Structure of the complex I-like molecule NDH of oxygenic photosynthesis

Laughlin, Thomas G.; Bayne, Andrew N; Trempe, Jean‐François; Savage, David F.; Davies, Karen M.

doi:10.1038/s41586-019-0921-0

Cited by 136 publications

(105 citation statements)

References 61 publications

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“…Instead, the electrons directly enter a chain of three iron-sulphur (FeS) centres in the ferredoxin (Fd)binding domain (Fig. 1d), similar to the recently characterised NDH-1L type photosynthetic complex I and membrane-bound hydrogenases [15][16][17][18] . The PQ-binding site is located ca.…”

Section: Resultsmentioning

confidence: 63%

Redox-coupled proton pumping drives carbon concentration in the photosynthetic complex I

et al. 2020

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Photosynthetic organisms capture light energy to drive their energy metabolism, and employ the chemical reducing power to convert carbon dioxide (CO 2 ) into organic molecules. Photorespiration, however, significantly reduces the photosynthetic yields. To survive under low CO 2 concentrations, cyanobacteria evolved unique carbon-concentration mechanisms that enhance the efficiency of photosynthetic CO 2 fixation, for which the molecular principles have remained unknown. We show here how modular adaptations enabled the cyanobacterial photosynthetic complex I to concentrate CO 2 using a redox-driven proton-pumping machinery. Our cryo-electron microscopy structure at 3.2 Å resolution shows a catalytic carbonic anhydrase module that harbours a Zn 2+ active site, with connectivity to protonpumping subunits that are activated by electron transfer from photosystem I. Our findings illustrate molecular principles in the photosynthetic complex I machinery that enabled cyanobacteria to survive in drastically changing CO 2 conditions.

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Section: Resultsmentioning

confidence: 63%

Redox-coupled proton pumping drives carbon concentration in the photosynthetic complex I

et al. 2020

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“…For many photosynthetic complexes, reference structures are available from angiosperms or even A. thaliana itself, but other complexes required use of structures from anciently divergent species, including bacteria and mammals (File S1), making inference of residue homology tenuous. Furthermore, even when structures from close relatives were available, they were sometimes known to be missing certain subunits ( van Bezouwen, et al 2017;Laughlin, et al 2019). Therefore, we did not analyze many subunits within these complexes because of their absence from reference structures or low level of sequence similarity, designating them simply as not available ("NA").…”

Section: Resultsmentioning

confidence: 99%

“…We hope that CyMIRA will serve as useful community resource in this respect. (Hooper, et al 2017) eSLDB 848 4427 69 (Pierleoni, et al 2007) PA-GOSUB 985 730 14 (Lu, et al 2005) SUBA experimental 1217 2128 785 (Hooper, et al 2017) SWISS PROT 311 657 20 (Boutet, et al 2007) TAIR 397 1598 266 (Reiser, et al 2017) LocDB 446 1527 234 (Rastogi and Rost 2011) PPDB 327 1570 73 (Sun, et al 2009) Organelle DB 512 276 11 (Wiwatwattana, et al 2007) Kurisu et al 2003;Friso et al 2004;Nelson et al 2004;Jensen et al 2007;Izumi et al 2012;Shikanai 2016;Bezouwen et al 2017;Laughlin et al 2019PPR Lurin et al 2004Toole et al 2008;Fujii et al 2010;Cheng et al 2016 Transcription and transcript maturation Hess and Borner 1999;Walter et al 2002;Gu et al 2003;Perrin et al 2004;Kuhn et al 2007;Schmidt von Braun et al 2007;Yu et al 2008;Canino et al 2009;Delannoy et al 2009;Chen et al 2010;Falcon de Longevialle et al 2010;Gobert et al 2010;Placido et al 2010;Richter et al 2010;Babiychuk et al 2011;Bryant et al 2011;Gerdes et al 2011;Sharwood et al 2011;Apitz et al 2014;…”

Section: Resultsmentioning

confidence: 99%

CyMIRA: The Cytonuclear Molecular Interactions Reference forArabidopsis

Forsythe

Sharbrough

Havird

et al. 2019

Preprint

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The function and evolution of eukaryotic cells depends upon direct molecular interactions between gene products encoded in nuclear and cytoplasmic genomes. Understanding how these cytonuclear interactions drive molecular evolution and generate genetic incompatibilities between isolated populations and species is of central importance to eukaryotic biology. Plants are an outstanding system to investigate such effects because of their two different genomic compartments present in the cytoplasm (mitochondria and plastids) and the extensive resources detailing subcellular targeting of nuclear-encoded proteins. However, the field lacks a consistent classification scheme for mitochondrial-and plastid-targeted proteins based on their molecular interactions with cytoplasmic genomes and gene products, which hinders efforts to standardize and compare results across studies. Here, we take advantage of detailed knowledge about the model angiosperm Arabidopsis thaliana to provide a curated database of plant cytonuclear interactions at the molecular level. CyMIRA (Cytonuclear Molecular Interactions Reference for Arabidopsis) is available at http://cymira.colostate.edu/ and https://github.com/dbsloan/cymira and will serve as a resource to aid researchers in partitioning evolutionary genomic data into functional gene classes based on organelle targeting and direct molecular interaction with cytoplasmic genomes and gene products. It includes 11 categories (and 27 subcategories) of different cytonuclear complexes and types of molecular interactions, and it reports residue-level information for cytonuclear contact sites. We hope that this framework will make it easier to standardize, interpret and compare studies testing the functional and evolutionary consequences of cytonuclear interactions.

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“…RNA editing defects may directly alter protein function or affect its ability to form complexes with other proteins (Hammani et al, 2009). NdhB encodes a subunit of the NDH complex (Laughlin et al, 2019), so we asked if this complex accumulates in the null qKW9 background using protein blots probed with antibodies against NdhH to monitor accumulation of the complex. In NIL-SK, the level of NdhH was reduced to less than 25% of NIL-ZHENG58 (Figure 5), suggesting that NdhB-246 RNA editing by qKW9 is important for normal accumulation of the NDH complex.…”

Section: Resultsmentioning

confidence: 99%

“…Plastid genomes encode 11 subunits (NdhA to NdhK) forming the core of the membrane arm of the L-shaped structure of the NDH complex (Laughlin et al, 2019). Multiple PPR genes regulate expression of ndh genes in Arabidopsis.…”

Section: Discussionmentioning

confidence: 99%

qKW9encodes a pentatricopeptide repeat protein affecting photosynthesis and grain filling in maize

Huang

Lü

Liu

et al. 2019

Preprint

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Kernel weight is an important yield component in maize that was selected during domestication. Many kernel weight genes have been identified through mutant analysis, and are mostly involved in the biogenesis and functional maintenance of organelles or other fundamental cellular activities. However, only a limited number of loci underlying quantitative variation in kernel weight have been cloned. Here we characterize a maize kernel weight QTL, qKW9 and find that it encodes a DYW motif pentatricopeptide repeat protein involved in C-to-U editing of NdhB, a subunit of the chloroplast NADH dehydrogenase-like complex. In a null qKW9 background, C-to-U editing of NdhB was abolished, and photosynthesis was reduced, suggesting that qKW9 regulates kernel weight by controling the maternal source of photosynthate for grain filling. Characterization of qKW9 highlights the importance of optimizing photosynthesis on maize grain yield production.

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Structure of the complex I-like molecule NDH of oxygenic photosynthesis

Cited by 136 publications

References 61 publications

Redox-coupled proton pumping drives carbon concentration in the photosynthetic complex I

Redox-coupled proton pumping drives carbon concentration in the photosynthetic complex I

CyMIRA: The Cytonuclear Molecular Interactions Reference forArabidopsis

qKW9encodes a pentatricopeptide repeat protein affecting photosynthesis and grain filling in maize

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