Plant B Vitamin Pathways and their Compartmentation: a Guide for the Perplexed

Gerdes, Svetlana; Lerma-Ortiz, Claudia; Frelin, Océane; Seaver, Samuel M. D.; Henry, Christopher S.; Crécy‐Lagard, Valérie de; Hanson, Andrew D.

doi:10.1093/jxb/ers208

Cited by 87 publications

(108 citation statements)

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“…First, there has been much research on the B vitamin contents of food plants and on B vitamin synthesis and metabolism in plants. However, the main, if not sole, driver for this valuable work has been plants as vitamin sources for humans rather than plants as vitamin sources for themselves (Fitzpatrick et al, 2012;Gerdes et al, 2012). This article takes the complementary position that "plants need their vitamins too" (Smith et al, 2007).…”

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Does Abiotic Stress Cause Functional B Vitamin Deficiency in Plants?

et al. 2016

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B vitamins are the precursors of essential metabolic cofactors but are prone to destruction under stress conditions. It is therefore a priori reasonable that stressed plants suffer B vitamin deficiencies and that certain stress symptoms are metabolic knock-on effects of these deficiencies. Given the logic of these arguments, and the existence of data to support them, it is a shock to realize that the roles of B vitamins in plant abiotic stress have had minimal attention in the literature (100-fold less than hormones) and continue to be overlooked. In this article, we therefore aim to explain the connections among B vitamins, enzyme cofactors, and stress conditions in plants. We first outline the chemistry and biochemistry of B vitamins and explore the concept of vitamin deficiency with the help of information from mammals. We then summarize classical and recent evidence for stress-induced vitamin deficiencies and for plant responses that counter these deficiencies. Lastly, we consider potential implications for agriculture.

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Does Abiotic Stress Cause Functional B Vitamin Deficiency in Plants?

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“…PlantSEED currently consists of 97 subsystems covering 209 pathways of plant primary and secondary metabolism. These foundational subsystems, which together encompass 1,384 metabolic reactions, were constructed from AraCyc pathways (6) and from curated functions and reactions in seven B-vitamin biosynthetic pathways (37). In addition, membrane energetic functions were encoded in 14 original subsystems that capture in detail individual membrane complexes and soluble components of respiratory and photosynthetic electron transport chains.…”

Section: Organizing Biochemical Pathways and Protein Families Into Sumentioning

confidence: 99%

High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource

Seaver

Gerdes²,

Frelin

et al. 2014

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

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The increasing number of sequenced plant genomes is placing new demands on the methods applied to analyze, annotate, and model these genomes. Today's annotation pipelines result in inconsistent gene assignments that complicate comparative analyses and prevent efficient construction of metabolic models. To overcome these problems, we have developed the PlantSEED, an integrated, metabolism-centric database to support subsystems-based annotation and metabolic model reconstruction for plant genomes. PlantSEED combines SEED subsystems technology, first developed for microbial genomes, with refined protein families and biochemical data to assign fully consistent functional annotations to orthologous genes, particularly those encoding primary metabolic pathways. Seamless integration with its parent, the prokaryotic SEED database, makes PlantSEED a unique environment for crosskingdom comparative analysis of plant and bacterial genomes. The consistent annotations imposed by PlantSEED permit rapid reconstruction and modeling of primary metabolism for all plant genomes in the database. This feature opens the unique possibility of modelbased assessment of the completeness and accuracy of gene annotation and thus allows computational identification of genes and pathways that are restricted to certain genomes or need better curation. We demonstrate the PlantSEED system by producing consistent annotations for 10 reference genomes. We also produce a functioning metabolic model for each genome, gapfilling to identify missing annotations and proposing gene candidates for missing annotations. Models are built around an extended biomass composition representing the most comprehensive published to date. To our knowledge, our models are the first to be published for seven of the genomes analyzed.systems biology | computational biochemistry | plant metabolism | plant genomics

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Plastid origin: who, when and why?

Roettger

Zimorski

et al. 2014

Acta Soc Bot Pol

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Plastid origin: 110 years since MereschkowskyPlastids are eukaryotic metabolic compartments responsible for photosynthesis [1] and a variety of metabolic functions including the biosynthesis of amino acids [2], nucleotides [3], lipids [4], and cofactors [5]. The importance of plastids to photosynthetic lineages of eukaryotes cannot be overstated. In 1905, Mereschkowsky proposed a fully articulated version of endosymbiotic theory positing that plastids originated from cyanobacteria that came to reside as symbionts in eukaryotic cells [6,7]. The theory did not make its way into mainstream biological thinking until it was revived in a synthesis by Margulis [8,9] that also incorporated Wallin's [10] -and Paul Portier's (published in French, cited in Sapp [11]) -ideas about endosymbiotic theory for mitochondrial origin, yet adorned by Margulis' own suggestion of a spirochaete origin of flagella. The spirochaete story never took hold, leaving endosymbiotic theory with three main players: the plastid, the mitochondrion, and its host, which is now understood to be an archaeon [12]. Well into the 1970s, resistance to the concept of endosymbiosis for the origin of plastids (and mitochondria) was stiff [13][14][15].With the availability of protein and DNA sequences, of which Mereschkowsky knew nothing, strong evidence had accumulated by the early 1980s that plastids originated through endosymbiosis from cyanobacteria, rather than autogenously [16]. However, there have been recurrent suggestions, starting with Mereschkowsky [6] and tracing into the 1970's [17], that there were several independent origins of plastids from cyanobacteria. Today it is widely, but not universally [18,19], accepted that plastids had a single origin. The strongest evidence for that view is that the protein import machinery, a good marker for endosymbiotic events [20], in the three lineages of Archaeplastida -eukaryotes with primary plastids [21] -consists of homologous host-originated components [22][23][24], which would not be the case had plastids in those lineages arisen from independent cyanobacterial symbioses.Genomics has enriched our understanding of plastid origin. We now know that the plastid genome has undergone extreme reduction while leaving its imprints in the nuclear genome through endosymbiotic gene transfer [25,26] and that plastids have spread across eukaryotes through symbiosis and become secondary and tertiary plastids [27]. Genomic data also supports the case for a single plastid origin. Despite some concerns about incomplete sampling and phylogenetic artifacts [18], recent analyses from different groups, incorporating improved phylogenetic algorithms and sampling of cyanobacteria, provide two lines of evidence, in addition to * Corresponding author. Email: bill@hhu.deHandling Editor: Andrzej Bodył INVITED REVIEW Acta Soc Bot Pol 83(4): 281-289 DOI: 10.5586/asbp.2014.045 Received: 2014-11-20 Accepted: 2014-12-04 Published electronically: 2014 Plastid origin: who, when and why?Chuan Ku, Mayo Roettger, Verena Zimorski, Shijulal...

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Plant B Vitamin Pathways and their Compartmentation: a Guide for the Perplexed

Cited by 87 publications

References 107 publications

Does Abiotic Stress Cause Functional B Vitamin Deficiency in Plants?

Does Abiotic Stress Cause Functional B Vitamin Deficiency in Plants?

High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource

Plastid origin: who, when and why?

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