Phylogenetic footprint of the plant clock system in angiosperms: evolutionary processes of Pseudo-Response Regulators

Abstract

BackgroundPlant circadian clocks regulate many photoperiodic and diurnal responses that are conserved among plant species. The plant circadian clock system has been uncovered in the model plant, Arabidopsis thaliana, using genetics and systems biology approaches. However, it is still not clear how the clock system had been organized in the evolutionary history of plants. We recently revealed the molecular phylogeny of LHY/CCA1 genes, one of the essential components of the clock system. The aims of this study are to reconstruct the phylogenetic relationships of angiosperm clock-associated PRR genes, the partner of the LHY/CCA1 genes, and to clarify the evolutionary history of the plant clock system in angiosperm lineages.ResultsIn the present study, to investigate the molecular phylogeny of PRR genes, we performed two approaches: reconstruction of phylogenetic trees and examination of syntenic relationships. Phylogenetic analyses revealed that PRR genes had diverged into three clades prior to the speciation of monocots and eudicots. Furthermore, copy numbers of PRR genes have been independently increased in monocots and eudicots as a result of ancient chromosomal duplication events.ConclusionsBased on the molecular phylogenies of both PRR genes and LHY/CCA1 genes, we inferred the evolutionary process of the plant clock system in angiosperms. This scenario provides evolutionary information that a common ancestor of monocots and eudicots had retained the basic components required for reconstructing a clock system and that the plant circadian clock may have become a more elaborate mechanism after the speciation of monocots and eudicots because of the gene expansion that resulted from polyploidy events.

Diurnal and circadian expression of clock-associated pseudo-response regulators in Populus trichocarpa

“…Based on the sequence information available in the Pt genome database (http:// www.phytozome.net/search.php), we designed primer sets to amplify the coding region of the PtPRR gene (Supplemental Data 3), and performed molecular cloning and sequence analyses to determine the sequences experimentally, using the synthesized complementary DNA derived from the total RNA from the leaves. Of the seven members of the PtPRR gene family, the determined amino acid sequences of three (PtPRR73, PtPRR9la and PtPRR9lb) were identical to the reported sequences, while the remaining four members (PtPRR1, PtPRR37, PtPRR5a and PtPRR5b) were largely consistent with sequences reported previously (Takata et al 2010;Supplemental Data 4). Quantitative PCR analysis was performed with a Lightcycle 480 II instrument (Roche, Indianapolis, IN, USA) and FS Universal SYBR ® Green…”

“…Genes associated with transcriptional/translational feedback loops in the eukaryotic circadian clock are core components that control the form of the central oscillator (Bell et al 2005;Locke et al 2006;McClung 2006). In the dicot Arabidopsis thaliana (At), identification of the circadian clock's molecular components has revealed the basic workings of the plant circadian clock (Harmer 2009;Takata et al 2010). Reciprocal transcriptional regulation between CIRCADIAN CLOCK-ASSOCIATED 1 (CCA1) and the homologous gene LATE ELONGATED HYPOCOTYL (LHY) and TIMING OF CAB EXPRESSION1 (TOC1), also called PSEUDO-RESPONSE REGULATOR1 (PRR1), has been proposed as the main feedback loop (Alabadí et al 2001;Mizoguchi et al 2002;Perales and Mas 2007).…”

“…In the Populus trichocarpa (Pt) genome (Tuskan et al 2006), seven genes homologous to AtPRRs including PtPRR1/TOC1 have been identified (Takata et al 2010; Supplemental Data 1 and 2). To ascertain whether all the PtPRR genes are involved in the poplar circadian rhythm, we assessed their expression patterns under different light conditions by quantitative RT-PCR.…”

Development of a marker system to discern the flowering type inBrassica rapacrops

“…생체리 듬은 식물의 생장과 발달에 직,간접적으로 관여하며 궁극적 으로 진화과정상의 적응과 농작물의 생산량에 영향을 미친 다 (Dodd et al 2005). 애기장대에서 PRR1(Pseudo-Response Regulators1)과 LHY/CCA1(Late Elongated Hypocotyl/Circadian Clock Associated 1)는 생체시계 조절 기작의 중심 유전자이다 (Harmer 2009;Takata et al 2010). TOC1 (TIMING OF CAB EXPRESSION 1)로도 알려진 PRR1 유전자는 특이한 구조 (pseudo-receiver domain과 CONSTANS motif)를 가진 애기장 대 PRR(pseudo-response regulator)군 중 하나이다 Matsushika et al, 2000;Murakami et al, 2003;.…”

“…5 개로 되어 있어 "PRR quintet"로도 불리는 이 유전자의 mRNA 는 해가 뜨고 난 후 순차적으로 발현이 축적이 되어 2~3시 간 간격을 두고 PRR9_PRR7_PRR5_PRR3_PRR1 순으로 발현 량이 최대로 되는 생체시계 유전자이다 (Matsushika et al, 2000;Mizuno and Nakamichi, 2005). 피자 식물 진화계통에 보 존되어 있으며, 벼(Oryza sativa)와 같은 외떡잎 식물과 포플 라(Populus trichocarpa)와 같은 목본류의 식물 등에 잘 보존 되어 있는 유전자로 진화과정을 거치면서 작물별로 보존된 유사유전자(paralogous genes)의 개수에 차이가 있다 (Murakami et al 2003;Ming et al 2008;Ramírez-Carvajal et al 2008;Takata et al 2010). 배추 게놈에서 발견된 PRR군 유전자는 11개이며, 그 중 PRR1은 2개(BrPRR1a와 BrPRR1b)로 일일 주기로 발현 하는 생체시계 유전자임이 확인되었다 (Lou et al 2012;Kim et al 2012 Fig.…”