Co- and post-translational modifications in Rubisco: unanswered questions

Houtz, Robert L.; Magnani, Roberta; Nayak, Nihar R.; Dirk, Lynnette M.A.

doi:10.1093/jxb/erm360

Cited by 61 publications

(54 citation statements)

References 120 publications

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“…This conclusion differs from a model of the SET8-nucleosome complex, in which the enzyme's iSET ␣-helix plays a prominent role in the interactions with the histone substrate (12). As might be expected, the N-terminal region of Rubisco containing the Lys-14 target methylation site is also highly conserved in nearly all higher plant forms of Rubisco (27) (Fig. S8).…”

Section: Resultscontrasting

confidence: 77%

Rubisco in complex with Rubisco large subunit methyltransferase

Raunser

Magnani

Huang

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

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SET domain protein lysine methyltransferases (PKMT) are a structurally unique class of enzymes that catalyze the specific methylation of lysine residues in a number of different substrates. Especially histone-specific SET domain PKMTs have received widespread attention because of their roles in the regulation of epigenetic gene expression and the development of some cancers. Rubisco large subunit methyltransferase (RLSMT) is a chloroplastlocalized SET domain PKMT responsible for the formation of trimethyl-lysine-14 in the large subunit of Rubisco, an essential photosynthetic enzyme. Here, we have used cryoelectron microscopy to produce an 11-Å density map of the Rubisco-RLSMT complex. The atomic model of the complex, obtained by fitting crystal structures of Rubisco and RLSMT into the density map, shows that the extensive contact regions between the 2 proteins are mainly mediated by hydrophobic residues and leucine-rich repeats. It further provides insights into potential conformational changes that may occur during substrate binding and catalysis. This study presents the first structural analysis of a SET domain PKMT in complex with its intact polypeptide substrate.electron microscopy ͉ LSMT ͉ SET domain ͉ single particle S ET [SU(VAR)3-9, E(Z), and TRX] domain protein lysine methyltransferases (PKMTs) are a structurally unique class of enzymes that catalyze the formation of site-specific methylated lysine residues in a number of different polypeptide substrates including cytochrome c (1, 2), histones (3), ribosomal proteins (3, 4), p53 (5), TAF10 (6), ␥-tocopherol methyltransferase (7), and ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) (8). All SET domain PKMTs have a unique and conserved structural motif that contains separate binding sites for the target protein substrate and the methyl donor, Sadenosylmethionine (AdoMet) (9). The mechanisms by which these enzymes achieve site-specific methylation is of great interest and histone-specific SET domain protein methyltransferases (HKMTs) have received widespread attention because of their roles in the regulation of epigenetic gene expression and the development of some cancers (9, 10). The specificity of several SET domain PKMTs has been examined through structural and biochemical analyses of ternary complexes with bound polypeptide substrates, but all of these studies used short synthetic polypeptide mimetics of the intact polypeptide substrate and therefore do not account for the potential influence of areas outside the immediate residues flanking the target lysine methylation site (11)(12)(13)(14)(15)(16). Rubisco large subunit methyltransferase (RLSMT) is a chloroplast-localized SET domain PKMT responsible for the formation of trimethyl-lysine-14 in the large subunit of Rubisco (8,17), an essential photosynthetic enzyme with a hexadecameric structure and large molecular mass (Ϸ534 kDa). Detailed information is available regarding the structure, catalytic mechanism, active site residues, and the kinetic reaction mechanism for pea RLSMT (7,8,17,18)...

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Section: Resultscontrasting

confidence: 77%

Rubisco in complex with Rubisco large subunit methyltransferase

Raunser

Magnani

Huang

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

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“…The lack of holoenzyme may also be attributed to posttranslational modification systems that are missing in E. coli (reviewed in Kamionka, 2011) but are present in Chlamydomonas (reviewed in Houtz et al, 2008), which might be essential for subtle structural changes to complement the differences in primary structure (Fig. 1) and encourage proper folding or assembly.…”

Section: Discussionmentioning

confidence: 99%

Engineering of chimeric eukaryotic/bacterial Rubisco large subunits in <i>Escherichia coli</i>

2016

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Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is a rate-limiting photosynthetic enzyme that catalyzes carbon fixation in the Calvin cycle. Much interest has been devoted to engineering this ubiquitous enzyme with the goal of increasing plant growth. However, experiments that have successfully produced improved Rubisco variants, via directed evolution in Escherichia coli, are limited to bacterial Rubisco because the eukaryotic holoenzyme cannot be produced in E. coli. The present study attempts to determine the specific differences between bacterial and eukaryotic Rubisco large subunit primary structure that are responsible for preventing heterologous eukaryotic holoenzyme formation in E. coli. A series of chimeric Synechococcus Rubiscos were created in which different sections of the large subunit were swapped with those of the homologous Chlamydomonas Rubisco. Chimeric holoenzymes that can form in vivo would indicate that differences within the swapped sections do not disrupt holoenzyme formation. Large subunit residues 1-97, 198-247 and 448-472 were successfully swapped without inhibiting holoenzyme formation. In all ten chimeras, protein expression was observed for the separate subunits at a detectable level. As a first approximation, the regions that can tolerate swapping may be targets for future engineering.

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“…(2) A putative Rubisco methyltransferase (RMT1) was upregulated 2.2-fold after 24 h HS that might mediate lysine trimethylation of the large SU. Although the role of this modification in Rubisco is not yet clear, the absence of methylation seems to reduce activities of other protein substrates of the land plant Rubisco methyltransferase (Houtz et al, 2008). (3) Photorespiration appears to increase under long-term HS.…”

Section: Calvin Cycle Activity Might Be Reduced Early After Onset Of mentioning

confidence: 99%

Systems-Wide Analysis of Acclimation Responses to Long-Term Heat Stress and Recovery in the Photosynthetic Model OrganismChlamydomonas reinhardtii

et al. 2014

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We applied a top-down systems biology approach to understand how Chlamydomonas reinhardtii acclimates to long-term heat stress (HS) and recovers from it. For this, we shifted cells from 25 to 42°C for 24 h and back to 25°C for ‡8 h and monitored abundances of 1856 proteins/protein groups, 99 polar and 185 lipophilic metabolites, and cytological and photosynthesis parameters. Our data indicate that acclimation of Chlamydomonas to long-term HS consists of a temporally ordered, orchestrated implementation of response elements at various system levels. These comprise (1) cell cycle arrest; (2) catabolism of larger molecules to generate compounds with roles in stress protection; (3) accumulation of molecular chaperones to restore protein homeostasis together with compatible solutes; (4) redirection of photosynthetic energy and reducing power from the Calvin cycle to the de novo synthesis of saturated fatty acids to replace polyunsaturated ones in membrane lipids, which are deposited in lipid bodies; and (5) when sinks for photosynthetic energy and reducing power are depleted, resumption of Calvin cycle activity associated with increased photorespiration, accumulation of reactive oxygen species scavengers, and throttling of linear electron flow by antenna uncoupling. During recovery from HS, cells appear to focus on processes allowing rapid resumption of growth rather than restoring pre-HS conditions.

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Co- and post-translational modifications in Rubisco: unanswered questions

Cited by 61 publications

References 120 publications

Rubisco in complex with Rubisco large subunit methyltransferase

Rubisco in complex with Rubisco large subunit methyltransferase

Engineering of chimeric eukaryotic/bacterial Rubisco large subunits in <i>Escherichia coli</i>

Systems-Wide Analysis of Acclimation Responses to Long-Term Heat Stress and Recovery in the Photosynthetic Model OrganismChlamydomonas reinhardtii

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