Protein Kinases and Phosphatases of the Plastid and Their Potential Role in Starch Metabolism

White-Gloria, Chris; Johnson, Jayde J.; Marritt, Kayla; Kataya, Amr R.A.; Vahab, Ahmad; Moorhead, Greg B. G.

doi:10.3389/fpls.2018.01032

Cited by 18 publications

(10 citation statements)

References 71 publications

(122 reference statements)

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“…Post-translational alteration of proteins involved in starch metabolism can involve protein phosphorylation (Kötting et al., 2010) or reduction/oxidation mechanisms (Glaring et al., 2012; Santelia et al., 2015). Little is known about protein phosphorylation influencing starch metabolism, although a recent paper has identified plastidially localized protein kinases and phosphatases that may interact with starch metabolic enzymes (White-Gloria et al., 2018), which is a first step in the study of this process. More is known about redox control as several genes involved in starch metabolism are known to be redox regulated (Fu et al., 1998; Ballicora et al., 2000; Tiessen et al., 2002; Sokolov et al., 2006; Valerio et al., 2011; Glaring et al., 2012; Seung et al., 2013; Shaik et al., 2014), and expression of thioredoxin-f increased starch amounts in tobacco leaves (Sanz-Barrio et al., 2013), although it is not clear which enzymes were affected.…”

Section: Introductionmentioning

confidence: 99%

Starch Trek: The Search for Yield

Lloyd

Kossmann

2019

Front. Plant Sci.

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Starch is a plant storage polyglucan that accumulates in plastids. It is composed of two polymers, amylose and amylopectin, with different structures and plays several roles in helping to determine plant yield. In leaves, it acts as a buffer for night time carbon starvation. Genetically altered plants that cannot synthesize or degrade starch efficiently often grow poorly. There have been a number of successful approaches to manipulate leaf starch metabolism that has resulted in increased growth and yield. Its degradation is also a source of sugars that can help alleviate abiotic stress. In edible parts of plants, starch often makes up the majority of the dry weight constituting much of the calorific value of food and feed. Increasing starch in these organs can increase this as well as increasing yield. Enzymes involved in starch metabolism are well known, and there has been much research analyzing their functions in starch synthesis and degradation, as well as genetic and posttranslational regulatory mechanisms affecting them. In this mini review, we examine work on this topic and discuss future directions that could be used to manipulate this metabolite for improved yield.

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Section: Introductionmentioning

confidence: 99%

Starch Trek: The Search for Yield

Lloyd

Kossmann

2019

Front. Plant Sci.

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“…Notably, insertions of other TEs were also frequently found in different receptor-like protein kinases and tyrosine protein kinases in our study. Protein kinase genes belong to one of the most proliferated gene superfamilies in plants, whose members are linked with a range of key metabolic and various plant-specific adaptation processes [ 146 , 147 , 148 , 149 ].…”

Section: Discussionmentioning

confidence: 99%

Comparative Study of Pine Reference Genomes Reveals Transposable Element Interconnected Gene Networks

Voronova

Rendón-Anaya

Ingvarsson

et al. 2020

Genes

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Sequencing the giga-genomes of several pine species has enabled comparative genomic analyses of these outcrossing tree species. Previous studies have revealed the wide distribution and extraordinary diversity of transposable elements (TEs) that occupy the large intergenic spaces in conifer genomes. In this study, we analyzed the distribution of TEs in gene regions of the assembled genomes of Pinus taeda and Pinus lambertiana using high-performance computing resources. The quality of draft genomes and the genome annotation have significant consequences for the investigation of TEs and these aspects are discussed. Several TE families frequently inserted into genes or their flanks were identified in both species’ genomes. Potentially important sequence motifs were identified in TEs that could bind additional regulatory factors, promoting gene network formation with faster or enhanced transcription initiation. Node genes that contain many TEs were observed in multiple potential transposable element-associated networks. This study demonstrated the increased accumulation of TEs in the introns of stress-responsive genes of pines and suggests the possibility of rewiring them into responsive networks and sub-networks interconnected with node genes containing multiple TEs. Many such regulatory influences could lead to the adaptive environmental response clines that are characteristic of naturally spread pine populations.

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“…Notably, insertions of other TEs were also frequently found in different receptor-like protein kinases and tyrosine protein kinases in our study. Protein kinase genes belong to one of the most proliferated gene superfamilies in plants, whose members are linked with a range of key metabolic and various plant-speci c adaptation processes (Stone and Walker, 1995;Lehti-Shiu et al, 2009;Lehti-Shiu and Shiu, 2012;White-Gloria et al, 2018).…”

Section: Discussionmentioning

confidence: 99%

Comparative study of pine reference genomes reveals transposable element interconnected gene networks

Voronova

Rendón-Anaya

Ingvarsson

et al. 2020

Preprint

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Background: Sequencing the giga-genomes of several pine species belonging to the ancient gymnosperm clade has enabled comparative genomic analyses of these widely distributed outcrossing tree species. Initial sequence studies have revealed the wide distribution and extraordinary diversity of transposable elements (TEs) that occupy the large intergenic spaces. Our previous investigations revealed significant variations of class I TEs within pine subpopulations, but inoculation with pathogen induced correlated expression of TE families in pine seedlings, suggesting TE co-localisation with stress-responsive genes. In this study, we analyzed the distribution of TEs in gene regions of the assembled genomes of Pinus taeda and Pinus lambertiana using high-performance computing resources.Results: The quality of draft genomes and the genome annotation have significant consequences for the investigation of TEs and these aspects are discussed. Several TE families were identified in both species genomes frequently inserted into genes or their flanks. The non-autonomous MITE3321 family found in gene flanking regions and provide TATA boxes, several ARR1, DOF, WRKY and GT-binding sites, which are important signals in plant transcription activation and stress-response regulation. Distribution of MITE3321 across gene non-coding regions suggests action of selective pressure on this sequences and formation of gene sub-networks, depending on the location of MITE insertions. DNA TE DTX184 could potentially form microRNAs or provide its target site, thereby connect about 200 important stress-responsive genes in both pine species. Several retrotransposons propagated in gene regions were also identified, such as Copia-1813 containing important light-responsive regulative sequences, however full- length structures of low-copy-number TEs couldn’t be verified in the current genome assemblies. Only rare gene homologs carried similar insertions, indicating that most transposition events occurred after separation of investigated pine species. Node genes that contain many types of interspersed repeats were identified and observed in multiple potential transposable element associated networks.Conclusions: This study demonstrated the increased accumulation of TEs in the introns of stress-responsive genes of pines and the probability of rewiring them in responsive networks and sub-networks interconnected with node genes containing multiple TEs. Many such regulatory influences could lead to the adaptive environmental response clines that are characteristic of naturally spread pine populations.

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Protein Kinases and Phosphatases of the Plastid and Their Potential Role in Starch Metabolism

Cited by 18 publications

References 71 publications

Starch Trek: The Search for Yield

Starch Trek: The Search for Yield

Comparative Study of Pine Reference Genomes Reveals Transposable Element Interconnected Gene Networks

Comparative study of pine reference genomes reveals transposable element interconnected gene networks

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