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Comparative Transcriptome Analysis Reveals the Molecular Mechanisms of Acetic Acid Reduction by Adding NaHSO3 in Actinobacillus succinogenes GXAS137 Cover

Comparative Transcriptome Analysis Reveals the Molecular Mechanisms of Acetic Acid Reduction by Adding NaHSO3 in Actinobacillus succinogenes GXAS137

Open Access
|Dec 2023

References

  1. Ahn JH, Jang YS, Lee SY. Production of succinic acid by metabolically engineered microorganisms. Curr Opin Biotechnol. 2016 Dec;42:54–66. https://doi.org/10.1016/j.copbio.2016.02.034
  2. Almqvist H, Pateraki C, Alexandri M, Koutinas A, Lidén G. Succinic acid production by Actinobacillus succinogenes from batch fermentation of mixed sugars. J Ind Microbiol Biotechnol. 2016 Aug;43(8):1117–1130. https://doi.org/10.1007/s10295-016-1787-x
  3. Arocho A, Chen B, Ladanyi M, Pan Q. Validation of the 2–ΔΔCt calculation as an alternate method of data analysis for quantitative PCR of BCR-ABL P210 transcripts. Diagn Mol Pathol. 2006 Mar;15(1):56–61. https://doi.org/10.1097/00019606-200603000-00009
  4. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000 May;25(1):25–29. https://doi.org/10.1038/75556
  5. Bradfield MFA, Nicol W. Continuous succinic acid production from xylose by Actinobacillus succinogenes. Bioprocess Biosyst Eng. 2016 Feb;39(2):233–244. https://doi.org/10.1007/s00449-015-1507-3
  6. Brzostek A, Gąsior F, Lach J, Żukowska L, Lechowicz E, Korycka-Machała M, Strapagiel D, Dziadek J. ATP-dependent ligases and AEP primases affect the profile and frequency of mutations in Mycobacteria under oxidative stress. Genes. 2021 Apr;12(4):547. https://doi.org/10.3390/genes12040547
  7. Bu D, Luo H, Huo P, Wang Z, Zhang S, He Z, Wu Y, Zhao L, Liu J, Guo J, et al. KOBAS-i: intelligent prioritization and exploratory visualization of biological functions for gene enrichment analysis. Nucleic Acids Res. 2021 Jul;49(W1):W317–W325. https://doi.org/10.1093/nar/gkab447
  8. Chang IS, Kim BH, Shin PK. Use of sulfite and hydrogen peroxide to control bacterial contamination in ethanol fermentation. Appl Environ Microbiol. 1997 Jan;63(1):1–6. https://doi.org/10.1128/aem.63.1.1-6.1997
  9. Chen S, Zhou Y, Chen Y, Gu J. Fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018 Sep 1;34(17):i884–i890. https://doi.org/10.1093/bioinformatics/bty560
  10. Chen S. Ultrafast one-pass FASTQ data preprocessing, quality control, and deduplication using fastp. iMeta.2023;2(2):e107. https://doi.org/10.1002/imt2.107
  11. Chiang YY, Nagarajan D, Lo YC, Chen CY, Ng IS, Chang CH, Lee DJ, Chang JS. Succinic acid fermentation with immobilized Actinobacillus succinogenes using hydrolysate of carbohydrate-rich microalgal biomass. Bioresour Technol. 2021 Dec;342:126014. https://doi.org/10.1016/j.biortech.2021.126014
  12. Christensen QH, Cronan JE. Lipoic acid synthesis: A new family of octanoyltransferases generally annotated as lipoate protein ligases. Biochemistry. 2010 Nov;49(46):10024–10036. https://doi.org/10.1021/bi101215f
  13. Danson MJ, Hale G, Perham RN. The role of lipoic acid residues in the pyruvate dehydrogenase multienzyme complex of Escherichia coli. Bio-chem J. 1981 Dec;199(3):505–511. https://doi.org/10.1042/bj1990505
  14. Dessie W, Xin F, Zhang W, Jiang Y, Wu H, Ma J, Jiang M. Opportunities, challenges, and future perspectives of succinic acid production by Actinobacillus succinogenes. Appl Microbiol Biotechnol. 2018 Dec;102(23):9893–9910. https://doi.org/10.1007/s00253-018-9379-5
  15. Eikmanns BJ, Blombach B. The pyruvate dehydrogenase complex of Corynebacterium glutamicum: An attractive target for metabolic engineering. J Biotechnol. 2014 Dec 20;192:339–345. https://doi.org/10.1016/j.jbiotec.2013.12.019
  16. Ferone M, Raganati F, Olivieri G, Marzocchella A. Bioreactors for succinic acid production processes. Crit Rev Biotechnol. 2019 May; 39(4):571–586. https://doi.org/10.1080/07388551.2019.1592105
  17. Freeman GG, Donald GMS. Fermentation processes leading to glycerol. I. The influence of certain variables on glycerol formation in the presence of sulfites. Appl Microbiol. 1957 Jul;5(4):197–210. https://doi.org/10.1128/am.5.4.197-210.1957
  18. Gene Ontology Consortium; Aleksander SA, Balhoff J, Carbon S, Cherry JM, Drabkin HJ, Ebert D, Feuermann M, Gaudet P, Harris NL, Hill DP, et al. The Gene Ontology knowledgebase in 2023. Genetics. 2023 May 4;224(1):iyad031. https://doi.org/10.1093/genetics/iyad031
  19. Guarnieri MT, Chou YC, Salvachúa D, Mohagheghi A, St John PC, Peterson DJ, Bomble YJ, Beckham GT. Metabolic engineering of Actinobacillus succinogenes provides insights into succinic acid biosynthesis. Appl Environ Microbiol. 2017 Aug;83(17):e00996–e17. https://doi.org/10.1128/AEM.00996-17
  20. Hernández-Plaza A, Szklarczyk D, Botas J, Cantalapiedra CP, Giner-Lamia J, Mende DR, Kirsch R, Rattei T, Letunic I, Jensen LJ, et al. eggNOG 6.0: enabling comparative genomics across 12 535 organisms. Nucleic Acids Res. 2023 Jan 6;51(D1):D389–D394. https://doi.org/10.1093/nar/gkac1022
  21. Irwin SV, Fisher P, Graham E, Malek A, Robidoux A. Sulfites inhibit the growth of four species of beneficial gut bacteria at concentrations regarded as safe for food. PLoS One. 2017 Oct;12(10): e0186629. https://doi.org/10.1371/journal.pone.0186629
  22. Isogai S, Takagi H. Enhancement of lysine biosynthesis confers high-temperature stress tolerance to Escherichia coli cells. Appl Microbiol Biotechnol. 2021 Sep;105(18):6899–6908. https://doi.org/10.1007/s00253-021-11519-0
  23. Jansen MLA, van Gulik WM. Towards large scale fermentative production of succinic acid. Curr Opin Biotechnol. 2014 Dec;30:190–197. https://doi.org/10.1016/j.copbio.2014.07.003
  24. Joshi RV, Schindler BD, McPherson NR, Tiwari K, Vieille C. Development of a markerless knockout method for Actinobacillus succinogenes. Appl Environ Microbiol. 2014 May;80(10):3053–3061. https://doi.org/10.1128/AEM.00492-14
  25. Kanehisa M, Furumichi M, Sato Y, Kawashima M, Ishiguro-Watanabe M. KEGG for taxonomy-based analysis of pathways and genomes. Nucleic Acids Res. 2023 Jan;51(D1):D587-D592 https://doi.org/10.1093/nar/gkac963
  26. Kanehisa M, Goto S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000 Jan;28(1):27–30. https://doi.org/10.1093/nar/28.1.27
  27. Kanehisa M. Toward understanding the origin and evolution of cellular organisms. Protein Sci. 2019 Nov;28(11):1947–1951. https://doi.org/10.1002/pro.3715
  28. Kertesz MA. Bacterial transporters for sulfate and organosulfur compounds. Res Microbiol. 2001 Apr;152(3–4):279–290. https://doi.org/10.1016/S0923-2508(01)01199-8
  29. Kim SN, Cho YB, Park JW, Kim OB. Adaptation of Methanosarcina barkeri 227 as acetate scavenger for succinate fermentation by Actinobacillus succinogenes. Appl Microbiol Biotechnol. 2020 May; 104(10):4483–4492. https://doi.org/10.1007/s00253-020-10494-2
  30. Klopfenstein DV, Zhang L, Pedersen BS, Ramírez F, Warwick Vesztrocy A, Naldi A, Mungall CJ, Yunes JM, Botvinnik O, Weigel M, et al. GOATOOLS: A Python library for Gene Ontology analyses. Sci Rep. 2018 Jul;8(1):10872. https://doi.org/10.1038/s41598-018-28948-z
  31. Leonardo MR, Cunningham PR, Clark DP. Anaerobic regulation of the adhE gene, encoding the fermentative alcohol dehydrogenase of Escherichia coli. J Bacteriol. 1993 Feb;175(3):870–878. https://doi.org/10.1128/jb.175.3.870-878.1993
  32. Li S, Ma J, Li S, Chen F, Song C, Zhang H, Jiang M, Shen N. Comparative transcriptome analysis unravels the response mechanisms of Fusarium oxysporum f.sp. cubense to a biocontrol agent, Pseudomonas aeruginosa Gxun-2. Int J Mol Sci. 2022 Dec;23(23):15432. https://doi.org/10.3390/ijms232315432
  33. Li Z, Lou Y, Ding J, Liu BF, Xie GJ, Ren NQ, Xing D. Metabolic regulation of ethanol-type fermentation of anaerobic acidogenesis at different pH based on transcriptome analysis of Ethanoligenens harbinense. Biotechnol Biofuels. 2020 Dec;13(1):101. https://doi.org/10.1186/s13068-020-01740-w
  34. Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014; 15(12):550. https://doi.org/10.1186/s13059-014-0550-8
  35. Lu J, Holmgren A. The thioredoxin antioxidant system. Free Radic Biol Med. 2014 Jan;66:75–87. https://doi.org/10.1016/j.freeradbiomed.2013.07.036
  36. Mara P, Fragiadakis GS, Gkountromichos F, Alexandraki D. The pleiotropic effects of the glutamate dehydrogenase (GDH) pathway in Saccharomyces cerevisiae. Microb Cell Fact. 2018 Dec;17(1):170. https://doi.org/10.1186/s12934-018-1018-4
  37. Mayr JA, Feichtinger RG, Tort F, Ribes A, Sperl W. Lipoic acid biosynthesis defects. J Inherit Metab Dis. 2014 Jul;37(4):553–563. https://doi.org/10.1007/s10545-014-9705-8
  38. McKinlay JB, Shachar-Hill Y, Zeikus JG, Vieille C. Determining Actinobacillus succinogenes metabolic pathways and fluxes by NMR and GC-MS analyses of 13C-labeled metabolic product isotopomers. Metab Eng. 2007 Mar;9(2):177–192. https://doi.org/10.1016/j.ymben.2006.10.006
  39. McKinlay JB, Vieille C. 13C-metabolic flux analysis of Actinobacillus succinogenes fermentative metabolism at different NaHCO3 and H2 concentrations. Metab Eng. 2008 Jan;10(1):55–68. https://doi.org/10.1016/j.ymben.2007.08.004
  40. McKinlay JB, Zeikus JG, Vieille C. Insights into Actinobacillus succinogenes fermentative metabolism in a chemically defined growth medium. Appl Environ Microbiol. 2005 Nov;71(11):6651–6656. https://doi.org/10.1128/AEM.71.11.6651-6656.2005
  41. Mo W, Wang M, Zhan R, Yu Y, He Y, Lu H. Kluyveromyces marxianus developing ethanol tolerance during adaptive evolution with significant improvements of multiple pathways. Biotechnol Biofuels 2019 Dec;12(1):63. https://doi.org/10.1186/s13068-019-1393-z
  42. Mohd Kamal K, Mahamad Maifiah MH, Zhu Y, Abdul Rahim N, Hashim YZH, Abdullah Sani MS. Isotopic tracer for absolute quantification of metabolites of the pentose phosphate pathway in bacteria. Metabolites. 2022 Nov;12(11):1085. https://doi.org/10.3390/metabo12111085
  43. Murphy GE, Jensen GJ. Electron cryotomography of the E. coli pyruvate and 2-oxoglutarate dehydrogenase complexes. Structure. 2005 Dec;13(12):1765–1773. https://doi.org/10.1016/j.str.2005.08.016
  44. Nag A, St John PCS, Crowley MF, Bomble YJ. Prediction of reaction knockouts to maximize succinate production by Actinobacillus succinogenes. PLoS One. 2018;13(1):e0189144. https://doi.org/10.1371/journal.pone.0189144
  45. Omwene PI, Yağcioğlu M, Öcal-Sarihan ZB, Ertan F, Keris-Sen ÜD, Karagunduz A, Keskinler B. Batch fermentation of succinic acid from cheese whey by Actinobacillus succinogenes under variant medium composition. 3 Biotech. 2021 Aug;11(8):389. https://doi.org/10.1007/s13205-021-02939-w
  46. Patel MS, Nemeria NS, Furey W, Jordan F. The pyruvate dehydrogenase complexes: Structure-based function and regulation. J Biol Chem. 2014 Jun;289(24):16615–16623. https://doi.org/10.1074/jbc.R114.563148
  47. Pateraki C, Skliros D, Flemetakis E, Koutinas A. Succinic acid production from pulp and paper industry waste: A transcriptomic approach. J Biotechnol. 2021 Jan;325:250–260. https://doi.org/10.1016/j.jbiotec.2020.10.015
  48. Pavlova SI, Jin L, Gasparovich SR, Tao L. Multiple alcohol dehydrogenases but no functional acetaldehyde dehydrogenase causing excessive acetaldehyde production from ethanol by oral streptococci. Microbiology. 2013 Jul;159(Pt_7):1437–1446. https://doi.org/10.1099/mic.0.066258-0
  49. Shen N, Li S, Li S, Wang Y, Zhang H, Jiang M. Reduced acetic acid formation using NaHSO3 as a steering agent by Actinobacillus succinogenes GXAS137. J Biosci Bioeng. 2023 Mar;135(3):203–209 https://doi.org/10.1016/j.jbiosc.2022.12.007
  50. Shen N, Wang Q, Qin Y, Zhu J, Zhu Q, Mi H, Wei Y, Huang R. Optimization of succinic acid production from cane molasses by Actinobacillus succinogenes GXAS137 using response surface methodology (RSM). Food Sci Biotechnol. 2014 Dec;23(6):1911–1919. https://doi.org/10.1007/s10068-014-0261-7
  51. Shen N, Wang Q, Zhu J, Qin Y, Liao S, Li Y, Zhu Q, Jin Y, Du L, Huang R. Succinic acid production from duckweed (Landoltia punctata) hydrolysate by batch fermentation of Actinobacillus succinogenes GXAS137. Bioresour Technol. 2016 Jul;211:307–312. https://doi.org/10.1016/j.biortech.2016.03.036
  52. Shen N, Zhang H, Qin Y, Wang Q, Zhu J, Li Y, Jiang MG, Huang R Efficient production of succinic acid from duckweed (Landolti punctata) hydrolysate by Actinobacillus succinogenes GXAS137 Bioresour Technol. 2018 Feb;250:35–42. https://doi.org/10.1016/j.biortech.2017.09.208
  53. Sirover MA. Structural analysis of glyceraldehyde-3-phosphate dehydrogenase functional diversity. Int J Biochem Cell Biol. 2014 Dec;57:20–26. https://doi.org/10.1016/j.biocel.2014.09.026
  54. Škerlová J, Berndtsson J, Nolte H, Ott M, Stenmark P. Structure of the native pyruvate dehydrogenase complex reveals the mechanism of substrate insertion. Nat Commun. 2021 Sep;12(1):5277. https://doi.org/10.1038/s41467-021-25570-y
  55. Solmonson A, DeBerardinis RJ. Lipoic acid metabolism and mitochondrial redox regulation. J Biol Chem. 2018 May;293(20):7522–7530. https://doi.org/10.1074/jbc.TM117.000259
  56. Taherzadeh MJ, Adler L, Lidén G. Strategies for enhancing fermentative production of glycerol – A review. Enzyme Microb Technol. 2002 Jul;31(1–2):53–66. https://doi.org/10.1016/S0141-0229(02)00069-8
  57. Taherzadeh MJ, Lidén G, Gustafsson L, Niklasson C. The effects of pantothenate deficiency and acetate addition on anaerobic batch fermentation of glucose by Saccharomyces cerevisiae. Appl Microbiol Biotechnol. 1996 Sep;46(2):176–182. https://doi.org/10.1007/s002530050801
  58. Tan JP, Luthfi AAI, Manaf SFA, Wu TY, Jahim JM. Incorporation of CO2 during the production of succinic acid from sustainable oil palm frond juice. J CO2 Util. 2018;26:595–601. https://doi.org/10.1016/j.jcou.2018.06.006
  59. Tong LL, Wang Y, Du YH, Yuan L, Liu MZ, Mu XY, Chen ZL, Zhang YD, He SJ, Li XJ, et al. Transcriptomic analysis of morphology regulatory mechanisms of microparticles to Paraisaria dubia in submerged fermentation. Appl Biochem Biotechnol. 2022 Oct; 194(10):4333–4347. https://doi.org/10.1007/s12010-022-03820-z
  60. Tsuji K, Yoon KS, Ogo S. Biochemical characterization of a bifunctional acetaldehyde-alcohol dehydrogenase purified from a facultative anaerobic bacterium Citrobacter sp. S-77. J Biosci Bioeng. 2016 Mar;121(3):253–258. https://doi.org/10.1016/j.jbiosc.2015.06.019
  61. Valadi H, Valadi Å, Ansell R, Gustafsson L, Adler L, Norbeck J, Blomberg A. NADH-reductive stress in Saccharomyces cerevisiae induces the expression of the minor isoform of glyceraldehyde-3-phosphate dehydrogenase (TDH1). Curr Genet. 2004 Feb;45(2): 90–95. https://doi.org/10.1007/s00294-003-0469-1
  62. Wang C, Ren X, Yu C, Wang J, Wang L, Zhuge X, Liu X. Physiological and transcriptional responses of Streptomyces albulus to acid stress in the biosynthesis of ε-poly-L-lysine. Front Microbiol. 2020 Jun;11:1379. https://doi.org/10.3389/fmicb.2020.01379
  63. Wang L, Hong H, Zhang C, Huang Z, Guo H. Transcriptome analysis of Komagataeibacter europaeus CGMCC 20445 responses to different acidity levels during acetic acid fermentation. Pol J Microbiol. 2021 Sep;70(3):305–313. https://doi.org/10.33073/pjm-2021-027
  64. Zhang H, Shen N, Qin Y, Zhu J, Li Y, Wu J, Jiang MG. Complete genome sequence of Actinobacillus succinogenes GXAS137, a highly efficient producer of succinic acid. Genome Announc. 2018 Feb; 6(8):e01562–17. https://doi.org/10.1128/genomeA.01562-17
  65. Zhang X, Ruan Y, Liu W, Chen Q, Gu L, Guo A. Transcriptome analysis of gene expression in Dermacoccus abyssi HZAU 226 under lysozyme stress. Microorganisms. 2020 May;8(5):707. https://doi.org/10.3390/microorganisms8050707
  66. Zhuang W, Balasubramanian N, Wang L, Wang Q, McDermott TR, Copié V, Wang G, Bothner B. Arsenate-induced changes in bacterial metabolite and lipid pools during phosphate stress. Appl Environ Microbiol. 2021 Feb;87(6):e02261–20. https://doi.org/10.1128/AEM.02261-20
DOI: https://doi.org/10.33073/pjm-2023-036 | Journal eISSN: 2544-4646 | Journal ISSN: 1733-1331
Language: English
Page range: 399 - 411
Submitted on: Jul 23, 2023
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Accepted on: Aug 28, 2023
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Published on: Dec 16, 2023
In partnership with: Paradigm Publishing Services
Publication frequency: 4 issues per year

© 2023 Shiyong Li, Chaodong Song, Hongyan Zhang, Yan Qin, Mingguo Jiang, Naikun Shen, published by Polish Society of Microbiologists
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License.