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Annotated Information


  • LIR1 interacts with LFNR.

In rice (Oryza sativa), LIR1(Os-LIR1) is an LFNR-interacting partner that strengthens the binding of LFNR to the membrane anchor[1]. LEAF-TYPE FERREDOXIN-NADP+ OXIDOREDUCTASE (LFNR) catalyzes electron transfer from ferredoxin (FD) to NADP+ during photosynthesis and generates the reducing power (as NADPH) required for carbon fixation[1]. Recently, two Arabidopsis chloroplast proteins, At-TROL and At-TIC62, have been shown to mediate anchoring of hydrophilic LFNR to the thylakoid membrane respectively[2][3][4][5][6][7]. LIR1 can increases the affinity between LFNR and TIC62 in Rice. LIR1 does not directly bind to TIC62, but rather, it interacts with LFNR(Figure3C),which increases the affinity of LFNR for TIC62[1]. There are two LFNR isoforms and LIR1 interacts with both of them.

  • Light-Dependent turnover of LIR1 regulates the membrane tethering of LFNR.

LIR1 content is regulated by light. Illumination of the plants induced rapid degradation of the LIR1 protein and also led to the release of LFNR from the thylakoid membrane[1]. The changes of LIR1 content slightly influence the total TIC62 content but has no effect on the accumulation of LFNR, however, markedly alter the distribution of LFNR between the soluble and membrane fractions both in the light and in the dark[1].


  • LIR1 Deficiency in Rice Results in Retarded Growth

In order to assess the physiological function of LIR1 in rice, lir1 knockout plants were produced using the CRISPR-Cas9 (clustered regulatory interspaced short palindromic repeat-associated proteins)approach. Sequencing of 30 T0 plants resulted in the identification of nine transgenic lines carrying mutations in LIR1, and three unique mutants were recovered in the T1 generation. All three mutant lines exhibited similar visual phenotypes, two lines (lir1-1 and lir1-2) were chosed to study the physiological effects of LIR1 deficiency in planta. Although the mutants exhibited retarded growth when grown hydroponically and in soil, they were fully viable and produced ~75% as many seeds as wild-type plants (Figure 1). Complementation of lir1 (lir1/PLIR1:LIR1-GFP) restored the growth of the mutant plants(Figure 2), indicating that the mutant phenotype in rice resulted from LIR1 deficiency[1].

Figure 1. Phenotypes,seed setting rate,yields of wild type,lir1-1 and lir1-2 mutant(from reference) [1].
Figure 2. Phenotypes, fresh weights, and molecular characteristics of 30-d-old wild-type, lir1-1, and two independent complementation lines [lir1/PLIR1:LIR1-GFP(from reference) [1].
  • Loss of LIR1 Reduces Photosynthetic Electron Transfer in Rice

The CO2 assimilation rate of the lir1 mutant was slightly but significantly reduced compared with wild type (Figure 3A). In accordance with the smaller plant size (Figure 1) and reduced CO2 fixation rate (Figure 3A) of the lir1 mutant compared with the wild type, the ETR(I) (electron transfer rate reflecting the capacity of PSI) was also reduced in the mutant, especially under higher actinic light intensities (Figure 3B). A similar trend was also observed for ETR(II), but the reduction was less prominent than that inETR(I) (Figure3C).Moreover, a slight increase innonphotochemical quenching (NPQ) was detected in the lir1 mutant (Figure 3D). Next, weexamined the kinetics of P700+ dark rereduction, which is used as an indicator of cyclic electron transfer [8][9][10][11]. As shown in (Figure 3E), the rereduction rate of P700+wasslower in the lir1 mutant than in the wild type[1].

Figure 3. Photosynthetic Properties of Wild-Type and Os-lir1 Plants(from reference) [1].

Expression Pattern

Figure 4. Expression of LIR1 mRNA and LIR1 protein in lir1/PLIR1:LIR1-GFP plants grown under a 12-h-light/12-h-dark photoperiod(from reference) [1].

LIR1 is regulated by light and expressed in a circadian manner. As a result, the allocation of LFNR between the stroma and chloroplast membrane is finetuned by light through the action of LIR1. Levels of LIR1 transcript increased following illumination, reaching a maximum at the end of the light period and dropping to a minimum at the end of the dark period[1][12][13]. However, marked accumulation of LIR1 was observed during the dark phase, whereas the LIR1 content decreased substantially upon the onset of illumination(Figure 4)[1] .

Subcellular localization

LIR1 is localized exclusively in chloroplasts. LIR1 is present as a soluble protein in the chloroplast stroma in addition to being bound to the thylakoid and envelope membranes[1] .

Knowledge Extension

Labs working on this gene

  • State Key Laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, Hangzhou 310058, P.R.China
  • National Engineering Technology Research Center for Slow and Controlled Release Fertilizers, Kingenta Ecological Engineering Group Co., Linyi, Shandong 276700, P.R. China
  • College of Life Science, Shaanxi Normal University, Xi’an, Shaanxi Province 710062, P.R. China
  • Molecular Plant Biology, Department of Biochemistry, University of Turku, FI-20014 Turku, Finland


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