CoChat
Sign Up
Cited by 17Photosynthetic Processes and MechanismsGenomics and Chromatin DynamicsBacterial Genetics and Biotechnology

The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.

Architecture of the spinach plastid-encoded RNA polymerase

Open access
Wang, Tongtong, Wang, Guang-Lei, Fang, Ying, Zhang, Yi, Peng, Wenxin, Zhou, Yue, Zhang, Aihong, Yu, Long-Jiang, Lu, Congming·2024·Nature Communications
DOI 10.1038/s41467-024-54266-2PMC PMC11561172

Published version of a preprint

Open this paper in CoChat — free account

Abstract

The plastid-encoded RNA polymerase serves as the principal transcription machinery within chloroplasts, transcribing over 80% of all primary plastid transcripts. This polymerase consists of a prokaryotic-like core enzyme known as the plastid-encoded RNA polymerase core, and is supplemented by newly evolved associated proteins known as PAPs. However, the architecture of the plastid-encoded RNA polymerase and the possible functions of PAPs remain unknown. Here, we present the cryo-electron microscopy structure of a 19-subunit plastid-encoded RNA polymerase complex derived from spinach (Spinacia oleracea). The structure shows that the plastid-encoded RNA polymerase core resembles bacterial RNA polymerase. Twelve PAPs and two additional proteins (FLN2 and pTAC18) bind at the periphery of the plastid-encoded RNA polymerase core, forming extensive interactions that may facilitate complex assembly and stability. PAPs may also protect the complex against oxidative damage and has potential functions in transcriptional regulation. This research offers a structural basis for future investigations into the functions and regulatory mechanisms governing the transcription of plastid genes. The plastid-encoded RNA polymerase serves as the principal transcription machinery within chloroplasts. Here, the authors present the cryo-electron microscopy structure of a 19-subunit plastid-encoded RNA polymerase complex derived from spinach.

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1038/s41467-024-54266-2

Cites

2 of 2 references verified0 citation errors · 0 not checkable

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Flagged first, then by citations

Research works printed but not linked: 67

  1. Timmis, J. N., Ayliffe, M. A., Huang, C. Y. & Martin, W. Endosymbiotic gene transfer: Organelle genomes forge eukaryotic chromosomes. Nat. Rev. Genet. 5, 123–135 (2004). · DOI
  2. Soll, J. & Schleiff, E. Protein import into chloroplasts. Nat. Rev. Mol. Cell Biol. 5, 198–208 (2004). · DOI
  3. Pogson, B. J. & Albrecht, V. Genetic dissection of chloroplast biogenesis and development: an overview. Plant Physiol. 155, 1545–1551 (2011). · DOI
  4. Zhang, Y., Tian, L. & Lu, C. Chloroplast gene expression: Recent advances and perspectives. Plant Commun. 4, 100611 (2023). · DOI
  5. Yagi, Y. & Shiina, T. Recent advances in the study of chloroplast gene expression and its evolution. Front. Plant Sci. 5, 61 (2014). · DOI
  6. Börner, T., Aleynikova, A. Y., Zubo, Y. O. & Kusnetsov, V. V. Chloroplast RNA polymerases: Role in chloroplast biogenesis. Biochim. Biophys. Acta 1847, 761–769 (2015). · DOI
  7. Legen, J. et al. Comparative analysis of plastid transcription profiles of entire plastid chromosomes from tobacco attributed to wild-type and PEP-deficient transcription machineries. Plant J. 31, 171–188 (2002). · DOI
  8. Zhelyazkova, P. et al. The Primary transcriptome of barley chloroplasts: Numerous noncoding RNAs and the dominating role of the plastid-encoded RNA polymerase. Plant Cell 24, 123–136 (2012). · DOI
  9. Pfannschmidt, T. et al. Plastid RNA polymerases: orchestration of enzymes with different evolutionary origins controls chloroplast biogenesis during the plant life cycle. J. Exp. Bot. 66, 6957–6973 (2015). · DOI
  10. Steiner, S., Schröter, Y., Pfalz, J. & Pfannschmidt, T. Identification of essential subunits in the plastid-encoded RNA polymerase complex reveals building blocks for proper plastid development. Plant Physiol. 157, 1043–1055 (2011). · DOI
  11. Ruedas, R. et al. Three-dimensional envelope and subunit interactions of the plastid-encoded RNA polymerase from Sinapis alba. Int. J. Mol. Sci. 23, 9922 (2022). · DOI · Paper page
  12. Yagi, Y., Ishizaki, Y., Nakahira, Y., Tozawa, Y. & Shiina, T. Eukaryotic-type plastid nucleoid protein pTAC3 is essential for transcription by the bacterial-type plastid RNA polymerase. Proc. Natl Acad. Sci. USA 109, 7541–7546 (2012). · DOI
  13. Pfalz, J., Liere, K., Kandlbinder, A., Dietz, K. J. & Oelmüller, R. pTAC2, -6, and -12 are components of the transcriptionally active plastid chromosome that are required for plastid gene expression. Plant Cell 18, 176–197 (2006). · DOI
  14. Williams-Carrier, R., Zoschke, R., Belcher, S., Pfalz, J. & Barkan, A. A major role for the plastid-encoded RNA polymerase complex in the expression of plastid transfer RNAs. Plant Physiol. 164, 239–248 (2014). · DOI
  15. Chang, S. H. et al. pTAC10, a key subunit of plastid-encoded RNA polymerase, promotes chloroplast development. Plant Physiol. 174, 435–449 (2017). · DOI
  16. Seo, D. H. et al. PEP-ASSOCIATED PROTEIN 3 regulates rice tiller formation and grain yield by controlling chloroplast biogenesis. Plant Physiol. 194, 805–818 (2024). · DOI
  17. Myouga, F. et al. A heterocomplex of iron superoxide dismutases defends chloroplast nucleoids against oxidative stress and is essential for chloroplast development in Arabidopsis. Plant Cell 20, 3148–3162 (2008). · DOI
  18. Wimmelbacher, M. & Börnke, F. Redox activity of thioredoxin z and fructokinase-like protein 1 is dispensable for autotrophic growth of Arabidopsis thaliana. J. Exp. Bot. 65, 2405–2413 (2014). · DOI
  19. Shi, C. et al. Conserved role of fructokinase-like protein 1 in chloroplast development revealed by a seedling-lethal albino mutant of pepper. Hortic. Res. 9, uhab084 (2022). · DOI
  20. Gilkerson, J., Perez-Ruiz, J. M., Chory, J. & Callis, J. The plastid-localized pfkB-type carbohydrate kinases FRUCTOKINASE-LIKE 1 and 2 are essential for growth and development of Arabidopsis thaliana. BMC Plant Biol. 12, 102 (2012). · DOI
  21. Gao, Z. P. et al. A functional component of the transcriptionally active chromosome complex, Arabidopsis pTAC14, interacts with pTAC12/HEMERA and regulates plastid gene expression. Plant Physiol. 157, 1733–1745 (2011). · DOI
  22. Arsova, B. et al. Plastidial thioredoxin z interacts with two fructokinase-like proteins in a thiol-dependent manner: evidence for an essential role in chloroplast development in Arabidopsis and Nicotiana benthamiana. Plant Cell 22, 1498–1515 (2010). · DOI
  23. Garcia, M. et al. An Arabidopsis homolog of the bacterial peptidoglycan synthesis enzyme MurE has an essential role in chloroplast development. Plant J. 53, 924–934 (2008). · DOI
  24. Yu, Q. B. et al. TAC7, an essential component of the plastid transcriptionally active chromosome complex, interacts with FLN1, TAC10, TAC12 and TAC14 to regulate chloroplast gene expression in Arabidopsis thaliana. Physiol. Plant. 148, 408–421 (2013). · DOI
  25. Huang, C. et al. The reduced plastid-encoded polymerase-dependent plastid gene expression leads to the delayed greening of the Arabidopsis fln2 mutant. PLoS ONE 8, e73092 (2013). · DOI
  26. Varadi, M. et al. AlphaFold protein structure database: massively expanding the structural coverage of protein-sequence space with high-accuracy models. Nucleic Acids Res 50, D439–D444 (2022). · DOI · Paper page
  27. Bergsland, K. J. & Haselkorn, R. Evolutionary relationships among eubacteria, cyanobacteria, and chloroplasts: evidence from the rpoC1 gene of Anabaena sp. strain PCC 7120. J. Bacteriol. 173, 3446–3455 (1991). · DOI
  28. Shen, L. et al. An SI3-σ arch stabilizes cyanobacteria transcription initiation complex. Proc. Natl. Acad. Sci. USA 120, e2219290120 (2023). · DOI
  29. Glyde, R. et al. Structures of bacterial RNA polymerase complexes reveal the mechanism of DNA loading and transcription initiation. Mol. Cell 70, 1111–1120 (2018). · DOI
  30. Zhang, G. et al. Crystal structure of Thermus aquaticus core RNA polymerase at 3.3 Å resolution. Cell 98, 811–824 (1999). · DOI · Paper page
  31. Lane, W. J. & Darst, S. A. Molecular evolution of multisubunit RNA polymerases: sequence analysis. J. Mol. Biol. 395, 671–685 (2010). · DOI
  32. Zhang, J., Palangat, M. & Landick, R. Role of the RNA polymerase trigger loop in catalysis and pausing. Nat. Struct. Mol. Biol. 17, 99–104 (2010). · DOI
  33. Toulokhonov, I., Zhang, J., Palangat, M. & Landick, R. A central role of the RNA polymerase trigger loop in active-site rearrangement during transcriptional pausing. Mol. Cell 27, 406–419 (2007). · DOI
  34. Mishanina, T. V., Palo, M. Z., Nayak, D., Mooney, R. A. & Landick, R. Trigger loop of RNA polymerase is a positional, not acid-base, catalyst for both transcription and proofreading. Proc. Natl Acad. Sci. USA 114, E5103–E5112 (2017). · DOI
  35. Mazumder, A., Lin, M., Kapanidis, A. N. & Ebright, R. H. Closing and opening of the RNA polymerase trigger loop. Proc. Natl Acad. Sci. USA 117, 15642–15649 (2020). · DOI
  36. Riaz-Bradley, A. Transcription in cyanobacteria: A distinctive machinery and putative mechanisms. Biochem. Soc. Trans. 47, 679–689 (2019). · DOI
  37. Qayyum, M. Z. et al. Structure and function of the Si3 insertion integrated into the trigger loop/helix of cyanobacterial RNA polymerase. Proc. Natl Acad. Sci. USA 121, e2311480121 (2024). · DOI
  38. Sevostyanova, A., Belogurov, G. A., Mooney, R. A., Landick, R. & Artsimovitch, I. The β subunit gate loop is required for RNA polymerase modification by RfaH and NusG. Mol. Cell 43, 253–262 (2011). · DOI
  39. Dillon, S. C., Zhang, X., Trievel, R. C. & Cheng, X. The SET-domain protein superfamily: Protein lysine methyltransferases. Genome Biol. 6, 227 (2005). · DOI
  40. Trievel, R. C., Flynn, E. M., Houtz, R. L. & Hurley, J. H. Mechanism of multiple lysine methylation by the SET domain enzyme Rubisco LSMT. Nat. Struct. Mol. Biol. 10, 545–552 (2003). · DOI
  41. Cramer, P. et al. Architecture of RNA polymerase II and implications for the transcription mechanism. Science 288, 640–649 (2000). · DOI
  42. Korzheva, N. et al. A structural model of transcription elongation. Science 289, 619–625 (2000). · DOI
  43. Gordon, E. J. et al. Crystal structure of UDP-N-acetylmuramoyl-L-alanyl-D-glutamate: meso-diaminopimelate ligase from Escherichia coli. J. Biol. Chem. 276, 10999–11006 (2001). · DOI
  44. Dunwell, J. M., Purvis, A. & Khuri, S. Cupins: the most functionally diverse protein superfamily? Phytochemistry 65, 7–17 (2004). · DOI
  45. Pfalz, J. et al. ZmpTAC12 binds single-stranded nucleic acids and is essential for accumulation of the plastid-encoded polymerase complex in maize. N. Phytol. 206, 1024–1037 (2015). · DOI
  46. Favier, A. et al. The plastid-encoded RNA polymerase-associated protein PAP9 is a superoxide dismutase with unusual structural features. Front. Plant Sci. 12, 668897 (2021). · DOI
  47. Gallie, D. R. & Chen, Z. Chloroplast-localized iron superoxide dismutases FSD2 and FSD3 are functionally distinct in Arabidopsis. PLoS ONE 14, e0220078 (2019). · DOI
  48. Perry, J. J. P., Shin, D. S., Getzoff, E. D. & Tainer, J. A. The structural biochemistry of the superoxide dismutases. Biochim. Biophys. Acta 1804, 245–262 (2010). · DOI
  49. Díaz, M. G. et al. Redox regulation of PEP activity during seedling establishment in Arabidopsis thaliana. Nat. Commun. 9, 50 (2018). · DOI
  50. Igarashi, K., Fujita, N. & Ishihama, A. Identification of a subunit assembly domain in the alpha subunit of Escherichia coli RNA polymerase. J. Mol. Biol. 218, 1–6 (1991). · DOI
  51. Windgassen, T. A. et al. Trigger-helix folding pathway and SI3 mediate catalysis and hairpin-stabilized pausing by Escherichia coli RNA polymerase. Nucleic Acids Res 42, 12707–12721 (2014). · DOI
  52. Guo, X. et al. Structural basis for NusA stabilized transcriptional pausing. Mol. Cell 69, 816–827.e4 (2018). · DOI
  53. Kang, J. Y. et al. RNA polymerase accommodates a pause RNA hairpin by global conformational rearrangements that prolong pausing. Mol. Cell 69, 802–815.e5 (2018). · DOI
  54. Ray-Soni, A., Mooney, R. A. & Landick, R. Trigger loop dynamics can explain stimulation of intrinsic termination by bacterial RNA polymerase without terminator hairpin contact. Proc. Natl Acad. Sci. USA 114, E9233–E9242 (2017). · DOI
  55. Abdelkareem, M. et al. Structural basis of transcription: RNA polymerase backtracking and its reactivation. Mol. Cell 75, 298–309.e294 (2019). · DOI
  56. Shin, Y. et al. Structural basis of ribosomal RNA transcription regulation. Nat. Commun. 12, 528 (2021). · DOI
  57. Kindgren, P. & Strand, Å. Chloroplast transcription, untangling the Gordian Knot. N. Phytol. 206, 889–891 (2015). · DOI
  58. Ederth, J., Artsimovitch, I., Isaksson, L. A. & Landick, R. The downstream DNA jaw of bacterial RNA polymerase facilitates both transcriptional initiation and pausing. J. Biol. Chem. 277, 37456–37463 (2002). · DOI
  59. Drennan, A. et al. Key roles of the downstream mobile jaw of Escherichia coli RNA polymerase in transcription initiation. Biochemistry 51, 9447–9459 (2012). · DOI
  60. do Prado, P. F. V. et al. Structure of the multi-subunit chloroplast RNA polymerase. Mol. Cell 84, 1–16 (2024). · DOI
  61. Wu, X.-X. et al. Cryo-EM structures of the plant plastid-encoded RNA polymerase. Cell 187, 1127–1144 (2024). · DOI
  62. Vergara-Cruces, Á. et al. Structure of the plant plastid-encoded RNA polymerase. Cell 187, 1145–1159 (2024). · DOI
  63. Punjani, A., Rubinstein, J. L., Fleet, D. J. & Brubaker, M. A. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat. Methods 14, 290–296 (2017). · DOI · Paper page
  64. Wagner, T. & Raunser, S. The evolution of SPHIRE-crYOLO particle picking and its application in automated cryo-EM processing workflows. Commun. Biol. 3, 61 (2020). · DOI
  65. Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Cryst. D. 66, 486–501 (2010). · DOI · Paper page
  66. Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Cryst. D. 66, 213–221 (2010). · DOI · Paper page
  67. Pettersen, E. F. et al. UCSF ChimeraX: Structure visualization for researchers, educators, and developers. Protein Sci. 30, 70–82 (2021). · DOI

Metadata

Authors
Wang, T., Wang, G.-L., Fang, Y., Zhang, Y., Peng, W., Zhou, Y., Zhang, A., Yu, L.-J., & Lu, C.
Affiliations
  • Shandong Agricultural University (CN)
  • Chinese Academy of Sciences (CN)
Corresponding author
  • Yu, Long-Jiang
  • Lu, Congming
ORCID
Venue
Nature Communications
Publisher
Springer Science and Business Media LLC
Published
2024-11-13
Volume
15
Issue
1
Pages
9838-9838
ISSN
2041-1723 (ISSN-L)
DOI
10.1038/s41467-024-54266-2
PMC
PMC11561172
OpenAlex
W4404311285
Cited by
17
References
2
Citations by year
2026: 8 · 2025: 8 · 2024: 1
FWCI
2.31
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature Communications (publishedVersion, cc-by-nc-nd)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
  • PubMed Central (publishedVersion, cc-by-nc-nd)
  • PubMed (publishedVersion)
  • RePEc: Research Papers in Economics (submittedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
Funders
  • National Natural Science Foundation of China (32000184, 32000444)
  • Natural Science Foundation of Shandong Province (ZR2019ZD48)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Photosynthetic Processes and Mechanisms
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
Keywords
plastid-encoded RNA polymerase, chloroplast transcription, PAPS, spinach, oxidative damage protection, transcriptional regulation, chloroplast gene expression
MeSH terms
Chloroplasts, Models, Molecular, Plant Proteins, DNA-Directed RNA Polymerases, Transcription, Genetic, Plastids, Spinacia oleracea, Cryoelectron Microscopy

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review