Comparative analysis of ABCB1 reveals novel structural and functional conservation between monocots and dicots

Abstract

Phytohormone auxin plays a critical role in modulating plant architecture by creating a gradient regulated via its transporters such as ATP-binding cassette (ABC) B1. Except for Arabidopsis and maize, where it was shown to interrupt auxin transport, ABCB1's presence, structure and function in crop species is not known. Here we describe the structural and putative functional organization of ABCB1 among monocots relative to that of dicots. Identified from various plant species following specific and stringent criteria, ZmABCB1's "true" orthologs sequence identity ranged from 56-90% at the DNA and 75-91% at the predicted amino acid (aa) level. Relative to ZmABCB1, the size of genomic copies ranged from −27 to +1.5% and aa from −7.7 to +0.6%. With the average gene size being similar (5.8 kb in monocots and 5.7 kb in dicots), dicots have about triple the number of introns with an average size of 194 bp (total 1743 bp) compared to 556 bp (total 1667 bp) in monocots. The intron-exon junctions across species were however conserved. N-termini of the predicted proteins were highly variable: in monocots due to mismatches and small deletions of 1-13 aa compared to large, species-specific deletions of up to 77 aa in dicots. The species-, family-and group-specific conserved motifs were identified in the N-terminus and linker region of protein, possibly responsible for the specific functions. The near-identical conserved motifs of Nucleotide Binding Domains (NBDs) in two halves of the protein showed subtle aa changes possibly favoring ATP binding to the N-terminus. Predicted 3-D protein structures showed remarkable similarity with each other and for the residues involved in auxin binding.

Overexpression of ABCB1 Transporter Confers Resistance to mTOR Inhibitor WYE-354 in Cancer Cells

“…ABCB1 is composed of 1280 amino acids expressed by a single-strand [30]. The basic structure of ABCB1 consists of four key regions, namely: two nucleoside binding domains (NBDs) and two hydrophobic transmembrane domains (TMDs) [31,32]. Each transmembrane region is composed of six transmembrane α-helices connected by hydrophilic rings, so that the ABCB1 polypeptide chains are embedded in the cell membrane.…”

Genome-wide analysis of the HSP101/CLPB gene family for heat tolerance in hexaploid wheat

“…Using a tblastx tool 61,62 , the rice sequences (Os05g0519700, Os03g0426900, Os02g0181900) were used as references and queries to retrieve the orthologs from the wheat sequence databases in NCBI (https://www.ncbi.nlm.nih.gov), Swissprot/ Uniprot (http://www.uniprot.org), and EnsemblPlants (http://plants.ensembl.org/Triticum_aestivum). The retrieved sequences were then confirmed as orthologs of CLPB following the criteria developed by Dhaliwal et al 63 . Briefly, orthologous sequences have to meet four criteria: the highest level of sequence identities and query coverage, the presence of domains and motifs of CLPB at the protein level, the relative size and distance among domains and motifs to be similar to the query, and that orthologs must retrieve the reference sequences at the first place when the basic local alignment (BLAST) against nucleotide or protein databases are performed.…”

Genome-wide analysis of the SPL/miR156 module and its interaction with the AP2/miR172 unit in barley

“…A search for conserved motifs within HvSPL proteins was performed by using the MEME 4.11.0 tool ( http://meme-suite.org/tools/meme ) 70 , 71 using default settings, except that the maximum width was 50, the minimum width was 6, and the maximum number of motifs to find was 10. The online WebLogo3 platform ( http://weblogo.threeplusone.com/ ) was used to create the sequence logo of the barley SBP domain.…”