Metabolic flux analysis of <italic style="font-style: italic">Shewanella</italic> sp. MR-4 with different terminal electron receptors

ZHENG Qingxiang

doi:10.12211/2096-8280.2022-052

您当前的位置：

首页 >

文章列表页 >

Metabolic flux analysis of Shewanella sp. MR-4 with different terminal electron receptors

Research Article | 更新时间：2025-03-20

- Metabolic flux analysis of Shewanella sp. MR-4 with different terminal electron receptors
- Synthetic Biology Journal Vol. 4, Issue 6, Pages: 1300-1320(2023)
- 作者机构：
  
  漳州人才发展集团有限公司，福建漳州 363000
- 作者简介：
- 基金信息：
- DOI：10.12211/2096-8280.2022-052
  CLC： Q816
- Received：23 September 2022，
  
  Revised：2022-11-16，
  
  Published：31 December 2023
- 稿件说明：
移动端阅览
郑庆祥. 希瓦氏菌Shewanella sp. MR-4在不同末端电子受体条件下的代谢通量分析［J］. 合成生物学， 2023， 4（6）： 1300-1320

ZHENG Qingxiang. Metabolic flux analysis of Shewanella sp. MR-4 with different terminal electron receptors［J］. Synthetic Biology Journal， 2023， 4（6）： 1300-1320
郑庆祥. 希瓦氏菌Shewanella sp. MR-4在不同末端电子受体条件下的代谢通量分析［J］. 合成生物学， 2023， 4（6）： 1300-1320 DOI： 10.12211/2096-8280.2022-052.

ZHENG Qingxiang. Metabolic flux analysis of Shewanella sp. MR-4 with different terminal electron receptors［J］. Synthetic Biology Journal， 2023， 4（6）： 1300-1320 DOI： 10.12211/2096-8280.2022-052.

摘要

本研究解析了

Shewanella

sp. MR-4在厌氧条件下以Fe

、延胡索酸、硝酸和二甲基亚砜（DMSO）为末端电子受体时代谢通量分布，发现在各种不同末端电子受体条件下细胞内代谢通量分布发生显著改变。与延胡索酸相比，在Fe

和硝酸为电子受体条件下，乙酸生成速率明显降低，而三羧酸循环代谢通量增加。同时，三羧酸循环回补反应存在显著差异：在延胡索酸为电子受体条件下，磷酸烯醇式丙酮酸羧化酶反应是唯一回补反应，而在Fe

和硝酸条件下苹果酸酶催化成为唯一回补反应。本研究在代谢通量分析基础上定量解析了还原力NADH合成和消耗，分析了电子流向变化，发现在不同末端电子受体条件下，NADH产生途径和反应发生明显变化。研究结果为希瓦氏菌代谢工程改造提供了一定理论依据。

Abstract

Shewanella

is ubiquitous in natural environments

known to show various unique activities

such as metal reduction and trimethylamine production. The metal reduction capability expands the range of electron acceptors and enables its application in producing current in microbial fuel cells. Previous work primarily focused on the model organism

Shewanella oneidensis

MR-1

based on which the metabolic models were constructed for three other strains including

Shewanella

sp. MR-4. Interestingly

the genetic similarity does not always coincide with metabolic phenotype similarity between these two strains

suggesting that potential regulatory effects affecting cellular phenotypes are present in

Shewanella

sp.

MR-4. This study analyzed the metabolic flux distribution of

Shewanella

sp. MR-4 when Fe

fumaric acid

nitric acid and dimethyl sulfoxide were used as electron acceptors under anaerobic conditions. The intracellular metabolic flux distribution was significantly changed with different electron acceptors. The formation rate of acetic acid was decreased

while the metabolic flux of the tricarboxylic acid (TC

A) cycle was increased with Fe

and nitric acid as electron acceptors

compared to that with fumaric acid. The anaplerotic reaction in the TCA cycle was also dramatically altered: the phosphoenolpyruvate carboxylase-catalyzed reaction or malic enzyme-catalyzed reaction is the only anaplerotic reaction with fumaric acid or Fe

and nitric acid as electron acceptor

respectively. Based on the metabolic flux map

quantitative analysis was performed to derive the synthesis and consumption rates of reducing agent NADH

and the change of electron transfer. It was found that NADH metabolism varies significantly with the electron acceptors tested. The results provide a theoretical basis for the future metabolic engineering of

Shewanella

and experimental evidences that can be used for future study of different phenotypes unaccounted for in previous models of

Shewanella

sp. MR-4 and MR-1.

关键词

Keywords

references

MYERS C R , NEALSON K H . Bacterial Manganese reduction and growth with manganese oxide as the sole electron acceptor [J ] . Science , 1988 , 240 ( 4857 ): 1319 - 1321 .

LARSEN I , LITTLE B , NEALSON K H , et al . Manganite reduction by Shewanella putrefaciens MR-4 [J ] . American Mineralogist , 1998 , 83 ( 11/12 ): 1564 - 1572 .

URRUTIA M M , RODEN E E , FREDRICKSON J K , et al . Microbial and surface chemistry controls on reduction of synthetic Fe(Ⅲ) oxide minerals by the dissimilatory iron-reducing bacterium Shewanella alga [J ] . Geomicrobiology Journal , 1998 , 15 ( 4 ): 269 - 291 .

CACCAVO F , BLAKEMORE R P , LOVLEY D R . A hydrogen-oxidizing, Fe(Ⅲ)-reducing microorganism from the Great Bay Estuary, New Hampshire [J ] . Applied and Environmental Microbiology , 1992 , 58 ( 10 ): 3211 - 3216 .

WIELINGA B , MIZUBA M M , HANSEL C M , et al . Iron promoted reduction of chromate by dissimilatory iron-reducing bacteria [J ] . Environmental Science & Technology , 2001 , 35 ( 3 ): 522 - 527 .

FARRENKOPF A M , DOLLHOPF M E , NI CHADHAIN S , et al . Reduction of iodate in seawater during Arabian Sea shipboard incubations and in laboratory cultures of the marine bacterium Shewanella putrefaciens strain MR-4 [J ] . Marine Chemistry , 1997 , 57 ( 3/4 ): 347 - 354 .

WILDUNG R E , GORBY Y A , KRUPKA K M , et al . Effect of electron donor and solution chemistry on products of dissimilatory reduction of technetium by Shewanella putrefaciens [J ] . Applied and Environmental Microbiology , 2000 , 66 ( 6 ): 2451 - 2460 .

LLOYD J R , YONG P , MACASKIE L E . Biological reduction and removal of Np(Ⅴ) by two microorganisms [J ] . Environmental Science & Technology , 2000 , 34 ( 7 ): 1297 - 1301 .

SALTIKOV C W , WILDMAN R A JR , NEWMAN D K . Expression dynamics of arsenic respiration and detoxification in Shewanella sp. strain ANA-3 [J ] . Journal of Bacteriology , 2005 , 187 ( 21 ): 7390 - 7396 .

BOUKHALFA H , ICOPINI G A , REILLY S D , et al . Plutonium(Ⅳ) reduction by the metal-reducing bacteria Geobacter metallireducens GS15 and Shewanella oneidensis MR1 [J ] . Applied and Environmental Microbiology , 2007 , 73 ( 18 ): 5897 - 5903 .

KLONOWSKA A , HEULIN T , VERMEGLIO A . Selenite and tellurite reduction by Shewanella oneidensis [J ] . Applied and Environmental Microbiology , 2005 , 71 ( 9 ): 5607 - 5609 .

CARPENTIER W , SANDRA K , DE SMET I , et al . Microbial reduction and precipitation of vanadium by Shewanella oneidensis [J ] . Applied and Environmental Microbiology , 2003 , 69 ( 6 ): 3636 - 3639 .

PERRY K A , KOSTKA J E , LUTHER G W 3 RD, et al. Mediation of sulfur speciation by a Black Sea facultative anaerobe[J ] . Science , 1993, 259 ( 5096 ): 801 - 803 .

KRAUSE B , NEALSON K H . Physiology and enzymology involved in denitrification by Shewanella putrefaciens [J ] . Applied and Environmental Microbiology , 1997 , 63 ( 7 ): 2613 - 2618 .

RINGØ E , STENBERG E , STRØM A R . Amino acid and lactate catabolism in trimethylamine oxide respiration of Alteromonas putrefaciens NCMB 1735 [J ] . Applied and Environmental Microbiology , 1984 , 47 ( 5 ): 1084 - 1089 .

GRALNICK J A , VALI H , LIES D P , et al . Extracellular respiration of dimethyl sulfoxide by Shewanella oneidensis strain MR-1 [J ] . Proceedings of the National Academy of Sciences of the United States of America , 2006 , 103 ( 12 ): 4669 - 4674 .

MYERS C R , MYERS J M . Fumarate reductase is a soluble enzyme in anaerobically grown Shewanella putrefaciens MR-1 [J ] . FEMS Microbiology Letters , 1992 , 98 ( 1/2/3 ): 13 - 19 .

ZHAO J S , MANNO D , BEAULIEU C , et al . Shewanella sediminis sp nov., a novel Na + -requiring and hexahydro-1,3,5-trinitro-1,3,5-triazine-degrading bacterium from marine sediment [J ] . International Journal of Systematic and Evolutionary Microbiology , 2005 , 55 ( Pt 4 ): 1511 - 1520 .

ZHAO J S , MANNO D , THIBOUTOT S , et al . Shewanella canadensis sp nov. and Shewanella atlantica sp. nov., manganese dioxide- and hexahydro-1,3,5-trinitro-1,3,5-triazine-reducing, psychrophilic marine bacteria [J ] . International Journal of Systematic and Evolutionary Microbiology , 2007 , 57 ( 9 ): 2155 - 2162 .

HAU H H , GRALNICK J A . Ecology and biotechnology of the genus Shewanella [J ] . Annual Review of Microbiology , 2007 , 61 : 237 - 258 .

肖翔 , 吴勇民 , 徐灿灿 , 等 . 金属还原菌希瓦氏菌厌氧呼吸能力及其在环境修复中的研究进展 [J ] . 微生物学通报 , 2012 , 39 ( 11 ): 1677 - 1686 .

XIAO X , WU Y M , XU C C , et al . Anaerobic respiratory capabilities of a metal-reducing microorganism Shewanella and its application in environmental remediation [J ] . Microbiology China , 2012 , 39 ( 11 ): 1677 - 1686 .

TANG Y J J , HWANG J S , WEMMER D E , et al . Shewanella oneidensis MR-1 fluxome under various oxygen conditions [J ] . Applied and Environmental Microbiology , 2007 , 73 ( 3 ): 718 - 729 .

TANG Y J J , MARTIN H G , DEUTSCHBAUER A , et al . Invariability of central metabolic flux distribution in Shewanella oneidensis MR-1 under environmental or genetic perturbations [J ] . Biotechnology Progress , 2009 , 25 ( 5 ): 1254 - 1259 .

TANG Y J J , MARTIN H G , DEHAL P S , et al . Metabolic flux analysis of Shewanella spp. reveals evolutionary robustness in central carbon metabolism [J ] . Biotechnology and Bioengineering , 2009 , 102 ( 4 ): 1161 - 1169 .

TANG Y J J , MEADOWS A L , KIRBY J , et al . Anaerobic central metabolic pathways in Shewanella oneidensis MR-1 reinterpreted in the light of isotopic metabolite labeling [J ] . Journal of Bacteriology , 2007 , 189 ( 3 ): 894 - 901 .

STOOKEY L L . Ferrozine— a new spectrophotometric reagent for iron [J ] . Analytical Chemistry , 1970 , 42 ( 7 ): 779 - 781 .

ALEF K , KLEINER D . Rapid and sensitive determination of microbial activity in soils and in soil aggregates by dimethylsulfoxide reduction [J ] . Biology and Fertility of Soils , 1989 , 8 ( 4 ): 349 - 355 .

MASUKO T , MINAMI A , IWASAKI N , et al . Carbohydrate analysis by a phenol-sulfuric acid method in microplate format [J ] . Analytical Biochemistry , 2005 , 339 ( 1 ): 69 - 72 .

ZAMBONI N , FENDT S M , RÜHL M , et al . 13 C-based metabolic flux analysis [J ] . Nature Protocols , 2009 , 4 ( 6 ): 878 - 892 .

PINCHUK G E , HILL E A , GEYDEBREKHT O V , et al . Constraint-based model of Shewanella oneidensis MR-1 metabolism: a tool for data analysis and hypothesis generation [J ] . PLoS Computational Biology , 2010 , 6 ( 6 ): e1000822 .

NANCHEN A , FUHRER T , SAUER U . Determination of metabolic flux ratios from 13 C-experiments and gas chromatography-mass spectrometry data [M/OL ] // Methods in molecular biology: metabolomics . Totowa, NJ, USA: Humana Press. 2007 , 358 : 177 - 197 [2022-09-01] . https://link.springer.com/protocol/10.1007/978-1-59745-244-1_11 https://link.springer.com/protocol/10.1007/978-1-59745-244-1_11 .

AYYASAMY P M , CHUN S H , LEE S H . Desorption and dissolution of heavy metals from contaminated soil using Shewanella sp. (HN-41) amended with various carbon sources and synthetic soil organic matters [J ] . Journal of Hazardous Materials , 2009 , 161 ( 2/3 ): 1095 - 1102 .

ONG W K , VU T T , LOVENDAHL K N , et al . Comparisons of Shewanella strains based on genome annotations, modeli ng, and experiments [J ] . BMC Systems Biology , 2014 , 8 : 31 .

CRUZ-GARCÍA C , MURRAY A E , KLAPPENBACH J A , et al . Respiratory nitrate ammonification by Shewanella oneidensis MR-1 [J ] . Journal of Bacteriology , 2007 , 189 ( 2 ): 656 - 662 .

INOHANA Y , KATSUYA S , KOGA R , et al . Shewanella algae relatives capable of generating electricity from acetate contribute to coastal-sediment microbial fuel cells treating complex organic matter [J ] . Microbes and Environments , 2020 , 35 ( 2 ): ME19161 .

REWATKAR P , GOEL S . Shewanella putrefaciens powered microfluidic microbial fuel cell with printed circuit board electrodes and soft-lithographic microchannel [J ] . Chemosphere , 2022 , 286 : 131855 .

DAI H N , DUONG NGUYEN T A , MY LE L P , et al . Power generation of Shewanella oneidensis MR-1 microbial fuel cells in bamboo fermentation effluent [J ] . International Journal of Hydrogen Energy , 2021 , 46 ( 31 ): 16612 - 16621 .

CHAUDHARY S , BANERJEE D K . Metal phase association of chromium in contaminated soils from an industrial area in Delhi [J ] . Chemical Speciation & Bioavailability , 2004 , 16 ( 4 ): 145 - 151 .

FREDRICKSON J K , ROMINE M F , BELIAEV A S , et al . Towards environmental systems biology of Shewanella [J ] . Nature Reviews Microbiology , 2008 , 6 ( 8 ): 592 - 603 .

LEMAIRE O N , MÉJEAN V , IOBBI-NIVOL C . The Shewanella genus: ubiquitous organisms sustaining and preserving aquatic ecosystems [J ] . FEMS Microbiology Reviews , 2020 , 44 ( 2 ): 155 - 170 .

FAN G , DUNDAS C M , GRAHAM A J , et al . Shewanella oneidensis as a living electrode for controlled radical polymerization [J ] . Proceedings of the National Academy of Sciences of the United States of America , 2018 , 115 ( 18 ): 4559 - 4564 .

Views

下载量

CSCD

Alert me when the article has been cited

提交

Tools

Publicity Resources

No data

Related Author

No data

Related Institution

No data

⁰

Metabolic flux analysis of Shewanella sp. MR-4 with different terminal electron receptors

DOI：10.12211/2096-8280.2022-052

摘要

Abstract

关键词

Keywords

references