Chloroplast RNA polymerase genes of Chlamydomonas reinhardtii exhibit an unusual structure and arrangement

Fong, Steven E.; Surzycki, Stefan

doi:10.1007/bf00351659

Cited by 33 publications

(17 citation statements)

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“…The core of the E. coli-like plastid-encoded RNA polymerase (PEP), which initiates transcription from sequences resembling E. coli s 70 -type promoters, consists of two a-subunits, and the b-, b'-, and b''-subunits encoded by the plastid genes rpoA, rpoB, rpoC1, and rpoC2, respectively (Igloi and Kössel, 1992). In C. reinhardtii, the rpoB and rpoC1 genes are further split in two parts (Fong and Surzycki, 1992;Maul et al, 2002). The a-subunit plays a role in the assembly of the polymerase complex.…”

Section: Loss Of Chloroplast Gene Transcription and Translation Affecmentioning

confidence: 99%

Repression of Essential Chloroplast Genes Reveals New Signaling Pathways and Regulatory Feedback Loops inChlamydomonas

et al. 2013

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Although reverse genetics has been used to elucidate the function of numerous chloroplast proteins, the characterization of essential plastid genes and their role in chloroplast biogenesis and cell survival has not yet been achieved. Therefore, we developed a robust repressible chloroplast gene expression system in the unicellular alga Chlamydomonas reinhardtii based mainly on a vitamin-repressible riboswitch, and we used this system to study the role of two essential chloroplast genes: ribosomal protein S12 (rps12), encoding a plastid ribosomal protein, and rpoA, encoding the a-subunit of chloroplast bacterial-like RNA polymerase. Repression of either of these two genes leads to the arrest of cell growth, and it induces a response that involves changes in expression of nuclear genes implicated in chloroplast biogenesis, protein turnover, and stress. This response also leads to the overaccumulation of several plastid transcripts and reveals the existence of multiple negative regulatory feedback loops in the chloroplast gene circuitry.

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Section: Loss Of Chloroplast Gene Transcription and Translation Affecmentioning

confidence: 99%

Repression of Essential Chloroplast Genes Reveals New Signaling Pathways and Regulatory Feedback Loops inChlamydomonas

et al. 2013

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“…Other features in 6 and ~' are indicated with contrasting patterns and labels. In 13, they are a large deletion found in several chloroplast RNA polymerases (Hudson et al 1988), a sequence resembling one found in the RNase barnase (Shirai and Go 1991), sites of substitutions leading to streptolydigin (Heisler et al 1993;Severinov et al 1993) or rifampicin (Lisitsyn et al 1984;Severinov et al 1993} resistance, location where f3 is divided in Chlamydomonas chloroplasts (Fong and Surzycki 1992), the major site of trypsin cleavage in E. coli RNA polymerase (Borukhov et al 1991), a deletable hinge region in ~ (Glass et al 1986), and sites where primer substrate analogs cross-link to the [3 subunit (Grachev et al 1989). Features noted in ~' are a putative Cys4-Zn 2+ motif conserved in most ~' homologs (Borukhov et al 1991), a sequence similarity to DNA polymerase I (Allison et al 1985), a site where ~' homologs are split in cyanobacteria and chloroplasts (Hudson et al 1988;Xie et al 1989;Igloi et al 1990;Shimada et al 1990;Fong and Surzycki 1992), a region in which Ama-resistance substitutions occur in Pol II ~' subunit homologs (Bartolomei and Corden 1987;Chen et al 1993), a site where the 3' end of the nascent transcript cross-links to ~' (Borukhov et al 1991), a site where an insertion occurs in the rice chloroplast ~' subunit (Shimada et al 1990), and a site where a large deletion occurs in M. leprae fY (Honore et al 1993).…”

Section: All But One Termination-altering Substitution Occurred In Fomentioning

confidence: 99%

Termination-altering amino acid substitutions in the beta' subunit of Escherichia coli RNA polymerase identify regions involved in RNA chain elongation.

Weilbaecher¹,

Hebron²,

Feng³

et al. 1994

Genes Dev.

118

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To identify regions of the largest subunit of RNA polymerase that are potentially involved in transcript elongation and termination, we have characterized amino acid substitutions in the 13' subunit of Escherichia coli RNA polymerase that alter expression of reporter genes preceded by terminators in vivo. Termination-altering substitutions occurred in discrete segments of [3', designated 2, 3a, 3b, 4a, 4b, 4c, and 5, many of which are highly conserved in eukaryotic homologs of 13'. Region 2 substitutions (residues 311-386) are tightly clustered around a short sequence that is similar to a portion of the DNA-binding cleft in E. coli DNA polymerase I. Region 3b (residues 718-798) corresponds to the segment of the largest subunit of RNA polymerase II in which amanitin-resistance substitutions occur. Region 4a substitutions (residues 933-936) occur in a segment thought to contact the transcript 3' end. Region 5 substitutions (residues 1308-1356) are tightly clustered in conserved region H near the carboxyl terminus of [3'. A representative set of mutant RNA polymerases were purified and revealed unexpected variation in percent termination at six different p-independent terminators. Based on the location and properties of these substitutions, we suggest a hypothesis for the relationship of subunits in the transcription complex.[Key Words: rpoC gene; [3' subunit; RNA polymerase; transcriptional termination] Received July 26, 1994; revised version accepted October 13, 1994.Escherichia coli RNA polymerase contains a core of four subunits: 6', 155 kD; [3, 150 kD; and two c~, 43 kD each. These subunits form a scaffold and catalytic center for synthesis of RNA on a double-stranded DNA template that appear to be conserved from bacteria to humans. The two largest subunits, 6' and B in E. coli, display significant sequence similarity to homologous subunits found in all multisubunit RNA polymerases (Allison et al. 1985; Jokerst et al. 1989; Young 1991 and references therein): Each contains eight to nine conserved, colinear segments, although no sequence conservation is evident between f3' and B. However, we currently lack a clear picture of how these conserved primary sequence motifs are positioned in the three-dimensional structure of RNA polymerase.In the transcription elongation complex (for review, see Das 1993;Chamberlin 1994;Chan and Landick 1994), RNA polymerase contacts the DNA over a 25-to ~Present address:

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“…The question marks indicate genes that have not yet been mapped but are assumed to be unlinked to known genes. Data for these operons are from the following: E. coli, Falk and Walker (1988) (1987) and Fong and Surzycki (1992). such as psbD/C, psaA/B, psbE/F/UJ, atpWE, and rpoB/Cl/C2, are conserved in both cyanobacteria and land plant chloroplast genomes.…”

Section: Gene Clusteringmentioning

confidence: 99%

“…Similarly, the present arrangement in C. paradoxa requires the transfer of the tsf and atplgenes to the nucleus (M. Annarella, V. L. Stirewalt, and D. A. Bryant, unpublished results). In the Chlamydomonas reinhardtii chloroplast genome, rpoC7 is apparently absent, whereas there are two rpoSlike genes (Fong and Surzycki, 1992). In addition, the rpo and atp clusters have been shuffled to scatter these genes around the genome.…”

Section: Gene Clusteringmentioning

confidence: 99%

A High-Resolution Gene Map of the Chloroplast Genome of the Red Alga Porphyra purpurea.

1993

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Extensive DNA sequencing of the chloroplast genome of the red alga Porphyra purpurea has resulted in the detection of more than 125 genes. Fifty-eight (approximately 46%) of these genes are not found on the chloroplast genomes of land plants. These include genes encoding 17 photosynthetic proteins, three tRNAs, and nine ribosomal proteins. In addition, nine genes encoding proteins related to biosynthetic functions, six genes encoding proteins involved in gene expression, and at least five genes encoding miscellaneous proteins are among those not known to be located on land plant chloroplast genomes. The increased coding capacity of the P. purpurea chloroplast genome, along with other characteristics such as the absence of introns and the consenration of ancestral operons, demonstrate the primitive nature of the f . purpurea chloroplast genome. In addition, evidence for a monophyletic origin of chloroplasts is suggested by the identification of two groups of genes that are clustered in chloroplast genomes but not in cyanobacteria. INTRODUCTIONThe complete DNA sequences of three photosynthetic land plant chloroplast genomes have revealed an enormous amount of functional and evolutionary information. The chloroplast genomes of tobacco (Shinozaki et al., 1986), rice (Hiratsuka et al., 1989), and the liverwort Marchantia polymorpha (Ohyama et al., 1986) have each been shown to contain 110 to 118 genes. The products of these genes are primarily involved in two processes: gene expresssion (59 to 60 genes) and photosynthesis (29 genes). In addition, 11 genes encoding subunits of NADPH dehydrogenase (Arizmendi et al., 1992) as well as a number of conserved open reading frames (ORFs) are contained on these genomes. The gene content of all land plant chloroplast genomes investigated is surprisingly conserved (for review, see Palmer, 1991).Alga1 chloroplast genomes, on the other hand, have not been so extensively characterized. Current information on the chloroplast genomes of chlorophyll a/b-containing algae suggest that their gene content is not too different from that of land plants, although a few genes that are absent from land plant chloroplast genomes (e.g., tufA in several species [Baldauf et al., 19901, rpl5 [Christopher and Hallick, 19891, and ccsA [Orsat et al., 19921 in Euglena gracilis) have been identified. Of greater significance, however, may be the observation of substantial genome rearrangements in green alga1 chloroplast genomes in the form of the splitting up of ancestral operons in several species of Chlamydomonas (e.g., Woessner et al., 1987) and the large number of introns, including introns within introns, To whom correspondence should be addressed. in E. gracilis (Christopher and Hallick, 1989; Copertino and Hallick, 1991). These observations are indicative of chloroplast genomes that are evolving under more relaxed constraints than land plant chloroplast genomes. lnformation about the gene content of chloroplast genomes from chromophyte (chlorophyll a/c-containing) and rhodophyte/glaucophyte (c...

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Chloroplast RNA polymerase genes of Chlamydomonas reinhardtii exhibit an unusual structure and arrangement

Cited by 33 publications

References 47 publications

Repression of Essential Chloroplast Genes Reveals New Signaling Pathways and Regulatory Feedback Loops inChlamydomonas

Repression of Essential Chloroplast Genes Reveals New Signaling Pathways and Regulatory Feedback Loops inChlamydomonas

Termination-altering amino acid substitutions in the beta' subunit of Escherichia coli RNA polymerase identify regions involved in RNA chain elongation.

A High-Resolution Gene Map of the Chloroplast Genome of the Red Alga Porphyra purpurea.

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