Genome-Wide Identification and Expression Analysis of Aquaporins in Tomato

The family of aquaporins, also called water channels or major intrinsic proteins, is characterized by six transmembrane domains that together facilitate the transport of water and a variety of low molecular weight solutes. They are found in all domains of life, but show their highest diversity in plants. Numerous studies identified aquaporins as important targets for improving plant performance under drought stress. The phylogeny of aquaporins is well established based on model species like Arabidopsis thaliana, which can be used as a template to investigate aquaporins in other species. In this study we comprehensively identified aquaporin encoding genes in tomato (Solanum lycopersicum), which is an important vegetable crop and also serves as a model for fleshy fruit development. We found 47 aquaporin genes in the tomato genome and analyzed their structural features. Based on a phylogenetic analysis of the deduced amino acid sequences the aquaporin genes were assigned to five subfamilies (PIPs, TIPs, NIPs, SIPs and XIPs) and their substrate specificity was assessed on the basis of key amino acid residues. As ESTs were available for 32 genes, expression of these genes was analyzed in 13 different tissues and developmental stages of tomato. We detected tissue-specific and development-specific expression of tomato aquaporin genes, which is a first step towards revealing the contribution of aquaporins to water and solute transport in leaves and during fruit development.     

Aquaporins in the eye: Expression,function, and roles in ocular disease

Background

All thirteen known mammalian aquaporins have been detected in the eye. Moreover, aquaporins have been identified as playing essential roles in ocular functions ranging from maintenance of lens and corneal transparency to production of aqueous humor to maintenance of cellular homeostasis and regulation of signal transduction in the retina.

Scope of review

This review summarizes the expression and known functions of ocular aquaporins and discusses their known and potential roles in ocular diseases.

Major conclusions

Aquaporins play essential roles in all ocular tissues. Remarkably, not all aquaporin function as a water permeable channel and the functions of many aquaporins in ocular tissues remain unknown. Given their vital roles in maintaining ocular function and their roles in disease, aquaporins represent potential targets for future therapeutic development.

General significance

Since aquaporins play key roles in ocular physiology, an understanding of these functions is important to improving ocular health and treating diseases of the eye. It is likely that future therapies for ocular diseases will rely on modulation of aquaporin expression and/or function. This article is part of a Special Issue entitled Aquaporins.     

青稞HvtAGO1基因的克隆及其在条纹病胁迫下的表达

AGO蛋白是RNA诱导沉默复合体的核心分子,在植物的生长、发育及胁迫响应中起重要作用.为探索青稞AGO基因在青稞抗条纹病病原菌过程中的作用机制,该研究以抗条纹病青稞品种‘昆仑14号’和感病品种‘Z1141’为材料,利用条纹病原菌侵染两品种,从感病前后的转录组测序结果中获得一个差异表达基因,克隆验证了该基因为HvtAGO...     

Genome-Wide Characterization of Aquaporins (aqps) in Lateolabrax maculatus: Evolution and Expression Patterns During Freshwater Acclimation

Marine Biotechnology - Aquaporin (aqp) proteins are a group of small integral membrane proteins that play crucial roles as pore channels for the transport of water and other small solutes across...     

The Rice B-Box Zinc Finger Gene Family: Genomic Identification,Characterization, Expression Profiling and Diurnal Analysis

Background

The B-box (BBX) -containing proteins are a class of zinc finger proteins that contain one or two B-box domains and play important roles in plant growth and development. The Arabidopsis BBX gene family has recently been re-identified and renamed. However, there has not been a genome-wide survey of the rice BBX (OsBBX) gene family until now.

Methodology/Principal Findings

In this study, we identified 30 rice BBX genes through a comprehensive bioinformatics analysis. Each gene was assigned a uniform nomenclature. We described the chromosome localizations, gene structures, protein domains, phylogenetic relationship, whole life-cycle expression profile and diurnal expression patterns of the OsBBX family members. Based on the phylogeny and domain constitution, the OsBBX gene family was classified into five subfamilies. The gene duplication analysis revealed that only chromosomal segmental duplication contributed to the expansion of the OsBBX gene family. The expression profile of the OsBBX genes was analyzed by Affymetrix GeneChip microarrays throughout the entire life-cycle of rice cultivar Zhenshan 97 (ZS97). In addition, microarray analysis was performed to obtain the expression patterns of these genes under light/dark conditions and after three phytohormone treatments. This analysis revealed that the expression patterns of the OsBBX genes could be classified into eight groups. Eight genes were regulated under the light/dark treatments, and eleven genes showed differential expression under at least one phytohormone treatment. Moreover, we verified the diurnal expression of the OsBBX genes using the data obtained from the Diurnal Project and qPCR analysis, and the results indicated that many of these genes had a diurnal expression pattern.

Conclusions/Significance

The combination of the genome-wide identification and the expression and diurnal analysis of the OsBBX gene family should facilitate additional functional studies of the OsBBX genes.     

Genome-Wide Identification of the F-box Gene Family and Expression Analysis under Drought and Salt Stress in Barley

The F-box protein-encoding gene family plays an essential role in plant stress resistance. In present study, 126 non-redundant F-box genes were identified in barley (Hordeum vulgare L., Hv). The corresponding proteins contained 165– 887 amino acid residues and all were amphiphilic, except 5 proteins. Phylogenetic analysis of F-box protein sequences in barley and stress-related F-box protein sequences in wheat and Arabidopsis thaliana (At) was used to classify barley F-box genes are divided into 9 subfamilies (A–I). A structure-based sequence alignment demonstrated that F-box proteins were highly conserved with a total of 10 conserved motifs. In total, 124 F-box genes were unevenly distributed on 7 chromosomes; another 2 genes have not been anchored yet. The gene structure analysis revealed high variability in the number of exons and introns in F-box genes. Comprehensive analysis of expression profiles and phylogenetic tree analysis, a total of 12 F-box genes that may be related to stress tolerance in barley were screened. Of the 12 detected F-box genes, 8 and 10 were upregulated after drought and salt stress treatments, respectively, using quantitative real-time polymerase chain reaction (qRT-PCR). This study is the first systematic analysis conducted on the F-box gene family in barley, which is of great importance for clarifying this family’s bioinformatic characteristics and elucidating its function in barley stress resistance. These results will serve as a theoretical reference for subsequent research on molecular regulation mechanisms, genetic breeding, and improvement.     

水通道蛋白AQP1,3,4,5在双峰驼肺中的表达

目的研究水通道蛋白AQPs在双峰驼肺中的表达情况,探讨双峰驼适应极干旱荒漠环境的呼吸生理机制。方法运用常规形态学统计方法和石蜡切片HE染色法对双峰驼肺组织形态结构进行统计与分析,免疫组化方法对双峰驼肺中AQPs的表达进行定位分析。结果双峰驼气管长且弯曲,肺较致密且含水量较黄牛高。免疫组化检测显示,在双峰驼肺中有AQP1、AQP3、AQP4和AQP5四种AQPs表达。其中,AQP1主要表达于肺毛细血管网、淋巴管以及气管上皮细胞顶膜面;AQP3主要表达于气管上皮基底细胞质膜上;AQP4主要分布于整个气管上皮杯状细胞基底侧细胞膜和肺泡Ⅱ型上皮细胞;AQP5表达于气管粘膜下腺腺体细胞管腔面和肺泡Ⅰ型上皮细胞膜上。结论呼吸道和肺组织形态学特征表明双峰驼对干旱沙漠环境具有很好的适应性,AQPs在双峰驼肺中的强烈表达,与气道润化、气道水平衡、气道表面液体层、肺内液体转运和肺内水平衡等生理过程有关,为其适应极干旱荒漠环境提供了分子生物学依据。     

Evaluation of Barley lncRNAs Expression Analysis in Salinity Stress

Long noncoding RNAs (lncRNAs) act important roles in a wide range of biological processes. The regulatory roles of lncRNAs are still poorly understood. One of the major problems of limiting plant productivity is the salinity in the worldwide that barley (Hordeum vulgare L.) seems to be relatively well adapted to salinity environments. The aim of this study is the investigation of lncRNAs’ expression levels on four barley genotypes (Hasat, Beysehir 99, Konevi 98 and Tarm 92) to 150 mM salt stress application during 3 days germination. Grains were placed randomly in petri dishes containing filter paper soaked in (a) only H₂O (control), (b) 150 mM NaCl for 72 h. RNA extraction were carried out using TriPure® reagent from root and shoot samples obtained after 150 mM salt treatment. Expression levels of CNT0018772 and CNT0031477 were determined by qPCR. Expression analysis demonstrated salinity effected expression levels of CNT0018772 and CNT0031477 on roots and shoots during germination. The expression levels of CNT0018772 for 150 mM salt applied groups were down-regulated raged between (log2–0.52 and–35.65) compared controls on roots and shoot. The expression levels of CNT0031477 in 150 mM salt applied groups were also down-regulated ranged between (log₂–10.40 and 33.59) compared controls on roots and shoot except for Tarm 92 variety. On the contrary, expression levels of CNT0031477 were up-regulated on root and shoot of Tarm 92. Comparison of CNT0018772 and CNT0031477 expression levels on roots, there was no significant difference between barley varieties compared to controls (p > 0.05). However, it was found there was statistically significant difference between 150 mM salt treatment and control groups for CNT0031477 expression levels (p < 0.05). It was determined Konevi 98 shoot control expression level was statistically higher than Tarm 92 shoot control. This is the first report about the lncRNAs expression levels of barley under salinity.     

Aquaporins: Structure, Systematics, and Regulatory Features

The review describes current views on the molecular structure, systematics, and functional regulation of aquaporins. These recently discovered channel proteins play a principal role in water transport across cell membranes in the majority of living organisms.     

中药止泻液对乳鼠轮状病毒肠炎水通道蛋白表达的影响

目的:用中药止泻液对轮状病毒肠炎乳鼠进行干预后,检测乳鼠空肠,回肠与近端结肠粘膜水通道蛋白(aquaporin,AQP)1,3,4,8mRNA的表达情况,研究中药止泻液对乳鼠轮状病毒肠炎AQP1,3,4,8mRNA表达的影响.方法:在实验条件下,用恒河猴SAll株轮状病毒感染6日龄乳鼠24h后,予各乳鼠灌注止泻液,每日3次,于接毒后48 h始,每天处死2只乳鼠,连续6天.采用实时荧光定量PCR方法对乳鼠的空肠,回肠与近端结肠黏膜细胞的AQP1,3,4,8 mRNA进行定性和相对定量分析研究,探讨中药止泻液对轮状病毒腹泻模型乳鼠肠道AQP1,3,4,8mRNA表达的影响.结果:结肠AQP1 mRNA在中药干预组乳鼠中表达量显著高于空白组(t=-3.47,P<0.05). AQP3,4,8mRNA表达量无统计学差异.在空肠,回肠中,中药干预组与空白组AQP1,3,4,8 mRNA袁达量均无统计学差异.结论:中药干预组乳鼠结肠AQP1 mRNA表达上升,提示中药止泻液能明显提高乳鼠结肠组织AQP1 mRNA的表达,通过增加结肠对水分的吸收,来达到收敛止泻的作用.在本研究中,中药止泻液对轮状病毒肠炎乳鼠肠道AQP3,4,8 mRNA表达没有明显的影响.     

Heterologous Expression of Tulip Petal Plasma Membrane Aquaporins in Pichia pastoris for Water Channel Analysis

Water channels formed by aquaporins (AQPs) play an important role in the control of water homeostasis in individual cells and in multicellular organisms. Plasma membrane intrinsic proteins (PIPs) constitute a subclass of plant AQPs. TgPIP2;1 and TgPIP2;2 from tulip petals are members of the PIP family. In this study, we overexpressed TgPIP2;1 and TgPIP2;2 in Pichia pastoris and monitored their water channel activity (WCA) either by an in vivo spheroplast-bursting assay performed after hypo-osmotic shock or by growth assay. Osmolarity, pH, and inhibitors of AQPs, protein kinases (PKs), and protein phosphatases (PPs) affect the WCA of heterologous AQPs in this expression system. The WCA of TgPIP2;2-expressing spheroplasts was affected by inhibitors of PKs and PPs, which indicates that the water channel of this homologue is regulated by phosphorylation in P. pastoris. From the results reported herein, we suggest that P. pastoris can be employed as a heterologous expression system to assay the WCA of PIPs and to monitor the AQP-mediated channel gating mechanism, and it can be developed to screen inhibitors/effectors of PIPs.The movement of water across cell membranes has long been thought to occur by free diffusion through the lipid bilayer. However, the discovery of the membrane protein CHIP28 in red blood cells has suggested the involvement of protein channels (29), and it is now well established that transmembrane water permeability is facilitated by aquaporins (AQPs), water channel proteins that are found in bacteria, fungi, plants, and animals (1, 7, 13, 24). AQPs contain six transmembrane α-helices and five connecting loops, and both the N and C termini are located in the cytosol. The monomers assemble into tetrameric complexes, with each monomer forming an individual water channel (11, 14, 24, 33). Apart from the exceptions of AQP11 and AQP12 from mice, as described by K. Ishibashi (15), AQPs have two signature Asn-Pro-Ala motifs, which are located in the second intracellular and the fifth extracellular loops, B and E.While 13 different AQPs have been identified in mammals (16), more than 33 AQP homologues have been discovered in plants (6, 17, 30). Plant AQPs fall into four subclasses: (i) the plasma membrane (PM) intrinsic proteins (PIPs), which are localized in the PM; (ii) the tonoplast intrinsic proteins (TIPs), which are localized in the vacuolar membranes; (iii) the nodulin-26-like intrinsic proteins; and (iv) the small basic intrinsic proteins (24). In Arabidopsis and maize, there are 13 PIPs, which can be divided further into two subfamilies, PIP1 and PIP2 (6, 17).The functions and mechanisms of regulation of plant AQPs have been extensively investigated (7, 13, 18, 24). There have been several reports on the water channel activity (WCA) of specific AQPs and their regulation by protein phosphorylation (3, 4, 8, 12, 18, 25, 32, 33). It has been shown that the WCA of the PIP2 member SoPIP2;1 from spinach is regulated by phosphorylation at two Ser residues (19, 33).The physiologically interesting temperature-dependent opening and closing of tulip (Tulipa gesneriana) petals occur concomitantly with water transport and are regulated by reversible phosphorylation of an undefined PIP (4, 5). Recently, four PIP homologues were isolated from tulip petals, and their WCAs have been analyzed by heterologous expression in Xenopus laevis oocytes (3). It has been shown that the tulip PIP TgPIP2;2 (DDBJ/EMBL/GenBank accession no. {"type":"entrez-nucleotide","attrs":{"text":"AB305617","term_id":"196259707","term_text":"AB305617"}}AB305617) is ubiquitously expressed in all organs of the tulip and that TgPIP2;2 is the most likely of the TgPIP homologues to be modulated by the reversible phosphorylation that regulates transcellular water transport and mediates petal opening and closing (3, 4). However, while the members of the PIP2 subfamily are characterized as water channels (6), TgPIP2;1 (DDBJ/EMBL/GenBank accession no. {"type":"entrez-nucleotide","attrs":{"text":"AB305616","term_id":"196259705","term_text":"AB305616"}}AB305616) shows no significant WCA in the oocyte expression system (3). There is growing interest in research on AQPs due to their crucial roles in the physiology of plants and animals (1, 16, 21-24, 26-28, 36). The assay of AQP channel activity is usually performed using either a X. laevis oocyte expression system (29) or a stopped-flow light-scattering spectrophotometer (35), both of which are not widely available. Furthermore, the complexity of these methods and requirement of expertise limit their high-throughput applications. In contrast, a Pichia pastoris expression system is simple to use, inexpensive, and feasible and can be used in high-throughput applications. Although a P. pastoris expression system has been shown to assay the WCA of a TIP (9), extensive research is necessary with other AQPs such as PIPs or AQPs present in intragranular membranes to establish whether this assay system can be used to characterize a water channel and study its regulation mechanisms. With this in view, in the study reported herein, TgPIP2;1 and TgPIP2;2 have been heterologously expressed in P. pastoris, and their WCAs have been assayed. The effects of several factors, such as osmolarity, pH, and inhibitors of protein kinases (PKs) and protein phosphatases (PPs), on the WCA of the recombinant P. pastoris have been investigated. Based on the results, we demonstrate that the P. pastoris heterologous expression system can be used to rapidly characterize PIP channels, to monitor the effects of mutations, and to score the effects of inhibitors and abiotic factors.     

不同来源大麦对条纹病抗性鉴定及遗传多样性分析

为了解不同来源大麦对条纹病的抗性及遗传多样性,本研究采用"三明治法"通过人工接种大麦条纹病菌对91份大麦材料进行抗性评价,并通过31对SSR标记对91份大麦材料进行遗传多样性和群体结构分析。结果表明,人工接种大麦条纹病菌后共鉴定出4份免疫、6份高抗、33份抗病、43份感病和5份高感大麦材料;31对SSR标记共检测出等位基因238个,平均每对标记可检测到7.677个等位基因,等位基因数的变幅为2～19;主基因频率变化范围为0.236～0.951,平均值为0.394;基因多样性指数的变幅为0.094～0.871,平均值为0.667;多态性信息含量变幅为0.091～0.860,平均值为0.613;遗传相似系数变异范围为0.103～1.000,平均值为0.522;在遗传相似系数为0.783水平上可将参试材料聚为3个大类群,各大类分别包含86份、2份和3份材料;群体遗传结构分析表明,供试大麦材料分为3个亚群,每个亚群分别包含47份、33份和11份材料,且在91份材料中,Q>0.6的材料占总数的97.80%。本研究经抗病鉴定及分子标记结果综合分析,可为挑选抗病亲本辅助抗大麦条纹病优良品种的选...     

Identification, Phylogeny, and Expression Analysis of Pto-like Genes in Pepper

The Pto gene from the wild tomato (Solanum pimpinellifolium Mill.) encodes a serine/threonine kinase that plays an important role in bacterial speck resistance in the cultivated tomato (Solanum lycopersicum Mill.). In this paper, 10 classes of Pto-like genes are identified using degenerate polymerase chain reaction (PCR) primers and database mining in pepper. Sequences alignment reveals that many features of the gene family, such as subdomains, autophosphorylation sites, and important amino acid residues for tomato Pto, are well conserved in pepper. A phylogenetic tree of pepper Pto-like genes along with those of other plant species, including tomato Pto genes, suggests that these genes share a common evolutionary origin, and they may have evolved prior to the divergence of monocotyledonous and dicotyledonous plants. Expression analysis has revealed that nine selected Pto-like genes can be detected in at least one of the tissues grown under normal growth conditions; however, these genes are differentially expressed. In addition, some of these genes are regulated by at least one of the subjected treatments, including hormones, abiotic stress, and pathogen infection. These findings will contribute to expanding our knowledge of the roles of Pto-like genes in growth, development, and stress tolerance in pepper.