Identification of novel salt stress-responsive microRNAs through sequencing and bioinformatic analysis in a unique halophilic <italic style="font-style: italic">Dunaliella</italic> <italic style="font-style: italic">salina</italic> strain

Fan GAO; Fangru NAN; Jia FENG; Junping LÜ; Qi LIU; Xudong LIU; Shulian XIE

Your Location：

Home >

Browse articles >

Identification of novel salt stress-responsive microRNAs through sequencing and bioinformatic analysis in a unique halophilic Dunaliella salina strain

Biology | Updated：2024-10-14

- Identification of novel salt stress-responsive microRNAs through sequencing and bioinformatic analysis in a unique halophilic Dunaliella salina strain
- Journal of Oceanology and Limnology Vol. 41, Issue 4, Pages: 1558-1574(2023)
- Affiliations：
  
  School of Life Science, Shanxi Key Laboratory for Research and Development of Regional Plants, Shanxi University, Taiyuan 030006, China
- Author bio：
  
  xiesl@sxu.edu.cn
- Funds：
- DOI：
  CLC：
- Received：16 March 2022，
  
  Accepted：22 April 2022，
  
  Online First：27 May 2022，
  
  Published：01 July 2023
- Accepted：
Scan QR Code
GAO Fan,NAN Fangru,FENG Jia,et al.Identification of novel salt stress-responsive microRNAs through sequencing and bioinformatic analysis in a unique halophilic Dunaliellasalina strain[J].Journal of Oceanology and Limnology,2023,41(04):1558-1574.
DOI：

GAO Fan,NAN Fangru,FENG Jia,et al.Identification of novel salt stress-responsive microRNAs through sequencing and bioinformatic analysis in a unique halophilic Dunaliellasalina strain[J].Journal of Oceanology and Limnology,2023,41(04):1558-1574. DOI：

摘要

Abstract

Dunaliella

salina

is a classic halophilic alga. However

its molecular mechanisms in response to high salinity at the post transcriptional level remain unknown. A unique halophilic alga strain

DS-CN1

was screened from four

salina

strains via cell biological

physiological

and biochemical methods. High-throughput sequencing of small RNAs (sRNAs) of DS-CN1 in culture medium containing 3.42-mol/L NaCl (SS group) or 0.05-mol/L NaCl (CO group) was performed on the BGISEQ-500 platform. The annotation and sequences of

salina

sRNAs were profiled. Altogether

44 novel salt stress-responsive microRNAs (miRNAs) with a relatively high C content

with the majority of them being 24 nt in length

were identified and characterized in DS-CN1. Twenty-one differentially expressed miRNAs (DEMs) in SS and CO were screened via bioinformatic analysis. A total of 319 putative salt stress-related genes targeted (104 overlapping genes) by novel miRNAs in this alga were screened based on our previous transcriptome sequencing research. Furthermore

these target genes were classified and enriched by GO and KEGG pathway analysis. Moreover

5 novel DEMs (dsa-mir3

dsa-mir16

dsa-mir17

and dsa-mir26 were significantly upregulated

and dsa-mir40 was significantly downregulated) and their corresponding 10 target genes involved in the 6 significantly enriched metabolic pathways were verified by quantitative real-time PCR. Next

their regulatory relationships were comprehensively analyzed. Lastly

a unique salt stress response metabolic network was constructed based on the novel DEM-target gene pairs. Taken together

our results suggest that 44 novel salt stress-responsive microRNAs were ide

ntified

and 4 of them might play important roles in

salina

upon salinity stress and contribute to clarify its distinctive halophilic feature. Our study will shed light on the regulatory mechanisms of salt stress responses.

关键词

Keywords

references

Alzahrani S M , Alaraidh I A , Khan M A et al . 2019 . Identification and characterization of salt-responsive microRNAs in Vicia faba by high-throughput sequencing . Genes , 10 ( 4 ): 303 , https://doi.org/10.3390/genes10040303 https://doi.org/10.3390/genes10040303 .

Ametaj B N , Bobe G , Lu Y et al . 2003 . Effect of sample preparation, length of time, and sample size on quantification of total lipids from bovine liver . Journal of Agricultural and Food Chemistry , 51 ( 8 ): 2105 - 2110 , https://doi.org/10.1021/jf0259011 https://doi.org/10.1021/jf0259011 .

Lokhande H A . 2023 . Bioinformatics analysis of miRNA sequencing data . Methods in Molecular Biology , 2595 : 225 - 237 . https://doi.org/10.1007/978-1-0716-2823-2_16 https://doi.org/10.1007/978-1-0716-2823-2_16

Axtell M J . 2013 . Classification and comparison of small RNAs from plants . Annual Review of Plant Biology , 64 : 137 - 159 , https://doi.org/10.1146/annurev-arplant-050312-120043 https://doi.org/10.1146/annurev-arplant-050312-120043 .

Axtell M J , Meyers B C . 2018 . Revisiting criteria for plant microRNA annotation in the era of big data . The Plant Cell , 30 ( 2 ): 272 - 284 , https://doi.org/10.1105/tpc.17.00851 https://doi.org/10.1105/tpc.17.00851 .

Barozai M Y K , Qasim M , Din M et al . 2018 . An update on the microRNAs and their targets in unicellular red alga Porphyridium cruentum . Pakistan Journal of Botany , 50 ( 2 ): 817 - 825 .

Billoud B , Nehr Z , Le Bail A et al . 2014 . Computational prediction and experimental validation of microRNAs in the brown alga Ectocarpus siliculosus . Nucleic Acids Research , 42 ( 1 ): 417 - 429 , https://doi.org/10.1093/nar/gkt856 https://doi.org/10.1093/nar/gkt856 .

Chen Y X , Bi C B , Zhang J et al . 2020 . Astaxanthin biosynthesis in transgenic Dunaliella salina (Chlorophyceae) enhanced tolerance to high irradiation stress . South African Journal of Botany , 133 : 132 - 138 , https://doi.org/10.1016/j.sajb.2020.07.008 https://doi.org/10.1016/j.sajb.2020.07.008 .

Chen Y X , Chen Y S , Shi C M et al . 2018 . SOAPnuke: a MapReduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data . Gigascience , 7 ( 1 ): gix 120 , https://doi.org/10.1093/gigascience/gix120 https://doi.org/10.1093/gigascience/gix120 .

Duché O , Trémoulet F , Namane A et al . 2002 . A proteomic analysis of the salt stress response of Listeria monocytogenes . FEMS Microbiology Letters , 215 ( 2 ): 183 - 188 , https://doi.org/10.1111/j.1574-6968.2002.tb11389.x https://doi.org/10.1111/j.1574-6968.2002.tb11389.x .

Evers M , Huttner M , Dueck A et al . 2015 . miRA: adaptable novel miRNA identification in plants using small RNA sequencing data . BMC Bioinformatics , 16 : 370 , https://doi.org/10.1186/s12859-015-0798-3 https://doi.org/10.1186/s12859-015-0798-3 .

Feng B H , Li G Y , Islam M et al . 2020a . Strengthened antioxidant capacity improves photosynthesis by regulating stomatal aperture and ribulose-1,5-bisphosphate carboxylase/oxygenase activity . Plant Science , 290 : 110245 , https://doi.org/10.1016/j.plantsci.2019.110245 https://doi.org/10.1016/j.plantsci.2019.110245 .

Feng K W , Nie X J , Cui L C et al . 2017 . Genome-wide identification and characterization of salinity stress-responsive miRNAs in wild emmer wheat ( Triticum turgidum ssp. dicoccoides ) . Genes (Basel) , 8 ( 6 ): 156 , https://doi.org/10.3390/genes8060156 https://doi.org/10.3390/genes8060156 .

Feng S Y , Hu L , Zhang Q H et al . 2020b . CRISPR/Cas technology promotes the various applica tion of Dunaliella salina system . Applied Microbiology and Biotechnology , 104 ( 20 ): 8621 - 8630 , https://doi.org/10.1007/s00253-020-10892-6 https://doi.org/10.1007/s00253-020-10892-6 .

Folch J , Lees M , Stanley G H S . 1957 . A simple method for the isolation and purification of total lipides from animal tissues . Journal of Biological Chemistry , 226 ( 1 ): 497 - 509 , https://doi.org/10.1016/S0021-9258(18)64849-5 https://doi.org/10.1016/S0021-9258(18)64849-5 .

Frukh A , Siddiqi T O , Khan M I R et al . 2020 . Modulation in growth, biochemical attributes and proteome profile of rice cultivars under salt stress . Plant Physiology and Biochemistry , 146 : 55 - 70 , https://doi.org/10.1016/j.plaphy.2019.11.011 https://doi.org/10.1016/j.plaphy.2019.11.011 .

Gao F , Nan F R , Feng J et al . 2021 . Transcriptome profile of Dunaliella salina in Yuncheng Salt Lake reveals salt-stress-related genes under different salinity stresses . Journal of Oceanology and Limnology , 39 ( 6 ): 2336 - 2362 , https://doi.org/10.1007/s00343-021-0164-4 https://doi.org/10.1007/s00343-021-0164-4 .

Gao F , Nan F R , Feng J et al . 2022 . Comparative morphological, physiological, biochemical and genomic studies reveal novel genes of Dunaliella bioculata and D . quartolecta in response to salt stress . Molecular Biology Reports , 49 ( 3 ): 1749 - 1761 , https://doi.org/10.1007/s11033-021-06984-9 https://doi.org/10.1007/s11033-021-06984-9 .

Gao X , Zhang F G , Hu J L et al . 2016 . MicroRNAs modulate adaption to multiple abiotic stresses in Chlamydomonas reinhardtii . Scientific Reports , 6 ( 1 ): 38228 , https://doi.org/10.1038/srep38228 https://doi.org/10.1038/srep38228 .

Garcia-Seco D , Zhang Y , Gutierrez-Mañero F J et al . 2015 . RNA-Seq analysis and transcriptome assembly for blackberry ( Rubus sp. var. Lochness) fruit . BMC Genomics , 16 ( 1 ): 5 , https://doi.org/10.1186/s12864-014-1198-1 https://doi.org/10.1186/s12864-014-1198-1 .

Jin H C , Sun Y , Yang Q C et al . 2010 . Screening of genes induced by salt stress from Alfalfa . Molecular Biology Reports , 37 ( 2 ): 745 - 753 , https://doi.org/10.1007/s11033-009-9590-7 https://doi.org/10.1007/s11033-009-9590-7 .

Joshi G A N , Chauhan C , Das S . 2021 . Sequence and functional analysis of MIR319 promoter homologs from Brassica juncea reveals regulatory diversification and altered expression under stress . Molecular Genetics and Genomics , 296 ( 3 ): 731 - 749 , https://doi.org/10.1007/s00438-021-01778-x https://doi.org/10.1007/s00438-021-01778-x .

Kalvari I , Argasinska J , Quinones-Olvera N et al . 2018 . Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families . Nucleic Acids Research , 46 ( D1 ): D335 - D342 , https://doi.org/10.1093/nar/gkx1038 https://doi.org/10.1093/nar/gkx1038 .

Kanesaki Y , Suzuki I , Allakhverdiev S I et al . 2002 . Salt stress and hyperosmotic stress regulate the expression of different sets of genes in Synechocystis sp. PCC 6803 . Biochemical and Biophysical Research Communications , 290 ( 1 ): 339 - 348 , https://doi.org/10.1006/bbrc.2001.6201 https://doi.org/10.1006/bbrc.2001.6201 .

Langdon W B . 2015 . Performance of genetic programming optimised Bowtie2 on genome comparison and analytic testing (GCAT) benchmarks . BioData Mining , 8 ( 1 ): 1 , https://doi.org/10.1186/s13040-014-0034-0 https://doi.org/10.1186/s13040-014-0034-0 .

Lin Y S , Wang B , Wang N H et al . 2019 . Transcriptome analysis of rare minnow ( Gobiocypris rarus ) infected by the grass carp reovirus . Fish & Shellfish Immunology , 89 : 337 - 344 , https://doi.org/10.1016/j.fsi.2019.04.013 https://doi.org/10.1016/j.fsi.2019.04.013 .

Liu Y , Lv J P , Feng J et al . 2019 . Treatment of real aquaculture wastewater from a fishery utilizing phytoremediation with microalgae . Journal of Chemical Technology & Biotechnology , 94 ( 3 ): 900 - 910 , https://doi.org/10.1002/jctb.5837 https://doi.org/10.1002/jctb.5837 .

Love M I , Huber W , Anders S . 2014 . Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 . Genome Biology , 15 ( 12 ): 550 , https://doi.org/10.1186/s13059-014-0550-8 https://doi.org/10.1186/s13059-014-0550-8 .

Ma K , Bao Q W , Wu Y et al . 2020 . Evaluation of microalgae as immunostimulants and recombinant vaccines for diseases prevention and control in aquaculture . Frontiers in Bioengineering and Biotechnology , 8 : 590431 , https://doi.org/10.3389/fbioe.2020.590431 https://doi.org/10.3389/fbioe.2020.590431 .

Mera R , Torres E , Abalde J . 2016 . Effects of sodium sulfate on the freshwater microalga Chlamydomonas moewusii : implications for the optimization of algal culture media . Journal of Phycology , 52 ( 1 ): 75 - 88 , https://doi.org/10.1111/jpy.12367 https://doi.org/10.1111/jpy.12367 .

Mishra A , Jha B . 2009 . Isolation and characterization of extracellular polymeric substances from micro-algae Dunaliella salina under salt stress . Bioresource Technology , 100 ( 13 ): 3382 - 3386 , https://doi.org/10.1016/j.biortech.2009.02.006 https://doi.org/10.1016/j.biortech.2009.02.006 .

Moayedi A , Yargholi B , Pazira E et al . 2019 . Investigated of desalination of saline waters by using Dunaliella salina algae and its effect on water ions . Civil Engineering Journal , 5 ( 11 ): 2450 - 2460 , https://doi.org/10.28991/cej-2019-03091423 https://doi.org/10.28991/cej-2019-03091423 .

Naik H K , Varadahalli R D . 2020 . Genomic identification of salt induced microRNAs in Niger ( Guizotia abyssinica Cass .) . Plant Gene , 23 : 100242 , https://doi.org/10.1016/j.plgene.2020.100242 https://doi.org/10.1016/j.plgene.2020.100242 .

Omidbakhshfard M A , Omranian N , Ahmadi F S et al . 2012 . Effect of salt stress on genes encoding translation-associated proteins in Arabidopsis thaliana . Plant Signaling & Behavior , 7 ( 9 ): 1095 - 1102 , https://doi.org/10.4161/psb.21218 https://doi.org/10.4161/psb.21218 .

Panahi B , Frahadian M , Dums J T et al . 2019 . Integration of cross species RNA-Seq meta-analysis and machine-learning models identifies the most important salt stress—responsive pathways in microalga Dunaliella . Frontiers in Genetics , 10 : 752 , https://doi.org/10.3389/fgene.2019.00752 https://doi.org/10.3389/fgene.2019.00752 .

Pandit A , Rai V , Sharma T R et al . 2011 . Differentially expressed genes in sensitive and tolerant rice varieties in response to salt-stress . Journal of Plant Biochemistry and Biotechnology , 20 ( 2 ): 149 - 154 , https://doi.org/10.1007/s13562-010-0022-5 https://doi.org/10.1007/s13562-010-0022-5 .

Rammuni M N , Ariyadasa T U , Nimarshana P H V et al . 2019 . Comparative assessment on the extracti on of carotenoids from microalgal sources: astaxanthin from H . pluvialis and β-carotene from D . salina . Food Chemistry , 277 : 128 - 134 , https://doi.org/10.1016/j.foodchem.2018.10.066 https://doi.org/10.1016/j.foodchem.2018.10.066 .

Rasouli M , Ostovar-Ravari A , Shokri-Afra H . 2014 . Characterization and improvement of phenol-sulfuric acid microassay for glucose-based glycogen . European Review for Medical and Pharmacological Sciences , 18 ( 14 ): 2020 - 2024 .

Saeed A I , Sharov V , White J et al . 2003 . TM4: a free, open-source system for microarray data management and analysis . Biotechniques , 34 ( 2 ): 374 - 378 , https://doi.org/10.2144/03342mt01 https://doi.org/10.2144/03342mt01 .

Sewe S O , Silva G , Sicat P et al . 2022 . Trimming and validation of Illumina short reads using Trimmomatic, Trinity assembly, and assessment of RNA-Seq data . In: Edwards D ed. Plant Bioinformatics . Humana, New York. p. 211 - 232 , https://doi.org/10.1007/978-1-0716-2067-0_11 https://doi.org/10.1007/978-1-0716-2067-0_11 .

Sun X M , Ren L J , Zhao Q Y et al . 2018 . Microalgae for the production of lipid and carotenoids: a review with focus on stress regulation and adaptation . Biotechnology for Biofuels , 11 ( 1 ): 272 , https://doi.org/10.1186/s13068-018-1275-9 https://doi.org/10.1186/s13068-018-1275-9 .

Tafreshi A H , Shariati M . 2009 . Dunaliella biotechnology: methods and applications . Journal of Applied Microbiology , 107 ( 1 ): 14 - 35 , https://doi.org/10.1111/j.1365-2672.2009.04153.x https://doi.org/10.1111/j.1365-2672.2009.04153.x .

Tammam A A , Fakhry E M , El-Sheekh M . 2011 . Effect of salt stress on antioxidant system and the metabolism of the reactive oxygen species in Dunaliella salina and Dunaliella tertiolecta . African Journal of Biotechnology , 10 ( 19 ): 3795 - 3808 . https://do 10.4314/AJB.V10I19 http://dx.doi.org/10.4314/AJB.V10I19

Tian Y H , Tian Y M , Luo X J et al . 2014 . Identification and characterization of microRNAs related to salt stress in broccoli, using high-throughput sequencing and bioinformatics analysis . BMC Plant Biology , 14 : 226 , https://doi.org/10.1186/s12870-014-0226-2 https://doi.org/10.1186/s12870-014-0226-2 .

Wu Y , Guo J , Cai Y M et al . 2016 . Genome-wide identification and characterization of Eutrema salsugineum microRNAs for salt tolerance . Physiologia Plantarum , 157 ( 4 ): 453 - 468 , https://doi.org/10.1111/ppl.12419 https://doi.org/10.1111/ppl.12419 .

Xu L , Gao F , Feng J et al . 2022 . Relationship between β-carotene accumulation and geranylgeranyl pyrophosphate synthase in different species of Dunaliella . Plants , 11 : 27 , https://doi.org/10.3390/plants11010027 https://doi.org/10.3390/plants11010027 .

Yang H J , Hu C X . 2020 . Regulation and remodeling of intermediate metabolite and membrane lipid during NaCl‐induced stress in freshwater microalga Micractinium sp. XJ-2 for biofuel production . Biotechnology and Bioengineering , 117 ( 12 ): 3727 - 3738 , https://doi.org/10.1002/bit.27528 https://doi.org/10.1002/bit.27528 .

Yang Y Q , Guo Y . 2018 . Elucidating the molecular mechanisms mediating plant salt-stress responses . New Phytologist , 217 ( 2 ): 523 - 539 , https://doi.org/10.1111/nph.14920 https://doi.org/10.1111/nph.14920 .

Yin Z J , Li Y , Zhu W D et al . 2018 . Identification, characterization, and expression patterns of TCP genes and microRNA319 in cotton . International Journal of Molecular Sciences , 19 ( 11 ): 3655 , https://doi.org/10.3390/ijms19113655 https://doi.org/10.3390/ijms19113655 .

Yu Y , Wu G W , Yuan H M et al . 2016 . Identification and characterization of miRNAs and targets in flax ( Linum usitatissimum ) under saline, alkaline, and saline-alkaline stresses . BMC Plant Biology , 16 ( 1 ): 124 , https://doi.org/10.1186/s12870-016-0808-2 https://doi.org/10.1186/s12870-016-0808-2 .

Zavřel T , Očenášová P , Sinetova M et al . 2018 . Determination of storage (starch/glycogen) and total saccharides content in algae and cyanobacteria by a phenol-sulfuric acid method . Bio-Protocol , 8 ( 15 ): e2966 , https://doi.org/10.21769/BioProtoc.2966 https://doi.org/10.21769/BioProtoc.2966 .

Zhang X Z , Tan G R , Huang Y J et al . 1989 . Plant Physiological Experimental Technique . Liaoning Science and Technology Press, Shenyang . (in Chinese)

Zhu F Y , Chen M X , Ye N H et al . 2018 . Comparative performance of the BGISEQ-500 and Illumina HiSeq4000 sequencing platforms for transcriptome analysis in plants . Plant Methods , 14 : 69 , https://doi.org/10.1186/s13007-018-0337-0 https://doi.org/10.1186/s13007-018-0337-0 .

Views

Downloads

CSCD

Alert me when the article has been cited

Submit

Tools

Publicity Resources

No data

Related Author

Fan GAO

Fangru NAN

Jia FENG

Junping LÜ

Qi Liu

Xudong LIU

Related Institution

No data

Address：Editorial Office of JOL, 88 Haijun Rd. Qingdao, 266000, China
Tel：+86-532-82898754 Email：jol@qdio.ac.cn
Technical support is provided by Beijing Founder electronics co., LTD 京ICP备09064830号-19 京公网安备11010802024621
It is recommended to read the content of this site in Chrome&IE9+. Please switch to extreme mode in browser 360.
Cookies We use cookies to help provide and enhance our service and tailor content. By continuing, you agree to the use of cookies.

⁰

Identification of novel salt stress-responsive microRNAs through sequencing and bioinformatic analysis in a unique halophilic Dunaliella salina strain

DOI：

摘要

Abstract

关键词

Keywords

references