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Transcriptomic responses of haloalkalitolerant bacterium Egicoccus halophilus EGI 80432T to highly alkaline stress

Abstract

The haloalkalitolerant bacterium Egicoccus halophilus EGI 80432T exhibits high adaptability to saline–alkaline environment. The salinity adaptation mechanism of E. halophilus EGI 80432T was fully understood based on transcriptome analyses and physiological responses; however, the alkaline response mechanism has not yet been investigated. Here, we investigated the alkaline response mechanism of E. halophilus EGI 80432T by a transcriptomic comparison. In this study, the genes involved in the glycolysis, TCA cycle, starch, and trehalose metabolism for energy production and storage, were up-regulated under highly alkaline condition. Furthermore, genes responsible for the production of acidic and neutral metabolites, i.e., acetate, pyruvate, formate, glutamate, threonine, and ectoine, showed increased expression under highly alkaline condition, compared with the control pH condition. In contrast, the opposite results were observed in proton capture or retention gene expression profiles, i.e., cation/proton antiporters and ATP synthases. The above results revealed that E. halophilus EGI 80432T likely tended to adopt an “acidic metabolites production” strategy in response to a highly alkaline condition. These findings would pave the way for further studies in the saline–alkaline adaptation mechanisms of E. halophilus EGI 80432T, and hopefully provide a new insight into the foundational theory and application in ecological restoration with saline–alkaline strains.

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Abbreviations

CPA:

Cation/proton antiporter

NCBI:

National Center for Biotechnology Information

SRA:

Sequence Read Archive

SNP:

Single-nucleotide polymorphisms

SD:

Shine–Dalgarno

DEG:

Differentially expressed gene

FPKM:

Fragments per kilobase of transcript sequence per millions of base pairs

GO:

Gene Ontology

KEGG:

Kyoto Encyclopedia of Genes and Genomes

qPCR:

Quantitative real-time PCR

cDNA:

Complementary DNA

TCA:

Tricarboxylic acid

References

  1. Anders S, Huber W (2013) Differential expression of RNA-Seq data at the gene level-the DESeq package. European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.359.7464. Accessed 24 Feb 2013

  2. Banciu HL, Sorokin DY (2013) Adaptation in haloalkaliphiles and natronophilic bacteria. In: Seckbach J, Oren A, Stanlotter H (eds) Polyextremophiles: life under multiple forms of stress. Cellular origin, life in extreme habitats and astrobiology 27. Springer, Dordrecht, pp 121–178. https://doi.org/10.1007/978-94-007-6488-0_5

    Chapter  Google Scholar 

  3. Busch A, Richter AS, Backofen R (2008) IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions. Bioinformatics 24(24):2849–2856. https://doi.org/10.1093/bioinformatics/btn544

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  4. Chen DD, Tian Y, Jiao JY, Zhang XT, Zhang YG, Dong ZY, Xiong MJ, Xiao M, Shu WS, Li WJ (2020) Comparative genomics analysis of Nitriliruptoria reveals the genomic differences and salt adaptation strategies. Extremophiles 24:249–264. https://doi.org/10.1007/s00792-019-01150-3

    CAS  Article  PubMed  Google Scholar 

  5. Chen DD, Fang BZ, Manzoor A, Liu YH, Li L, Mohamad OAA, Shu WS, Li WJ (2021) Revealing the salinity adaptation mechanism in halotolerant bacterium Egicoccus halophilus EGI 80432T by physiological analysis and comparative transcriptomics. Appl Microbiol Biotechnol 105:2497–2511. https://doi.org/10.1007/s00253-021-11190-5

    CAS  Article  PubMed  Google Scholar 

  6. Cheng B, Meng YW, Cui TB, Li CF, Tao F, Yin HJ, Yang CY, Xu P (2016) Alkaline response of a halotolerant alkaliphilic Halomonas strain and functional diversity of its Na+(K+)/H+ antiporters. J Biol Chem 291(50):26056–26065. https://doi.org/10.1074/jbc.M116.751016

    CAS  Article  PubMed  Google Scholar 

  7. Chew J, Zilm PS, Fuss JM, Gully NJ (2012) A proteomic investigation of Fusobacterium nucleatum alkaline-induced biofilms. BMC Microbiol 12:189. https://doi.org/10.1186/1471-2180/12/189

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  8. Guo J, Ma ZP, Gao JS, Zhao JH, Wei L, Liu J, Xu N (2019) Recent advances of pH homeostasis mechanisms in Corynebacterium glutamicum. World J Microbiol Biotechnol 35:192. https://doi.org/10.1007/s11274-019-2770-2

    CAS  Article  PubMed  Google Scholar 

  9. Hicks DB, Krulwich TA (1995) The respiratory chain of alkaliphilic bacteria. Biochim Biophy Acta 1229:303–314. https://doi.org/10.1016/0005-2728(95)00024-D

    Article  Google Scholar 

  10. Hicks DB, Liu J, Fujisawa M, Krulwich TA (2010) F1F0-ATP synthases of alkaliphilic bacteria: Lessons from their adaptations. Biochim Biophys Acta, Bioenerg 1797:1362–1377. https://doi.org/10.1016/j.bbabio.2010.02.028

    CAS  Article  Google Scholar 

  11. Hofacker IL, Stadler PF (2006) Memory efficient folding algorithms for circular RNA secondary structures. Bioinformatics 22(10):1172–1176. https://doi.org/10.1093/bioinformatics/btl023

    CAS  Article  PubMed  Google Scholar 

  12. Ito M, Morino M, Krulwich TA (2017) Mrp antiporters have important roles in diverse bacteria and archaea. Front Microbiol 8:2325. https://doi.org/10.3389/fmicb.2017.02325

    Article  PubMed  PubMed Central  Google Scholar 

  13. Jiang J, Sun YF, Tang X, He CN, Shao YL, Tang YJ, Zhou WW (2018) Alkaline pH shock enhanced production of validamycin A in fermentation of Streptomyces hygroscopicus. Bioresour Technol 249:234–240. https://doi.org/10.1016/j.biortech.2017.10.012

    CAS  Article  PubMed  Google Scholar 

  14. Kingsford CL, Ayanbule K, Salzberg SL (2007) Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake. Genome Biol 8:R22. https://doi.org/10.1186/gb-2007-8-2-r22

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  15. Krulwich TA, Hicks DB, Ito M (2009) Cation/proton antiporter complements of bacteria: why so large and diverse? Mol Microbiol 74(2):257–260. https://doi.org/10.1111/j.1365-2958.2009.06842.x

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  16. Krulwich TA, Sachs G, Padan E (2011) Molecular aspects of bacterial pH sensing and homeostasis. Nat Rev Microbiol 9(5):330–343. https://doi.org/10.1038/nrmicro2549

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  17. Kurahashi M, Fukunaga Y, Sakiyama Y, Harayama S, Yokota A (2010) Euzebya tangerina gen. nov., sp. nov., a deeply branching marine actinobacterium isolated from the sea cucumber Holothuria edulis, and proposal of Euzebyaceae fam. nov., Euzebyales ord. nov. and Nitriliruptoridae subclassis nov. Int J Syst Evol Microbiol 60:2314–2319. https://doi.org/10.1099/ijs.0.016543-0

    CAS  Article  PubMed  Google Scholar 

  18. Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9(4):357–359. https://doi.org/10.1038/nmeth.1923

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  19. Lewis RJ, Krulwich TA, Reynafarje B, Lehningere AL (1983) Respiration-dependent proton translocation in alkalophilic Bacillus firmus RAB and its non-alkalophilic mutant Derivative*. J Biol Chem 258:2109–2111. https://doi.org/10.1016/S0021-9258(18)32891-6

    CAS  Article  PubMed  Google Scholar 

  20. Liang MH, Jiang JG, Wang L, Zhu JH (2020) Transcriptomic insights into the heat stress response of Dunaliella bardawil. Enzyme Microb Technol 132:109436. https://doi.org/10.1016/j.enzmictec.2019.109436

    CAS  Article  PubMed  Google Scholar 

  21. Liu XM, Wu XL, Gao W, Qu JB, Chen Q, Huang CY, Zhang JX (2019) Protective roles of trehalose in Pleurotus pulmonarius during heat stress response. J Integr Agric 18(2):428–437. https://doi.org/10.1016/S2095-3119(18)62010-6

    CAS  Article  Google Scholar 

  22. Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real time quantitative PCR and the 2-ΔΔCT method. Methods 25(4):402–408. https://doi.org/10.1006/meth.2001.1262

    CAS  Article  Google Scholar 

  23. Mamo G (2020) Challenges and adaptations of life in alkaline habitats. Adv Biochem Eng Biotechnol 172:85–134. https://doi.org/10.1007/10_2019_97

    CAS  Article  PubMed  Google Scholar 

  24. Mao XZ, Cai T, Olyarchuk JG, Wei LP (2005) Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary. Bioinformatics 21(19):3787–3793. https://doi.org/10.1093/bioinformatics/bti430

    CAS  Article  PubMed  Google Scholar 

  25. Matsuno T, Yumoto I (2015) Bioenergetics and the role of soluble cytochromes c for alkaline adaptation in gram-negative alkaliphilic Pseudomonas. BioMed Res Int. https://doi.org/10.1155/2015/847945

    Article  PubMed  PubMed Central  Google Scholar 

  26. McClure R, Balasubramanian D, Sun Y, Bobrovskyy M, Sumby P, Genco CA, Vanderpool CK, Tjaden B (2013) Computational analysis of bacterial RNA-Seq data. Nucleic Acids Res 41:e140. https://doi.org/10.1093/nar/gkt444

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  27. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA (2020) The genome analysis toolkit: a mapreduce framework for analyzing next-generation DNA sequencing data. Genome Res 20:1297–1303. https://doi.org/10.1101/gr.107524.110

    CAS  Article  Google Scholar 

  28. Papa S, Lorusso M, Capitanio N (1994) Mechanistic and phenomenological features of proton pumps in the respiratory chain of mitochondria. J Bioenerg Biomembr 26:609–618. https://doi.org/10.1007/BF00831535

    CAS  Article  PubMed  Google Scholar 

  29. Raymond-Bouchard I, Whyte LG (2017) From transcriptomes to metatranscriptomes: cold adaptation and active metabolisms of psychrophiles from cold environments. In: Margesin R (ed) Psychrophiles: from biodiversity to biotechnology. Springer, New York, pp 437–445. https://doi.org/10.1007/978-3-319-57057-0_18

    Chapter  Google Scholar 

  30. Reina-Bueno M, Argandoña M, Nieto JJ, Hidalgo-García A, Iglesias-Guerra F, Delgado MJ, Vargas C (2012) Role of trehalose in heat and desiccation tolerance in the soil bacterium Rhizobium etli. BMC Microbiol 12:207. https://doi.org/10.1186/1471-2180-12-207

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  31. Shu BS, Wu YX, Qu MQ, Pu XH, Wu ZZ, Lin JT (2020) Comparative transcriptomic analyses revealed genes and pathways responsive to heat stress in Diaphorina citri. Gene 727:144246. https://doi.org/10.1016/j.gene.2019.144246

    CAS  Article  PubMed  Google Scholar 

  32. Slonczewski JL, Fujisawa M, Dopson M, Krulwich TA (2009) Cytoplasmic pH measurement and homeostasis in bacteria and archaea. Adv Microb Physiol 55:1–317. https://doi.org/10.1016/S0065-2911(09)05501-5

    CAS  Article  PubMed  Google Scholar 

  33. Songserm P, Srimongkol P, Thitiprasert S, Tanasupawat S, Cheirsilp B, Assabumrungrat S, Karnchanatat A, Thongchul N (2020) Differential gene expression analysis of Aspergillus terreus reveals metabolic response and transcription suppression under dissolved oxygen and pH stress. J Evol Biochem Physiol 56(6):577–586. https://doi.org/10.1134/S0022093020060101

    CAS  Article  Google Scholar 

  34. Sorokin DY, Pelt SV, Tourova TP, Evtushenko LI (2009) Nitriliruptor alkaliphilus gen. nov., sp. nov., a deeplineage haloalkaliphilic actinobacterium from soda lakes capable of growth on aliphatic nitriles, and proposal of Nitriliruptoraceae fam. nov. and Nitriliruptorales ord. nov. Int J Syst Evol Microbiol 59:248–253. https://doi.org/10.1099/ijs.0.002204-0

    CAS  Article  PubMed  Google Scholar 

  35. Stolyar S, He Q, He Z, Yang Z, Borglin SE, Joyner D, Huang K, Alm E, Hazen TC, Zhou J, Wall J, Arkin AP, Stahl DA (2007) Response of Desulfovibrio vulgaris to alkaline stress. J Bacteriol 189(24):8944–8952. https://doi.org/10.1128/JB.00284-07

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  36. Suzek BE, Ermolaeva MD, Schreiber M, Salzberg SL (2001) A probabilistic method for identifying start codons in bacterial genomes. Bioinformatics 17:1123–1130. https://doi.org/10.1093/bioinformatics/17.12.1123

    CAS  Article  PubMed  Google Scholar 

  37. Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, Baren MJ, Salzberg SL, Wold BJ, Pachter L (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 28:511–515. https://doi.org/10.1038/nbt.1621

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  38. Wang DK, Hao ZQ, Zhao JS, Jin Y, Huang J, Zhou RQ, Wu CD (2019) Comparative physiological and transcriptomic analyses reveal salt tolerance mechanisms of Zygosaccharomyces rouxii. Process Biochem 82:59–67. https://doi.org/10.1016/j.procbio.2019.04.009

    CAS  Article  Google Scholar 

  39. Xu L, Sun C, Huang MM, Wu YH, Yuan CQ, Dai WH, Ye KX, Han BN, Xu XW (2019) Complete genome sequence of Euzebya sp. DY32-46, a marine Actinobacteria isolated from the Pacific Ocean. Mar Genomics 44:65–69. https://doi.org/10.1016/j.margen.2018.09.008

    Article  Google Scholar 

  40. Yin Q, Zhang L, Song ZM, Wu YH, Hu ZL, Zhang XH, Zhang Y, Yu M, Xu Y (2018) Euzebya rosea sp. nov., a rare actinobacterium isolated from the East China Sea and analysis of two genome sequences in the genus Euzebya. Int J Syst Evol Microbiol 68:2900–2905. https://doi.org/10.1099/ijsem.0.002917

    CAS  Article  PubMed  Google Scholar 

  41. Young MD, Wakefield MJ, Smyth GK, Oshlack A (2010) Gene ontology analysis for RNA-seq: accounting for selection bias. Genome Biol 11:R14. https://doi.org/10.1186/gb-2010-11-2-r14

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  42. Zhang YG, Chen JY, Wang HF, Xiao M, Yang LL, Guo JW, Zhou EM, Zhang YM, Li WJ (2016a) Egicoccus halophilus gen. nov., sp. nov., a halophilic, alkalitolerant actinobacterium and proposal of Egicoccaceae fam. nov. and Egicoccales ord. nov. Int J Syst Evol Microbiol 66:530–535. https://doi.org/10.1099/ijsem.0.000749

    CAS  Article  PubMed  Google Scholar 

  43. Zhang YG, Wang HF, Yang LL, Zhou XK, Zhi XY, Duan YQ, Xiao M, Zhang YM, Li WJ (2016b) Egibacter rhizosphaerae gen. nov., sp. nov., an obligately halophilic, facultatively alkaliphilic actinobacterium and proposal of Egibaceraceae fam. nov. and Egibacterales ord. nov. Int J Syst Evol Microbiol 66:283–289. https://doi.org/10.1099/ijsem.0.000713

    CAS  Article  PubMed  Google Scholar 

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Acknowledgements

This work was supported by the National Natural Science Foundation of China (nos. 91751206, 32000084 and 32061143043) and China Postdoctoral Science Foundation (No. 2019M662952).

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DDC, WSS, and WJL conceived and designed the research. DDC conducted the experiments, analyzed the data, and wrote the original draft. YHL, SW, and BBL analyzed the data and modified the first draft of this manuscript. AM and SXG conducted the review and editing. DDC, YHL, HCJ, and WJL provided funding. All authors read and approved the manuscript.

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Correspondence to Wen-Sheng Shu or Wen-Jun Li.

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Chen, DD., Ahmad, M., Liu, YH. et al. Transcriptomic responses of haloalkalitolerant bacterium Egicoccus halophilus EGI 80432T to highly alkaline stress. Extremophiles (2021). https://doi.org/10.1007/s00792-021-01239-8

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Keywords

  • Egicoccus halophilus
  • Transcriptomic comparison
  • Alkaline response