skip to main content


Title: Cross‐species complementation reveals conserved functions for EARLY FLOWERING 3 between monocots and dicots
Abstract

Plant responses to the environment are shaped by external stimuli and internal signaling pathways. In both the model plantArabidopsis thaliana(Arabidopsis) and crop species, circadian clock factors are critical for growth, flowering, and circadian rhythms. Outside ofArabidopsis,however, little is known about the molecular function of clock gene products. Therefore, we sought to compare the function ofBrachypodium distachyon(Brachypodium) andSetaria viridis(Setaria) orthologs ofEARLY FLOWERING3,a key clock gene inArabidopsis. To identify both cycling genes and putativeELF3functional orthologs inSetaria, a circadianRNA‐seq dataset and online query tool (Diel Explorer) were generated to explore expression profiles ofSetariagenes under circadian conditions. The function ofELF3orthologs fromArabidopsis, Brachypodium,andSetariawas tested for complementation of anelf3mutation inArabidopsis. We find that both monocot orthologs were capable of rescuing hypocotyl elongation, flowering time, and arrhythmic clock phenotypes. Using affinity purification and mass spectrometry, our data indicate that BdELF3 and SvELF3 could be integrated into similar complexesin vivoas AtELF3. Thus, we find that, despite 180 million years of separation,BdELF3andSvELF3can functionally complement loss ofELF3at the molecular and physiological level.

 
more » « less
NSF-PAR ID:
10046066
Author(s) / Creator(s):
 ;  ;  ;  ;  ;  ;  ;  ;  ;  ;  ;  
Publisher / Repository:
Wiley Blackwell (John Wiley & Sons)
Date Published:
Journal Name:
Plant Direct
Volume:
1
Issue:
4
ISSN:
2475-4455
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. Summary

    The flowering plantArabidopsis thalianais a dicot model organism for research in many aspects of plant biology. A comprehensive annotation of its genome paves the way for understanding the functions and activities of all types of transcripts, includingmRNA, the various classes of non‐codingRNA, and smallRNA. TheTAIR10 annotation update had a profound impact on Arabidopsis research but was released more than 5 years ago. Maintaining the accuracy of the annotation continues to be a prerequisite for future progress. Using an integrative annotation pipeline, we assembled tissue‐specificRNA‐Seq libraries from 113 datasets and constructed 48 359 transcript models of protein‐coding genes in eleven tissues. In addition, we annotated various classes of non‐codingRNAincluding microRNA, long intergenicRNA, small nucleolarRNA, natural antisense transcript, small nuclearRNA, and smallRNAusing published datasets and in‐house analytic results. Altogether, we identified 635 novel protein‐coding genes, 508 novel transcribed regions, 5178 non‐codingRNAs, and 35 846 smallRNAloci that were formerly unannotated. Analysis of the splicing events andRNA‐Seq based expression profiles revealed the landscapes of gene structures, untranslated regions, and splicing activities to be more intricate than previously appreciated. Furthermore, we present 692 uniformly expressed housekeeping genes, 43% of whose human orthologs are also housekeeping genes. This updated Arabidopsis genome annotation with a substantially increased resolution of gene models will not only further our understanding of the biological processes of this plant model but also of other species.

     
    more » « less
  2. Abstract

    The circadian clock is an internal molecular oscillator and coordinates numerous physiological processes through regulation of molecular pathways. Tissue‐specific clocks connected by mobile signals have previously been found to run at different speeds inArabidopsis thalianatissues. However, tissue variation in circadian clocks in crop species is unknown. In this study, leaf and tuber global gene expression in cultivated potato under cycling and constant environmental conditions was profiled. In addition, we used a circadian‐regulated luciferase reporter construct to study tuber gene expression rhythms. Diel and circadian expression patterns were present among 17.9% and 5.6% of the expressed genes in the tuber. Over 500 genes displayed differential tissue specific diel phases. Intriguingly, few core circadian clock genes had circadian expression patterns, while all such genes were circadian rhythmic in cultivated tomato leaves. Furthermore, robust diel and circadian transcriptional rhythms were observed among detached tubers. Our results suggest alternative regulatory mechanisms and/or clock composition is present in potato, as well as the presence of tissue‐specific independent circadian clocks. We have provided the first evidence of a functional circadian clock in below‐ground storage organs, holding important implications for other storage root and tuberous crops.

     
    more » « less
  3. Summary

    Many plants require prolonged exposure to cold to acquire the competence to flower. The process by which cold exposure results in competence is known as vernalization. InArabidopsis thaliana, vernalization leads to the stable repression of the floral repressorFLOWERING LOCUS Cvia chromatin modification, including an increase of trimethylation on lysine 27 of histone H3 (H3K27me3) by Polycomb Repressive Complex 2 (PRC2). Vernalization in pooids is associated with the stable induction of a floral promoter,VERNALIZATION1(VRN1). From a screen for mutants with a reduced vernalization requirement in the model grassBrachypodium distachyon, we identified two recessive alleles ofENHANCER OF ZESTELIKE 1(EZL1).EZL1is orthologous toA. thalianaCURLY LEAF 1, a gene that encodes the catalytic subunit ofPRC2.B. distachyon ezl1mutants flower rapidly without vernalization in long‐day (LD) photoperiods; thus,EZL1is required for the proper maintenance of the vegetative state prior to vernalization. Transcriptomic studies inezl1revealed mis‐regulation of thousands of genes, including ectopic expression of several floral homeotic genes in leaves. Loss ofEZL1results in the global reduction of H3K27me3 and H3K27me2, consistent with this gene making a major contribution toPRC2 activity inB. distachyon. Furthermore, inezl1mutants, the flowering genesVRN1andAGAMOUS(AG) are ectopically expressed and have reduced H3K27me3. Artificial microRNAknock‐down of eitherVRN1orAGinezl1‐1mutants partially restores wild‐type flowering behavior in non‐vernalized plants, suggesting that ectopic expression inezl1mutants may contribute to the rapid‐flowering phenotype.

     
    more » « less
  4. Summary

    The altered carbon assimilation pathway of crassulacean acid metabolism (CAM) photosynthesis results in an up to 80% higher water‐use efficiency than C3photosynthesis in plants making it a potentially useful pathway for engineering crop plants with improved drought tolerance. Here we surveyed detailed temporal (diel time course) and spatial (across a leaf gradient) gene and microRNA(miRNA) expression patterns in the obligateCAMplant pineapple [Ananas comosus(L.) Merr.]. The high‐resolution transcriptome atlas allowed us to distinguish betweenCAM‐related and non‐CAMgene copies. A differential gene co‐expression network across green and white leaf diel datasets identified genes with circadian oscillation,CAM‐related functions, and source‐sink relations. Gene co‐expression clusters containingCAMpathway genes are enriched with clock‐associatedcis‐elements, suggesting circadian regulation ofCAM. About 20% of pineapple microRNAs have diel expression patterns, with several that target keyCAM‐related genes. Expression and physiology data provide a model forCAM‐specific carbohydrate flux and long‐distance hexose transport. Together these resources provide a list of candidate genes for targeted engineering ofCAMinto C3photosynthesis crop species.

     
    more » « less
  5. Summary

    Emerging evidence indicates a close connection between cell‐cycle progression and the plant immune responses. In Arabidopsis,MODIFIER OFsnc1‐1(MOS1) modulates a number of processes including endoreduplication and plant disease resistance, but the molecular mechanism underlying this modulation was not fully understood. Here, we provide biochemical and genetic evidence thatTEOSINTE BRANCHED1,CYCLOIDEA,PCF1 (TCP) transcription factorsTCP15 and its homologues are mediators ofMOS1 function in the immune response and are likely to be also involved in cell‐cycle control.MOS1 andTCPproteins have a direct physical interaction. They both bind to the promoter of the immune receptor geneSUPRESSOR OFnpr1‐1,CONSTITUTIVE1(SNC1) and modulate its expression and consequently immune responses.MOS1 andTCP15 both affect the expression of cell‐cycle genesD‐typeCYCLIN3;1(CYCD3;1), which may mediate theMOS1 function in cell‐cycle modulation. In addition,CYCD3;1overexpression upregulates immune responses, andSNC1expression. This study investigated and revealed a role forMOS1 in transcriptional regulation throughTCP15 and its homologues. This finding suggests the coordination of cell‐cycle progression and plant immune responses at multiple levels.

     
    more » « less