Genome-wide analysis of immunophilin FKBP genes and expression patterns in Zea mays

Abstract

ABSTRACT. The receptors for the immunosuppression drugs FK506 and rapamycin are called FKBPs (FK506-binding proteins). FKBPs comprise a large family; they are found in many species, including bacteria, fungi, animals, and plants. As a class of peptidyl-prolyl cistrans isomerase enzymes, the FKBP genes have been the focus of recent studies on plant stress tolerance and immunology. We identified and analyzed gene families encoding these proteins in maize using computational and molecular biology approaches. Thirty genes were found to encode putative FKBPs according to their FK506-binding domain. The FKBP genes can be classified into single domain and multiple domain members based on the number of the domains. By analysis of the physical locations, the 30 FKBP genes were found to be widely distributed on 10 chromosomes. After analysis of the FKBP phylogenetic tree in the maize genome, we found that the 30 genes revealed two major clades. Gene duplication played a major role in the evolution of FKBP genes, which suggests that the FKBP genes in maize have a pattern significantly different from that of these genes in rice. Based on semi-quantitative RT-PCR, we found that the 30 FKBPs were expressed differently in various tissues in maize, which suggests FKBP genes and expression patterns in Zea mays that FKBP genes play different roles in each tissue. Several FKBPs were expressed at higher levels in roots, indicating that these genes in maize may have similar or overlapping functions.

Microbial Peptidyl-Prolyl cis / trans Isomerases (PPIases): Virulence Factors and Potential Alternative Drug Targets

“…Many FKBPs, although initially associated with immunomodulatory processes, were later found to be expressed at much higher degrees in brain tissue, with neuroprotective or neuroregenerative properties, and hence are considered important factors in neurological diseases (25,62). Differential expression in tissues and during development was also observed for plant PPIases, such as in the case of maize or wheat (56,63). All these data are indicative of the physiologic versatility of this protein family.…”

A systems biology approach uncovers a gene co-expression network associated with cell wall degradability in maize

“…The first two genes belonged to module M4. ZmFKB20-1 which was one of only two DE genes already identified in the targeted QTL6.05 support interval [38] belongs to the FK506-binding protein family, which contains up to 30 paralogous genes in the maize genome [77,99]. Although historically linked to immunosuppression and proline bond rotation, the physiological importance of FK506-binding proteins extends general protein folding to diverse biological processes, including hormone signaling, DNA transcription and protein trafficking.…”

Elucidation of Abiotic Stress Signaling in Plants

“…stress conditions, the time point of expression (in hours or days) is given c Only experimentally determined or high-confi dence interactions are listed d Confi rmed experimentally using promoter-GUS analysis by Cheng et al ( 2005 ), Kamiya et al ( 2006 ), Mei et al ( 2009 ), Pittman et al ( 2004 ), Wang et al ( 2012 ), Zhao et al ( 2009b ) e Confi rmed experimentally using Northern blotting or RT-PCR by Catalá et al ( 2003 ), Cheng et al ( 2002 , 2005 ), Cho et al ( 2012 ), Conn et al ( 2011 ), Edmond et al ( 2009 ), Hirschi ( 1999 ), Hirschi et al ( 2000 ), Kamiya et al ( 2005 , 2006 , 2012 ), Liu et al ( 2011 ), Singh et al ( 2014 ),Wang et al ( 2012 ) f Confi rmed experimentally using fl uorescent protein fusions or fractionation byCheng et al ( , 2005,Edmond et al ( 2009), Hirschi et al ( 2000,Kamiya et al ( 2006 ),Wang et al ( 2012 ) g Confi rmed experimentally using yeast-2 hybrid, split ubiquitin analysis or biofl uorescence complementation analysis by), Cheng et al ( 2004a,Zhao et al ( 2004a , b ) …”