nuclear control of plastid and mitochondrial development in higher

P1: ARS/sny P2: ARS/ary QC: ARS/anil T1: ARS

April 13, 1998 16:13 Annual Reviews AR060-18

Annu. Rev. Plant Physiol. Plant Mol. Biol. 1998. 49:453–80Copyright c© 1998 by Annual Reviews. All rights reserved

NUCLEAR CONTROL OF PLASTIDAND MITOCHONDRIALDEVELOPMENT INHIGHER PLANTS

P. Leon and A. ArroyoDepartamento de Biologia Molecular de Plantas, Instituto de Biotecnolog´ıa UNAM,Cuernavaca, Morelos 62250 Mexico; e-mail: [email protected]

S. MackenzieDepartment of Agronomy, Lilly Hall of Life Sciences, Purdue University, WestLafayette, Indiana 47907

KEY WORDS: organelle biogenesis, transcriptional regulation, posttranscriptional regulation,chloroplast mutants, mitochondrial mutants

ABSTRACT

The nucleus must coordinate organelle biogenesis and function on a cell andtissue-specific basis throughout plant development. The vast majority of plastidand mitochondrial proteins and components involved in organelle biogenesis areencoded by nuclear genes. Molecular characterization of nuclear mutants hasilluminated chloroplast development and function. Fewer mutants exist that af-fect mitochondria, but molecular and biochemical approaches have contributedto a greater understanding of this organelle. Similarities between organelles andprokaryotic regulatory molecules have been found, supporting the prokaryoticorigin of chloroplasts and mitochondria. A striking characteristic for both mito-chondria and chloroplast is that most regulation is posttranscriptional.

CONTENTS

INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 454

A DEVELOPMENTAL CONSIDERATION. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 455

NUCLEAR REGULATION OF THE EARLY PHASES OF CHLOROPLASTDEVELOPMENT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 455

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Initial Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 455MUTANTS THAT AFFECT EARLY CHLOROPLAST DEVELOPMENT. . . . . . . . . . . . . . 456

Early Developmental Mutants. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 456Pigment Mutants. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 457

NUCLEAR REGULATION DURING CHLOROPLAST DEVELOPMENT. . . . . . . . . . . . . 458Division . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 458Transcription . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 459Posttranscriptional Processing. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 460Nuclear Regulation of Targeting. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 463

NUCLEAR SIGNALS FOR CHLOROPLAST DEVELOPMENT. . . . . . . . . . . . . . . . . . . . . 464Light Regulation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 464

MUTATIONAL ANALYSIS OF PLANT MITOCHONDRIA . . . . . . . . . . . . . . . . . . . . . . . . . 465

NUCLEAR REGULATION OF MITOCHONDRIAL GENE EXPRESSION. . . . . . . . . . . . . 466Regulation of Transcription. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 466Transcript Processing. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 467Transcript Editing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 468Translational/Posttranslational Regulation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 469

NUCLEAR INFLUENCE ON THE MITOCHONDRIAL GENOME. . . . . . . . . . . . . . . . . . . 470

PERSPECTIVES. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 472

INTRODUCTION

It is generally believed that higher plant evolution occurred through two differ-ent endosymbiotic events, both involving prokaryotic organisms. Eukaryoticcells initially acquired mitochondria through endosymbiosis of a bacterium.Later, the chloroplast was derived from a cyanobacteria-type organism (149).Mitochondria and plastids each contain an autonomous genome, yet the nu-cleus now plays a major role in determining organelle properties, because itencodes the majority of the genes required for function and maintenance. Thepresence of organelle genes in two different cellular compartments creates anobvious regulatory problem. The cell must coordinate the expression of nuclear-encoded genes, present in only one or a few copies per cell, with the expressionof organellar-encoded genes present in several hundred or even thousands ofcopies. Coordinate control is a necessity for mitochondrial and chloroplastfunction and likely requires new regulatory pathways not present in the originalendosymbionts (48).

Many of the structural genes required for the photosynthetic and respiratoryreactions have been cloned and sequenced. We have much less informationabout the many nuclear genes required in development. This is a broad subjectfor study, as higher plants contain a variety of differentiated plastids types, re-flecting cell and tissue type (85). This review concentrates primarily on recentadvances in organelle development and function in vascular plants. Recent pub-lished reviews cover other photosynthetic organisms such asChlamydomonasandEuglena(45, 54, 142, 160).



CONTROL OF PLASTID AND MITOCHONDRIAL DEVELOPMENT 455

A DEVELOPMENTAL CONSIDERATION

Plastids exhibit a very clear developmental program. All plastids are derivedfrom proplastids present in meristematic cells (85). Upon cell differentiation,proplastids also differentiate. Plastids can also redifferentiate in response toexternal environmental signals (85). The best characterized differentiation pro-cess results in a chloroplast.

Almost every step of plastid development depends on the direct action ofnuclear-encoded molecules. Molecules required in the initial stages of organelledifferentiation could affect all plastid types, whereas molecules necessary atlater stages should affect only one plastid type.

Chloroplast differentiation appears to start very early during plant develop-ment. The leaf primordia that develop from the apical meristem contain mes-ophyll tissue from which most of the chloroplasts will be derived. Mesophyllchloroplasts can then undergo further differentiation, as is well-documented fordifferentiation of mesophyll and bundle sheath chloroplasts of C4 plants (124).

Microscopic studies have provided a sequential picture of the events duringplastid differentiation (95). Further refinement of these events at the molecularlevel has been difficult. It is possible that many events during chloroplast dif-ferentiation are concurrent or occur in such a brief period that they cannot bedissected with the available techniques. In monocot leaves initial differentia-tion events include DNA replication and production of the chloroplast decodingapparatus (11, 123). Production of thylakoid membranes and accumulation ofspecific photosynthetic complexes are detected in later stages (85, 123).

The study of the participation of nuclear genes in plastid development hasbenefited from the isolation and characterization of an enormous number ofmutants, many of which will be described in this review. In contrast to the well-defined developmental program of the chloroplast, the mitochondrion does nothave an obvious developmental program. However, it is clear that mitochondriaplay essential roles throughout cellular differentiation and take on a pronouncedrole at particular points in higher plant development.

NUCLEAR REGULATION OF THE EARLY PHASESOF CHLOROPLAST DEVELOPMENT

Initial StepsTranscription is a central regulatory point during the early stages of chloroplastdifferentiation (54, 123). Transcription is low in the proplastid, and is activatedin the immature chloroplast (11). In parallel, the synthesis of both the transcrip-tion and translation apparatus takes place (63). Several lines of evidence suggesta nuclear origin for the enzyme responsible for initial transcriptional activity in



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the chloroplast (69, 70, 74, 122). For example, in the parasitic plantEpifagusvirginiana, which lacks the chloroplast-encoded subunits of RNA polymerase,and in thealbostriansbarley mutant, which lacks ribosomes, transcription ofparticular plastid genes has been detected (70, 122).

Allison et al (2) have shown that a subset of the chloroplast-encoded genesare transcribed by a second RNA polymerase in which at least some sub-units are nuclear-encoded. The role of this nuclear-encoded RNA polymerase(NEP polymerase) seems to be primarily, but not exclusively, the expressionof housekeeping genes during the early phases of chloroplast development(54, 123, 160). Among the genes transcribed by this enzyme are the rRNAgenes (2), ribosomal proteins (70), and therpoB operon (72), which encodesthe subunits of the plastid-encoded RNA polymerase. Candidates for the NEPenzyme have been purified from spinach (97). NEP is probably encoded bythe RpoPtgene recently isolated fromArabidopsis(68); it shares importantsimilarities with phage-type RNA polymerases.

Concomitant with transcription of the rRNA genes, nuclear-encoded ribo-somal proteins are synthesized (63) and imported into the chloroplast to formribosomes, in preparation for translation in later stages of development. Thecurrent view is that the nucleus initiates chloroplast differentiation and provideskey components of the transcriptional and translational machinery required forlater stages of development (123).

MUTANTS THAT AFFECT EARLY CHLOROPLASTDEVELOPMENT

Early Developmental MutantsAlthough many chloroplast developmental mutants have been isolated, few ofthem affect initial events in organelle biogenesis. Because the plastid producesmany essential compounds such as hormones, lipids, and cofactors, mutationsthat interrupt these pathways will probably disrupt both plastid biogenesis andplant function. Theamidophosphoribosyl-transferase deficient(atd) mutantfrom Arabidopsisis an example; chloroplast development is arrested at anearly stage inatd lines because one of the genes encoding the ATase enzyme,(ATase2gene) is disrupted; a key enzyme of purine biosynthesis. This nucleargene provides the only ATase activity in photosynthetic tissue, but a secondgene might permit purine biosynthesis in other tissues (170).

Similar examples of fundamental mutants includedcl from tomato (80),dag from Antirrhinum (18), and theArabidopsisalbino T-DNA taggedcla1-1(110). Plastids present in these plants are very small, with almost no thylakoid




membrane, and thus resemble proplastids. mRNA analyses showed thatCLA1,DAG, andDCL genes are normally expressed not only in photosynthetic butalso in nonphotosynthetic tissue, suggesting that these genes are probably re-quired for the development of different plastid types. In bothcla1-1(J Estevez,A Arroyo, A Cantero & P Leon, unpublished results) anddag (18) plants,chloroplasts and etioplasts are abnormal. Each of these genes encodes a novelplastid-localized protein of unknown function. Null mutations of theDCLgene cause embryo abortion (JS Keddie & W Gruissem, unpublished data).Proteins homologous to CLA1 are found in photosynthetic and nonphotosyn-thetic prokaryotes; recent data indicate that this protein may be involved in thebiosynthesis of a novel isoprenoid pathway conserved in evolution (J Estevez,A Arroyo, A Cantero & P Leon, unpublished results). At the morphologicallevel,daganddcl plants apparently lack palisade cells (18, 80).

Similar alterations occur in plastids after disruption of thePALE CRESS(PAC), IMMUTANTS(IM ), and ATD genes ofArabidopsis(139, 170, 178).Because it seems unlikely that all these genes directly regulate leaf differenti-ation, a novel signaling system during early plastid development has been hy-pothesized that would affect the final divisions of mesophyll cells in the prepal-isade stage (18). Compelling evidence indicates that a factor originating in thechloroplast signals its developmental stage to the nucleus, coordinating the ex-pression of many nuclear-encoded genes (reviewed in 162, 165). Alterations inthis signal transduction pathway do not have any obvious impact on mesophyllmorphology. These results suggest that multiple signals might exist to ensureproper coordination between cell and organelle during plastid development.

Genes involved in early plastid development have also been described in C4maize plants. Phenotypic characteristics of thebsd3(R Roth & J Langlade,unpublished data) mutant resemble those described above, with no thylakoidformation and alterations in different plastid types. However, in thebsd3mu-tant, neither the morphology of the photosynthetic tissue nor accumulation ofthe C4 nuclear-encoded photosynthetic genes is altered. These results suggestthat, in contrast to what it is found in C3 plants, leaf development in C4 plantssuch as maize might not rely on chloroplast signals for final differentiation.

Pigment MutantsDirect participation of pigment biosynthesis in chloroplast development hasbeen difficult to establish because of pleiotropy. Several mutants with alteredchlorophyll accumulation have been described (158). In all cases, chloroplastdevelopment was arrested at initial membrane assembly, suggesting that chloro-phyll synthesis and chloroplast development may be interdependent (174). Be-cause these kinds of mutations can disrupt different metabolic activities, loss of



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chlorophyll along with other plastid components might represent secondary ef-fects (62). Recent data that support the hypothesis that chlorophyll productionhas the potential to influence organelle development come from work withmutants altered in chlorophylla/b ratio (40) and theolive (oli) mutant fromAntirrhinum(73). TheOLI gene seems to encode a key enzyme of the chloro-phyll biosynthetic pathway, the porphyrin IX Mg-chelatase.oli conditionallyaffects chlorophyll synthesis and organelle development, and the chloroplastsin this mutant contain thylakoids but no grana. This phenotype seems to bethe direct result of a block in chlorophyll biosynthesis, not a result of photo-oxidation (73). Chlorophyllb–deficient mutants usually result in smaller pho-tosynthetic unit sizes (115), possibly because of LHC destabilization and anabnormal thylakoid membrane system (39). Chlorophyll appears to be neces-sary for either translation or stability of the nuclear-encoded apoproteins of thelight-harvesting complex and the formation of grana-deficient thylakoid mem-branes (64, 88). Gene disruptions at other steps of chlorophyll biosynthesis dis-play alterations in plastid development even in the dark, where photo-oxidativedamage does not exist, supporting the hypothesis that chlorophyll is involveddirectly (39, 64, 146, 158).

NUCLEAR REGULATION DURING CHLOROPLASTDEVELOPMENT

DivisionOrganelle division is a fundamental process in chloroplast and mitochondrialbiogenesis. With the recent isolation of several mutants fromArabidopsisthaliana, Pyke and coworkers have contributed to our understanding of themolecular basis of control of chloroplast division (135, 136). These mutants,namedarc for “accumulation and replication of the chloroplast,” demonstratethat several nuclear genes are required. Interestingly, all mutants analyzed sofar show a reduction in chloroplast number per mesophyll cell, but no obviousplant morphological alterations (134a, 135). It is likely that the total amount ofchloroplast material within a cell is the important parameter for cell functionrather than chloroplast number.

Physiological analysis of mostarc mutants shows plastid division to be al-tered only in chloroplast (134a). An exception is thearc6mutant, the most ex-treme mutation isolated, which may affect division at the proplastid state (134a)the gene affected in thearc6 mutant appears to be a homolog of theFtsZpro-tein, implicated in bacterial cell division (12, 31, 131).FtsZ, which polymerizessimilarly to eukaryotic cytoskeletal elements, may be a progenitor of tubulin




(38), which raises the intriguing possibility that the mechanism of organelledivision may be, to some degree, conserved between prokaryotes and plants.

TranscriptionAlthough transcriptional control is the key element setting expression of nuclear-encoded plastid-localized gene products (90), the relative transcription rates ofmany chloroplast-encoded genes are constant in different tissues and at differentdevelopmental stages. This suggests that posttranscriptional events may pre-dominate in chloroplast gene regulation (29). Evidence suggests, however, thatstage-specific transcriptional regulation occurs during leaf maturation. For ex-ample, some plastid-encoded genes fluctuate in transcription levels in responseto factors such as light and plastid type (103, 114, 123, 138). This is the casefor the light-activated genes such aspsbAin barley and maize (86),psbD-psbCin barley (150), andpetG from maize (59). Similarly, the transcription ratesof rbcL, psbA, andatpB/Egenes fromArabidopsisare specifically reduced inamyloplasts (77). All these genes are preferentially transcribed by the better-characterized plastid-encoded RNA polymerase (74). It is tempting to attributethe selectivity of the transcriptional response during chloroplast development tothe interaction of the core RNA polymerase with specific regulatory molecules(103). These factors might be available only under certain conditions and inthis way might regulate gene transcription during development.

Two types of factors seem to play a role in the regulation of chloroplasttranscription: factors that bind DNA only in the presence of the RNA poly-merase (sigma-like factors) and sequence-specific proteins acting as activatorsor repressors. Several sigma-like factors have been recognized (102, 167). Forexample, a 90-kDa sigma-like factor from mustard is present in young butnot in mature spinach leaves (96). In contrast, the transcriptional activity ofchloroplasts and etioplasts in mustard appears to be modulated by differen-tial phosphorylation of three sigma factors in response to light (166). In thisway only dephosphorylated factors permit efficient transcription initiation ofpromoters like that ofpsbA. The most likely candidate responsible for phos-phorylation of these sigma-like factors is a serine/threonine kinase found toassociate with the active transcription complex (103).

Evidence has emerged recently for a number of sequence-specific bindingfactors that might also modulate expression of photosynthetic genes under spe-cific conditions. A nuclear factor involved in differential light-mediated tran-scription of thepsbDgene has been isolated (84). This element (AGF) inter-acts at a specific site within the promoter region of thepsbDgene and sharessimilarity with a specific DNA binding factor, CDF2 (for chloroplast DNAbinding factor 2), isolated recently (76). Both factors have similar properties,



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suggesting that they may belong to a larger family of DNA-binding proteins,but their specific function remains to be seen.

Posttranscriptional ProcessingPosttranscriptional and translational events play a major role in regulating thedifferential accumulation of many plastid-encoded mRNAs during chloroplastdevelopment (for extensive reviews, see 53, 54, 114, 142). Most chloroplast-encoded genes are transcribed as polycistronic units (53). These precursorsundergo a series of complex maturation events that include processing of themature mRNAs, although only inChlamydomonas(98, 141, 142) the impor-tance of posttranscriptional processing understood. One of the few exceptionsin higher plants is theCRP1gene from maize, which seems to be requiredfor the efficient translation of two chloroplast mRNAs (pet Aandpet D) (9).This gene affects processing of thepetDmRNA in such a way that the mono-cistronic transcript is absent, implying a mechanistic link between RNA pro-cessing and translation. It is hypothesized that in this mutant the petD proteinis no longer synthesized, because the ribosome cannot initiate within the poly-cistronic mRNA, due to masking of the translation initiation region. TheCRP1gene has been cloned, but the encoded protein shows no significant similarityto any known protein (M Walker & A Barkan, unpublished data).

In contrast to processing, mRNA stability seems to be important for the ac-cumulation of several photosynthetic mRNAs required during the transitionfrom proplastid to chloroplast. For example, as measured by run-on exper-iments, steady state levels of thepsbAand atpB transcripts increase duringgreening of etiolated spinach cotyledons without changes in the transcriptionrate (29). In addition, the stability of several chloroplast-encoded transcriptsseems to be dramatically increased during chloroplast development in barley(83) and spinach (51). Stabilization seems to occur by the correct process-ing of the polycistronic mRNAs in the differentiated chloroplasts, whereas inproplastids these mRNAs appear to be rapidly degraded (53). It has recentlybeen established that nuclear-encoded enzymes are required for correct mRNAprocessing (66). Both exo- and endoribonuclease activities are found in a high-molecular-weight complex that binds near stem and loop sequences found inthe 3′ region of chloroplast transcripts (53, 114, 142). Although this complexhas not been fully characterized, similarities have been postulated with a ri-bonucleolytic complex (“degradosome”) inEscherichia coli(66). In additionto the action of the chloroplast high-molecular-weight complex, stabilizationof transcripts requires additional factors that inhibit rapid degradation (53, 66).One of these factors is a nuclear-encoded 28-kDa protein (28RNP) (53) thatinteracts with both the transcript and the high-molecular-weight complex (66).This protein is differentially expressed during plant development, is modified by




phosphorylation, and is likely necessary to direct the correct 3′-end processingof plastid transcripts under particular developmental conditions (66).

Unexpectedly, polyadenylation is the signal for degradation of specific chloro-plast transcripts. Following the endonucleolytic cleavage events in thepetDmRNA by components of the high-molecular-weight complex, the productsare then polyadenylated (89). By increasing susceptibility to degradation inresponse to conditions such as light, polyadenylation seems to play a criticalrole in regulating chloroplast transcript stability. For example, in dark-adaptedplants, the extent of polyadenylatedpetD-specific transcripts is higher than inplants grown in light (89). This unexpected process is probably not restrictedto a particular transcript and will most likely require the action of additionalnuclear regulatory factors.

The modulation of transcript stability during the differentiation of chloro-plasts in C4 plants has also been documented. In the dimorphic cells of the C4plant, the photosynthetic genes are expressed in a cell-specific manner. Thecharacterization of plants altered in bundle sheath cell differentiation in maizehas led to identification of a nuclear gene (Bsd2) that influences the regulationof transcript stability and/or translation ofrbcL mRNA. In this mutant, chloro-plast development is prevented in bundle shealth cells; this is likely the resultof photo-oxidative damage in the absence of the RuBPCase protein in thesecells (145). It is conceivable that the product of theBsd2gene might interactin a sequence-specific manner with therbcL mRNA in bundle sheath cells tostabilize this transcript.

A few other mutants have been described that alter stability of specific RNAtranscripts, including the maizehcf2andhcf6mutations (118). Still others havea more general effect on the stability of multiple transcripts such ashcf38frommaize (7, 118) and thehcf109andhcf5mutants fromArabidopsis(35, 116).

In both mitochondria and chloroplasts unspliced transcripts can accumulateto high levels (177). The role of splicing in the regulation of chloroplast de-velopment in higher plants has not been extensively studied, but recent studiesin maize show that the relative abundance of spliced and unspliced transcriptsdiffers among plastid types. Compared to chloroplasts, unspliced forms pre-dominate in both amyloplasts and proplastids (6). RNA splicing could exertcontrol in plastid development by regulating the abundance of plastid-encodedproteins.

Probably the best evidence for participation of splicing in chloroplast de-velopment comes from the work with thecrs (chloroplast RNA splicing) mu-tants in maize. Chloroplast genes in higher plants contain multiple group IIintrons, from both the A and B subgroups (117). These introns are capable ofself-splicing in vitro; genetic evidence indicates thattrans-acting factors arerequired for efficient splicing in vivo (148). Recently, two nuclear genes,crs1



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andcrs2, were reported to be required for the proper splicing of group II intronsin maize chloroplasts (79). Mutation atcrs1specifically blocks splicing of theatpF type IIA intron that encodes subunit I of the chloroplast ATP synthase,whereas mutation at the recently clonedcrs2gene blocks the splicing of manygroup IIB introns. Disruption of chloroplast development in these mutants pro-vides important biological evidence for the structural division of type II intronsbecause different splicing factors are required to process IIA and IIB introns.Previously described mutants might also reflect splicing deficiencies. For ex-ample, in plants with the nuclear geneiojap (ij ) splicing of most IIA intronsis defective (16). Whether there is a direct relationship betweenij andcrs1remains to be deduced.

Translational and posttranslational regulation has been documented inChla-mydomonas, Euglena, and higher plants (45, 54, 142, 160). This control couldunderlie the rapid changes in protein accumulation prominent in several pho-tosynthetic factors during chloroplast development; for example, the productof thepsbAtranscripts does not accumulate during senescence of bean leaves(10), in etiolated leaves (159), in roots, and in cultured cells (71). Transla-tional control is possible at several steps, but the best analyzed so far is duringribosome binding to the mRNA. Both 5′ and 3′ untranslated leader (UTR)sequences play important roles during translation in eukaryotes, and severalcis-acting sequences have been identified (45). Nuclear-encoded proteins havebeen identified that interact with specific stem-loop sequences in the 5′ UTR ofchloroplast transcripts in several organisms (27, 65, 71). These 5′ UTR bindingcomplexes seem to modulate ribosome binding, acting as translational activa-tors or repressors (28, 114). The nuclear-encoded factors identified to date aremostly fromChlamydomonas; these factors can regulate the translation of eitherindividual or a group of transcripts (45, 142). In higher plants, a specific proteinfactor(s) was recently demonstrated to be required for the efficient translation ofpsbAmRNA in an in vitro translation system from tobacco chloroplasts. Thisfactor interacts with specific elements of the 5′ UTR of thepsbAmRNA (71).This approach has an enormous potential to analyze the molecular mechanismsof translational regulation in vascular plants.

Coordinate protein accumulation for different photosynthetic protein com-plexes depends on translational control. It is known that in order to maintain thestoichiometric levels of different plastid complexes, their subunits are rapidlydegraded when prevented from assembling (142). Until now, the molecularmechanism has been little studied, but evidence currently exists to suggest it asan important point of translational regulation. For example, inChlamydomonasmutants, the accumulation of cytochromef decreases in the absence of othergenes of the cytochromeb6 f complex (petBor petD), although its transcriptlevel remains unchanged. The most likely interpretation of this phenomenon




is the direct autoregulation of the cytochromef so that when unassembled, itstranslation is attenuated (160).

A similar mechanism appears to be present in higher plants. It has beenshown that the translation of the large subunit protein (LS) of the Rubiscoenzyme is controlled by levels of the small subunit (SS). The levels of therbcL transcript remain unchanged, again suggesting translational regulation.Though the mechanism underlying this mode of regulation is still unclear, onemight postulate that proteins such as SS may act as activators during translationof therbcL transcript (144).

Posttranslational proteolysis is important during plastid differentiation. Forexample, during chloroplast to chromoplast differentiation, massive degrada-tion of the photosynthetic complexes and the accumulation of new sets of pro-teins must occur (111). Likewise, photosystem D1 protein is specifically de-graded after damage by oxygen radicals during electron transport (92), and thisdegradation is mediated by a specific protease (75). Several nuclear proteinsinvolved in proteolytic degradation in chloroplasts have been identified. Thegene homologous to ClpA, a subunit of the ATP-dependent serine protease(Clp) (47), is nuclear-encoded and transported into the chloroplast (81), whereit may be involved in the degradation of soluble and thylakoidal proteins (151).This offers a means by which the nucleus may regulate protein accumulationduring specific stages in the biogenesis of the organelle. This subject, thoughnot yet extensively studied, likely represents a very important point in plastiddevelopmental regulation.

Concomitant with the accumulation of the photosynthetic complexes, exten-sive proliferation of thylakoid membranes and the formation of granal stacksoccurs in maturing chloroplast. It has been suggested that incorporation of thelight-harvesting complex (LHCII) into the thylakoid membrane plays an impor-tant role in thylakoid stacking inChlamydomonasand higher plants (35, 158).Only recently has participation of other nuclear genes been analyzed (36). Oneinteresting example is development of transgenicArabidopsisplants with lowlevels of a dynamin-like gene (ADL1), which show a greatly reduced thylakoidmembranes and an increase in lipid granules. Because dynamin-like proteinsin other systems are involved in the formation of membrane vesicles (180), itis proposed that the nuclear-encodedADL1 gene participates in thylakoid bio-genesis in higher plants (JM Park, JH Cho, SG Kang, HJ Jang, KT Pih, et al,unpublished data).

Nuclear Regulation of TargetingThe proper allocation of the nuclear-encoded subunits is required for organellefunctionality and development. Plastids have developed an elaborate sortingsystem to ensure proper targeting of multimeric protein complexes. The presence



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of three distinct membranes requires that proteins are incorporated into thechloroplast and later reallocated within the organelle (21). General aspects ofchloroplast protein import have been known for some time, but the mechanismsfor sorting and import are just beginning to be elucidated. Most genes involvedin this process are nuclear-encoded, and their proper expression regulates cor-rect targeting during chloroplast development (21).

A fairly detailed picture has emerged recently for the integration of proteinsinto the thylakoid membrane. Mutations in four nuclear genes of maize inter-fere with plastid biogenesis by disrupting the translocation of thylakoid proteins(8). Mutations in thetha1andtha5genes affect a SecA-type pathway, whereasmutations in thehcf106and tha4 genes disrupt a DpH pathway that dependson pH (112, 172). These nuclear mutations are recessive and result in pale-green, nonphotosynthetic seedlings that die after endosperm depletion. Thetha1mutant affects chloroplast development specifically in the mesophyll cellsin which giant grana are found, but does not apparently affect bundle sheathchloroplasts that look normal (173). In thehcf106mutant, both plastid typesare abnormal (112).tha1encodes a chloroplast-localized SecA protein homol-ogous to the SecA protein fromE. coli. This suggests that at least one of theplastid targeting mechanisms is similar to the prokaryoticsecA/Y/E pathway(173). Recently thetha4gene has also been cloned; it is closely related to anopen reading frame of unknown function ofSynechocystis. In tha4plants theDph pathway is disrupted; this pathway may have evolved from a cyanobacte-rial progenitor (M Walker & A Barkan, unpublished data). It is unknown whytwo distinct translocation pathways exist for the tylakoidal proteins and whatthe differences are between both mechanisms. Given the recent identificationof the proteins involved in tylakoidal protein import, important progress in thefuture is expected.

NUCLEAR SIGNALS FOR CHLOROPLASTDEVELOPMENT

Light RegulationOrganelle development and plant development respond to external signals,particularly light. Light regulation is mediated by the photoreceptors: a phy-tochromes, blue/UV-A cryptochromes, and the UV-A and -B receptors. Sev-eral nuclear genes are part of the signal transduction system coupling lightto plastid and plant development (19, 37, 137). Mutants with a de-etiolatedphenotype—det, fus, andcopclasses—have a morphology when grown in thedark similar to light-grown wild-type seedlings (91, 137, 173a); these mutants




have altered expression of several nuclear- and chloroplast-encoded photosyn-thetic genes (119, 137). The plastids indet1, cop1, andcop9develop a maturethylakoid system when grown in the dark, even though they do not accumu-late chlorophyll. These mutants together with severalfus mutants also affectthe amyloplast, by promoting differentiation of a chloroplast, resulting in aconstitutive default photomorphogenic developmental pathway (91, 119). Incontrast, other de-etiolated mutants such asdet2show no impact in chloroplastdevelopment (20). Several of the genes affected in these mutants have beencloned (30, 100, 132, 176), and the characteristics and localization of their geneproducts suggest that they may be nuclear regulators (17). The COP1 proteinis probably one of the best studied light regulators; it is a negative transcrip-tional regulator capable of direct interaction with upstream DNA sequences ofits target genes (137). Other genes such as COP8, COP9, and COP11, seemedto act in the same pathway (176a).

The cue mutants, were selected to identify elements that play a positiverole during de-etiolation inArabidopsis(99, 105). Mostcuegenes influencechloroplast development in the light and appear to modulate expression levelsof particular nuclear-encoded photosynthetic genes.CUE1 encodes a phos-phate/phosphoenolpyruvate translocator (PPT) of the chloroplast inner enve-lope membrane (42, 161). PPT is likely required early in chloroplast devel-opment; loss of this function probably directly influences signals from thechloroplast that affect nuclear expression of light-regulated genes.

MUTATIONAL ANALYSIS OF PLANTMITOCHONDRIA

Unlike the chloroplast case, there are few mutations in mitochondrial devel-opment. Most loss of function mutation in mitochondria are lethal unlessmaintained in a heteroplasmic state (125). Some dominant mitochondrial mu-tations, resulting from expression of novel open reading frames in mtDNA,survive in higher plants. For the most part, these mutations lead to a similarphenotype of pollen inviability known as cytoplasmic male sterility (cms) (61).This maternally inherited trait has been reported in over 150 plant species, andin all cases examined in detail results from expression of novel mitochondrialpolypeptides. Usually, these novel polypeptides contain at least one hydropho-bic domain, likely facilitating membrane association. Eachcms-associatedpolypeptide identified has been unique, and their modes of action are unclear.

Cmsmutations have proven particularly useful in defining nuclear regulationof mitochondrial functions. Nuclear suppressors of thecmsphenotype are read-ily identified as nuclear fertility restorer (Rf) genes. In the majority of cases,Rf



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genes act as single, dominant loci, though examples exist of polygenic restorersystems. Nuclear-directed mitochondrial functions identified via the analysisof fertility restoration mechanisms include mitochondrial transcript process-ing (154, 164, 182), posttranscriptional functions (157, 185), possible modesof biochemical detoxification (26), and alteration of mitochondrial genomeorganization (108).

NUCLEAR REGULATION OF MITOCHONDRIALGENE EXPRESSION

Regulation of TranscriptionA particularly unusual feature of plant mitochondria is the variable and com-plex pattern of transcripts arising from a given mitochondrial gene. Variation intranscript size can arise from use of multiple transcription start sites and termi-nation sites (50). Complexity is compounded by posttranscriptional processing,described below.

Transcriptional regulation of mitochondrial gene expression does occur, al-though it does not appear to be the predominant means of gene modulation.For example, tissue-specific differences in transcript accumulation have beendetected in various tissues of the maize seedling using in situ hybridization(101). It is unknown whether these differences reflect cell-specific changes intranscription rate, as opposed to posttranscriptional processes; it it clear thatcell-to-cell modulation of mitochondrial expression can occur. Plant mitochon-drial transcription appears to be mediated by at least one nuclear-encoded RNApolymerase bearing striking similarity to the RNA polymerases of bacterio-phages T7, T3, and SP6 (68).

Data to date suggest that variation in promoter strength is likely a primaryinfluence on relative transcription rates (15, 41, 50). Nuclear factors regulatingtranscription rate or promoter selection are difficult to detect. Perhaps the mostcompelling demonstration of nuclear influence on mitochondrial transcriptionis described in aZea mays/Zea perennisalloplasmic line. A single nuclear gene,designatedMct, influences promoter selection in the cytochrome oxidase sub-unit II (coxII) gene in maize (22, 126). Transcriptional initiation at position−907 produces the predominantcoxII transcript of∼1900 nucleotides. ThedominantMct allele apparently directs transcriptional initiation at a secondsite (−347) upstream to thecoxII locus. Interestingly, this alternate initiationsite, detected as a shortercoxII transcript, does not conform to the consen-sus promoter sequence described for maize. This provides the first evidencethat specific cofactors may influence promoter selection in plant mitochondria,unlike yeasts and mammalian systems.




Certain nuclear-directed changes in mitochondrial transcript levels appear tobe tissue-specific. This has been suggested by in situ hybridization studies ofmaize seedling tissues, where several mitochondrial transcripts appeared to bepresent at different levels depending on tissue type (101). Similar studies indeveloping anthers of sunflower demonstrated a marked accumulation ofatpA,atp9, cob, and rrn26 transcripts in young meiotic cells, with a concomitantincrease in their respective protein products (157). Moreover,orf522transcriptsdecrease incmssunflower; the encoded 15-kDa protein is observed in antherswhen the nuclearRf gene, likely acting posttranscriptionally, is present (121).These results imply that nuclear-directed modulation of mitochondrial geneexpression may occur in a cell-specific pattern. Further support comes fromobservations incmsPetunia where restoration of fertility by a nuclearRf geneis associated with the tissue-specific reduction in a particular transcript derivedfrom thepcfmitochondrial region (185).

Transcript ProcessingNuclear background influences mitochondrial transcription patterns in partic-ular genomic regions. For example, nuclear background alters transcriptionof atpA in the Ogura cytoplasm of radish (109) and thecmsgene (T-urf 13)in the T cytoplasm of maize. TheT-urf13sterility-associated sequence is co-transcribed with theorf 221 open reading frame. Specific lines of maize re-vealed a marked influence of nuclear background on its pattern of transcription(82). Rocheford & Pring (1994) demonstrated that the transcript changes werenot only a function of the mitochondrial genomic environment encompass-ing theT-urf13/orf221 region but also of dominant nuclear gene action influ-encing the pattern of posttranscriptional processing these transcripts undergo(143).

Transcript processing is a widespread phenomenon in plant mitochondriathough not yet well understood mechanistically. It was first deduced by theobservation that unusually complex transcript in certain regions of the plant mi-tochondrial genome were produced not only by multiple transcription start andstop sites, but also by internal transcript processing (reviewed in 50). Althoughthe role of processing in gene regulation is not yet clear, nuclear regulationof transcript processing could be an important means of mitochondrial genesuppression. This conclusion is based on the observation that three differentnuclearRf loci directly influence transcript processing within the respectivemitochondrialcms-associated regions.

In cms-T maize, perhaps the most well-investigated example of cytoplas-mic male sterility, fertility restoration requires dominant allels of two unlinkednuclear loci,Rf1andRf2(94). Compelling evidence demonstrates that the prod-uct ofRf1, essential though not sufficient to restore fertility, directly influences



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transcript processing of theT-urf13mitochondrial region (182). Processing ofT-urf13 transcripts appears to be directly associated with a marked reductionin the expression of the encoded 13-kDa T-URF13 polypeptide (43). The ac-tion of Rf2will be discussed in a later section. In sorghum line IS1112C,cmsis associated with expression of theorf107open reading frame (164). Again,fertility restoration is associated with altered processing oforf107 transcripts,and the concomitant reduction in the accumulation of a 12-kDa polypeptidepresumed to be the gene product (164). Of particular interest is the obser-vation that the transcript processing sites described in bothcms-T maize andcmssorghum share sequence features (34), implying that sequence motifs existwithin plant mitochondrial genes that may act as targets for nuclear-directedgene modulation.

cms in the Brassica napus(oilseed rape) Polima cytoplasm is associatedwith aberrant expression of a region encoding theatp6gene cotranscribed witha downstream chimeric sequence,orf224 (152). Fertility restoration, condi-tioned by either of two dominant single nuclear loci, results in a transcriptprocessing event that generates predominantly monocistronicatp6 transcripts(152, 153). Generation of monocistronicatp6 transcripts cosegregates with asingle dominant fertility restorer locus,Rfp1(154). Most intriguing, however,is the observation that an alternate recessive allele at this locus, (rfp1) or a sec-ond locus tightly linked torfp1, influences transcript processing of two othermitochondrial genes not associated with sterility,nad4and accl1-like genethat may be involved in cytochromec biogenesis. At all four processing sitesunderRfp1or rfp1 control, there is UUGUGG or UUGUUG, a sequence motif,located very near the processing site.

Transcript EditingOne of the more surprising features distinguishing plant mitochondrial geneexpression from that of yeast and mammals is the extensive editing of plantmitochondrial transcripts. The biochemistry and pattern of transcript editinghas been reviewed recently (49, 60). The mechanisms regulating the rate ofediting, as well as the local sequence features determining sites to be edited,are not yet understood. Evidence to date indicates that local features of theediting site are important (24, 55, 56) and that sites that alter codons may bepreferentially edited (181). Nuclear genotype (181) as well as tissue type,developmental stage, and growth conditions may influence the extentof transcript editing (52). Perhaps the most definitive evidence of nuclearinfluence on transcript editing involves differentialnad3 editing in a partic-ular Petunia mitochondrial genotype when combined with different nuclearbackgrounds. The extent ofnad3 editing changes dramatically in responseto different nuclear backgrounds, with a high extent of editing segregating




as a single dominant nuclear locus. Interestingly, this genetic variation forextent of transcript editing pertained exclusively tonad3; this implies speci-ficity in nuclear control of editing and predicts that additional nuclear factorsexist.

Translational/Posttranslational RegulationRelatively little evidence currently exists for nuclear-directed, translational reg-ulation in plant mitochondria. In contrast, several nuclear factors influencetranslation of specific mitochondrial genes in yeast (44). In plants, sequenceconservation exist upstream of some mitochondrial start codons, but it is notclear whether these sequences actually function as specific binding sites fortranslational components (134). Furthermore, although particular mitochon-drial polypeptide differences have been associated with changes in plant nuclearbackground (23), it is not yet determined whether the protein differences resultfrom differential transcription or translation.

Perhaps more provocative at this stage is the accumulating evidence suggest-ing surprisingly limited regulation of translation in mitochondria, particularly inlight of extensive translational control in plastids. One unexpected observationof transcript editing is that both edited and unedited transcripts are transla-tionally competent. Both edited and partially edited transcripts appear to berepresented in association with polysomes (57, 106). Moreover, little discrim-ination by the ribosome occurs with regard to untranslated leader sequences ortranscript splicing status (184).

It may be argued that polysome association does not, in itself, demonstratenonselective translation. Using antibodies against the predicted polypeptideproduct of therps12 unedited transcript, compelling evidence demonstratesthat polypeptides are produced from partially edited or unedited transcripts, aswell as edited forms (107, 133). Not unexpectedly, these aberrant polypeptidesare not incorporated into functional ribosomes (133).

These observations raise the obvious general question about the fate of aber-rant translation products, and why they are not more commonly detected withinplant mitochondria. One explanation may be differences in half-life for productsof edited vs unedited transcripts. Although protein import and the concomitantprocessing events associated with import have been well described (reviewedin 46, 179), little is yet known about posttranslational proteolysis of mitochon-drial gene products. Mitochondrial proteolysis has been best detailed in yeast,where several proteases, both matrix and membrane-localized, have been char-acterized (reviewed in 140). In plants, no proteolytic activity has been detectedin the matrix of mitochondria, but limited activity is detected within the innermembrane; and there is some indication that this activity may be involved inthe proteolysis of unassembled, imported proteins (87).



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In common bean, posttranslational regulation of thecms-associated mito-chondrial protein appears to occur in vegetative tissues. In bean,cmsis associ-ated with the expression of a 239–amino acid polypeptide, (ORF239) (1, 67) thataccumulates only in reproductive tissues, with no detectable ORF239 in vegeta-tive (seedling, leaf, or root) tissues (1). More extensive investigation shows thatthe ORF239 protein is subject to proteolysis in vegetative tissues, dependent inpart on a mitochondrial protease related to thelonhomologs of yeast (163, 171)and human (175; R Sarria, A Lyznik, E Vallejos & S Mackenzie, submittedmanuscript). Whether this newly identified plant protease is involved in thedegradation of other aberrant mitochondrial gene products remains an activearea of inquiry.

Detoxification of metabolic poisons is a quite unexpected means of influenc-ing mitochondrial functions posttranslationally. TheRf2 fertility restorer genein cms-Tmaize encodes a putative aldehyde dehydrogenase (26). Although thefunction of this gene in fertility restoration is not yet clear, recent biochemicalstudies have confirmed its enzymatic activity identity (P Schnable, personalcommunication). It has been speculated that theRf2 gene product may playa role in the detoxification of a pollen-specific product that interacts with theT-URF13 protein to cause premature tapetal breakdown.

NUCLEAR INFLUENCE ON THE MITOCHONDRIALGENOME

The plant mitochondrial genome, now fully sequenced inArabidopsis(169)andMarcantia(128), is organized in a much more complex and variable struc-ture than is observed in other higher eukaryotes (reviewed in 183). In mosthigher plants, this organization is defined by the presence of recombinationallyactive repeated sequences that allow for high- and low-frequency inter- andintramolecular recombination events to occur (3). The physical organizationof the mitochondrial genome in plants has been difficult to define. Althoughmost genomes map as circular molecules defined by overlapping clones, directphysical observation by pulsed field gel electrophoresis, electron microscopy,and other procedures has indicated that the genome may consist of both lin-ear and circular forms, with molecules much larger than the multiple circlesconstructed by clone analysis (3, 14, 130).

The nucleus definitely affects mitochondrial genome organization. One valueof the remarkable mitochondrial DNA variation existing within plant familiesis the information it provides regarding evolution of this unusual genome andthe cellular forces molding current organization. Examination of variationwithin the legume family (Fabaceae) provides striking evidence for the ongoingevolutionary transfer of functional genetic information from the mitochondrion




to the nucleus via RNA intermediates (25, 127). This evolutionary transfer ofmitochondrial genes to the nucleus has presented some intriguing problems,most notably the requirement to move tRNA into mitochondria (33). Thereis evidence that this transfer likely requires association with the appropriateaminoacyl tRNA synthase to mediate transmembrane import (32).

A multipartite genome organization exists in the mitochondrion of most plantspecies, with each molecule containing only a portion of the genetic informa-tion. Overall structure is further complicated by the variable stoichiometry ofspecific subgenomic regions. Remarkably, in several plant species, a subset ofmitochondrial DNA molecules, atypical genomic organizations termed “sub-limons,” can be retained indefinitely in nearly undetectable levels (155, 156).The relative copy number of the various mitochondrial DNA forms and theirrecombinational activity appears to be under nuclear control. One of the mostpronounced examples is the observed loss of a mitochondrial genomic moleculein response to a single nuclear gene in common bean. Thecms-associated mito-chondrial mutation in common bean,pvs-orf239, appears to be maintained on asingle 210-kb molecule within a tripartite mitochondrial genome organization(78). Introduction of a single dominant nuclear factor,Fr, results in a genomicshift of thepvs-orf239–containing molecule to substoichiometric levels withinthe genome, thus restoring pollen fertility (H Janska, R Sarria, M Woloszynska,M Arrieta-Montiel & S Mackenzie, manuscript submitted).

The development of alloplasmic lines, derived by recurrent backcrossingstrategies or protoplast fusion to combine different mitochondrial and nucleargenotypes, routinely gives rise to changes in relative stoichiometries and mito-chondrial genomic rearrangements inNicotiana(5, 13, 58),Brassica(93, 104),andTriticum (120, 129, 168). In some cases, it has been possible to identifyspecific nuclear loci essential to establishing compatibility in individual nuclear-cytoplasmic combinations (4). Moreover, particular nuclear-cytoplasmic ge-netic combinations in maize can be predicted to give rise to a high frequencyof specific mitochondrial mutations. These mutations, referred to collectivelyas nonchromosomal stripe mutations, generally result in loss of mitochondrialgene function, leaf striping, severe growth impairment, and infertility;ncsmutations are maintained in a heteroplasmic state with wild-type, functionalmitochondria (125). Severalncsmutations affect in distinct loci and have arisenby what appear to be different molecular events.

In Arabidopsis, the appearance of mitochondrial mutations is likewise associ-ated with modification of the nuclear genotype. In the case ofArabidopsis, mu-tation at a single dominant nuclear gene,CHM, yields mitochondrial genomicrearrangements (113). Notably, the mutant mitochondrial forms arising uponCHM mutation are already present in the wild-type lines at substoichiometriclevels (147), implying that the role of theCHM locus, like that of theFr locus



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in bean, may be to suppress copy number of mutant mitochondrial forms.Efforts are ongoing to determine whether theFr locus in cmsbean involvehomologous functions (B Li & S Mackenzie, personal communication).

PERSPECTIVES

Chloroplast and mitochondrial development are regulated by complex intracel-lular interactions. In the case of the plastids, it is likely that the discrete nuclearfactors set the program that determines to a large degree the stage of organelledevelopment. In contrast, plastid signaling to the nucleus may be continualthroughout development. In the next few years, we will likely see importantadvances in the characterization of chloroplast signals that trigger changes innuclear expression.

In the past years, we have seen an important number of breakthroughs inseveral aspects of the chloroplast field as protein import, transcription, andposttranscriptional events. Now a clearer picture is emerging of the regulatoryevents that take place in each of these processes. Collectively, in the nearfuture, it will be possible to understand the surprising variety of regulatorymechanisms that in concert permit chloroplast development. In the years tocome, the implementation of new approaches will contribute to the identificationof molecules required for alternative plastid development pathways. Novelclasses of genetic loci inArabidopsisdefine unsolved steps of early chloroplastdifferentiation. Detailed study of these genes during plant development willcertainly help us understand the mechanisms operating in early chloroplastdevelopment.

In mitochondrial research, several laboratories are now quite close to cloningadditional fertility restorers involved in transcript processing, as well as theCHM andFr loci involved in differential amplification of the genome. A sur-prising picture emerges as we investigate mitochondrial regulation; namely,that the mitochondrial genome is permitted to expend what would appear to betremendous energy in the execution of transcription and, in most cases, trans-lation of products destined for rapid turnover. These observations imply that,unlike prokaryotes, factors other than energy conservation may be most influ-ential in plant mitochondria. We predict that future investigations will discoverthe impetus for retaining functions as perplexing as substoichiometric genomicforms and prolific editing functions. Until such time, the plant mitochondrialgenome remains an enigma.

ACKNOWLEDGMENTS

We thank everyone who provided us with reprints, preprints, and unpublishedresults of their recent work, and especially K Pyke and D Stern for sharing




their expertise on selected topics. In addition, we thank Helena Porta, KennethLuehrsen, and Stewart Gillmor for critical reading of the manuscript. The workin our laboratories was supported by a grant of the DGAPA program IN206294and the Pew Charitable Trust to PL and from the USDA, National ScienceFoundation, and National Institutes of Health-GMS to SM.

Visit the Annual Reviews home pageathttp://www.AnnualReviews.org.

Literature Cited

1. Abad A, Mehrtens B, Mackenzie S.1995. Specific expression in reproduc-tive tissues and fate of a mitochondrialsterility-associated protein in cytoplas-mic male sterile bean.Plant Cell7:271–85

2. Allison L, Simon L, Maliga P. 1996.Deletion of rpoB reveals a second dis-tinct transcription system in plastids ofhigher plants.EMBO J.15:2802–9

3. Andre C, Levy A, Walbot V. 1992. Smallrepeated sequences and the structureof plant mitochondrial genomes.TrendsGenet.8:128–32

4. Asakura N, Nakamura C, Ohtsuka I.1997. RAPD markers linked to the nu-clear gene fromTriticum timopheeviithat confers compatibility withAegilopssquarrosacytoplasm on alloplasmic du-rum wheat.Genome40:201–10

5. Aviv D, Galun E. 1987. Chondriomeanalysis in sexual progenies of Nicotianacybrids.Theor. Appl. Genet.73:821–26

6. Barkan A. 1989. Tissue-dependent plas-tid RNA splicing in maize: transcriptsfrom four plastid genes are predomi-nantly unspliced in leaf meristems androots.Plant Cell1:437–45

7. Barkan A, Miles D, Taylor W. 1986.Chloroplast gene expression in nuclear,photosyntetic mutants of maize.EMBOJ. 5:1421–27

8. Barkan A, Voelker R, Mendel-HartvigJ, Johnson D, Walker M. 1995. Ge-netic analysis of chloroplast biogenesisin higher plants.Physiol. Plant.93:163–70

9. Barkan A, Walker M, Nolasco M, John-son D. 1994. A nuclear mutation inmaize blocks the processing and transla-tion of several chloroplast mRNAs andprovides evidence for the differentialtranslation of alternative mRNA forms.EMBO J.13:3170–81

10. Bate NJ, Straus NA, Thompson JE.

1990. Expression of chloroplast photo-synthetic genes during leaf senescence.Plant Physiol.80:217–25

11. Baumgartner BJ, Rapp JC, Mullet JE.1989. Plastid transcription activity andDNA copy number increase early inbarley chloroplast development.PlantPhysiol.89:1011–18

12. Begg K, Donachie WD. 1985. Cell shapeand division inEscherichia coli:exper-iments with shape and division mutants.J. Bacteriol.163:615–22

13. Belliard G, Vedel F, Pelletier G. 1979.Mitochondrial recombination in cyto-plasmic hybrids ofNicotiana tabacumby protoplast fusion.Nature281:401–3

14. Bendich AJ. 1993. Reaching for thering: the study of mitochondrial genomestructure.Curr. Genet.24:279–90

15. Binder S, Marchfelder A, Brennicke A.1996. Regulation of gene expressionin plant mitochondria.Plant Mol. Biol.32:303–14

16. Byrne M, Taylor WC. 1996. Analysisof Mutator-induced mutations in theIo-jap gene of maize.Mol. Gen. Genet.252:216–20

17. Chamovitz DA, Wei N, Osterlund MT,von Arnim AG, Staub JM, et al. 1996.The COP9 complex, a novel multisub-unit nuclear regulator involved in lightcontrol of a plant developmental switch.Cell 86:115–21

18. Chatterjee M, Sparvoli S, Edmunds C,Garosi P, Findlay K, Martin C. 1996.DAG, a gene required for chloroplast dif-ferentiation and palisade development inAntirrhinum majus. EMBO J.15:4194–207

19. Chory J. 1993. Out of darkness: mu-tants reveal pathways controlling light-regulated development in plants.TrendsGenet.9:167–72

20. Chory J, Nagpal P, Peto CA. 1991. Phe-notypic and genetic analysis ofdet2, a



474 LEON ET AL

new mutant that affects light-regulatedseedling development inArabidopsis.Plant Cell3:445–59

21. Cline K, Henry R. 1996. Import and rout-ing of nucleus-encoded chloroplast pro-teins.Annu. Rev. Cell Dev. Biol.12:1–26

22. Cooper P, Butler E, Newton KJ. 1990.Identification of a maize nuclear genewhich influences the size and numberof cox2 transcripts in mitochondria ofperennial teosintes.Genetics126:461–67

23. Cooper P, Newton KJ. 1989. Maize nu-clear background regulates the synthesisof a 22-kDa polypeptide inZea luxuri-ansmitochondria.Proc. Natl. Acad. Sci.USA86:7423–26

24. Covello PS, Gray MW. 1990. Differ-ences in editing at homologous sites inmessenger RNAs from angiosperm mi-tochondria.Nucleic Acids Res.18:5189–96

25. Covello PS, Gray MW. 1992. Silent mi-tochondrial and active nuclear genes forsubunit 2 of cytochrome c oxidase (cox2)in soybean: evidence for RNA-mediatedgene transfer.EMBO J.11:3815–20

26. Cui XQ, Wise RP, Schnable PS.1996. Therf2 nuclear restorer gene ofmale sterile T-cytoplasm maize.Science272:1334–36

27. Danon A, Mayfield SP. 1991. Light regu-lated translational activators: identifica-tion of chloroplast gene specific mRNAbinding proteins.EMBO J. 10:3993–4001

28. Danon A, Mayfield SP. 1994. ADP-dependent phosphorylation regulatesRNA-binding in vitro: implications inlight-modulated translation.EMBO J.13:2227–35

29. Deng X-W, Gruissem W. 1987. Controlof plastid gene expression during devel-opment: the limited role of transcrip-tional regulation.Cell 49:379–87

30. Deng X-W, Matsui M, Wei N, WagnerD, Chu AM, et al. 1992.COP1, an Ara-bidopsis regulatory gene, encodes a pro-tein with both a zinc-binding motif anda Gβ homologous domain.Cell 27:791–801

31. de Souza D, Osteryoung K, Pyke KA.1997. Molecular genetics of chloroplastdevelopment inArabidopsis. Int. Conf.Arabidopsis Res., 8th, Madison, Wis.

32. Dietrich A, Marechaldorouard L, Car-neiro V, Cosset A, Small I. 1996. A sin-gle base change prevents import of cy-tosolic tRNA (ala) into mitochondria intransgenic plants.Plant J.10:913–18

33. Dietrich A, Small I, Cosset A, Weil

JH, Marechaldrouard L. 1996. Edit-ing and import—strategies for providingplant mitochondria with a complete setof functional transfer RNAs.Biochimie78:518–29

34. Dill CL, Wise RP, Schnable PS. 1998.Rf8 and Rf∗ mediate uniqueT-urf13-transcript accumulation, revealing a mi-tochondrial consensus sequence associ-ated with RNA processing and restora-tion of pollen fertility in T-cytoplasmmaize.Genetics.In press

35. Dinkins RD, Bandaranayake H, BaezaL, Griffiths AJF, Green BR. 1997.hcf5,a nuclear photosynthetic electron trans-port mutant ofArabidopsis thalianawitha pleiotropic effect on chloroplast geneexpression.Plant Physiol. 113:1023–31

36. Dormann P, Hoffmann-Benning S,Balbo I, Benning C. 1995. Isolationand characterization of an Arabidopsismutant deficient in the thylakoid lipiddigalactosyl diacylglycerol.Plant Cell7:1801–10

37. Duckett CM, Gray JC. 1995. Illumi-nating plant development.BioEssays17:101–3

38. Erickson HP. 1995. FtsZ, a prokaryotichomolog of tubulin?Cell 80:367–70

39. Falbel TG, Meehl JB, Staehelin LA.1996. Severity of mutant phenotype ina series of chlorophyll-deficient wheatmutants depends on light intensity andthe severity of the block in chlorophyllsynthesis.Plant Physiol.112:821–32

40. Falbel TG, Staehelin LA. 1994. Char-acterization of a family of chlorophyll-deficient wheat and barley mutants withdefects in the Mg-insertion step onchlorophyll biosynthesis.Plant Physiol.104:639–48

41. Finnegan PM, Brown GG. 1990. Tran-scriptional and post-transcriptional reg-ulation of RNA levels in maize mito-chondria.Plant Cell2:71–83

42. Fisher K, Kammerer B, Gutensohn M,Arbirger B, Weber A, et al. 1997. A newclass of plastidic phosphate transloca-tors: a putative link between primaryand secondary metabolism by the phos-phoenolpyruvate/phosphate antiporter.Plant Cell9:453–62

43. Forde BG, Oliver RJC, Leaver CJ. 1978.Variation in mitochondrial translationproducts associated with male-sterile cy-toplasms in maize.Proc. Natl. Acad. Sci.USA75:3841–45

44. Fox TD. 1996. Genetics of mito-chondrial translation. InTranslationalControl, ed. J Hershey, M Mathews,




N Sonenberg, pp. 733–58. Cold SpringHarbor, NY: Cold Spring Harbor Lab.Press

45. Gillham NW, Boynton JE, Hauser CR.1994. Translational regulation of geneexpression in chloroplast and mitochon-dria.Annu. Rev. Genet.28:71–93

46. Glaser E, Ljoling S, Szigyarto C, Erik-sson AC. 1996. Plant mitochondrial pro-tein import: precursor processing is ca-talysed by the integrated mitochondrialprocessing peptidase (MPP)/bc1 com-plex and degradation by the ATP-depen-dent proteinase.Biochem. Biophys. Acta1275:33–37

47. Gottesman S, Wickner S, Maurizi MR.1997. Protein quality control: triage bychaperones and proteases.Genes Dev.11:815–23

48. Gray MW. 1992. The endosymbionthypothesis revisited.Int. Rev. Cytol.141:233–357

49. Gray MW. 1996. RNA editing in plantorganelles—a fertile field.Proc. Natl.Acad. Sci. USA96:8157–59

50. Gray MW, Hanic-Joyce PJ, CovelloPS. 1992. Transcription, processing andediting in plant mitochondria.Annu. Rev.Plant Physiol. Plant Mol. Biol.43:145–75

51. Green CD, Hollingsworth MJ. 1992.Expression of the large ATP synthasegene cluster in spinach plastids duringlight-induced development.Plant Phys-iol. 100:1164–70

52. Grosskopf D, Mulligan RM. 1996. De-velopmental and tissue-specificity ofRNA editing in mitochondria of suspen-sion-cultured maize cells and seedlings.Curr. Genet.29:556–63

53. Gruissem W, Schuster G. 1993. Controlof mRNA degradation in organelles. InControl of Messenger RNA Stability, ed.J Belasco, G Brawerman, pp. 329–65.New York: Academic

54. Gruissem W, Tonkyn JC. 1993. Controlmechanisms of plastid gene expression.Crit. Rev. Plant Sci.12:19–55

55. Gualberto JM, Bonnard G, LamattinaL, Grienenberger JM. 1991. Expressionof the wheat mitochondrialnad3-rps12transcription unit: correlation betweenediting and mRNA maturation.PlantCell 3:1109–20

56. Gualberto JM, Weil JH, GrienenbergerJM. 1990. Editing of the wheatcoxIIItranscript: evidence for twelve C to Uand one U to C conversions and for se-quence similarities around editing sites.Nucleic Acids Res.18:3771–76

57. Gualberto JM, Wintz H, Weil JH, Grie-

nenberger JM. 1988. The genes cod-ing for subunit 3 of NADH dehydro-genase and for ribosomal protein S12are present in the wheat and maizemitochondrial genome and are co-tran-scribed.Mol. Gen. Genet.215:118–27

58. Hakansson G, Glimelius K. 1991. Exten-sive nuclear influence on mitochondrialtranscription and genome structure inmale-fertile and male-sterile alloplasmicNicotiana materials.Mol. Gen. Genet.229:380–88

59. Haley J, Bogorad L. 1990. Alternativepromoters are used for genes withinmaize chloroplast polycistronic tran-scription units.Plant Cell2:323–33

60. Hanson M, Sutton C, Lu B. 1996.Plant organelle gene expression-alteredby RNA editing.Trends Plant Sci.1:57–64

61. Hanson MR. 1991. Plant mitochondrialmutations and male sterility.Annu. Rev.Genet.25:461–86

62. Harpster MH, Mayfield SP, Taylor WC.1984. Effects of pigment-deficient mu-tants on the accumulation of photosyn-thetic proteins in maize.Plant Mol. Biol.3:59–71

63. Harrak H, Langrange T, Bisanz-SeyerC, Lerbs-Mache S, Mache R. 1995.The expression of nuclear encodingplastid ribosomal proteins precedes theexpression of chloroplast gene duringearly phases of chloroplast development.Plant Physiol.108:685–92

64. Harrison MA, Nemson JA, Melis A.1993. Assembly and composition of thechlorophyll a-b light harvesting com-plex of barley: immunochemical analy-sis of the chlorophyllb-less and chloro-phyll b-deficient mutants.Photosynth.Res.38:141–51

65. Hauser CR, Gillham NW, Boynton JE.1996. Translational regulation of chloro-plast genes. Proteins binding to the 5′-untranslated regions of chloroplast mR-NAs in Chlamydomonas reinhardtii. J.Biol. Chem.271:1486–97

66. Hayes R, Kudla J, Schuster G, GabayL, Maliga P, Gruissem W. 1996. Chloro-plast mRNA 3′-end processing by a highmolecular weight protein complex isregulated by nuclear encoded RNA bind-ing proteins.EMBO J.15:1132–41

67. He S, Abad AR, Gelvin SB, MackenzieSA. 1996. A cytoplasmic male sterility-associated mitochondrial protein causespollen disruption in transgenic tobacco.Proc. Natl. Acad. Sci. USA93:11763–68

68. Hedtke B, Borner T, Weihe A. 1997. Mi-tochondrial and chloroplast phage-type



476 LEON ET AL

RNA polymerases inArabidopsis. Sci-ence277:809–11

69. Hess WR, Muller A, Nagy F, BornerT. 1994. Ribosome-deficient plastids af-fect transcription of light-induced nu-clear genes: genetic evidence for aplastid-derived signal.Mol. Gen. Genet.242:305–12

70. Hess WR, Prombona A, Fieder B, Subra-manian AR, Borner T. 1993. Chloroplastrps15 and therpoB/C1/C2 gene clus-ter are strongly transcribed in ribosome-deficient plastids: evidence for a func-tioning nonchloroplast encoded RNApolymerase.EMBO J.12:563–71

71. Hirose T, Sugiura M. 1996.Cis-actingelements andtrans-acting factors for ac-curate translation of chloroplastpsbAmRNAs: development of an in vitrotranslation system from tobacco chloro-plasts.EMBO J.15:1687–95

72. Hu J, Bogorad L. 1990. Maize chloro-plast RNA polymerase: the 180-, 120-,and 38-kilodalton polypeptides are en-coded in chloroplast genes.Proc. Natl.Acad. Sci. USA87:1531–35

73. Hudson A, Carpenter R, Doyle S, CoenES. 1993.Olive: a key gene required forchlorophyll biosynthesis inAntirrhinummajus. EMBO J.12:3711–19

74. Igloi GL, Kossel H. 1992. The transcrip-tional apparatus of chloroplast.Crit. Rev.Plant Sci.10:525–58

75. Inagaki N, Fujita S, Satoh K. 1989. Sol-ubilization and partial purification of athylakoidal enzyme of spinach involvedin the processing of D1 protein.FEBSLett.246:218–22

76. Iratni R, Baeza R, Andreeva A, MacheR, Lerbs-Mache S. 1994. Regulation ofthe rDNA transcription in chloroplasts:promoter exclusion by a constitutive re-pression.Genes Dev.8:2928–38

77. Isono K, Niwa Y, Satoh K, Kobayashi H.1997. Evidence for transcriptional regu-lation of plastid photosynthesis genes inArabidopsis thalianaroots.Plant Phys-iol. 114:623–30

78. Janska H, Mackenzie SA. 1993. Unusualmitochondrial genome organization incytoplasmic male sterile common beanand the nature of cytoplasmic reversionto fertility. Genetics135:869–79

79. Jenkins BD, Kulhanek DJ, Barkan A.1997. Nuclear mutations that blockgroup II RNA splicing in maize chloro-plast reveal several intron classes withdistinct requirements for splicing fac-tors.Plant Cell9:283–96

80. Keddie JS, Carroll B, Jones JDG, Gruis-sem W. 1996. TheDCL gene of tomato

is required for chloroplast develop-ment and palisade cell morphogenesis inleaves.EMBO J.15:4208–17

81. Keegstra K, Olsen LJ, Theg SM. 1989.Chloroplastic precursors and their trans-port across the envelope membranes.Annu. Rev. Plant Physiol. Plant Mol.Biol. 40:471–501

82. Kennell JC, Wise RP, Pring DR. 1987.Influence of nuclear background on tran-scription of a maize mitochondrial re-gion associated with Texas male sterilecytoplasm.Mol. Gen. Genet.210:399–406

83. Kim MY, Christopher DA, Mullet JE.1993. Direct evidence for selective mod-ulation of psbA, rpoA, rbcL and 16SRNA stability during barley chloroplastdevelopment.Plant Mol. Biol. 22:447–63

84. Kim MY, Mullet JE. 1995. Identifica-tion of a sequence-specific DNA bind-ing factor required for transcriptionof the barley chloroplast blue light–responsivepsbD-psbCpromoter.PlantCell 7:1445–57

85. Kirk JTO, Tilney-Bassett RAE. 1978.The Plastids: Their Chemistry, Struc-ture, Growth and Inheritance. Amster-dam: Elsevier/North Holland. 960 pp.

86. Klein RR, Mullet JE. 1990. Light-induced transcription of chloroplastgenes.psbA transcription is differen-tially enhanced in illuminated barely.J.Biol. Chem.265:1895–902

87. Knorpp C, Szigyarto C, Glaser E. 1996.Evidence for a novel ATP-dependentmembrane-associated protease in spi-nach leaf mitochondria.Biochem. J.310:527–31

88. Krol M, Spangfort MD, Huner NPA,Oquist G, Gustafsson P, Jansson S. 1995.Chlorophyll a/b binding proteins, pig-ment conversions and early light inducedproteins in a chlorophyllb-less barleymutant.Plant Physiol.107:873–83

89. Kudla J, Hayes R, Gruissem W. 1996.Polyadenylation accelerates degrada-tion of chloroplast mRNA.EMBO J.15:7137–46

90. Kuhlemeier C. 1992. Transcriptionaland post-transcriptional regulation ofgene expression in plants.Plant Mol.Biol. 19:1–14

91. Kwok SF, Piekos B, Mis´era S, DengX-W. 1996. A complement of tenessential and pleiotropic ArabidopsisCOP/DET/FUS genes is necessary forrepression of photomorphogenesis indarkness.Plant Physiol.110:731–42

92. Kyle DJ, Ohad I, Arntzen CJ. 1984.




Membrane protein damage and repair:selective loss of a quinone-protein func-tion in chloroplast membranes.Proc.Natl. Acad. Sci. USA81:4070–74

93. Landgren M, Zetterstrand M, Sund-berg, Glimelius K. 1996. Alloplasmicmale-sterileBrassica lines containingB. tournefortiimitochondria express anORF 3′ of the atp6 gene and a 32 kDaprotein.Plant Mol. Biol.32:879–90

94. Laughnan JR, Gabay-Laughnan S. 1983.Cytoplasmic male sterility in maize.Annu. Rev. Genet.17:27–48

95. Leech RM. 1986. Stability and plastic-ity during chloroplast development. InPlasticity in Plants, ed. D Jennings, ATrewavas, pp. 121–53. Cambridge: Soc.Exp. Biol. Symp., 40

96. Lerbs S, Brautigam E, Mache R. 1988.DNA-dependent RNA polymerase ofspinash chloroplast: Characterization ofα a-like andσ -like polypeptides.Mol.Gen. Genet.211:459–64

97. Lerbs-Mache S. 1993. The 110-kDapolypeptide of spinach plastid DNA-dependent RNA polymerase: single-subunit enzyme or catalytic core of mul-timeric enzyme complexes?Proc. Natl.Acad. Sci. USA90:5509–13

97a. Levings CS, Vasil I, eds. 1995.TheMolecular Biology of Plant Mitochon-dria. Boston: Kluwer

98. Levy H, Kindle KL, Stern D. 1997. Anuclear mutation that affects the 3′ pro-cessing of several mRNAs in Chlamy-domonas chloroplasts.Plant Cell9:825–36

99. Li H-M, Culligan K, Dixon RA, Chory J.1995.CUE1: a mesophyll cell-specificpositive regulator of light-controlledgene expression in Arabidopsis.PlantCell 7:1599–610

100. Li JM, Nagpal P, Vitart V, McMorrisTC, Chory J. 1996. A role for brassino-steroids in light-dependent developmentof Arabidopsis. Science272:398–401

101. Li X-Q, Zhang M, Brown GG. 1996.Cell-specific expression of mitochon-drial transcripts in maize seedlings.Plant Cell8:1961–75

102. Link G. 1994. Plastid differentiation: or-ganelle promoters and transcription fac-tors. InPlant Promoters and Transcrip-tion Factors, ed. L Nover, pp. 63–83.Heidelberg: Springer-Verlag

103. Link G. 1996. Green life: control ofchloroplast gene transcription.BioEs-says18:465–71

104. Liu JH, Landgren M, Glimelius K. 1996.Transfer of theB. tournefortiicytoplasmto B. napusfor the production of cyto-

plasmic male sterileB. napus. Physiol.Plant96:123–29

105. Lopez-Juez E, Stretfield S, Chory J.1996. Light signals and autoregulatedchloroplast development. InRegulationof Plant Growth and Development byLight, ed. WR Briggs, RL Heath, EMTobin, pp. 144–52. Rockville, MD: Am.Soc. Plant Physiol.

106. Lu BW, Hanson MR. 1996. Fully editedand partially editednad9transcripts dif-fer in size and both are associated withpolysomes in potato mitochondria.Nu-cleic Acids Res.24:1369–74

107. Lu BW, Wilson RK, Phreaner CG, Mul-ligan RM, Hanson MR. 1996. Proteinpolymorphism generated by differentialRNA editing of a plant mitochondrialrps12 gene.Mol. Cell Biol. 16:1543–49

108. Mackenzie SA, Chase CD. 1990. Fertil-ity restoration is associated with loss of aportion of the mitochondrial genome incytoplasmic male sterile common bean.Plant Cell2:905–12

109. Makaroff CA, Apel IJ, Palmer JD.1990. Characterization of radish mi-tochondrialatpA: influence of nuclearbackground on transcription ofatpA-associated sequences and relationshipwith male sterility. Plant Mol. Biol.15:735–46

110. Mandel MA, Feldmann KA, Herrera-Estrella L, Rocha-Sosa M, Leon P. 1996.CLA1, a novel gene required for chloro-plast development, is highly conservedin evolution.Plant J.9:649–58

111. Marano M, Serra E, Orellano E, CarrilloN. 1993. The path of chromoplast devel-opment in fruits and flowers.Plant Sci.94:1–17

112. Martienssen RA, Barkan A, Freeling M,Taylor WC. 1989. Molecular cloningof a maize gene involved in photosyn-thetic membrane organization that is reg-ulated by Robertson’sMutator. EMBOJ. 8:1633–39

113. Martınez-Zapater JM, Gil P, Capel J,Somerville CR. 1992. Mutations at theArabidopsis CHM locus promote re-arrangements of the mitochondrial ge-nome.Plant Cell4:889–99

114. Mayfield SP, Yohn CB, Cohen A, DanonA. 1995. Regulation of chloroplast geneexpression.Annu. Rev. Plant Physiol.Plant Mol. Biol.46:147–66

115. Melis A. 1991. Dynamics of photosyn-thetic membrane composition and func-tion. Biochim. Biophys. Acta1058:87–106

116. Meurer J, Meierhoff K, Westhoff P.



478 LEON ET AL

1996. Isolation of high chlorophyll-fluorescence mutants ofArabidopsisthaliana and their characterisation byspectroscopy, immunoblotting and nor-thern hybridization.Planta198:385–96

117. Michel F, Umesono K, Ozeki H. 1989.Comparative and functional anatomy ofgroup II catalytic introns—A review.Gene82:5–30

118. Miles D. 1994. The role of high chloro-phyll fluroscence photosynthesis mu-tants in the analysis of chloroplast thy-lakoid membrane assembly and func-tion. Maydica39:35–45

119. Millar AJ, McGrath RB, Chua N-H.1994. Phytochrome phototransductionpathways.Annu. Rev. Genet.28:325–49

120. Mohr S, Schulte-Kappert E, OdenbachW, Oettler G, Kuck U. 1993. Mito-chondrial DNA of cytoplasmic male-sterileTriticum timopheevi: rearrange-ment of upstream sequences of theatp6and orf25 genes.Theor. Appl. Genet.86:259–68

121. Moneger F, Smart CJ, Leaver CJ. 1994.Nuclear restoration of cytoplasmic malesterility in sunflower is associated withthe tissue-specific regulation of a novelmitochondrial gene.EMBO J. 13:8–17

122. Morden CW, Wolfe KH, de PamphilisCW, Palmer JD. 1991. Plastid transla-tion and transcription genes in a nonpho-tosynthetic plant: intact, missing andpseudo genes.EMBO J.10:3281–88

123. Mullet JE. 1993. Dynamic regulation ofchloroplast transcription.Plant Physiol.103:309–13

124. Nelson T, Langdale JA. 1989. Patternsof leaf development in C4 plants.PlantCell 1:3–13

125. Newton KJ. 1995. Aberrant growth phe-notypes associated with mitochondrialgenome rearrangements in higher plants.See Ref. 97a, pp. 585–96

126. Newton KJ, Winberg B, Yamato K,Lupold S, Stern DB. 1995. Evidence fora novel mitochondrial promoter preced-ing thecox2gene of perennial teosintes.EMBO J.14:585–93

127. Nugent JM, Palmer JD. 1991. RNA-mediated transfer of the genecoxII fromthe mitochondrion to the nucleus duringflowering plant evolution.Cell 66:473–81

128. Oda K, Yamato K, Ohta E, NakamuraY, Takemura M, et al. 1992. Gene or-ganization deduced from the completesequence of liverwortMarchantia poly-morphamitochondrial DNA: a primitive

form of plant mitochondrial genome.J.Mol. Biol. 223:1–7

129. Ogihara Y, Futami K, Tsuji K, Mu-rai K. 1997. Alloplasmic wheats withAegilops crassacytoplasm which ex-press photoperiod-sensitive homeotictransformations of anthers, show al-terations in mitochondrial DNA struc-ture and transcription.Mol. Gen. Genet.255:45–53

130. Oldenburg DJ, Bendich AJ. 1996. Sizeand structure of replicating mitochon-drial DNA in cultured tobacco cells.Plant Cell8:447–61

131. Osteryoung KW, Vierling E. 1995. Con-served cell and organelle division.Na-ture376:473–74

132. Pepper A, Delaney T, Washburn T, PooleD, Chory J. 1994.DET1, a negative regu-lator of light-mediated development andgene expression in Arabidopsis, encodesa novel nuclear-localized protein.Cell78:109–16

133. Phreaner CG, Williams MA, MulliganRM. 1996. Incomplete editing ofrps12transcripts results in the synthesis ofpolymorphic polypeptides in plant mi-tochondria.Plant Cell8:107–17

134. Pring DR, Mullen JA, Kempken F. 1992.Conserved sequence blocks 5′ to startcodons of plant mitochondrial genes.Plant Mol. Biol.19:313–17

134a. Pyke KA. 1997. The genetic control ofplastid division in higher plants.Am. J.Bot.84:1017–27

135. Pyke KA, Leech RM. 1992. Chloroplastdivision and expansion is radically al-tered by nuclear mutations inArabidop-sis thaliana. Plant Physiol.99:1005–8

136. Pyke KA, Leech RM. 1994. A geneticanalysis of chloroplast division and ex-pansion inArabidopsis thaliana. PlantPhysiol.104:201–7

137. Quail PH, Boylan MT, Parks BM, ShortTW, Xu Y, Wagner D. 1995. Phyto-chromes: photosensory perception andsignal transduction.Science268:675–80

138. Rapp JC, Baumgartner BJ, Mullet J.1992. Quantitative analysis of transcrip-tion and RNA levels of 15 barley chloro-plast genes. Transcription rates andmRNA levels vary over 300-fold; pre-dicted mRNA stabilities vary 30-fold.J.Biol. Chem.267:21404–11

139. Reiter RS, Coomber SA, Bourett TM,Bartley GE, Scolnik PA. 1994. Controlof leaf and chloroplast development bythe Arabidopsis genepale cress. PlantCell 6:1253–64

140. Rep M, Grivell LA. 1996. The role




of protein degradation in mitochondrialfunction and biogenesis.Curr. Genet.30:367–80

141. Rochaix JD. 1992. Post-transcriptionalsteps in the expression of chloroplastgenes.Annu. Rev. Cell Biol.8:1–28

142. Rochaix JD. 1996. Post-transcriptionalregulation of chloroplast gene expres-sion in Chlamydomonas reinhardtii.Plant Mol. Biol.32:327–41

143. Rocheford TR, Kennell JC, Pring DR.1992. Genetic analysis of nuclear con-trol of T-urf13/orf221 transcription in Tcytoplasm maize.Theor. Appl. Genet.84:891–98

144. Rodermel S, Haley J, Jiang C-Z, Tsai C-H, Bogorad L. 1996. A mechanism forintergenomic integration: abundance ofribulose biphosphate carboxilase small-subunit protein influences the translationof the large-subunit mRNA.Proc. Natl.Acad. Sci. USA93:3881–85

145. Roth R, Hall LN, Brutnell TP, LangdaleJA. 1996.bundle sheath defective 2, amutation that disrupts the coordinate de-velopment of bundle sheath and meso-phyll cells in the maize leaf.Plant Cell8:915–27

146. Runge S, van Cleve B, Lebedev N,Armstrong G, Apel K. 1995. Isola-tion and classification of chlorophyll-deficientxanthamutants ofArabidopsisthaliana. Planta197:490–500

147. Sakamoto W, Kondo H, Murata M, Mo-toyoshi F. 1996. Altered mitochondrialgenome expression in a maternal dis-torted leaf mutant of Arabidopsis in-duced by chloroplast mutator.Plant Cell8:1377–90

148. Saldanha R, Mohr G, Belfort M, Lam-bowitz AM. 1993. Group I and group IIintrons.FASEB J.7:15–24

149. Schwartz RM, Dayhoff MO. 1978. Ori-gins of prokaryotes, eukaryotes, mi-tochondria, and chloroplast.Science199:395–403

150. Sexton TB, Christopher DA, Mullet JE.1990. Light-induced swich in barleypsbD-psbCpromoter utilization: a novelmechanism regulating chloroplast geneexpression.EMBO J.9:4485–94

151. Shanklin J, DeWitt ND, Flanagan JM.1995. The stroma of higher plant plas-tids contain ClpP and ClpC, functionalhomologs ofEscherichia coliClpP andClpA: an archetypal two-componentATP-dependent protease.Plant Cell7:1713–22

152. Singh M, Brown GG. 1991. Suppres-sion of cytoplasmic male sterility by nu-clear genes alters expression of a novel

mitochondrial gene region.Plant Cell3:1349–62

153. Singh M, Brown GG. 1993. Characteri-zation of expression of a mitochondrialgene region associated with the Bras-sica “Polima” CMS: developmental in-fluences.Curr. Genet.24:316–22

154. Singh M, Hamel N, Menassa R, Li X-Q, Young B, et al. 1996. Nuclear genesassociated with a single Brassica CMSrestorer locus influence transcripts ofthree different mitochondrial gene re-gions.Genetics143:505–16

155. Small ID, Isaac PG, Leaver CJ. 1987.Stoichiometric differences in DNAmolecules containing theatpAgene sug-gest mechanisms for the generation ofmitochondrial diversity in maize.EMBOJ. 6:865–69

156. Small ID, Suffolk R, Leaver CJ.1989. Evolution of plant mitochondrialgenomes via sub-stoichiometric inter-mediates.Cell 58:69–76

157. Smart CJ, Moneger F, Leaver CJ. 1994.Cell-specific regulation of gene ex-pression in mitochondria during antherdevelopment in sunflower.Plant Cell6:811–25

158. Somerville CR. 1986. Analysis of pho-tosynthesis with mutants of higher plantsand algae.Annu. Rev. Plant Physiol.37:467–507

159. Staub JM, Maliga P. 1993. Accumula-tion of the D1 polypeptide in tobaccoplastids is regulated via the untranslatedregion of thepsbA mRNA. EMBO J.12:601–6

160. Stern DB, Higgs DC, Yang J. 1997. Tran-scription and translation in chloroplasts.Trends Plant Sci.2:308–15

161. Streatfield SJ, Post-Beittenmiller D,Chory J. 1997. Analysis of thecuel(cabunderexpressed) mutant ofArabidopsisthaliana. Int. Conf. Arabidopsis Res.,8th, Madison, Wis.

162. Susek R, Chory J. 1992. A tale of twogenomes: role of a chloroplast sig-nal in coordinating nuclear and plastidgenome expression.Aust. J. Plant Phys-iol. 19:387–99

163. Suzuki CK, Suda K, Wang N, Schatz G.1994. Requirement for the yeast geneLON in intramitochondrial proteolysisand maintenance of respiration.Science264:273–76

164. Tang HV, Pring DR, Shaw LC, SalazarRA, Muza FR, et al. 1996. Tran-script processing internal to a mitochon-drial open reading frame is correlatedwith fertility restoration in male-sterilesorghum.Plant J.10:123–33



480 LEON ET AL

165. Taylor WC. 1989. Regulatory inter-actions between nuclear and plastidgenomes.Annu. Rev. Plant Physiol.Plant Mol. Biol.40:211–33

166. Tiller K, Link G. 1993. Phosphorylationand dephosphorylation affect functionalcharacteristics of chloroplast and etio-plast transcription systems from mustard(Sinapis albaL.). EMBO J.12:1745–53

167. Troxler RF, Zhang F, Hu J, Bogorad L.1994. Evidence thatσ factors are com-ponents of chloroplast RNA polymerase.Plant Physiol.104:753–59

168. Tsunewaki K. 1993. Genome-plasmoninteractions in wheat.Jpn. J. Genet.68:1–34

169. Unseld M, Marienfeld JR, Brandt P,Brennicke A. 1997. The mitochondrialgenome ofArabidopsis thalianacon-tains 57 genes in 366,924 nucleotides.Nat. Genet.15:57–61

170. van der Graaff E. 1997.Developmen-tal mutants of Arabidopsis thaliana ob-tained after T-DNA transformation. PhDthesis. Leiden Univ. 179 pp.

171. Van Dyck L, Pearce DA, ShermanF. 1994. PIM1 encodes a mitochon-drial ATP-dependent protease that is re-quired for mitochondrial function in theyeastSaccharomyces cerevisiae. J. Biol.Chem.269:238–42

172. Voelker R, Barkan A. 1995. Two nuclearmutations disrupt distinct pathways fortargeting proteins to the chloroplast thy-lakoid.EMBO J.14:3905–14

173. Voelker R, Mendel-Hartvig J, Barkan A.1997. Transposon-disruption of a maizenuclear gene,tha1, encoding a chloro-plast SecA homologue: in vivo role ofcp-SecA in thylakoid protein targeting.Genetics145:467–78

173a. von Arnim A, Deng X-W. 1996. Lightcontrol of seedling development.Annu.Rev. Plant Physiol. Plant. Mol. Biol.47:215–43

174. von Wettstein D, Henningsen KW,Boynton JE, Kannangara GC, NielsenOF. 1971. The genetic control of chloro-plast development in barley. InAuton-omy and Biogenesis of Mitochondriaand Chloroplast, ed. N Boardman, ALinnae, R Smillie, pp. 205–23. Amster-dam: North-Holland

175. Wang N, Gottesman S, Willingham M,Gottesman MM, Maurizi MR. 1993.

A human mitochondrial ATP-dependentprotease that is highly homologous tobacterialLonprotease.Proc. Natl. Acad.Sci. USA90:11247–51

176. Wei N, Chamovitz DA, Deng X-W.1994. Arabidopsis COP9 is a compo-nent of a novel signaling complex medi-ating light control of development.Cell78:117–24

176a. Wei N, Deng X-W. 1996. The role ofthe COP/DET/FUS genes in light con-trol of Arabidopsis seedling develop-ment.Plant Physiol.112:871–78

177. Westhoff P, Hermann RG. 1988. Com-plex RNA maturation in chloroplasts.Eur. J. Biochem.171:551–64

178. Wetzel CM, Jiang C, Meehan LJ, Voy-tas DF, Rodermel SR. 1994. Nuclear-organelle interactions: theimmutansvariegation mutant ofArabidopsis isplastid autonomous and impaired incarotenoid biosynthesis.Plant J.6:161–75

179. Whelan J, Glaser E. 1997. Protein im-port into plant mitochondria.Plant Mol.Biol. 33:771–89

180. Wilsbach K, Payne GS. 1993. Vps1p, amember of the dynamin GTPase family,is necessary for Golgi membrane proteinretention inSaccharomyces cerevisiae.EMBO J.12:3049–59

181. Wilson RK, Hanson MR. 1996. Pref-erential RNA editing at specific siteswithin transcripts of two plant mitochon-drial genes does not depend on transcrip-tional context or nuclear genotype.Curr.Genet.30:502–8

182. Wise RP, Dill CL, Schnable PS. 1996.Mutator-induced mutations of therf1nuclear fertility restorer of T-cytoplasmmaize alter the accumulation ofT-urf13 mitochondrial transcripts.Genet-ics143:1383–94

183. Wolstenholme DR, Fauron CM-R. 1995.Mitochondrial genome organization.See Ref. 97a, pp. 1–60

184. Yang AJ, Mulligan RM. 1993. Distribu-tion of maize mitochondrial transcriptsin polysomal RNA: evidence for nonse-lectivity in recruitment of mRNAs.Curr.Genet.23:532–36

185. Young EG, Hanson MR. 1987. A fusedmitochondrial gene associated with cy-toplasmic male sterility is developmen-tally regulated.Cell 50:41–49

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nuclear control of plastid and mitochondrial development in higher