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Background  The ubiquitin 26S proteasome system (UPS) selectively degrades cellular proteins, which results in physiological changes to eukaryotic cells. F-box proteins are substrate adaptors within the UPS and are responsible for the diversity of potential protein targets. Plant genomes are enriched in F-box genes, but the vast majority of these have unknown roles. This work investigated the  Arabidopsis  F-box gene  F-BOX STRESS INDUCED 1  ( FBS1 ) for its effects on gene expression in order elucidate its previously unknown biological function.    Results  Using publically available Affymetrix ATH1 microarray data, we show that  FBS1  is significantly co-expressed in abiotic stresses with other well-characterized stress response genes, including important stress-related transcriptional regulators. This gene suite is most highly expressed in roots under cold and salt stresses. Transcriptome analysis of  fbs1–1  knock-out plants grown at a chilling temperature shows that hundreds of genes require  FBS1  for appropriate expression, and that these genes are enriched in those having roles in both abiotic and biotic stress responses. Based on both this genome-wide expression data set and quantitative real-time PCR (qPCR) analysis, it is apparent that  FBS1  is required for elevated expression of many jasmonic acid (JA) genes that have established roles in combatting environmental stresses, and that it also controls a subset of JA biosynthesis genes.  FBS1  also significantly impacts abscisic acid (ABA) regulated genes, but this interaction is more complex, as  FBS1  has both positive and negative effects on ABA-inducible and ABA-repressible gene modules. One noteworthy effect of  FBS1  on ABA-related stress processes, however, is the restraint it imposes on the expression of multiple class I  LIPID TRANSFER PROTEIN  ( LTP ) gene family members that have demonstrated protective effects in water deficit-related stresses.    Conclusion    FBS1  impacts plant stress responses by regulating hundreds of genes that respond to the plant stress hormones JA and ABA. The positive effect that  FBS1  has on JA processes and the negative effect it has on at least some ABA processes indicates that it in part regulates cellular responses balanced between these two important stress hormones. More broadly then,  FBS1  may aid plant cells in switching between certain biotic (JA) and abiotic (ABA) stress responses. Finally, because  FBS1  regulates a subset of JA biosynthesis and response genes, we conclude that it might have a role in tuning hormone responses to particular circumstances at the transcriptional level.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-017-3864-6) contains supplementary material, which is available to authorized users.

Transcriptome analysis uncovers Arabidopsis F-BOX STRESS INDUCED 1 as a regulator of jasmonic acid and abscisic acid stress gene expression