

“The former exhibits monooxygenase activity, catalyzing the oxidative conversion of NTA to iminodiacetate (IDA) and glyoxylate in the presence of FMNH2 and O2.”

What the sources say

• ?Not checked — no full text of the sourcecites [165] Xu Y, Mortimer MW, Fisher TS, Kahn ML, Brockman FJ, Xun L. 1997. Cloning, sequencing, and analysis of a gene cluster from Chelatobacter heintzii ATCC 29600 encoding nitrilotriacetate monooxygenase and NADH: flavin mononucleotide oxidoreductase. J Bacteriol 179: 1112– 1116. doi: 10.1128/jb.179.4.1112-1116.1997 9023192 PMC178806 source

In the paper

“There are two known classes of F− channels, which appear to have evolved independently of each other: fluoride-specific members of the CLC family and the Fluc family of proteins.”

In the paper

“The Fluc proteins are small, homodimeric permeases (175), with extremely high specificity for the fluoride anion (10,000-fold versus chloride) (176).”

What the sources say

• Not checked yet

  Checked before — its earlier verdict is held back until a new check runs.

  cites [175] McIlwain BC, Gundepudi R, Koff BB, Stockbridge RB. 2021. The fluoride permeation pathway and anion recognition in Fluc family fluoride channels. Elife 10: e69482. doi: 10.7554/eLife.69482 34250906 PMC8315801 source
• Not checked yet

  Checked before — its earlier verdict is held back until a new check runs.

  cites [176] Stockbridge RB, Koide A, Miller C, Koide S. 2014. Proof of dual-topology architecture of Fluc F− channels with monobody blockers. Nat Commun 5: 5120. doi: 10.1038/ncomms6120 25290819 PMC4265568 source

In the paper

“In addition, the TauABC and SsuABC transport systems are not interchangeable due to no shared membrane component or ATPase between the periplasmic binding proteins of these two systems (153, 156).”

What the sources say

• ?Not checked — no full text of the sourcecites [153] van der Ploeg JR, Eichhorn E, Leisinger T. 2001. Sulfonate-sulfur metabolism and its regulation in Escherichia coli. Arch Microbiol 176: 1– 8. doi: 10.1007/s002030100298 11479697 source
• Not checked yetcites [156] Eichhorn EE. 2000. Sulfonate-sulfur assimilation in Escherichia coli Doctoral dissertation, ETH Zurich

In the paper

“The majority of enzymes discussed in this review are either intracellular or membrane bound.”