Genome-Wide Identification and Expression Profiling of ATP-Binding Cassette (ABC) Transporter Gene Family in Pineapple (Ananas comosus (L.) Merr.) Reveal the Role of AcABCG38 in Pollen Development.

Piaojuan Chen,Yi Li,Ziyan Zhang,Syed Muhammad Azam,Liping Liu,Zia Ur Rahman,Maokai Yan,Yanhui Liu,Lihua Zhao,Yuan Qin,Zhimin Hou,Bingyan Hu

doi:10.3389/fpls.2017.02150

Piaojuan Chen, Yi Li + Show 10 more

Open Access

https://doi.org/10.3389/fpls.2017.02150

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Abstract

Pineapple (Ananas comosus L.) cultivation commonly relies on asexual reproduction which is easily impeded by many factors in agriculture production. Sexual reproduction might be a novel approach to improve the pineapple planting. However, genes controlling pineapple sexual reproduction are still remain elusive. In different organisms a conserved superfamily proteins known as ATP binding cassette (ABC) participate in various biological processes. Whereas, till today the ABC gene family has not been identified in pineapple. Here 100 ABC genes were identified in the pineapple genome and grouped into eight subfamilies (5 ABCAs, 20 ABCBs, 16 ABCCs, 2 ABCDs, one ABCEs, 5 ABCFs, 42 ABCGs and 9 ABCIs). Gene expression profiling revealed the dynamic expression pattern of ABC gene family in various tissues and different developmental stages. AcABCA5, AcABCB6, AcABCC4, AcABCC7, AcABCC9, AcABCG26, AcABCG38 and AcABCG42 exhibited preferential expression in ovule and stamen. Over-expression of AcABCG38 in the Arabidopsis double mutant abcg1-2abcg16-2 partially restored its pollen abortion defects, indicating that AcABCG38 plays important roles in pollen development. Our study on ABC gene family in pineapple provides useful information for developing sexual pineapple plantation which could be utilized to improve pineapple agricultural production.

Highlights

The ATP-binding cassette (ABC) gene family is one of the largest expressed gene subfamilies (Campa et al, 2008)
To identify the ATP binding cassette (ABC) gene family in pineapple, the HMMER3.0 (Eddy, 2011) was used to get ABC protein sequences containing PFAM ABC domain (PF00005) in pineapple genome database downloaded from the Phytozome v12.1
A total of 100 ABC genes were identified in the pineapple genome by BLAST and phylogenetic analysis with Arabidopsis ABC proteins

Summary

Introduction

The ATP-binding cassette (ABC) gene family is one of the largest expressed gene subfamilies (Campa et al, 2008). Most ABC transporter subfamilies had highly conservative amino acid sequence domains: the nucleotide-binding domain (NBDs) and the transmembrane domains (TMDs) including five or six helices (Higgins and Linton, 2004). The signature motif is unique to ABC proteins while the Walker A and Walker B motif are responsible for nucleotide binding (Davidson et al, 2008). ABC transporter proteins have been classified into two categories based on the length of structural domain: full-sized transporters (two NBDs and two TMDs) and half-sized transporters (one NBD) (Davidson et al, 2008). The ABCE and ABCF subfamilies lack of TMDs domain and do not function as transporter. ABCE (Y39E4B.1) had been reported for regulating transcription and translation in eukaryotes (Zhao et al, 2004)

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