Plant Molecular Biology

, Volume 66, Issue 1–2, pp 33–46 | Cite as

Nuclear, chloroplast, and mitochondrial transcript abundance along a maize leaf developmental gradient

  • A. Bruce Cahoon
  • Elizabeth M. Takacs
  • Richard M. Sharpe
  • David B. Stern


In maize, the chloroplast chromosome encodes 104 genes whose roles are primarily in photosynthesis and gene expression. The 2,000–3,000 nuclear gene products that localize to plastids are required both to encode and regulate plastid gene expression as well as to underpin each aspect of plastid physiology and development. We used a new “three-genome” maize biogenesis cDNA microarray to track abundance changes in nuclear, chloroplast and mitochondrial transcripts in stage 2 semi-emerged leaf blades of one month-old maize plants. We report the detection and quantification of 433 nuclear, 62 chloroplast, and 27 mitochondrial transcripts, with the majority of the nuclear transcripts predicted or known to encode plastid proteins. The data were analyzed as ratios of expression of individual transcripts in the green tip (mature chloroplasts) versus the yellow base of the leaf (etioplasts). According to the microarray data at least 51 plastid genes and 121 nuclear genes are expressed at least two-fold higher in the tip of the leaf. Almost all (25) mitochondrial and 177 nuclear transcripts were expressed at least 2–fold higher in the leaf base. Independent quantification of a subset of each transcript population by RNA gel blot analysis and/or quantitative real time RT-PCR concurred with the transcript ratios determined by the array. Ontological distribution of the transcripts suggests that photosynthesis-related RNAs were most highly abundant in the leaf tip and that energy use genes were most highly expressed in the base. Transcripts whose products are used in plastid translation constituted the largest single ontological group with relatively equal numbers of genes in the three expression categories, defined as higher in tip, higher in base, or equally expressed in tip and base.


Chloroplast Maize Leaf development Microarray Mitochondria 



plastid targeted proteins


quantitative, real-time, reverse transcriptase polymerase chain reaction


expressed sequence tag

Supplementary material

11103_2007_9250_MOESM1_ESM.doc (22 kb)
Table S1Primers Used for Quantitative Real Time RT-PCR Analysis. Sets were designed based on GenBank accessions. The members of each set have a similar annealing temperature and are predicted to resist forming secondary structure at or above these temperatures. Amplicons are 75–150 bases in size (DOC 22 kb)
11103_2007_9250_MOESM2_ESM.xls (470 kb)
Table S2Microarray elements. A complete list of the elements included on the maize three genome microarray developed at Boyce Thompson Institute. Listed are nuclear, chloroplast, and mitochondrial genes as well as positive control spots, negative control spots, and blanks (XLS 469 kb)
11103_2007_9250_MOESM3_ESM.xls (36 kb)
Table S3Chloroplast transcripts. A list of the protein-coding chloroplast transcripts detected by the microarray experiments which passed the data quality screens described in Materials and Methods. The genes are arranged by their Tip:Base ratio from the smallest ratio to the largest (XLS 36 kb)
11103_2007_9250_MOESM4_ESM.xls (22 kb)
Table S4Mitochondrial transcripts. A list of the protein-coding mitochondrial transcripts detected by the microarray experiments which passed the data quality screens described in Materials and Methods. The genes are arranged by their Tip:Base ratio from the smallest ratio to the largest (XLS 21 kb)
11103_2007_9250_MOESM5_ESM.xls (70 kb)
Table S5Nuclear gene transcripts, higher in base. A list of the nuclear transcripts with a Tip:Base ratio which suggested they were most abundant in the base of the leaf. The genes are arranged by their Tip:Base ratio from smallest (expressed most extremely in the base) to ratios close to the cutoff of 0.5 (0.5 represents a two-fold difference in transcript abundance in the base and the tip) (XLS 70 kb)
11103_2007_9250_MOESM6_ESM.xls (54 kb)
Table S6Nuclear gene transcripts, no change. A list of the nuclear transcripts with a Tip:Base ratio which suggested there was less than two-fold abundance difference between the base and the tip. The genes are arranged by their Tip:Base ratios from just above two-fold higher in the base (0.5) to just below two fold higher in the tip (2.0) (XLS 54 kb)
11103_2007_9250_MOESM7_ESM.xls (50 kb)
Table S7Nuclear gene transcripts, higher in tip. A list of the nuclear transcripts with a Tip:Base ratio which suggested they were most abundant in the tip of the leaf. The genes are arranged by their Tip:Base ratios from smallest (just above a two-fold difference in expression) to ratios indicating an extremely high transcript abundance in the tip versus the base (XLS 50 kb)
11103_2007_9250_MOESM8_ESM.xls (66 kb)
Table S8MapMan Asignments. Nuclear genes with Arabidopsis homologs recognized by the MapMan program are listed. Bin designations are listed for each maize gene along with their array-derived expression ratios and the corresponding Arabidopsis locus numbers (XLS 66 kb)


  1. Allison LA, Simon LD, Maliga P (1996) Deletion of rpoB reveals a second distinct transcription system in plastids of higher plants. EMBO J 15:2802–2809PubMedGoogle Scholar
  2. Baba K, Schmidt J, Espinosa-Ruiz A, Villarejo A, Shiina T, Gardestrom P, Sane AP, Bhalerao RP (2004) Organellar gene transcription and early seedling development are affected in the rpoT;2 mutant of Arabidopsis. Plant J 38:38–48PubMedCrossRefGoogle Scholar
  3. Baginsky S, Siddique A, Gruissem W (2004) Proteome analysis of tobacco bright yellow-2 (BY-2) cell culture plastids as a model for undifferentiated heterotrophic plastids. J Proteome Res 3:1128–1137PubMedCrossRefGoogle Scholar
  4. Barkan A (1988) Proteins encoded by a complex chloroplast transcription unit are each translated from both monocistronic and polycistronic mRNAs. Embo J 7:2637–2644PubMedGoogle Scholar
  5. Barkan A (1989) Tissue-dependent plastid RNA splicing in maize: transcripts from four plastid genes are predominantly unspliced in leaf meristems and roots. Plant Cell 1:437–445PubMedCrossRefGoogle Scholar
  6. Barkan A, Goldschmidt-Clermont M (2000) Participation of nuclear genes in chloroplast gene expression. Biochimie 82:559–572PubMedCrossRefGoogle Scholar
  7. Baumgartner BJ, Rapp JC, Mullet JE (1989) Plastid transcription activity and DNA copy number increase early in barley chloroplast development. Plant Physiol 89:1011–1018PubMedGoogle Scholar
  8. Baumgartner BJ, Rapp JC, Mullet JE (1993) Plastid genes encoding the transcription/translation apparatus are differentially transcribed early in barley (Hordeum vulgare) chloroplast development (evidence for selective stabilization of psbA mRNA). Plant Physiol 101:781–791PubMedGoogle Scholar
  9. Blomqvist LA, Ryberg M, Sundqvist C (2006) Proteomic analysis of the etioplast inner membranes of wheat (Triticum aestivum) by two-dimersional electrophoresis and mass spectrometry. Physiol Plant 128:368–381CrossRefGoogle Scholar
  10. Bollenbach TJ, Schuster G, Stern DB (2004) Cooperation of endo- and exo-ribonucleases in chloroplast mRNA turnover. Prog Nucleic Acid Res Mol Biol 78:305–337PubMedCrossRefGoogle Scholar
  11. Cahoon AB, Cunningham KA, Bollenbach TJ, Stern DB (2003) Maize BMS cultured cell lines survive with massive plastid gene loss. Curr Genet 44:104–113PubMedCrossRefGoogle Scholar
  12. Cahoon AB, Harris FM, Stern DB (2004) Analysis of developing maize plastids reveals two mRNA stability classes correlating with RNA polymerase type. EMBO Rep 5:801–806PubMedCrossRefGoogle Scholar
  13. Cahoon AB, Komine Y, Stern DB (2006) Plastid Transcription: Competition, Regulation, and Promotion by Plastid- and Nuclear-Encoded Polymerases. In: Wise RRH, Kenneth J (eds) The structure and function of plastids, vol 23. SpringerGoogle Scholar
  14. Chang CC, Sheen J, Bligny M, Niwa Y, Lerbs-Mache S, Stern DB (1999) Functional analysis of two maize cDNAs encoding T7-like RNA polymerases. Plant Cell 11:911–926PubMedCrossRefGoogle Scholar
  15. Choquet Y, Wollman FA (2002) Translational regulations as specific traits of chloroplast gene expression. FEBS Lett 529:39–42PubMedCrossRefGoogle Scholar
  16. Clarke AK, Gustafsson P, Lidholm JA (1994) Identification and expression of the chloroplast clpP gene in the conifer Pinus contorta. Plant Mol Biol 26:851–862PubMedCrossRefGoogle Scholar
  17. Czechowski T, Bari RP, Stitt M, Scheible WR, Udvardi MK (2004) Real-time RT-PCR profiling of over 1400 Arabidopsis transcription factors: unprecedented sensitivity reveals novel root- and shoot-specific genes. Plant J 38:366–379PubMedCrossRefGoogle Scholar
  18. Danon A (1997) Translational regulation in the chloroplast. Plant Physiol 115:1293–1298PubMedCrossRefGoogle Scholar
  19. Draghici S, Khatri P, Eklund AC, Szallasi Z (2006) Reliability and reproducibility issues in DNA microarray measurements. Trends Genet 22:101–109PubMedCrossRefGoogle Scholar
  20. Emanuel C, Weihe A, Graner A, Hess WR, Borner T (2004) Chloroplast development affects expression of phage-type RNA polymerases in barley leaves. Plant J 38:460–472PubMedCrossRefGoogle Scholar
  21. Emanuelsson O, Nielsen H, Brunak S, von Heijne G (2000) Predicting subcellular localization of proteins based on their N-terminal amino acid sequence. J Mol Biol 300:1005–1016PubMedCrossRefGoogle Scholar
  22. Fedoroff NV (2002) RNA-binding proteins in plants: the tip of an iceberg? Curr Opin Plant Biol 5:452–459PubMedCrossRefGoogle Scholar
  23. Ferro M, Salvi D, Brugiere S, Miras S, Kowalski S, Louwagie M, Garin J, Joyard J, Rolland N (2003) Proteomics of the chloroplast envelope membranes from Arabidopsis thaliana. Mol Cell Proteomics 2:325–345PubMedGoogle Scholar
  24. Fey V, Wagner R, Brautigam K, Prannschmidt T (2005) Photosynthetic redox control of nuclear gene expression. J Exp Bot 56:1491–1498PubMedCrossRefGoogle Scholar
  25. Firestein GS, Pisetsky DS (2002) DNA microarrays: boundless technology or bound by technology? Guidelines for studies using microarray technology. Arthritis Rheum 46:859–861PubMedCrossRefGoogle Scholar
  26. Freeling MLB (1994) The Maize Leaf. In: Freeling MWV (ed) The Maize handbook. Springer-Verlag, New York, pp 17–28Google Scholar
  27. Friso G, Giacomelli L, Ytterberg AJ, Peltier JB, Rudella A, Sun Q, Wijk KJ (2004) In-depth analysis of the thylakoid membrane proteome of Arabidopsis thaliana chloroplasts: new proteins, new functions, and a plastid proteome database. Plant Cell 16:478–499PubMedCrossRefGoogle Scholar
  28. Goldschmidt-Clermont M (1998) Coordination of nuclear and chloroplast gene expression in plant cells. Int Rev Cytol 177:115–180PubMedGoogle Scholar
  29. Gray JC, Sullivan JA, Wang JH, Jerome CA, MacLean D (2003) Coordination of plastid and nuclear gene expression. Philos Trans R Soc Lond B Biol Sci 358:135–144; discussion 144–135PubMedCrossRefGoogle Scholar
  30. Hajdukiewicz PT, Allison LA, Maliga P (1997) The two RNA polymerases encoded by the nuclear and the plastid compartments transcribe distinct groups of genes in tobacco plastids. EMBO J 16:4041–4048PubMedCrossRefGoogle Scholar
  31. Han C-d, Patrie W, Polacco M, Coe EH (1993) Aberrations in plastid transcripts and deficiency of plastid DNA in striped and albino mutations of maize. Planta 191:552–563Google Scholar
  32. Heazlewood JL, Tonti-Filippini J, Verboom RE, Millar AH (2005) Combining experimental and predicted datasets for determination of the subcellular location of proteins in Arabidopsis. Plant Physiol 139:598–609PubMedCrossRefGoogle Scholar
  33. Hedtke B, Borner T, Weihe A (2000) One RNA polymerase serving two genomes. EMBO Rep 1:435–440PubMedCrossRefGoogle Scholar
  34. Herrin DL, Nickelsen J (2004) Chloroplast RNA processing and stability. Photosynth Res 82:301–314PubMedCrossRefGoogle Scholar
  35. Hess WR, Prombona A, Fieder B, Subramanian AR, Borner T (1993) Chloroplast RPS15 and the RPOB/C1/C2 gene cluster are strongly transcribed in ribosome-deficient plastids: evidence for a functioning non-chloroplast encoded RNA polymerase. EMBO J 12:563–571PubMedGoogle Scholar
  36. Hoober JK (1984) Chloroplasts. Plenum, New York and LondonGoogle Scholar
  37. Hricova A, Quesada V, Micol JL (2006) The SCABRA3 nuclear gene encodes the plastid RpoTp RNA polymerase, which is required for chloroplast biogenesis and mesophyll cell proliferation in Arabidopsis. Plant Physiol 141:942–956PubMedCrossRefGoogle Scholar
  38. Hudson GS, Holton TA, Whitfield PR, Bottomley W (1988) Spinach chloroplast rpoBC genes encode three subunits of the chloroplast RNA polymerase. J Mol Biol 200:639–654PubMedCrossRefGoogle Scholar
  39. Jiao S, Thornsberry JM, Elthon TE, Newton KJ (2005) Biochemical and molecular characterization of photosystem I deficiency in the NCS6 mitochondrial mutant of maize. Plant Mol Biol 57:303–13PubMedCrossRefGoogle Scholar
  40. Khan MS (2005) Unraveling the complexities of plastid transcription in plants. Trends Biotechnol 23:535–538PubMedCrossRefGoogle Scholar
  41. Kleffmann T, Russenberger D, von Zychlinski A, Christopher W, Sjolander K, Gruissem W, Baginsky S (2004) The Arabidopsis thaliana chloroplast proteome reveals pathway abundance and novel protein functions. Curr Biol 14:354–362PubMedCrossRefGoogle Scholar
  42. Komatsu S, Muhammad A, Rakwal R (1999) Separation and characterization of proteins from green and etiolated shoots of rice (Oryza sativa L.): towards a rice proteome. Electrophoresis 20:630–636PubMedCrossRefGoogle Scholar
  43. Kubicki A, Steinmuller K, Westhoff P (1994) Differential transcription of plastome-encoded genes in the mesophyll and bundle-sheath chloroplasts of the monocotyledonous NADP-malic enzyme-type C4 plants maize and Sorghum Google Scholar
  44. Leech RM, Rumsby MG, Thomson WW (1973) Plastid differentiation, acyl lipid, and fatty acid changes in developing green maize leaves. Plant Physiol 52:240–245PubMedGoogle Scholar
  45. Liere K, Maliga P (2001) Plastid RNA Polymerases in Higher Plants. In: Aro E-M, Andersson B (eds) Regulation of photosynthesis, vol 11. Kluwer Academic, pp 39–49Google Scholar
  46. Lonosky PM, Zhang X, Honavar VG, Dobbs DL, Fu A, Rodermel SR (2004) A proteomic analysis of maize chloroplast biogenesis. Plant Physiol 134:560–574PubMedCrossRefGoogle Scholar
  47. Lopez-Juez E, Pyke KA (2005) Plastids unleashed: their development and their integration in plant development. Int J Dev Biol 49:557–577PubMedCrossRefGoogle Scholar
  48. Maier RM, Neckermann K, Igloi GL, Kossel H (1995) Complete sequence of the maize chloroplast genome: gene content, hotspots of divergence and fine tuning of genetic information by transcript editing. J Mol Biol 251:614–628PubMedCrossRefGoogle Scholar
  49. Majeran W, Cai Y, Sun Q, van Wijk KJ (2005) Functional differentiation of bundle sheath and mesophyll maize chloroplasts determined by comparative proteomics. Plant Cell 17:3111–3140PubMedCrossRefGoogle Scholar
  50. Masuda T, Takamiya K (2004) Novel insights into the enzymology, regulation and physiological functions of light-dependent protochlorophyllide oxidoreductase in angiosperms. Photosynth Res 81:1–29PubMedCrossRefGoogle Scholar
  51. Meurer J, Berger A, Westhoff P (1996) A nuclear mutant of Arabidopsis with impaired stability on distinct transcripts of the plastid psbB, psbD/C, ndhH, and ndhC operons. Plant Cell 8:1193–1207PubMedCrossRefGoogle Scholar
  52. Minoda A, Nagasawa K, Hanaoka M, Horiuchi M, Takahashi H, Tanaka K (2005) Microarray profiling of plastid gene expression in a unicellular red alga, Cyanidioschyzon merolae. Plant Mol Biol 59:375–385PubMedCrossRefGoogle Scholar
  53. Monde RA, Schuster G, Stern DB (2000) Processing and degradation of chloroplast mRNA. Biochimie 82:573–582PubMedCrossRefGoogle Scholar
  54. Nadon R, Shoemaker J (2002) Statistical issues with microarrays: processing and analysis. Trends Genet 18:265–271PubMedCrossRefGoogle Scholar
  55. Nagashima A, Hanaoka M, Motohashi R, Seki M, Shinozaki K, Kanamaru K, Takahashi H, Tanaka K (2004) DNA microarray analysis of plastid gene expression in an Arabidopsis mutant deficient in a plastid transcription factor sigma, SIG2. Biosci Biotechnol Biochem 68:694–704PubMedCrossRefGoogle Scholar
  56. Nakamura T, Furuhashi Y, Hasegawa K, Hashimoto H, Watanabe K, Obokata J, Sugita M, Sugiura M (2003) Array-based analysis on tobacco plastid transcripts: preparation of a genomic microarray containing all genes and all intergenic regions. Plant Cell Physiol 44:861–867PubMedCrossRefGoogle Scholar
  57. Peltier JB, Cai Y, Sun Q, Zabrouskov V, Giacomelli L, Rudella A, Ytterberg AJ, Rutschow H, van Wijk KJ (2006) The Oligomeric Stromal Proteome of Arabidopsis thaliana Chloroplasts. Mol Cell Proteomics 5:114–133PubMedCrossRefGoogle Scholar
  58. Peltier JB, Friso G, Kalume DE, Roepstorff P, Nilsson F, Adamska I, van Wijk KJ (2000) Proteomics of the chloroplast: systematic identification and targeting analysis of lumenal and peripheral thylakoid proteins. Plant Cell 12:319–341PubMedCrossRefGoogle Scholar
  59. Pfannschmidt T, Liere K (2005) Redox regulation and modification of proteins controlling chloroplast gene expression. Antioxid Redox Signal 7:607–618PubMedCrossRefGoogle Scholar
  60. Porubleva L, Vander Velden K, Kothari S, Oliver DJ, Chitnis PR (2001) The proteome of maize leaves: use of gene sequences and expressed sequence tag data for identification of proteins with peptide mass fingerprints. Electrophoresis 22:1724–1738PubMedCrossRefGoogle Scholar
  61. Richly E, Leister D (2004) An improved prediction of chloroplast proteins reveals diversities and commonalities in the chloroplast proteomes of Arabidopsis and rice. Gene 329:11–16PubMedCrossRefGoogle Scholar
  62. Rochaix JD (1996) Post-transcriptional regulation of chloroplast gene expression in Chlamydomonas reinhardtii. Plant Mol Biol 32:327–341PubMedCrossRefGoogle Scholar
  63. Rochaix JD (2006) The role of nucleus- and chloroplast-encoded factors in the synthesis of the photosynthetic apparatus. In: Wise RRH, Kenneth J (eds) The Structure and Function of Plastids, vol 23. SpringerGoogle Scholar
  64. Schubert M, Petersson UA, Haas BJ, Funk C, Schroder WP, Kieselbach T (2002) Proteome map of the chloroplast lumen of Arabidopsis thaliana. J Biol Chem 277:8354–8365PubMedCrossRefGoogle Scholar
  65. Shiina T, Tsunoyama Y, Nakahira Y, Khan MS (2005) Plastid RNA polymerases, promoters, and transcription regulators in higher plants. Int Rev Cytol 244:1–68PubMedCrossRefGoogle Scholar
  66. Staehelin LA (2003) Chloroplast structure: from chlorophyll granules to supra-molecular architecture of thylakoid membranes. Photosynth Res 76:185–196PubMedCrossRefGoogle Scholar
  67. Stern DB, Hanson MR, Barkan A (2004) Genetics and genomics of chloroplast biogenesis: maize as a model system. Trends Plant Sci 9:293–301PubMedCrossRefGoogle Scholar
  68. Strand A, Kleine T (2006) Plastid-to-Nucleus Signalling. In: Wise RRH, Kenneth J (eds) The structure and function of plastids, vol 23. SpringerGoogle Scholar
  69. Sugita M, Sugiura M (1996) Regulation of gene expression in chloroplasts of higher plants. Plant Mol Biol 32:315–326PubMedCrossRefGoogle Scholar
  70. Sylvester AW, Cande WZ, Freeling M (1990) Division and differentiation during normal and liguleless-1 maize leaf development. Development 110:985–1000PubMedGoogle Scholar
  71. Thimm O, Blasing O, Gibon Y, Nagel A, Meyer S, Kruger P, Selbig J, Muller LA, Rhee SY, Stitt M (2004) MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant J 37:914–939PubMedCrossRefGoogle Scholar
  72. Trifa Y, Lerbs-Mache S (2000) Extra-ribosomal function(s) of the plastid ribosomal protein L4 in the expression of ribosomal components in spinach. Mol Gen Genet 263:642–647PubMedCrossRefGoogle Scholar
  73. Trifa Y, Privat I, Gagnon J, Baeza L, Lerbs-Mache S (1998) The nuclear RPL4 gene encodes a chloroplast protein that co-purifies with the T7-like transcription complex as well as plastid ribosomes. J Biol Chem 273:3980–3985PubMedCrossRefGoogle Scholar
  74. van Wijk KJ (2004) Plastid proteomics. Plant Physiol Biochem 42:963–977PubMedCrossRefGoogle Scholar
  75. von Zychlinski A, Kleffmann T, Krishnamurthy N, Sjolander K, Baginsky S, Gruissem W (2005) Proteome analysis of the rice etioplast: metabolic and regulatory networks and novel protein functions. Mol Cell Proteomics 4:1072–1084CrossRefGoogle Scholar
  76. Weihe A, Hedtke B, Borner T (1997) Cloning and characterization of a cDNA encoding a bacteriophage-type RNA polymerase from the higher plant Chenopodium album. Nucleic Acids Res 25:2319–2325PubMedCrossRefGoogle Scholar
  77. Zengel JM, Lindahl L (1990) Ribosomal protein L4 stimulates in vitro termination of transcription at a NusA-dependent terminator in the S10 operon leader. Proc Natl Acad Sci USA 87:2675–2679PubMedCrossRefGoogle Scholar
  78. Zuker M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31:3406–3415PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2007

Authors and Affiliations

  • A. Bruce Cahoon
    • 1
  • Elizabeth M. Takacs
    • 2
    • 3
  • Richard M. Sharpe
    • 1
  • David B. Stern
    • 2
  1. 1.Department of BiologyMiddle Tennessee State UniversityMurfreesboroUSA
  2. 2.Boyce Thompson Institute for Plant ResearchIthacaUSA
  3. 3.Department of Plant BiologyCornell UniversityIthacaUSA

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