Comparative analysis of contextual bias around the translation initiation sites in plant genomes

Gupta, Paras; Rangan, Latha; Ramesh, Tharmalingam; Gupta, Mudit

doi:10.1016/j.jtbi.2016.06.015

Cited by 20 publications

(19 citation statements)

References 34 publications

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“…Very recently, with the whole-genome data from many plant species, a similar survey was done using seven monocots and seven dicots. The most favorable context for translation initiation determined by comparisons with protein abundance was GCNAUGGC in monocots, AANAUGGC in dicots and GCNAUGGC in plants in general (Gupta et al, 2016).…”

Section: Leaky Scanningmentioning

confidence: 99%

Translation regulation in plants: an interesting past, an exciting present and a promising future

2017

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SUMMARYChanges in gene expression are at the core of most biological processes, from cell differentiation to organ development, including the adaptation of the whole organism to the ever-changing environment. Although the central role of transcriptional regulation is solidly established and the general mechanisms involved in this type of regulation are relatively well understood, it is clear that regulation at a translational level also plays an essential role in modulating gene expression. Despite the large number of examples illustrating the critical role played by translational regulation in determining the expression levels of a gene, our understanding of the molecular mechanisms behind such types of regulation has been slow to emerge. With the recent development of high-throughput approaches to map and quantify different critical parameters affecting translation, such as RNA structure, protein-RNA interactions and ribosome occupancy at the genome level, a renewed enthusiasm toward studying translation regulation is warranted. The use of these new powerful technologies in well-established and uncharacterized translation-dependent processes holds the promise to decipher the likely complex and diverse, but also fascinating, mechanisms behind the regulation of translation.

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Section: Leaky Scanningmentioning

confidence: 99%

Translation regulation in plants: an interesting past, an exciting present and a promising future

2017

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“…Whereas monocot mRNAs contain higher frequencies of À3G/+4G nucleotides, À3A/+4G are more frequent in dicot mRNAs. It should be pointed out that the 5 0 -UTRs of monocot mRNAs are GC-rich, whereas those of dicots are AU-rich sequences [31][32][33]40,41,43]. Moreover, we have noticed that, among the consensus sequences of the plant species here scrutinized, the À2M position is well conserved ( Table 2).…”

Section: Key Figurementioning

confidence: 73%

“…Within the supergroup Archaeplastida (Plantae), several species of green plants (land plants and green algae) have been analyzed (Table S3). They possess strong Kozak motifs as the consensus TIS context [31][32][33]36,[40][41][42][43]. The frequencies of TISs containing guanine at positions À3 and +4 were observed to be different between monocotyledon and dicotyledon mRNAs.…”

Section: Key Figurementioning

confidence: 99%

Conservation and Variability of the AUG Initiation Codon Context in Eukaryotes

Hernández

Osnaya

Pérez-Martı́nez

2019

Trends in Biochemical Sciences

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“…Coding sequences of twelve fluorescent proteins selected were obtained from the following sources: mTurquoise2 (Goedhart et al, 2012), mTFP1 [GenBank accession number DQ676819.1, (Ai et al, 2006)], mClover3 (Bajar et al, 2016), mNeonGreen [GenBank accession number KC295282.1, (Shaner et al, 2013)], mCitrine (Griesbeck et al, 2001), mYPet [the monomerizing mutation A206K was introduced into the YPet sequence (Nguyen and Daugherty, 2005) to generate mYPet], mKOκ [7 amino acid mutations (K49E, P70V, K185E, K188E, S192D, S196G, L210Q) were introduced into the mKO sequence with GenBank accession number AB128821.1 to generate mKOκ, (Tsutsui et al, 2008)], tdTomato (Shaner et al, 2004), TagRFP-T [GenBank accession number EU582019.1, (Shaner et al, 2008)], mRuby3 (Bajar et al, 2016), mCardinal (Chu et al, 2014), mKate2 (Shcherbo et al, 2009). Prior to synthesis for GoldenGate cloning (Weber et al, 2011), coding sequences were modified such that the codon encoding valine at position 2 of each open reading frame was mutated to code for an alanine (GCG) to achieve a partial match to the Kozak consensus sequence used in monocots (Nakagawa et al, 2008; Joshi et al, 1997; Gupta et al, 2016), codon-optimized for rice using the codon optimization tool by Integrated DNA Technologies, and domesticated for the GoldenGate cloning system. Where relevant, the GFP cryptic intron (Haseloff et al, 1997) and potential intron sites identified by NetPlantGene Server (Hebsgaard et al, 1996) were neutralized.…”

Section: Methodsmentioning

confidence: 99%

Fluorescent reporters for functional analysis in rice leaves

Luginbuehl

El‐Sharnouby

Wang

et al. 2019

Preprint

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Fluorescent reporters have facilitated non-invasive imaging in multiple plant species and thus allowed analysis of processes ranging from gene expression and protein localization through to cellular patterning. However, in rice, a globally important crop and model species, there are relatively few reports of fluorescent proteins being used in leaves. Fluorescence imaging is particularly difficult in the rice leaf blade, likely due to a high degree of light scattering in this tissue. To address this, we investigated approaches to improve deep imaging in mature rice leaf blades. We found that ClearSee treatment, which has previously been used to visualise fluorescent reporters in whole tissues of plants, led to improved imaging in rice. Removing epidermal and subtending mesophyll cell layers was faster than ClearSee, and also reduced light scattering such that imaging of fluorescent proteins in deeper leaf layers was possible. To expand the range of fluorescent proteins suitable for imaging in rice, we screened twelve whose spectral profiles spanned most of the visible spectrum. This identified five proteins, mTurquoise2, mClover3, mNeonGreen, mKOκ and tdTomato that are robustly expressed and visible in mesophyll cells of stably transformed plants. Using microparticle bombardment, we show that mTurquoise2 and mNeonGreen can be used for simultaneous multicolour imaging of different sub-cellular compartments. Overall, we conclude that mTurquoise2, mClover3, mNeonGreen, mKOκ and tdTomato are suitable for high resolution live imaging of rice leaves, both after transient and stable transformation. Along with the rapid microparticle bombardment method, which allows transient transformation of major cell types in the leaf blade, these fluorescent reporters should greatly facilitate the analysis of gene expression and cell biology in rice.One sentence summaryWe report five fluorescent reporters suitable for functional analysis in rice leaves.

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Comparative analysis of contextual bias around the translation initiation sites in plant genomes

Cited by 20 publications

References 34 publications

Translation regulation in plants: an interesting past, an exciting present and a promising future

Translation regulation in plants: an interesting past, an exciting present and a promising future

Conservation and Variability of the AUG Initiation Codon Context in Eukaryotes

Fluorescent reporters for functional analysis in rice leaves

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