Exploring the fate of mRNA in aging seeds: protection, destruction, or slow decay?

Fleming, Margaret B.; Patterson, Eric; Reeves, Patrick A.; Richards, Christopher M.; Gaines, Todd A.; Walters, Christina

doi:10.1093/jxb/ery215

Cited by 47 publications

(66 citation statements)

References 63 publications

(97 reference statements)

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“…Germability decrease is accompanied by a reduction in total RNA content and RNA integrity [ 33 , 40 , 41 ]. Fleming et al [ 42 ] demonstrated in soybean that longer transcripts were more likely to be damaged and postulated that this was due to the impact of reactive oxygen species. It has been proven that, during germination, the seeds translate stored mRNAs using stored ribosomes [ 43 , 44 ].…”

Section: Discussionmentioning

confidence: 99%

Low RIN Value for RNA-Seq Library Construction from Long-Term Stored Seeds: A Case Study of Barley Seeds

Puchta

Boczkowska

Groszyk

2020

Genes

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Seed aging is a complex biological process and its fundamentals and mechanisms have not yet been fully recognized. This is a key issue faced by research teams involved in the collection and storage of plant genetic resources in gene banks every day. Transcriptomic changes associated with seed aging in the dry state have barely been studied. The aim of the study was to develop an efficient protocol for construction of RNA-Seq libraries from long-term stored seeds with very low viability and low RNA integrity number (RIN). Here, barley seeds that have almost completely lost their viability as a result of long-term storage were used. As a control, fully viable seeds obtained in the course of field regeneration were used. The effectiveness of protocols dedicated to RNA samples with high and low RIN values was compared. The experiment concluded that library construction from low viable or long-term stored seeds with degraded RNA (RIN < 3) should be carried out with extraordinary attention due to the possibility of uneven degradation of different RNA fractions.

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Section: Discussionmentioning

confidence: 99%

Low RIN Value for RNA-Seq Library Construction from Long-Term Stored Seeds: A Case Study of Barley Seeds

Puchta

Boczkowska

Groszyk

2020

Genes

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“…The RIN is an index with a value in the range one to 10 (fully degraded RNA to intact RNA) and RNA-Seq protocols typically require total RNA with a value of at least eight [82]. Analyses of seed longevity carried out using the RIN as an index in pea [83,84], soybean [85,86], carrot, crimson clover, lettuce, onion, safflower, sesame, sorghum, tomato, and watermelon [84], revealed a positive and significant correlation between seed viabilities and RIN values in most species. Moreover, the RIN decreased prior to the loss of seed viability.…”

Section: Total Rna Degradation During Seed Agingmentioning

confidence: 99%

“…Among more than 20 different types of base damage caused by hydroxyl radicals, the most prevalent oxidized base in RNA is 8-oxoguanine [57]. Nonetheless, no significant correlation was observed between seed storage time and the relative abundance of 8-oxoguanine in total RNA [86], suggesting that RNA damage occurs by random oxidative attack on the molecule.…”

Section: Total Rna Degradation During Seed Agingmentioning

confidence: 99%

“…The transcriptomes of aged or deteriorated seeds including stored mRNAs have been analyzed in order to understand how gene expression contributes to the loss of seed longevity. The latest discovery is that aging soybean seed transcripts are broken non-specifically by free radical attack at random bases and that greater fragmentation occurs in longer transcripts [86]. Many of the shortest (<1200 bp) transcripts were relatively intact even after long-term seed storage and were mainly involved in ribosomal and translational functions, underlining the importance of stored mRNAs in the reconstitution of the translational machinery for germination.…”

Section: Transcriptome Profiles In Aged/deteriorated Seedsmentioning

confidence: 99%

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Lost in Translation: Physiological Roles of Stored mRNAs in Seed Germination

Sano

Rajjou

North

2020

Plants

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Seeds characteristics such as germination ability, dormancy, and storability/longevity are important traits in agriculture, and various genes have been identified that are involved in its regulation at the transcriptional and post-transcriptional level. A particularity of mature dry seeds is a special mechanism that allows them to accumulate more than 10,000 mRNAs during seed maturation and use them as templates to synthesize proteins during germination. Some of these stored mRNAs are also referred to as long-lived mRNAs because they remain translatable even after seeds have been exposed to long-term stressful conditions. Mature seeds can germinate even in the presence of transcriptional inhibitors, and this ability is acquired in mid-seed development. The type of mRNA that accumulates in seeds is affected by the plant hormone abscisic acid and environmental factors, and most of them accumulate in seeds in the form of monosomes. Release of seed dormancy during after-ripening involves the selective oxidation of stored mRNAs and this prevents translation of proteins that function in the suppression of germination after imbibition. Non-selective oxidation and degradation of stored mRNAs occurs during long-term storage of seeds so that the quality of stored RNAs is linked to the degree of seed deterioration. After seed imbibition, a population of stored mRNAs are selectively loaded into polysomes and the mRNAs, involved in processes such as redox, glycolysis, and protein synthesis, are actively translated for germination.

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“…However, the quantitative relationship of the At3g08030 transcript level with aging time or seed germination frequency was not determined. Recently, Fleming et al (Fleming et al, 2018b) observed fragmentation of stored mRNAs in soybean embryonic axis by transcriptomic analysis and suggested that mRNA breaks occur at random positions.…”

Section: Degradation Of Stored Mrnas Is Highly Correlated With Aging mentioning

confidence: 99%

Arabidopsis Seed Stored mRNAs are Degraded Constantly over Aging Time, as Revealed by New Quantification Methods

Zhao

Wang

et al. 2020

Front. Plant Sci.

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How plant seeds age remains poorly understood and effective tools for monitoring seed aging are lacking. Dry seeds contain various stored mRNAs which are believed to be required for protein synthesis during early stages of seed germination. We reasoned that seed stored mRNAs would undergo degradation during seed aging, based on the propensity of mRNAs to degrade. We performed RT-PCR and qPCR analyses to study the changes in stored mRNA levels of Arabidopsis seeds during aging. All stored mRNAs analyzed were gradually degraded in both naturally and artificially aged seeds. The difference in Ct values between aged and control seeds (DCt value) was highly correlated with the mRNA fragment size and seed aging time. We derived mathematical equations for estimating the relative amount of undamaged stored mRNAs and frequency of the breakdown at one nucleotide level for individual mRNAs. Stored mRNAs were found to break down randomly. The frequency of breaks per nucleotide per day, which we named b value, remained fairly constant under the same aging conditions over aging time. This parameter should allow the effects of different conditions on the degradation of stored mRNAs to be quantitatively compared. Also, we showed that the change in stored mRNA levels could serve as a more precise biomarker for seed aging assessment than three existing methods. These methods and findings will advance the studies of stored mRNAs and seed ageing in plants, and likely slow RNA degradation in non-plant systems.

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Exploring the fate of mRNA in aging seeds: protection, destruction, or slow decay?

Abstract: Aged soybean seeds show widespread cleavage of long mRNA transcripts with no particular relationship to transcript function, consistent with extant hypotheses of aging mechanisms.

Cited by 47 publications

References 63 publications

Low RIN Value for RNA-Seq Library Construction from Long-Term Stored Seeds: A Case Study of Barley Seeds

Low RIN Value for RNA-Seq Library Construction from Long-Term Stored Seeds: A Case Study of Barley Seeds

Lost in Translation: Physiological Roles of Stored mRNAs in Seed Germination

Arabidopsis Seed Stored mRNAs are Degraded Constantly over Aging Time, as Revealed by New Quantification Methods

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