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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: closed (30 April 2020) | Viewed by 21446

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Special Issue Editor

Prof. Dr. Greg C. Vanlerberghe

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Guest Editor

Department of Biological Sciences and Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
Interests: plant mitochondria; alternative oxidase; respiratory carbon metabolism; environmental and stress biology; interactions of respiration and photosynthesis; plant responses to global change; water deficit; high CO2, mitochondrial stress-signaling; reactive oxygen and nitrogen species; anaerobic metabolism; plant-cell death mechanisms; plant–pathogen interactions; comparative approaches to cellular energetics

Special Issue Information

Dear Colleagues,

Respiratory pathways (glycolysis, oxidative pentose-phosphate pathway, tricarboxylic-acid cycle, mitochondrial electron-transport chain, oxidative phosphorylation), along with the pathways of photosynthesis in the chloroplast, represent the core of plant carbon and energy metabolism. Since plants are sessile organisms, these pathways must function under a wide range of environmental and stress conditions in order to support growth effectively. A significant body of knowledge describes, in mechanistic detail, how photosynthesis responds and acclimates to changes in key environmental variables such as irradiance, temperature, water and nutrient availability, and CO₂ concentration in the atmosphere. However, how respiration responds to these and other environmental parameters remains much more uncertain, and mechanistic insights are generally lacking. In part, this may relate to the complex, diverse, and often-unique roles of respiration in an autotrophic organism. These include the need to provide extensive substrate for biosynthesis (anabolic respiration), as well as the need to coordinate with and indeed optimize photosynthetic metabolism. In part, these unique roles may rely upon plant-specific respiratory components, found in both the cytosol and mitochondrion, which introduce alternate routes for the processing of respiratory intermediates.

This Special Issue invites both original research and review articles that advance our understanding of how plant respiration responds to the environment and how the unique components of respiratory metabolism support acclimation to the environment. Contributions that describe interactions between respiration and photosynthesis, or how respiration responds to global change factors, are also welcome.

Prof. Dr. Greg C. Vanlerberghe
Guest Editor

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Keywords

Plant respiratory pathways
Acclimation to environment
Anabolic respiration
Photosynthesis–respiration interactions
Global-change factors
Plant carbon and energy metabolism
Alternate metabolic routes
Plant-specific respiratory components

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Published Papers (6 papers)

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Research

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25 pages, 11077 KiB

Open AccessArticle

Conserved and Opposite Transcriptome Patterns during Germination in Hordeum vulgare and Arabidopsis thaliana

by Yanqiao Zhu, Oliver Berkowitz, Jennifer Selinski, Andreas Hartmann, Reena Narsai, Yan Wang, Peisheng Mao and James Whelan

Int. J. Mol. Sci. 2020, 21(19), 7404; https://doi.org/10.3390/ijms21197404 - 7 Oct 2020

Cited by 7 | Viewed by 3386

Abstract

Seed germination is a critical process for completion of the plant life cycle and for global food production. Comparing the germination transcriptomes of barley (Hordeum vulgare) to Arabidopsis thaliana revealed the overall pattern was conserved in terms of functional gene ontology; however, many oppositely responsive orthologous genes were identified. Conserved processes included a set of approximately 6000 genes that peaked early in germination and were enriched in processes associated with RNA metabolism, e.g., pentatricopeptide repeat (PPR)-containing proteins. Comparison of orthologous genes revealed more than 3000 orthogroups containing almost 4000 genes that displayed similar expression patterns including functions associated with mitochondrial tricarboxylic acid (TCA) cycle, carbohydrate and RNA/DNA metabolism, autophagy, protein modifications, and organellar function. Biochemical and proteomic analyses indicated mitochondrial biogenesis occurred early in germination, but detailed analyses revealed the timing involved in mitochondrial biogenesis may vary between species. More than 1800 orthogroups representing 2000 genes displayed opposite patterns in transcript abundance, representing functions of energy (carbohydrate) metabolism, photosynthesis, protein synthesis and degradation, and gene regulation. Differences in expression of basic-leucine zippers (bZIPs) and Apetala 2 (AP2)/ethylene-responsive element binding proteins (EREBPs) point to differences in regulatory processes at a high level, which provide opportunities to modify processes in order to enhance grain quality, germination, and storage as needed for different uses. Full article

(This article belongs to the Special Issue Plant Respiration)

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16 pages, 2772 KiB

Open AccessArticle

Genome-Wide Association Study Unravels LRK1 as a Dark Respiration Regulator in Rice (Oryza sativa L.)

by Mingnan Qu, Jemaa Essemine, Ming Li, Shuoqi Chang, Tiangen Chang, Gen-Yun Chen and Xin-Guang Zhu

Int. J. Mol. Sci. 2020, 21(14), 4930; https://doi.org/10.3390/ijms21144930 - 13 Jul 2020

Cited by 8 | Viewed by 3065

Abstract

Respiration is a major plant physiological process that generates adenosine triphosphate (ATP) to support the various pathways involved in the plant growth and development. After decades of focused research on basic mechanisms of respiration, the processes and major proteins involved in respiration are well elucidated. However, much less is known about the natural variation of respiration. Here we conducted a survey on the natural variation of leaf dark respiration (R_d) in a global rice minicore diversity panel and applied a genome-wide association study (GWAS) in rice (Oryza sativa L.) to determine candidate loci associated with R_d. This rice minicore diversity panel consists of 206 accessions, which were grown under both growth room (GR) and field conditions. We found that R_d shows high single-nucleotide polymorphism (SNP) heritability under GR and it is significantly affected by genotype-environment interactions. R_d also exhibits strong positive correlation to the leaf thickness and chlorophyll content. GWAS results of R_d collected under GR and field show an overlapped genomic region in the chromosome 3 (Chr.3), which contains a lead SNP (3m29440628). There are 12 candidate genes within this region; among them, three genes show significantly higher expression levels in accessions with high R_d. Particularly, we observed that the LRK1 gene, annotated as leucine rich repeat receptor kinase, was up-regulated four times. We further found that a single significantly associated SNPs at the promoter region of LRK1, was strongly correlated with the mean annual temperature of the regions from where minicore accessions were collected. A rice lrk1 mutant shows only ~37% R_d of that of WT and retarded growth following exposure to 35 °C for 30 days, but only 24% reduction in growth was recorded under normal temperature (25 °C). This study demonstrates a substantial natural variation of R_d in rice and that the LRK1 gene can regulate leaf dark respiratory fluxes, especially under high temperature. Full article

(This article belongs to the Special Issue Plant Respiration)

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19 pages, 2681 KiB

Open AccessArticle

Identification of Alternative Mitochondrial Electron Transport Pathway Components in Chickpea Indicates a Differential Response to Salinity Stress between Cultivars

by Crystal Sweetman, Troy K. Miller, Nicholas J. Booth, Yuri Shavrukov, Colin L.D. Jenkins, Kathleen L. Soole and David A. Day

Int. J. Mol. Sci. 2020, 21(11), 3844; https://doi.org/10.3390/ijms21113844 - 28 May 2020

Cited by 11 | Viewed by 2554

Abstract

All plants contain an alternative electron transport pathway (AP) in their mitochondria, consisting of the alternative oxidase (AOX) and type 2 NAD(P)H dehydrogenase (ND) families, that are thought to play a role in controlling oxidative stress responses at the cellular level. These alternative electron transport components have been extensively studied in plants like Arabidopsis and stress inducible isoforms identified, but we know very little about them in the important crop plant chickpea. Here we identify AP components in chickpea (Cicer arietinum) and explore their response to stress at the transcript level. Based on sequence similarity with the functionally characterized proteins of Arabidopsis thaliana, five putative internal (matrix)-facing NAD(P)H dehydrogenases (CaNDA1-4 and CaNDC1) and four putative external (inter-membrane space)-facing NAD(P)H dehydrogenases (CaNDB1-4) were identified in chickpea. The corresponding activities were demonstrated for the first time in purified mitochondria of chickpea leaves and roots. Oxidation of matrix NADH generated from malate or glycine in the presence of the Complex I inhibitor rotenone was high compared to other plant species, as was oxidation of exogenous NAD(P)H. In leaf mitochondria, external NADH oxidation was stimulated by exogenous calcium and external NADPH oxidation was essentially calcium dependent. However, in roots these activities were low and largely calcium independent. A salinity experiment with six chickpea cultivars was used to identify salt-responsive alternative oxidase and NAD(P)H dehydrogenase gene transcripts in leaves from a three-point time series. An analysis of the Na:K ratio and Na content separated these cultivars into high and low Na accumulators. In the high Na accumulators, there was a significant up-regulation of CaAOX1, CaNDB2, CaNDB4, CaNDA3 and CaNDC1 in leaf tissue under long term stress, suggesting the formation of a stress-modified form of the mitochondrial electron transport chain (mETC) in leaves of these cultivars. In particular, stress-induced expression of the CaNDB2 gene showed a striking positive correlation with that of CaAOX1 across all genotypes and time points. The coordinated salinity-induced up-regulation of CaAOX1 and CaNDB2 suggests that the mitochondrial alternative pathway of respiration is an important facet of the stress response in chickpea, in high Na accumulators in particular, despite high capacities for both of these activities in leaf mitochondria of non-stressed chickpeas. Full article

(This article belongs to the Special Issue Plant Respiration)

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18 pages, 4033 KiB

Open AccessArticle

Transcriptional and Metabolic Changes Associated with Phytoglobin Expression during Germination of Barley Seeds

by Somaieh Zafari, Kim H. Hebelstrup and Abir U. Igamberdiev

Int. J. Mol. Sci. 2020, 21(8), 2796; https://doi.org/10.3390/ijms21082796 - 17 Apr 2020

Cited by 14 | Viewed by 2929

Abstract

To understand how the class 1 phytoglobin is involved in germination process via the modulation of the nitric oxide (NO) metabolism, we performed the analysis of physiological and molecular parameters in the embryos of transgenic barley (Hordeum vulgare L. cv Golden Promise) plants differing in expression levels of the phytoglobin (Pgb1) gene during the first 48 h of germination. Overexpression of Pgb1 resulted in a higher rate of germination, higher protein content and higher ATP/ADP ratios. This was accompanied by a lower rate of NO emission after radicle protrusion, as compared to the wild type and downregulating line, and a lower rate of S-nitrosylation of proteins in the first hours postimbibition. The rate of fermentation estimated by the expression and activity of alcohol dehydrogenase was significantly higher in the Pgb1 downregulating line, the same tendency was observed for nitrate reductase expression. The genes encoding succinate dehydrogenase and pyruvate dehydrogenase complex subunits were more actively expressed in embryos of the seeds overexpressing Pgb1. It is concluded that Pgb1 expression in embryo is essential for the maintenance of redox and energy balance before radicle protrusion, when seeds experience low internal oxygen concentration and exerts the effect on metabolism during the initial development of seedlings. Full article

(This article belongs to the Special Issue Plant Respiration)

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25 pages, 4761 KiB

Open AccessArticle

Dynamic Transcriptome Analysis Reveals Uncharacterized Complex Regulatory Pathway Underlying Dose IBA-Induced Embryogenic Redifferentiation in Cotton

by Yupeng Fan, Xiaoman Yu, Huihui Guo, Junmei Wei, Haixia Guo, Li Zhang and Fanchang Zeng

Int. J. Mol. Sci. 2020, 21(2), 426; https://doi.org/10.3390/ijms21020426 - 9 Jan 2020

Cited by 9 | Viewed by 3015

Abstract

The somatic embryogenesis (SE) process of plants is regulated by exogenous hormones. During the SE, different genes sensitively respond to hormone signals through complex regulatory networks to exhibit plant totipotency. When cultured in indole-3-butyric acid (IBA) concentration gradient medium supplemented with 0 mg dm⁻³, 0.025 mg dm⁻³, and 0.05 mg dm⁻³ IBA, the callus differentiation rate first increased then decreased in cotton. To characterize the molecular basis of IBA-induced regulating SE, transcriptome analysis was conducted on embryogenic redifferentiation. Upon the examination of the IBA’s embryogenic inductive effect, it was revealed that pathways related to plant hormone signal transduction and alcohol degradation were significantly enriched in the embryogenic responsive stage (5 days). The photosynthesis, alcohol metabolism and cell cycle pathways were specifically regulated in the pre-embryonic initial period (20 days). Upon the effect of the IBA dose, in the embryogenic responsive stage (5 days), the metabolism of xenobiotics by the cytochrome P450 pathway and secondary metabolism pathways of steroid, flavonoid, and anthocyanin biosynthesis were significantly enriched. The phenylpropanoid, brassinosteroid, and anthocyanin biosynthesis pathways were specifically associated in the pre-embryonic initial period (20 days). At different developmental stages of embryogenic induction, photosynthesis, flavonoid biosynthesis, phenylpropanoid biosynthesis, mitogen-activated protein kinase (MAPK) signaling, xenobiotics metabolism by cytochrome P450, and brassinosteroid biosynthesis pathways were enriched at low a IBA concentration. Meanwhile, at high IBA concentration, the carbon metabolism, alcohol degradation, circadian rhythm and biosynthesis of amino acids pathways were significantly enriched. The results reveal that complex regulating pathways participate in the process of IBA-induced redifferentiation in cotton somatic embryogenesis. In addition, collections of potential essential signaling and regulatory genes responsible for dose IBA-induced efficient embryogenic redifferentiation were identified. Quantitative real-time PCR (qRT-PCR) was performed on the candidate genes with different expression patterns, and the results are basically consistent with the RNA-seq data. The results suggest that the complicated and concerted IBA-induced mechanisms involving multiple cellular pathways are responsible for dose-dependent plant growth regulator-induced SE. This report represents a systematic study and provides new insight into molecular signaling and regulatory basis underlying the process of dose IBA-induced embryogenic redifferentiation during SE. Full article

(This article belongs to the Special Issue Plant Respiration)

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Review

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19 pages, 1580 KiB

Open AccessReview

In Vivo Metabolic Regulation of Alternative Oxidase under Nutrient Deficiency—Interaction with Arbuscular Mycorrhizal Fungi and Rhizobium Bacteria

by José Ortíz, Carolina Sanhueza, Antònia Romero-Munar, Javier Hidalgo-Castellanos, Catalina Castro, Luisa Bascuñán-Godoy, Teodoro Coba de la Peña, Miguel López-Gómez, Igor Florez-Sarasa and Néstor Fernández Del-Saz

Int. J. Mol. Sci. 2020, 21(12), 4201; https://doi.org/10.3390/ijms21124201 - 12 Jun 2020

Cited by 11 | Viewed by 4231

Abstract

The interaction of the alternative oxidase (AOX) pathway with nutrient metabolism is important for understanding how respiration modulates ATP synthesis and carbon economy in plants under nutrient deficiency. Although AOX activity reduces the energy yield of respiration, this enzymatic activity is upregulated under stress conditions to maintain the functioning of primary metabolism. The in vivo metabolic regulation of AOX activity by phosphorus (P) and nitrogen (N) and during plant symbioses with Arbuscular mycorrhizal fungi (AMF) and Rhizobium bacteria is still not fully understood. We highlight several findings and open questions concerning the in vivo regulation of AOX activity and its impact on plant metabolism during P deficiency and symbiosis with AMF. We also highlight the need for the identification of which metabolic regulatory factors of AOX activity are related to N availability and nitrogen-fixing legume-rhizobia symbiosis in order to improve our understanding of N assimilation and biological nitrogen fixation. Full article

(This article belongs to the Special Issue Plant Respiration)

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