Abstract
Cassava (Manihot esculenta) is an important tropical subsistence crop that is severely affected by cassava brown streak disease (CBSD) in East Africa. The disease is caused by Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV). Both have a (+)-sense single-stranded RNA genome with a 5’ covalently-linked viral protein, which functionally resembles the cap structure of mRNA, binds to eukaryotic translation initiation factor 4E (eIF4E) or its analogues, and then enable the translation of viral genomic RNA in host cells. To characterize cassava eIF4Es and their potential role in CBSD tolerance and susceptibility, we cloned five eIF4E transcripts from cassava (accession TMS60444). Sequence analysis indicated that the cassava eIF4E family of proteins consisted of one eIF4E, two eIF(iso)4E, and two divergent copies of novel cap-binding proteins (nCBPs). Our data demonstrated experimentally the coding of these five genes as annotated in the published cassava genome and provided additional evidence for refined annotations. Illumina resequencing data of the five eIF4E genes were analyzed from 14 cassava lines tolerant or susceptible to CBSD. Abundant single nucleotide polymorphisms (SNP) and biallelic variations were observed in the eIF4E genes; however, most of the SNPs were located in the introns and non-coding regions of the exons. Association studies of non-synonymous SNPs revealed no significant association between any SNP of the five eIF4E genes and the tolerance or susceptibility to CBSD. However, two SNPs in two genes were weakly associated with the CBSD responses but had no direct causal-effect relationship. SNPs in an intergenic region upstream of eIF4E_me showed a surprising strong association with CBSD responses. Digital expression profile analysis showed differential expression of different eIF4E genes but no significant difference in gene expression was found between susceptible and tolerant cassava accessions despite the association of the intergenic SNPs with CBSD responses.
Highlights
The eukaryotic translation initiation factor 4E (eIF4E) family of eukaryotic initiation factor proteins play a crucial role in the initiation of cap-dependent translation of any RNA messenger. eIF4E or its homologue binds to the 7-methylguanosine (m7G) cap at the 5’ end of the mRNA in eukaryotes [1,2]
We reported here the cloning and analysis of the transcripts from five cassava eIF4E genes: eIF4E_me, eIF(iso)4E_me1, eIF(iso)4E_me2, nCBP_me1, and nCBP_me2 (Fig 2)
Data provided in this paper verified annotations from Cassava Genome V6.1 experimentally and provided additional data to refine the annotation of these five genes. eIF4E_me, eIF(iso)4E_me2, and nCBP_me2 were expressed at a significantly higher level than eIF(iso)4E_me1 and nCBP_me1, Fig 5
Summary
The eIF4E family of eukaryotic initiation factor proteins play a crucial role in the initiation of cap-dependent translation of any RNA messenger. eIF4E or its homologue binds to the 7-methylguanosine (m7G) cap at the 5’ end of the mRNA in eukaryotes [1,2]. Especially in dicots, several genes code for a small family of eIF4E and eIF(iso)4E proteins [1] These homologues presumably provide both redundancy and differential regulation during mRNA translation. Knockout and/or downregulation of eIF4E or eIF(iso)4E in Arabidopsis is tolerated and plants show little sign of impairment, depletion of both leads to a dwarf phenotype [6,7]. In addition to these two types of canonical translation initiation factors, plants encode novel cap binding proteins (nCBP) [1,8,9] that interact with eIF4G and actively participate in mRNA translation [9]
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
