Dataset Information

Identification and analysis of alternative splicing events in Phaseolus vulgaris and Glycine max.

ABSTRACT:

Background

The vast diversification of proteins in eukaryotic cells has been related with multiple transcript isoforms from a single gene that result in alternative splicing (AS) of primary transcripts. Analysis of RNA sequencing data from expressed sequence tags and next generation RNA sequencing has been crucial for AS identification and genome-wide AS studies. For the identification of AS events from the related legume species Phaseolus vulgaris and Glycine max, 157 and 88 publicly available RNA-seq libraries, respectively, were analyzed.

Results

We identified 85,570 AS events from P. vulgaris in 72% of expressed genes and 134,316 AS events in 70% of expressed genes from G. max. These were categorized in seven AS event types with intron retention being the most abundant followed by alternative acceptor and alternative donor, representing ~75% of all AS events in both plants. Conservation of AS events in homologous genes between the two species was analyzed where an overrepresentation of AS affecting 5'UTR regions was observed for certain types of AS events. The conservation of AS events was experimentally validated for 8 selected genes, through RT-PCR analysis. The different types of AS events also varied by relative position in the genes. The results were consistent in both species.

Conclusions

The identification and analysis of AS events are first steps to understand their biological relevance. The results presented here from two related legume species reveal high conservation, over ~15-20 MY of divergence, and may point to the biological relevance of AS.

SUBMITTER: Iniguez LP

PROVIDER: S-EPMC5568362 | biostudies-literature | 2017 Aug

REPOSITORIES: biostudies-literature

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Publications

Identification and analysis of alternative splicing events in Phaseolus vulgaris and Glycine max.

Iñiguez Luis P LP Ramírez Mario M Barbazuk William B WB Hernández Georgina G

BMC genomics 20170822 1

<h4>Background</h4>The vast diversification of proteins in eukaryotic cells has been related with multiple transcript isoforms from a single gene that result in alternative splicing (AS) of primary transcripts. Analysis of RNA sequencing data from expressed sequence tags and next generation RNA sequencing has been crucial for AS identification and genome-wide AS studies. For the identification of AS events from the related legume species Phaseolus vulgaris and Glycine max, 157 and 88 publicly av ...[more]

PMID: 28830361

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Project description:BACKGROUND: The PolyGalacturonase-Inhibiting Proteins (PGIP) of plant cell wall limit the invasion of phytopathogenic organisms by interacting with the enzyme PolyGalacturonase (PG) they secrete to degrade pectin present in the cell walls. PGIPs from different or same plant differ in their inhibitory activity towards the same PG. PGIP2 from Phaseolus vulgaris (Pv) inhibits the PG from Fusarium moniliforme (Fm) although PGIP1, another member of the multigene family from the same plant sharing 99% sequence similarity, cannot. Interestingly, PGIP3 from Glycine max (Gm) which is a homologue of PGIP2 is capable of inhibiting the same PG although the extent of similarity is lower and is 88%. It therefore appears that subtle changes in the sequence of plant PGIPs give rise to different specificity for inhibiting pathogenic PGs and there exists no direct dependence of function on the extent of sequence similarity. RESULTS: Structural information for any PGIP-PG complex being absent, we resorted to molecular modelling to gain insight into the mechanism of recognition and discrimination of PGs by PGIPs. We have built homology models of PvPGIP1 and GmPGIP3 using the crystal structure of PvPGIP2 (1OGQ) as template. These PGIPs were then docked individually to FmPG to elucidate the characteristics of their interactions. The mode of binding for PvPGIP1 to FmPG considerably differs from the mode observed for PvPGIP2-FmPG complex, regardless of the high sequence similarity the two PGIPs share. Both PvPGIP2 and GmPGIP3 despite being relatively less similar, interact with residues of FmPG that are known from mutational studies to constitute the active site of the enzyme. PvPGIP1 tends to interact with residues not located at the active site of FmPG. Looking into the electrostatic potential surface for individual PGIPs, it was evident that a portion of the interacting surface for PvPGIP1 differs from the corresponding region of PvPGIP2 or GmPGIP3. CONCLUSION: van der Waals and electrostatic interactions play an active role in PGIPs for proper recognition and discrimination of PGs. Docking studies reveal that PvPGIP2 and GmPGIP3 interact with the residues constituting the active site of FmPG with implications that the proteins bind/block FmPG at its active site and thereby inhibit the enzyme.

Dataset Information

Identification and analysis of alternative splicing events in Phaseolus vulgaris and Glycine max.

Background

Results

Conclusions

Publications

Identification and analysis of alternative splicing events in Phaseolus vulgaris and Glycine max.

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