Integrative bioinformatics approaches reveal key hub genes in cyanobacteria: insights from Synechocystis sp. PCC 6803 and Geminocystis sp. NIES-3708 under abiotic stress conditions

Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410

Article  PubMed  CAS  Google Scholar 

Babele PK, Kumar J, Chaturvedi V (2019) Proteomic de-regulation in cyanobacteria in response to abiotic stresses. Front Microbiol 10:1315

Article  PubMed  PubMed Central  Google Scholar 

Baldi P, Brunak S, Chauvin Y, Andersen CA, Nielsen H (2000) Assessing the accuracy of prediction algorithms for classification: an overview. Bioinformatics 16(5):412–424

Article  PubMed  CAS  Google Scholar 

Braun V, Hantke K (2011) Recent insights into iron import by bacteria. Curr Opin Chem Biol 15(2):328–334

Article  PubMed  CAS  Google Scholar 

Campbell D (1996) Complementary chromatic adaptation alters photosynthetic strategies in the cyanobacterium Calothrix. Microbiology 142:1255–1263

Article  PubMed  CAS  Google Scholar 

Červený J, Sinetova MA, Zavřel T, Los DA (2015) Mechanisms of high temperature resistance of synechocystis sp. PCC 6803: an impact of histidine kinase 34. Life (Basel) 5:676–699

PubMed  Google Scholar 

Cheng Y, Zhang T, Wang L, Chen W (2020) Transcriptome analysis reveals isiA-regulatory mechanisms underlying iron depletion and oxidative-stress acclimation in Synechocystis sp. Strain PCC 6803. Appl Environ Microbiol 86(13):100517–100520

Article  Google Scholar 

Dunne R, Reguant R, Ramarao-Milne P, Szul P, Sng LMF, Lundberg M, Twine NA, Bauer DC (2023) Thresholding Gini variable importance with a single-trained random forest: An empirical Bayes approach. Comput Struct Biotechnol J 21:4354–4360

Article  PubMed  PubMed Central  CAS  Google Scholar 

Fulda S, Mikkat S, Huang F, Huckauf J, Marin K, Norling B, Hagemann M (2006) Proteome analysis of salt stress response in the cyanobacterium Synechocystissp. strain PCC 6803. Proteomics 6(9):2733–2745

Article  PubMed  CAS  Google Scholar 

Ge SX, Jung D, Yao R (2020) ShinyGO: a graphical gene-set enrichment tool for animals and plants. Bioinformatics 36:2628–2629

Article  PubMed  CAS  Google Scholar 

Hamid JS, Hu P, Roslin NM, Ling V, Greenwood CM, Beyene J (2009) Data integration in genetics and genomics: methods and challenges. Hum Gen Prot. https://doi.org/10.4061/2009/869093

Article  Google Scholar 

Hernandez-Prieto MA, Futschik ME (2012) CyanoEXpress: A web database for exploration and visualisation of the integrated transcriptome of cyanobacterium Synechocystissp. PCC6803. Bioinformation 8(13):634–638

Article  PubMed  PubMed Central  Google Scholar 

Hidayat N, Putri MN, Kurniawan R (2024) Nannochloropsis sp phytoplankton culture technique laboratory scale. South East Asian Mar Sci J 1:73–76

Google Scholar 

Jia A, Zheng Y, Chen H, Wang Q (2021) Regulation and functional complexity of the chlorophyll-binding protein IsiA. Front Microbiol 17(12):774107

Article  Google Scholar 

Kaneko T, Sato S, Kotani H, Tanaka A, Asamizu E, Nakamura Y, Miyajima N, Hirosawa M, Sugiura M, Sasamoto S et al (1996) Sequence analysis of the genome of the unicellular cyanobacterium Synechocystissp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions. DNA Res 3:109–136

Article  PubMed  CAS  Google Scholar 

Karimi-Fard A, Saidi A, Tohidfar M, Saxena A (2023) Identification of key responsive genes to some abiotic stresses in arabidopsis thaliana at the seedling stage based on coupling computational biology methods and machine learning. J Appl Biotechnol Reports 10:1079–1090

CAS  Google Scholar 

Karimi-Fard A, Saidi A, TohidFar M, Emami SN (2024) Novel candidate genes for environmental stresses response in Synechocystis sp. PCC 6803 revealed by machine learning algorithms. Braz J Microbiol 55:1219–1229

Article  PubMed  CAS  Google Scholar 

Katoh H, Hagino N, Grossman AR, Ogawa T (2001) Genes essential to iron transport in the cyanobacterium Synechocystissp. strain PCC 6803. J Bacteriol 183(9):2779–2784

Article  PubMed  PubMed Central  CAS  Google Scholar 

Kaushik MS, Singh P, Tiwari B, Mishra AK (2016) Ferric uptake regulator (FUR) protein: properties and implications in cyanobacteria. Ann Microbiol 66:61–75

Article  CAS  Google Scholar 

Klähn S, Mikkat S, Riediger M, Georg J, Hess WR, Hagemann M (2021) Integrative analysis of the salt stress response in cyanobacteria. Biol Direct 16:26

Article  PubMed  PubMed Central  Google Scholar 

Kopf M, Klähn S, Scholz I, Matthiessen JK, Hess WR, Voß B (2014) Comparative analysis of the primary transcriptome of Synechocystissp. PCC 6803. DNA Res 21:527–539

Article  PubMed  PubMed Central  CAS  Google Scholar 

Krynická V, Georg J, Jackson PJ, Dickman MJ, Hunter CN, Futschik ME, Hess WR, Komenda J (2019) Depletion of the FtsH1/3 proteolytic complex suppresses the nutrient stress response in the cyanobacterium Synechocystissp. strain PCC 6803. Plant Cell 31:2912–2928

Article  PubMed  PubMed Central  Google Scholar 

Langfelder P, Horvath S (2008) WGCNA: an R package for weighted correlation network analysis. BMC Bioinform 9:559

Article  Google Scholar 

Leek JT, Johnson WE, Parker HS, Jaffe AE, Storey JD (2012) The sva package for removing batch effects and other unwanted variation in high-throughput experiments. Bioinformatics 28:882–883

Article  PubMed  PubMed Central  CAS  Google Scholar 

Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods 25:402–408

Article  PubMed  CAS  Google Scholar 

Moorthy K, Mohamad MS (2011) Random forest for gene selection and microarray data classification. Bioinformation 7:142–146

Article  PubMed  PubMed Central  Google Scholar 

Ogawa K, Yoshikawa K, Matsuda F, Toya Y, Shimizu H (2018) Transcriptome analysis of the cyanobacterium Synechocystissp. PCC 6803 and mechanisms of photoinhibition tolerance under extreme high light conditions. J Biosci Bioeng 126:596–602

Article  PubMed  CAS  Google Scholar 

Palani S, Lakshmanan P, Kumanan G (2021) Influence of process parameters on the machinability of nickel aluminum bronze alloy by electrochemical micromachining process–A desirability analysis approach. Mater Today: Proceed 46:1033–1038

CAS  Google Scholar 

Pathak J, Rajneesh, Maurya PK, Singh SP, Häder D-P, Sinha RP (2018) Cyanobacterial farming for environment friendly sustainable agriculture practices: innovations and perspectives. Front Environ Sci. https://doi.org/10.3389/fenvs.2018.00007

Article  Google Scholar 

Perveen N, Dinesh MR, Sankaran M, Ravishankar KV, Krishnajee HG, Hanur VS, Alamri S, Kesawat MS, Irfan M (2023) Comparative transcriptome analysis provides novel insights into molecular response of salt-tolerant and sensitive polyembryonic mango genotypes to salinity stress at seedling stage. Front Plant Sci 14:1152485

Article  PubMed  PubMed Central  Google Scholar 

Qiu GW, Lou WJ, Sun CY, Yang N, Li ZK, Li DL, Zang SS, Fu FX, Hutchins DA, Jiang HB, Qiu BS (2018) Outer membrane iron uptake pathways in the model cyanobacterium Synechocystis sp. Strain PCC 6803. Appl Environ Microbiol 17 84(19):101512-e01518

Google Scholar 

Riediger M, Hernández-Prieto MA, Song K, Hess WR, Futschik ME (2021) Genome-wide identification and characterization of Fur-binding sites in the cyanobacteria Synechocystis sp. PCC 6803 and PCC 6714. DNA Res 28(6):dsab023

Article  PubMed  PubMed Central  Google Scholar 

Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, Smyth GK (2015) limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucl Acids Res 43:e47

Article  PubMed  PubMed Central  Google Scholar 

Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13:2498–2504

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