Features of Plastid Genes

Features of Plastid Genes

Maize plastid genes for the large subunit of ribulose bisphosphate carboxylase（rc-L），the beta and epsilon subunits of the coupling factor CFi（cfl-BE），the ribosonial protein S4（rp-S4），subunit Ⅲ of CF0（cfo-Ⅲ），the alpha subunit of CFi（cfl-A），photogene 32［32］or ps2B，ie，the gene for the the B protein of photosystem 2，plus seven UORFs have been sequenced to date［33-35；S.R.Rodermel and L.Bogorad.unpublished；U.Kück.L.Fish.and L.Bogorad，unpublished；E.T.Krebbers，K.M.T.Muskavitch.and L.Bogorad.unpublished；A.Steinmetz and L.Bogorad.unpublished；L.Mclntosh and L.Bogorad.unpublished.］In all，DNA sequences have been determined for 11 polypeptides containing an aggregate of more than 5，000 amino acids.In addition，genes for 12 tRNAs have been sequenced［25，27，36，37；E.T.Krebbers，A.Steinmetz，and L.Bogorad，unpublished］.

Conserved sequences upstream of transcription start sites for a number of plastid genes from maize and other plants resemble prokaryotic promoters.A consensus sequence is［37］：

Variations on this consensus sequence are considerable and nested pairs of such conserved sequences occur upstream of the coding regions of a few genes.At the present time，however，there is no direct experimental evidence that these conserved sequences serve as recognition sites for plastid DNA-dependent RNA polymerase.

Another feature observed in this first plastid gene to be sequenced-maize rc-L［33］is the presence of a short nucleotide sequence complementary to nucleotides at the 3'end of maize 16S rRNA［29］.This sequence is analogous to the Shine-Dalgarno sequence of E.coli messenger RNAs；it occurs a few nucleotides upstream of the translation start site.Such sequences（given as they would appear in the transcription product of the gene）that have been seen in plastid genes of maize and other plants are shown in Table 1.These sequences vary in the number of nucleotides complementary to 16S rRNA as well as in the distance between the complementary sequence and the 5'end of the initiating methionine translation codon.There is no homologous plastid translation system available at present to determine whether these differences significantly influence the relative translation frequency of different mRNAs.There is one case in which such a sequence has not been recognized at the expected location［41］.

Unlike mitochondria，chloroplast genes use the universal code for amino acids.All of the codons possible in the universal code are employed in one protein or another that has been sequenced to date.The data in Table 2 show codon synonym usage distribution for some amino acids of three maize and one tobacco plastid genes［33-35，38］.In the bottom section of the table are the synonyms most highly preferred in the plastid genes but the bias is not the same in different plastid genes（eg，Tyr/UAU in rp-S4 and cfl-B vs re-L）.Differences between ribosomal protein genes rp-S4 and rp-S19 may be due to differences in the organisms from which the genes were sequenced，maize and tobacco，respectively.(https://www.daowen.com)

Two kinds of overlaps of coding regions have been observed in the maize plastid chromosome.A gene for a 1.6-kb transcript overlaps divergently the gene for tRNAHis［26］.Another overlap has been observed in the coding sequences for the beta and epsilon subunics of CF1［34］.In the latter case，the last A of the triplet coding for lysine becomes，together with the U and G of the 3'terminal codon of the mRNA for the beta subunit of CF1，part of the translation initiation codon for the epsilon subunit.

As described above，in the polycistronic message for the beta and epsilon subunits of CF1the coding regions overlap with a one nucleotide frameshift.There are other cases in the maize plastid chromosome in which two genes are transcribed in a single RNA molecule although the genes themselves are well separated from one another.One example is the single transcript containing messages for cfo-Ⅲ and cfl-A［S.R.Rodermel and L.Bogorad，unpublished］.

Maize chloroplast genes for alanine，isoleucine，leucine，and valine tRNAs（tA-UGG，tI-GAU，tL-UAA，and tV-UAC）contain introns［25，36；E.T.Krebbers，A.Steinmetz，and L.Bogorad，unpublished］.The introns range in size from 468 to 949 bp and，unlike nuclear genes for tRNAs in yeast，the introns are not always at the same position in the tRNA gene.For example，the intron in the tL splits the anticodon while in the other three genes the introns are within the anticodon loop but at different locations.

In summary，we have a fairly clear idea of consistent（but not necessarily universal）features of plastid genes but the number of cases studied is comparatively small and thus we may have a rather narrow view of the range of variation that occurs.These features are the presence of conserved sequences resembling prokaryotic promoters associated with each gene or each transcript；the presence of a Shine Dalgarno-like sequence upstream of the translation start site of most genes；and the use of the universal nucleotide code for amino acids.The more variable features include divergent overlaps of coding regions and frameshift overlaps in the same strand；polycistronic as well as monocistronic messages，and introns.