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Molecular Evolution and Nucleotide Sequences of the Maize Plastid Genes for the Cy Subunit of CFI (Atpa)And the Proteolipid Subunit of Cfo (Atph)

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Molecular Evolution and Nucleotide Sequences of the Maize Plastid Genes for the Cy Subunit of CFI (Atpa)And the Proteolipid Subunit of Cfo (Atph) Copyright 0 1987 by the Genetics Society of America Molecular Evolution and Nucleotide Sequences of the Maize Plastid Genes for the cy Subunit of CFI (atpA)and the Proteolipid Subunit of CFo (atpH) Steven R. Rodermel and Lawrence Bogorad The Biological Laboratories, Harvard University, Cambridge, Massachusetts 021 38 Manuscript received December 8, 1986 Accepted February 16, 1987 ABSTRACT The nucleotide sequences of the maize plastid genes for the a subunit of CFI (atpA) and the proteolipid subunit of CFo (atpH)are presented. The evolution of these genes among higher plants is characterized by a transition mutation bias of about 2:l and by rates of synonymous and nonsynony- mous substitution which are much lower than similar rates for genes from other sources. This is consistent with the notion that the plastid genome is evolving conservatively in primary sequence. Yet, the mode and tempo of sequence evolution of these and other plastidencoded coupling factor genes are not the same. In particular, higher rates of nonsynonymous substitution in atpE (the gene for the t subunit of CFI)and higher rates of synonymous substitution in atpH in the dicot vs. monocot lineages of higher plants indicate that these sequences are likely subject to different evolutionary constraints in these two lineages. The 5‘- and 3‘- transcribed flanking regions of atpA and atpH from maize, wheat and tobacco are conserved in size, but contain few putative regulatory elements which are conserved either in their spatial arrangement or sequence complexity. However, these regions likely contain variable numbers of “species-specific”regulatory elements. The present studies thus suggest that the plastid genome is not a passive participant in an evolutionary process governed by a more rapidly changing, readily adaptive, nuclear compartment, but that novel strategies for the coordinate expression of genes in the plastid genome may arise through rapid evolution of the flanking sequences of these genes. HE genes for the constituent proteins of the FROMMand EDELMAN1983; DENO,SHINOZAKI and T plastid coupling factor for photophosphoryla- SUGIURA1983, 1984; BOVENBERGet al. 1984; tion (CFt-CFo complex) are dispersed between the HUTTLYand GRAY1984; KO, STRAUSand WILLIAMS genomes of the plastid and nucleus. In all species 1984; ZURAWSKI and CLEGG1984; OLIVER1984; examined to date, atpA, atpB, atpE, atpF, atpH and PHILLIPS1985; BIRDet al. 1985; RODERMELand Bo- atpZ (for the a, /3 and E subunits of CFI and subunits GORAD 1985, 1986). Among higher plants, the nu- I, I11 and IV of CFo, respectively) are encoded in the cleotide sequences of all the plastid-encoded coupling plastid DNA, while atPC, atpD and atpG (for the y factor genes have been reported in tobacco (SHINO- and 6 subunits of CF, and subunit I1 of CFo, respec- ZAKI et al. 1983a; DENO, SHINOZAKIand SUGIURA tively) are encoded in the nuclear genome and trans- 1983,1984)and wheat (HOWEet al. 1982,1985;BIRD ported into the plastid post-translationally (e.g., MEN- et al. 1985;J. C. GRAY,unpublished data). In addition, DIOLA-MORGENTHALER,MORGENTHALER and PRICE among angiosperms the sequence of atpBE has been 1976; BOUTHYETTEand JAGENDORF1978; NELSON, reported in maize (KREBBERSet al. 1982, spinach NELSONand SCHATZ1980; NECHUSHTAIet al. 198 1 ; (ZURAWSKI,BOTTOMLEY and WHITFELD1982), barley WE~THOFFet al. 198 1, 1985; WATANABEand PRICE (ZURAWSKI and CLEGG1984), and pea (WHITFELD, 1982). The plastid-encoded genes appear to be highly ZURAWSKI and BOTTOMLEY1983), and the sequences conserved in their sequence arrangement among most of atpH and atpZ have been reported for spinach (ALT higher plant plastid DNAs. at@ and atpE are clus- et al. 1983) and pea (COZENSet aE. 1986), respectively. tered in one transcription unit, either partially over- The nucleotide sequences of atpA and atpH from lapping or immediately adjacent to one another, while maize are presented in the current studies. atpZ, atpH, atpF and atpA are clustered (in this polar- Although the striking conservation of sequence con- ity) in another transcription unit some distance away tent and arrangement of the plastid-encoded coupling from the atpBE locus on the plastid chromosome (e.g., factor genes is in accord with the notion that the WESTHOFFet al. 1981, 1985; KREBBERSet al. 1982; molecular evolution of angiosperm plastid DNAs is HOWEet al. 1982, 1983; DEHEJJet al. 1983; FLUHR, distinctly conservative in nature (reviewed in PALMER 1985a,b), little is known about the mode and tempo The sequence data presented in this article have been submitted to the EMBL/GenBank Data Libraries under the accession number Y00310. of sequence change in various regions of the plastid Genetics 116: 127-139 (May, 1987) 128 S. R. Rodermel and L. Bogorad chromosome. Comparative DNA hybridization and RNAses change in activity during greening, the flank- restriction site polymorphism analyses have shown ing regions of atpA and atpH likely contain transcrip- that sequences within the large inverted repeat struc- tion initiation and/or termination sequences involved ture (characteristic of most higher plant plastid DNAs) in the photoregulation of transcript levels. Since com- are evolving more slowly than sequences within the plex transcript patterns have also been observed for single copy regions of the chromosome (PALMER the region of the plastid chromosome bearing atpA 1985a). However, other than these global studies, and atpH in wheat (BIRDet al. 1985) and tobacco detailed investigations of nucleotide divergence in the (FLUHR,FROMM and EDELMAN1983; DENO,SHINO- plastid DNA are extremely limited, and have been ZAKI and SUGIURA1984), it was hoped that compara- restricted in the case of protein-coding genes to com- tive sequence analyses of these regions might reveal parative studies of rbcL (the gene for the large subunit conserved sequence elements that may be involved in of ribulose bisphosphate carboxylase), at#, and atpE transcriptional and/or processing activities. The data (SHINOZAKIet al. 1983b; ZURAWSKI, CLEGG and in this report indicate, however, that these, and other, BROWN1984; ZURAWSKIand CLEGC 1984). These putative regulatory elements in these regions are not analyses have demonstrated that the patterns and particularly conserved among these three species. levels of nucleotide substitution are the same in these This is reflected in rates of nucleotide divergence in three genes in comparisons between maize and barley, these regions which equal, or vastly exceed, synony- indicating that each codon position is evolving at mous substitution rates (depending upon the se- about the same rate in these genes in these two mon- quences compared). However, the data are not incon- ocots (ZURAWSKIand CLEGG1984). One purpose of sistent with the notion that these regions contain this study was to ascertain whether other plastid cou- variable numbers of “species-specific”regulatory ele- pling factor genes are evolving like atpB and atpE in ments. the monocots, and to investigate whether the mode and tempo of sequence evolution of these genes is MATERIALS AND METHODS similar in the dicot, as well as monocot, angiosperm The plasmids pZmc527, pZmc415 and pZrl2 contain Zea lineages. The data show that the coupling factor genes mays plastid DNA restriction fragments BamHI 3, BamHI differ in their patterns of nucleotide substitution both 24, and EcaRI b, respectively, cloned in pBR322 (RODERMEL and BOGORAD1985). The nucleotide sequences of portions within and between the two lineages, and that these of these fragments containing the genes for the a subunit differences are manifested in differing constraints on of CF, (atpA) and subunit 111 of CF, (atpH) (RODERMELand nonsynonymous or synonymous codon selection. BOGORAD,1985, 1986), were determined by the MAXAM- Another purpose of this investigation was to exam- GILBERTchemical cleavage method (1 980). High resolution S-1 nuclease mapping experiments were ine the patterns of nucleotide substitution in the 5‘- performed by procedures modified from BERKand SHARP and 3 ’-transcribed regions flanking the protein coding (1977). Total cell RNA (1 50 fig) from 16-hr-greened maize sequences of atPA and atpH. Previous comparative seedlings (RODERMELand BOCORAD1985) was mixed with analyses of the flanking regions of plastid-coding approximately 100 ng of DNA (5’4abeled at a single end) genes, though limited, have shown that the 5’-flanking in a total volume of 50 pl hybridization buffer [SOW deion- ized formamide/l mM Na2EDTA (pH 8.0)/0.4 M NaCl/4O region of rbcL is evolving at about half the synony- mM PIPES (pH 6.4)) The sample was incubated for 10 min mous substitution rate of the gene itself in compari- at 80” to denature the DNA, and then transferred to 41” sons between maize and barley, indicating this region for 16 hr. Following the addition of 400 pl ice cold S-1 is selectively constrained in its sequence evolution with nuclease buffer [0.28 M NaC1/0.05 M sodium acetate (pH 4.6)/4.5 mM ZnS04/20 pg carrier tRNA], the sample was respect to the third codon position (ZURAWSKI,CLECC incubated with S-1 nuclease (75 units, New England Nu- and BROWN1984). The constraints in this region were clear) for 30 min at 37”. After phenol/chloroform extrac- attributed to conserved sequence requirements for tion, the ethanol precipitate was vacuum desiccated, resus- promoter-binding. Northern hybridization experi- pended in sequencing dye, and electrophoresed through 8% ments have established that atpA and atpH from maize polyacrylamide/7 M urea sequencing gels
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