uORFs: Important Cis-Regulatory Elements in Plants

Zhang, Ting; Wu, Anqi; Yue, Yaping; Zhao, Yu

doi:10.3390/ijms21176238

“…In contrast, the PC2-3 ORF is located in the 5′ UTR of an mRNA transcribed from a cassava gene encoding a PPR repeat protein (Manes.13G072800). Small ORFs in 5′ UTRs have been implicated in negative control of translation, and they can impact protein expression in a variety of plant processes, including the host defense response ( 56 ). SEGS-2-related sequences in the cassava genome are often found in 5′ UTRs, suggesting that they are involved in translational control of many genes.…”

Section: Discussionmentioning

confidence: 99%

A New Type of Satellite Associated with Cassava Mosaic Begomoviruses

Aimone

¹

,

Leon

²

,

Dallas

³

et al. 2021

J Virol

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Cassava mosaic disease (CMD), which is caused by single-stranded DNA begomoviruses, severely limits cassava production across Africa. A previous study showed that CMD symptom severity and viral DNA accumulation increase in cassava in the presence of a DNA sequence designated as SEGS-2 ( s equence e nhancing g eminivirus s ymptoms). We report here that when SEGS-2 is co-inoculated with African cassava mosaic virus (ACMV) onto Arabidopsis thaliana , viral symptoms increase. Transgenic Arabidopsis with an integrated copy of SEGS-2 inoculated with ACMV also display increased symptom severity and viral DNA levels. Moreover, SEGS-2 enables Cabbage leaf curl virus (CaLCuV) to infect a geminivirus resistant Arabidopsis thaliana accession. Although SEGS-2 is related to cassava genomic sequences, an earlier study showed that it occurs as episomes and is packaged into virions in CMD-infected cassava and viruliferous whiteflies. We identified SEGS-2 episomes in SEGS-2 transgenic Arabidopsis. The episomes occur as both double-stranded and single-stranded DNA, with the single-stranded form packaged into virions. In addition, SEGS-2 episomes replicate in tobacco protoplasts in the presence, but not the absence, of ACMV DNA-A. SEGS-2 episomes contain a SEGS-2 derived promoter and an open reading frame with the potential to encode a 75-amino acid protein. An ATG mutation at the beginning of the SEGS-2 coding region does not enhance ACMV infection in A. thaliana . Together, the results established that SEGS-2 is a new type of begomovirus satellite that enhances viral disease through the action of a SEGS-2 encoded protein that may also be encoded in the cassava genome. IMPORTANCE Cassava is an important root crop in the developing world and a food and income crop for more than 300 million African farmers. Cassava is rising in global importance and trade as the demands for biofuels and commercial starch increase. More than half of the world’s cassava is produced in Africa, where it is primarily grown by smallholder farmers, many of whom are from the poorest villages. Although cassava can grow under high temperature, drought and poor soil conditions, its production is severely limited by viral diseases. Cassava mosaic disease (CMD) is one of the most important viral diseases of cassava and can cause up to 100% yield losses. We provide evidence that SEGS-2, which was originally isolated from cassava crops displaying severe and atypical CMD symptoms in Tanzanian fields, is a novel begomovirus satellite that can compromise the development of durable CMD resistance.

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“…In contrast, the PC2-3 ORF is located in the 5’ UTR of an mRNA transcribed from a cassava gene encoding a PPR repeat protein (Manes.13G072800). Small ORFs in 5’ UTRs have been implicated in negative control of translation, and they can impact protein expression in a variety of plant processes, including the host defense response (Zhang et al, 2020). SEGS-2 -related sequences in the cassava genome are often found in 5’ UTRs, suggesting that they may be involved in translational control of many genes.…”

Section: Discussionmentioning

confidence: 99%

A New Type of Satellite associated with Cassava Mosaic Begomoviruses

Aimone

¹

,

Leon

²

,

Dallas

³

et al. 2021

Preprint

View full text Add to dashboard Cite

Cassava mosaic disease (CMD), which is caused by single-stranded DNA begomoviruses, severely limits cassava production across Africa. A previous study showed that CMD symptom severity and viral DNA accumulation increase in cassava in the presence of a DNA sequence designated as SEGS-2 (sequence enhancing geminivirus symptoms). We report here that when SEGS-2 is co-inoculated with African cassava mosaic virus (ACMV) onto Arabidopsis thaliana, viral symptoms increase. Transgenic Arabidopsis with an integrated copy of SEGS-2 inoculated with ACMV also display increased symptom severity and viral DNA levels. Moreover, SEGS-2 enables Cabbage leaf curl virus (CaLCuV) to infect a geminivirus resistant Arabidopsis accession. Although SEGS-2 is related to cassava genomic sequences, an earlier study showed that it occurs as episomes and is packaged into virions in CMD-infected cassava and viruliferous whiteflies. We identified SEGS-2 episomes in SEGS-2 transgenic Arabidopsis. The episomes occur as both double-stranded and single-stranded DNA, with the single-stranded form packaged into virions. In addition, SEGS-2 episomes replicate in tobacco protoplasts in the presence, but not the absence, of ACMV DNA-A. SEGS-2 episomes contain a SEGS-2 derived promoter and an open reading frame with the potential to encode a 75-amino acid protein. An ATG mutation at the beginning of the SEGS-2 coding region does not enhance ACMV infection in Arabidopsis. Together, the results established that SEGS-2 is a new type of begomovirus satellite that enhances viral disease through the action of a SEGS-2 encoded protein that may also be encoded in the cassava genome.

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“…In many cases, many genes that regulate important traits require a high rate of translation to achieve crop improvement, rather than loss or reduction of function (Xu et al, 2017;Reis et al, 2020). Upstream open reading frames (uORFs) are important cis-regulatory elements in the 5′ leading sequence of eukaryotic mRNAs, and usually inhibit the translation initiation of downstream ORFs through ribosome stalling (Zhang et al, 2020;Kurihara, 2020). Fine-tuning the translation by regulating uORFs can effectively improve the translation efficiency of target genes for the improvement of crop traits (Figure 1E).…”

Section: Expression Regulationmentioning

confidence: 99%

Crop Quality Improvement Through Genome Editing Strategy

Yang

¹

,

Xu

²

,

Shen

³

et al. 2022

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Good quality of crops has always been the most concerning aspect for breeders and consumers. However, crop quality is a complex trait affected by both the genetic systems and environmental factors, thus, it is difficult to improve through traditional breeding strategies. Recently, the CRISPR/Cas9 genome editing system, enabling efficiently targeted modification, has revolutionized the field of quality improvement in most crops. In this review, we briefly review the various genome editing ability of the CRISPR/Cas9 system, such as gene knockout, knock-in or replacement, base editing, prime editing, and gene expression regulation. In addition, we highlight the advances in crop quality improvement applying the CRISPR/Cas9 system in four main aspects: macronutrients, micronutrients, anti-nutritional factors and others. Finally, the potential challenges and future perspectives of genome editing in crop quality improvement is also discussed.

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uORFs: Important Cis-Regulatory Elements in Plants

Cited by 41 publications

References 95 publications

A New Type of Satellite Associated with Cassava Mosaic Begomoviruses

A New Type of Satellite Associated with Cassava Mosaic Begomoviruses

A New Type of Satellite associated with Cassava Mosaic Begomoviruses

Crop Quality Improvement Through Genome Editing Strategy

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