Molecular Evolution of the <Emphasis Type="Italic">CPP-like</Emphasis> Gene Family in Plants: Insights from Comparative Genomics of <Emphasis Type="Italic">Arabidopsis</Emphasis> and Rice

CPP-like genes are members of a small family which features the existence of two similar Cys-rich domains termed CXC domains in their protein products and are distributed widely in plants and animals but do not exist in yeast. The members of this family in plants play an important role in development of reproductive tissue and control of cell division. To gain insights into how CPP-like genes evolved in plants, we conducted a comparative phylogenetic and molecular evolutionary analysis of the CPP-like gene family in Arabidopsis and rice. The results of phylogeny revealed that both gene loss and species-specific expansion contributed to the evolution of this family in Arabidopsis and rice. Both intron gain and intron loss were observed through intron/exon structure analysis for duplicated genes. Our results also suggested that positive selection was a major force during the evolution of CPP-like genes in plants, and most amino acid residues under positive selection were disproportionately located in the region outside the CXC domains. Further analysis revealed that two CXC domains and sequences connecting them might have coevolved during the long evolutionary period.     

Genomewide Structural Annotation and Evolutionary Analysis of the Type I MADS-Box Genes in Plants

Abstract The type I MADS-box genes constitute a largely unexplored subfamily of the extensively studied MADS-box gene family, well known for its role in flower development. Genes of the type I MADS-box subfamily possess the characteristic MADS box but are distinguished from type II MADS-box genes by the absence of the keratin-like box. In this in silico study, we have structurally annotated all 47 members of the type I MADS-box gene family in Arabidopsis thaliana and exerted a thorough analysis of the C-terminal regions of the translated proteins. On the basis of conserved motifs in the C-terminal region, we could classify the gene family into three main groups, two of which could be further subdivided. Phylogenetic trees were inferred to study the evolutionary relationships within this large MADS-box gene subfamily. These suggest for plant type I genes a dynamic of evolution that is significantly different from the mode of both animal type I (SRF) and plant type II (MIKC-type) gene phylogeny. The presence of conserved motifs in the majority of these genes, the identification of Oryza sativa MADS-box type I homologues, and the detection of expressed sequence tags for Arabidopsis thaliana and other plant type I genes suggest that these genes are indeed of functional importance to plants. It is therefore even more intriguing that, from an experimental point of view, almost nothing is known about the function of these MADS-box type I genes.     

Genomewide comparative phylogenetic and molecular evolutionary analysis of tubby-like protein family in Arabidopsis, rice, and poplar

Tubby-like proteins, which are characterized by a highly conserved tubby domain, play an important role in the maintenance and function of neuronal cells during postdifferentiation and development in mammals. In additional to the tubby domain, most tubby-like proteins in plants also possess an F-box domain. Plants also appear to harbor a large number of TLP genes. To gain insight into how TLP genes evolved in plants, we conducted a comparative phylogenetic and molecular evolutionary analysis of the tubby-like protein gene family in Arabidopsis, rice, and poplar. Genomewide screening identified 11 TLP genes in Arabidopsis, 14 in rice, and 11 in poplar. Phylogenetic trees, domain organizations, and intron/exon structures classified this family into three subfamilies and indicated that species-specific expansion contributed to the evolution of this family in plants. We determined that in rice and poplar, the tubby-like protein family had expanded mainly through segmental duplication events. Tissue-specific expression analysis indicated that functional diversification of the duplicated TLP genes was a major feature of long-term evolution. Our results also demonstrated that the tubby and F-box domains had co-evolved during the evolution of proteins containing both domains.     

Genome-wide analysis of SINA family in plants and their phylogenetic relationships(dagger).

SINA genes in plants are part of a multigene family with 5 members in Arabidopsis thaliana, 10 members in Populus trichocarpa, 6 members in Oryza sativa, at least 6 members in Zea mays and at least 1 member in Physcomitrella patens. Six members in maize were confirmed by RT-PCR. All SINAs have one RING domain and one SINA domain. These two domains are highly conserved in plants. According to the motif organization and phylogenetic tree, SINA family members were divided into 2 groups. In addition, through semi-quantitative RT-PCR analysis of maize members and Digital Northern analysis of Arabidopsis and rice members, we found that the tissue expression patterns are more diverse in monocot than in Arabidopsis.     

Auxin response factor family in rice

We isolated 11 rice genes homologous to the genes encoding auxin response factors (ARFs) in Arabidopsis. All of the genes encoded a well-conserved amino acid sequence in the N-terminal region, which is considered to be a DNA-binding domain (DBD). Phylogenetic analysis based on comparison of the DBDs indicated that rice has one or two closely related orthologs corresponding to a given respective ARF gene in Arabidopsis. We also analyzed the amino acid sequences of another conserved domain in the C-terminal conserved domain (CTD), which was shared by almost all the rice ARFs, with the exception of OsETTIN1 and OsETTIN2. These results agreed well with the evolutionary relationship deduced from the DBD comparison. In contrast to many ARFs, OsETTIN1 and OsETTIN2 do not contain the conserved C-terminal domain, but do share another consensus motif that is also found in Arabidopsis ETTIN. All of the above observations indicate that rice has functionally diversified ARF genes whose structures and functions correspond to those of various Arabidopsis ARFs, with one or two rice ARFs corresponding to a given Arabidopsis ARF. Thus, auxin signal transduction mechanisms may be well conserved between monocot and dicot plants.     

Molecular analyses of the rice <Emphasis Type="Italic">glutamate dehydrogenase</Emphasis> gene family and their response to nitrogen and phosphorous deprivation

Glutamate dehydrogenases (GDH, EC 1.4.1.2~4) are ubiquitous enzymes encoded by GDH genes. So far, at least two GDH members have been characterized in plants, but most members of this family in rice remains to be characterized. Here, we show that four putative GDH genes (OsGDH1-4) are present in the rice genome. The GDH sequences from rice and other species can be classified into two types (I and II). OsGDH1-3 belonged to type II genes, whereas OsGDH4 belonged to type I like gene. Our data implied that the expansion rate of type I genes was much slower than that of type II genes and species-specific expansion contributed to the evolution of type II genes in plants. The expression levels of the different members of GDH family in rice were evaluated using quantitative real-time PCR and microarray analysis. Gene expression patterns revealed that OsGDH1, OsGDH2, and OsGDH4 are expressed ubiquitously in various tissues, whereas OsGDH3 expression is glumes and stamens specific. The expression of the OsGDH family members responded differentially to nitrogen and phosphorus-deprivation, indicating their roles under such stress conditions. Implications of the expression patterns with respect to the functions of these genes were discussed. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Analysis of castor bean ribosome-inactivating proteins and their gene expression during seed development

Ribosome-inactivating proteins (RIPs) are enzymes that inhibit protein synthesis after depurination of a specific adenine in rRNA. The RIP family members are classified as type I RIPs that contain an RNA-N-glycosidase domain and type II RIPs that contain a lectin domain (B chain) in addition to the glycosidase domain (A chain). In this work, we identified 30 new plant RIPs and characterized 18 Ricinus communis RIPs. Phylogenetic and functional divergence analyses indicated that the emergence of type I and II RIPs probably occurred before the monocot/eudicot split. We also report the expression profiles of 18 castor bean genes, including those for ricin and agglutinin, in five seed stages as assessed by quantitative PCR. Ricin and agglutinin were the most expressed RIPs in developing seeds although eight other RIPs were also expressed. All of the RIP genes were most highly expressed in the stages in which the endosperm was fully expanded. Although the reason for the large expansion of RIP genes in castor beans remains to be established, the differential expression patterns of the type I and type II members reinforce the existence of biological functions other than defense against predators and herbivory.     

Versatile casein kinase 1: Multiple locations and functions

Members of casein kinase 1 (CK1) are evolutionarily conserved eukaryotic protein kinases, which play fundamental roles in various cellular, physiological and developmental processes. One of the key mechanisms by which the activity of these multifunctional CK1 members is controlled appears to be their specific spatiotemporal compartmentalization within the cell. Plant genomes encode dozens of CK1 homologs, the function of which are not yet well characterized, however, evolutionary conservation of these genes predicts their fundamental roles in plants. Characterization of Arabidopsis CK1-like 6 (CKL6) that we have recently reported sheds new light on the existence of parallel and unique aspects of the mechanism involved in specific subcellular targeting as well as cellular function of CK1 in plants. In this addendum, I will focus my discussion on the versatility of CKL6 partitioning at different subcellular compartments and propose that this capability likely reflects its multiple functions in modulating an array of cellular targets.Key words: protein phosphorylation, microtubule dynamics/organization, casein kinase 1, microtubule-binding domain, cell expansion, Arabidopsis     

Type II Opsins: Evolutionary Origin by Internal Domain Duplication?

Opsins are a large group of proteins with seven transmembrane segments (TMSs) that are found in all domains of life. There are two types of opsins that are sometimes considered nonhomologous: type I is known from prokaryotes and some eukaryotes, while type II is known only from Eumetazoan animals. Type II opsins are members of the family of G-protein coupled receptors (GPCRs), which facilitate signal transduction across cell membranes. While previous studies have concluded that multiple transmembrane-containing protein families-including type I opsins-originated by internal domain duplication, the origin of type II opsins has been speculated on but never tested. Here we show that type II opsins do not appear to have originated through a similar internal domain duplication event. This provides further evidence that the two types of opsins are nonhomologous, indicating a convergent evolutionary origin, in which both groups of opsins evolved a seven-TM structure and light sensitivity independently. This convergence may indicate an important role for seven-TM protein structure for retinal-based light sensitivity.     

普通烟草LBD基因家族的全基因组序列鉴定与表达分析

LBD是一类具有LOB(lateral organ boundaries)结构域的基因家族,在植物发育过程中起到非常重要的作用。采用生物信息学方法,根据拟南芥LBD基因序列鉴定了普通烟草基因组中的LBD基因,并对家族成员进行了序列特征、系统发育和表达谱分析。结果表明:普通烟草基因组中共有98个LBD基因成员,其基因结构相对简单,一般含有1~3个外显子。LBD基因家族可分成I和II两大类,两类均含有CX_2CX_6CX_3C保守结构域,但II类不含有LX_6LX_3LX_6L形成的"卷曲螺旋"二级结构,根据与拟南芥LBD蛋白构建的系统发育树则可细分成5个亚家族(Ia、Ib、Ic、Id和II)。将LBD基因与表达序列标签(EST)比对,发现36个基因有EST证据;EST、芯片数据和转录组数据分析表明:LBD基因具有不同的组织表达模式,部分基因表现出组织特异性。这些研究结果为普通烟草LBD基因家族功能的深入研究奠定了基础。     

黄瓜全基因组热激转录因子(HSFs)的鉴定与表达分析

热激转录因子 (Heat shock factors, HSFs) 普遍存在于整个生物界。尽管植物HSFs的DNA 结合域具有较高的保守性, 但其结构特征、生物功能具有多样化的特点。本文利用黄瓜(Cucumis sativus L.)全基因组测序结果, 运用生物信息学方法鉴定了黄瓜HSFs, 并对其数量、序列特征、染色体定位以及系统发育关系等进行分析。结果表明, 黄瓜至少含有21个HSFs基因家族成员, 编码184～560个氨基酸, 分子量21.2~62.3 kDa, 等电点(PI)4.70~9.10; 序列比对发现这些成员都具有转录因子特有的DNA结合域(DNA binding domain, DBD); 染色体定位分析表明, 除Csa026480之外, 其余HSFs不均匀分布在黄瓜7条染色体上。从拟南芥(Arabidopsis thaliana)和黄瓜HSFs系统发育树可以看出, 这些转录因子分为3个分支, 其中Ⅰ分支进一步可分为3类(A、B、C类), 系统发育分析揭示黄瓜HSFs蛋白存在9对直系同源蛋白, 3对旁系同源蛋白, 表明HSF转录因子基因家族的多样化发生在黄瓜和拟南芥分化之前。EST表达分析发现这些热激转录因子参与黄瓜的果实、雌花和两性花的发育与形成; 通过qRT-PCR分析, 发现这些基因在黄瓜苗期应对高温热激响应中表达水平存在显著的差异。研究结果为进一步分析黄瓜热激转录因子奠定了基础。     

Comparative analysis of cation/proton antiporter superfamily in plants

The cation/proton antiporter superfamily is associated with the transport of monovalent cations across membranes. This superfamily was annotated in the Arabidopsis genome and some members were functionally characterized. In the present study, a systematic analysis of the cation/proton antiporter genes in diverse plant species was reported. We identified 240 cation/proton antiporters in alga, moss, and angiosperm. A phylogenetic tree was constructed showing these 240 members are separated into three families, i.e., Na⁺/H⁺ exchangers, K⁺ efflux antiporters, and cation/H⁺ exchangers. Our analysis revealed that tandem and/or segmental duplications contribute to the expansion of cation/H⁺ exchangers in the examined angiosperm species. Sliding window analysis of the nonsynonymous/synonymous substitution ratios showed some differences in the evolutionary fate of cation/proton antiporter paralogs. Furthermore, we identified over-represented motifs among these 240 proteins and found most motifs are family specific, demonstrating diverse evolution of the cation/proton antiporters among three families. In addition, we investigated the co-expressed genes of the cation/proton antiporters in Arabidopsis thaliana. The results showed some biological processes are enriched in the co-expressed genes, suggesting the cation/proton antiporters may be involved in these biological processes. Taken together, this study furthers our knowledge on cation/proton antiporters in plants.     

Unraveling the Distribution and Evolution of miR156 targeted SPLs in Plants by Phylogenetic Analysis

Squamosa promoter binding protein like genes (SPLs) are critical during plant development and mostly regulated by miR156. However, little is known about phylogenetic distribution and evolutionary patterns of miR156 targeted SPLs. In this study, 183 SPLs from nine genome sequenced species representing algae, bryophytes, lycophyte, monocots, and eudicots were computationally analyzed. Our results showed that miR156 responsive elements (MREs) on SPLs were present in land plants but absent from unicellular green algae. Phylogenetic analysis revealed that miR156 targeted SPLs only distributed in group II not group I of land plants, suggesting they originated from a common ancestor. In addition, group II were further divided into seven subgroups (IIa IIg) and miR156 targeted SPLs distributed in some specific members of SPLs from six subgroups except subgroup IId. Such distribution pattern was well elucidated by gene structure evolution of miR156 targeted SPLs based on the correlation of phylogenetic classification and gene structure. They could suffer from the exon loss events combined with MREs loss during evolution. Moreover, gene duplication contributed to the abundance of miR156 targeted SPLs, which had significantly increased after angiosperms and lower plants split. With Arabidopsis as the model species, we found segmental and tandem gene duplications predominated during miR156 targeted SPLs expansion. Taken together, these results provide better insights in understanding the function diversity and evolution of miR156 targeted SPLs in plants.