BackgroundMultidrug and toxic compound extrusion (MATE) transporter proteins are present in all organisms. Although the functions of some MATE gene family members have been studied in plants, few studies have investigated the gene expansion patterns, functional divergence, or the effects of positive selection.ResultsForty-five MATE genes from rice and 56 from Arabidopsis were identified and grouped into four subfamilies. MATE family genes have similar exon-intron structures in rice and Arabidopsis; MATE gene structures are conserved in each subfamily but differ among subfamilies. In both species, the MATE gene family has expanded mainly through tandem and segmental duplications. A transcriptome atlas showed considerable differences in expression among the genes, in terms of transcript abundance and expression patterns under normal growth conditions, indicating wide functional divergence in this family. In both rice and Arabidopsis, the MATE genes showed consistent functional divergence trends, with highly significant Type-I divergence in each subfamily, while Type-II divergence mainly occurred in subfamily III. The Type-II coefficients between rice subfamilies I/III, II/III, and IV/III were all significantly greater than zero, while only the Type-II coefficient between Arabidopsis IV/III subfamilies was significantly greater than zero.A site-specific model analysis indicated that MATE genes have relatively conserved evolutionary trends. A branch-site model suggested that the extent of positive selection on each subfamily of rice and Arabidopsis was different: subfamily II of Arabidopsis showed higher positive selection than other subfamilies, whereas in rice, positive selection was highest in subfamily III. In addition, the analyses identified 18 rice sites and 7 Arabidopsis sites that were responsible for positive selection and for Type-I and Type-II functional divergence; there were no common sites between rice and Arabidopsis. Five coevolving amino acid sites were identified in rice and three in Arabidopsis; these sites might have important roles in maintaining local structural stability and protein functional domains.ConclusionsWe demonstrate that the MATE gene family expanded through tandem and segmental duplication in both rice and Arabidopsis. Overall, the results of our analyses contribute to improved understanding of the molecular evolution and functions of the MATE gene family in plants.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-016-0895-0) contains supplementary material, which is available to authorized users.

No abstract

High-molecular-weight glutenin subunit (HMW-GS) possessing nutritional and breadmaking quality is highly expressed in endosperm of wheat (Triticum aestivum L.) and its relative species. The main aim of this study was to explore the transcription initiator characteristics correlating to the high-level expression of HMW-GS genes. The 5¢-untranslated regions of HMW-GS gene Ax null, Dx2, Bx7, By8, and Dy12 in cultivar 'Chinese Spring' were cloned by 5¢-full rapid amplification of complementary DNA ends technology. The HMW-GS gene contained generally three or four transcription initiators, which tightly clustered in a region of 15 nucleotides. The consensus sequence of initiators I, II, and III was an adenine flanked by two pyrimidine bases on each side, namely, YYAYY. The transcriptional initiation efficiencies of these initiators varied dramatically from 3.3 to 90%, and initiators I and II adjacent to the 5¢-end together contributed 83.3 to 93.4%. A mutation from A to T at transcription start site in Ax null worked at far lower efficiency than its counterpart I in Dx2, Bx7, By8, and Dy12. our results indicated that the initiator cluster contributed to the high-level expression of HMW-GS genes in wheat endosperm. Understanding the mechanism involved in the high-level expression may be applied in plant breeding for improving agronomic traits of crops, e.g., qualities, yields, growth, or resistance to stress.

The human tissue kallikrein-related (KLK) proteases are a multigene family of 15 serine proteases, many of which are over-expressed in prostate cancer. Prostate-specific antigen (PSA), a member of this family, is the current serum biomarker for detection and monitoring of prostate cancer. The related prostatic protease, KLK2/KLK2 is also emerging as an additional biomarker for prostate cancer. We have demonstrated that KLK4/KLK4 may also be a useful biomarker for prostate cancer as KLK4/KLK4 expression is higher in the pre-malignant prostatic intra-epithelial neoplasia (PIN) lesion, adenocarcinoma and bone metastasis compared to benign/normal glands. Of interest, there are over 70 KLK splice variants many of which are cancer-specific in their expression and which encode truncated KLK proteins that would not be catalytically active. At least one of these variants, KLK4-205, is nuclear localized which is a novel site for a serine protease-related protein. The functional role of this variant or the native PSA, KLK2 or KLK4 proteases in cancer progression are not fully elucidated, although several biochemical studies suggest a matrix degrading role either directly or indirectly via the activation of urinary plasminogen activator and other factors. In order to further demonstrate a functional role at the cell biology level, we have stably-transfected the prostate cancer PC3 cell line with prepro-PSA, -KLK2 and -KLK4. No change in the proliferative or invasive capacity of these transfected cells was observed, but PSA and KLK4, but not KLK2, over-expression elicited a morphological change and increased migration to various chemo-attractants. We also observed a loss of the cell adhesion protein, E-cadherin and down-regulation of a number of other cell adhesion molecules (desmoplakin, junction plakoglobin, claudin-3 and claudin-7) while expression of the mesenchymal marker, vimentin, was increased. These changes are indicative of an epithelial to mesenchymal transition (EMT) and a more aggressive phenotype. KLK4:PC3 cells showed significantly greater attachment to collagen I and IV and increased migration towards conditioned media from an osteoblastic cell line (Saos-2). PSA and KLK4 expression was also increased in LNCaP:Saos 2 cell co-cultures. These data provide compelling evidence for a role for these kallikrein-related serine proteases in more aggressive disease especially bone metastasis and highlight their potential as biomarkers and therapeutic targets.