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TCP34, a Nuclear-Encoded Response Regulator-Like TPR Protein of Higher Plant Chloroplasts

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TCP34, a Nuclear-Encoded Response Regulator-Like TPR Protein of Higher Plant Chloroplasts doi:10.1016/j.jmb.2005.12.079 J. Mol. Biol. (2006) 357, 535–549 TCP34, a Nuclear-encoded Response Regulator-like TPR Protein of Higher Plant Chloroplasts P. Weber1†, H. Fulgosi1†, I. Piven1,L.Mu¨ ller2, K. Krupinska2 V. H. Duong1, R. G. Herrmann1 and A. Sokolenko1* 1Department fu¨r Biologie I We describe the identification of a novel chloroplast protein, designated Bereich Botanik, Ludwig- TCP34 (tetratricopeptide-containing chloroplast protein of 34 kDa) due to Maximilians-Universita¨t the presence of three tandemly arranged tetratricopeptide repeat (TPR) Menzingerstr. 67, 80638 arrays. The presence of the genes encoding this protein only in the genomes Mu¨nchen, Germany of higher plants but not in photosynthetic cyanobacterial prokaryotes suggests that TCP34 evolved after the separation of the higher plant 2Institut fu¨r Botanik, lineage. The in vitro translated precursor could be imported into intact Universita¨t Kiel, spinach chloroplasts and the processed products showed stable association Olshausenstr. 40, with thylakoid membranes. Using a specific polyclonal antiserum raised 24098 Kiel, Germany 1 2 against TCP34, three protein variants were detected. Two forms, T and T , were associated with the thylakoid membranes and one, S1, was found released in the stroma. TCP34 protein was not present in etioplasts and appeared only in developing chloroplasts. The ratio of membrane-bound and soluble forms was maximal at the onset of photosynthesis. The high molecular mass thylakoid TCP34 variant was found in association with a transcriptionally active protein/DNA complex (TAC) from chloroplasts and recombinant TCP34 showed specific binding to Spinacia oleracea chloroplast DNA. Two TCP34 forms, T1 and S1, were found to be phosphorylated. An as yet unidentified phosphorelay signal may modulate its capability for plastid DNA binding through the phosphorylation state of the putative response regulator-like domain. Based on the structural properties and biochemical analyses, we discuss the putative regulatory function of TCP34 in plastid gene expression. q 2005 Elsevier Ltd. All rights reserved. Keywords: DNA-binding; post-transcriptional regulation; signal trans- *Corresponding author duction; TAC; TPR array Introduction are synthesized in the cytosol and subsequently imported into the organelle.1–6 Both, genetic and The expression of chloroplast genes coding for biochemical data suggest that these factors act components of the photosynthetic machinery either as constituents of the organellar transcrip- depends largely on nucleus-encoded factors that tion/translation machinery or are involved in various post-transcriptional processes, such as RNA stabilization and processing.7–10 Recent work † P.W. and H.F. contributed equally to this work. indicates that several chloroplast proteins involved Present addresses: P. Weber, Institut fu¨ r Neuropatho- in post-transcriptional steps of chloroplast gene logie, Ludwig-Maximilians-Universita¨t, Marchioninistr. expression contain tetratricopeptide repeat (TPR) or 17, 81377 Mu¨ nchen, Germany; H. Fulgosi, Department of TPR-like motifs, which usually interact with large Molecular Genetics, Ruder Bosˇkovic´ Institute, Zagreb, protein complexes.11,12 TPR arrays consist of a Croatia; V. H. Duong, Centre of Biotechnology, Vietnam repeated, degenerated stretch of 34 amino acid National University, Hanoi, Vietnam. residues and are presumed to form helix-turn Abbreviations used: TAC, transcriptionally active chromosomes; TCP34, tetratricopeptide-containing poly- structures acting as scaffolds to mediate protein– protein interactions and often in the assembly/ peptide; TPR, tetratricopeptide repeat; PEP, encoded 13,14 RNA polymerase. disassembly of multiprotein complexes. E-mail address of the corresponding author: The level of expression of chloroplast genes [email protected] varies considerably during plastid development 0022-2836/$ - see front matter q 2005 Elsevier Ltd. All rights reserved. 536 TCP34, a Response Regulator-like TPR Protein and differentiation, and is substantially influenced reported, i. e. in rhodoplasts from the raphidophytic by changes in light intensity and quality. Protein alga Heterosigma akashiwo.26 phosphorylation and redox control are considered Here, we report the identification and characteri- to provide regulatory feed-back connections zation of a novel nucleus-encoded, plastid-located between photosynthesis and organellar gene polypeptide of 37.2 kDa, designated TCP34 (tetra- expression. Activation and coordination of these tricopeptide-containing chloroplast protein of mechanisms require a precise sensing and regu- 34 kDa). The protein possesses remarkable struc- lation which can, in principle, be managed by tural features and specifically binds to plastid “classical” two-component systems consisting of a protein–DNA complexes, suggesting a regulatory sensor kinase and its cognate response regulator.15–17 role in plastid gene expression by means of protein– The sensor component recognizes environmental protein and/or protein–DNA interactions. stimuli through phosphorylation of a conserved histidine residue within its kinase domain. Sub- sequently, the phosphoryl group is transferred to a Results conserved aspartate residue in the receiver domain of the response regulator component. As a con- Isolation and characterization of a spinach cDNA sequence of the phosphorylation-induced confor- encoding a novel chloroplast precursor protein mational change, the output activity of the response regulator is modulated. Several proteins similar to During the course of studies aimed at isolating components involved in animal and fungal signal thylakoid protein kinases and molecular compo- transduction pathways have been identified in nents involved in regulation of photosynthesis and various compartments of the plant cell.18–21 To chloroplast gene expression, a spinach cDNA elucidate an entire plant signal transduction path- encoding a novel tetratricopeptide-containing poly- way incorporating a two-component regulatory peptide, designated TCP34, was identified. The full- system, the output activity of plant response length cDNA contained a single open reading frame regulator proteins must be known. Whereas various of 1237 bp that coded for a polypeptide of 339 bacterial response regulator proteins are known, amino acid residues (Figure 1(a)) with a predicted and function as transcription factors in the regu- molecular mass of 38.2 kDa. The protein-coding lation of gene expression, only a limited number of sequence starts from ATG at position 61, which is plant counterparts with DNA-binding activities embedded in a typical plant translation initiation have been isolated so far. Among 14 Arabidopsis consensus sequence AACAATGGC.27 The ATG thaliana response regulator homologues identified codon is preceded by an in-frame upstream stop up to now,20,22–24 two, ARR1 and ARR2, have codon, implying that it represents the codon for the been found to bind double-stranded DNA in a potential initiator methionine. The 30 end of the sequence-specific manner. They both appear to cDNA carried a poly(A) sequence. operate as transcriptional activators in the The most recent protein databases were searched expression of nuclear genes.22,25 For plastids, only with the deduced 339 amino acid sequence as the oneresponseregulator-likeproteinhasbeen query using the BLAST and FASTA3 programs at Figure 1. (a) Schematic presentation of functional domains and amino acid sequence of spinach TCP34 precursor protein. The hydrophilic protein contains a single predicted membrane-anchoring (MA) domain located at the C terminus (italics in the sequence). The putative response regulator-like domain (RR) is in boldface. Asp95, the putative phosphorylation site in that domain, is presented in italic boldface. The two serine-rich regions S56–S73, and S268–S298 are in grey italic boldface. The TPR domain is underlined. Two histidine residues within the second TPR unit are in grey boldface. A single cysteine residue is indicated with an asterisk, a putative processing site of the transit peptide (TP) by an arrow. HLH, helix-loop-helix. The numbers below the protein scheme indicate the amino acid range of each domain. (b) Predicted secondary structure of TCP34. The smaller cylinder depicts six TPR amphipatic helices forming a bulky moiety with exposed charged residues. Larger cylinders represent two helices forming a putative helix-loop-helix domain. The separating loop is highly negatively charged. Regions rich in serine are indicated with S; interchanging charged residues are represented by C or K. The protein is presumed to be anchored monotopically in the thylakoid membrane with its carboxy-terminal hydrophobic stretch. TCP34, a Response Regulator-like TPR Protein 537 the NCBI and GenomeNet www-services. A search factors29 and the catalytic domain of PPZ1 phos- of the A. thaliana databases revealed only a single phatase.30 The charged region, integrating the helix- homologous gene (At3g26580) encoding a protein loop-helix motif, and the serine-rich segment of unknown function with 67% identity. Northern together form an w140 residue long domain similar analysis of total RNA isolated from spinach and to the CheY superfamily of two-component A. thaliana seedlings revealed a single transcript of response regulators (Figure 2(b)). A crucial feature 2.0 kb (data not shown), which argues for an of these components is the conservation of D34, D95 absence of alternative splicing of the TCP34 and K147 (corresponding
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