Five-group distribution of the Shaker-like K+ channel family in higher plants

Abstract In higher plants, potassium channels of the Shaker family have been shown to play crucial roles in the uptake of K⁺ from the soil solution and subsequent transport of this ion at the cell, tissue, and organ levels. In the model plant Arabidopsis thaliana, this family is composed of nine members, which are the best characterized among plant channels at the protein, gene, and functional property levels. Plant Shaker channels share a common structure: a hydrophobic core composed of six transmembrane segments, a long cytoplasmic C-terminal region harboring a putative cyclic nucleotide binding domain, and a K_HA domain. Many channels also contain an ankyrin domain between the putative cyclic nucleotide binding domain and the K_HA domain. The analysis of 44 Shaker channels from plants revealed a five-group classification. The members of each group share high sequence and structure similarities. This grouping also correlates with the diversification of the functional properties of the proteins, as members of an individual group have roughly the same electrophysiological characteristics. Analysis of the intron positions showed that the gene structures are also quite well conserved within the five groups. A correlation linking the evolution of the sequences and the positioning of the introns was established. Finally, a moss sequence provided additional clues about the hypothetical structure of an ancestor of the present channels and suggested that the diversification of plant Shaker channels happened before the separation of monocots and dicots and after the separation of bryophytes and tracheophytes.     

Molecular studies of collagen genes

In this paper, information about the structure and function of collagen genes family coding the main proteins of connective tissue of higher organisms is summarized. The structure of collagen proteins, their precursors and the main properties of corresponding mRNA and cDNA are discussed. The data are presented on evolution of collagen genes and their association with the human hereditary diseases of connective tissue.     

A dynamic history of gene duplications and losses characterizes the evolution of the SPARC family in eumetazoans

The vertebrates share the ability to produce a skeleton made of mineralized extracellular matrix. However, our understanding of the molecular changes that accompanied their emergence remains scarce. Here, we describe the evolutionary history of the SPARC (secreted protein acidic and rich in cysteine) family, because its vertebrate orthologues are expressed in cartilage, bones and teeth where they have been proposed to bind calcium and act as extracellular collagen chaperones, and because further duplications of specific SPARC members produced the small calcium-binding phosphoproteins (SCPP) family that is crucial for skeletal mineralization to occur. Both phylogeny and synteny conservation analyses reveal that, in the eumetazoan ancestor, a unique ancestral gene duplicated to give rise to SPARC and SPARCB described here for the first time. Independent losses have eliminated one of the two paralogues in cnidarians, protostomes and tetrapods. Hence, only non-tetrapod deuterostomes have conserved both genes. Remarkably, SPARC and SPARCB paralogues are still linked in the amphioxus genome. To shed light on the evolution of the SPARC family members in chordates, we performed a comprehensive analysis of their embryonic expression patterns in amphioxus, tunicates, teleosts, amphibians and mammals. Our results show that in the chordate lineage SPARC and SPARCB family members were recurrently recruited in a variety of unrelated tissues expressing collagen genes. We propose that one of the earliest steps of skeletal evolution involved the co-expression of SPARC paralogues with collagenous proteins.     

大白菜NHX基因家族的鉴定与表达分析

Na+/H+逆向转运蛋白(Na+/H+antiporter,NHX)基因家族在植物响应盐胁迫中发挥重要作用。本研究鉴定了大白菜NHX基因家族成员,并分析了大白菜NHX基因(Brassica rapa ssp.Pekinensis NHX,BrNHXs)响应高温、低温、干旱和盐胁迫等非生物逆境的表达模式。结果表明,在大白菜中共鉴定到9个NHX基因家族成员,分布在大白菜的6条染色体上,其氨基酸数目在513–1154 aa之间,相对分子量集中在56804.22–127856.66 kDa,等电点位于5.35–7.68之间。该基因家族成员主要存在于液泡中,基因结构完整,外显子的数目介于11–22之间。大白菜NHX基因家族编码的蛋白质二级结构都具有α-螺旋、β-转角和不规则卷曲结构,其中α-螺旋发生频率较高。实时荧光定量PCR(quantitative real-time PCR,qRT-PCR)分析显示,该基因家族成员在高温、低温、干旱和盐胁迫下均有不同程度地响应,且在不同时间表达差异显著。以BrNHX02和BrNHX09对这4种胁迫的响应最为显著,表达量在处理72 h时均显著上调,可作为候选基因进一步验证其功能。     

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.     

S100 and S100 fused-type protein families in epidermal maturation with special focus on S100A3 in mammalian hair cuticles

Epithelial Ca²⁺-regulation, which governs cornified envelope formation in the skin epidermis and hair follicles, closely coincides with the expression of S100A3, filaggrin and trichohyalin, and the post-translational modification of these proteins by Ca²⁺-dependent peptidylarginine deiminases. This review summarizes the current nomenclature and evolutional aspects of S100 Ca²⁺-binding proteins and S100 fused-type proteins (SFTPs) classified as a separate protein family with special reference to the molecular structure and function of S100A3 dominantly expressed in hair cuticular cells. Both S100 and SFTP family members are identified by two distinct types of Ca²⁺-binding loops in an N-terminal pseudo EF-hand motif followed by a canonical EF-hand motif. Seventeen members of the S100 protein family including S100A3 are clustered with seven related genes encoding SFTPs on human chromosome 1q21, implicating their association with epidermal maturation and diseases. Human S100A3 is characterized by two disulphide bridges and a preformed Zn²⁺-pocket, and may transfer Ca²⁺ ions to peptidylarginine deiminases after its citrullination-mediated tetramerization. Phylogenetic analysis utilizing current genome databases suggests that divergence of the S100A3 gene coincided with the emergence of hair, a defining feature of mammals, and that the involvement of S100A3 in epithelial Ca²⁺-cycling occurred as a result of a skin adaptation in terrestrial mammals.     

Insights into early extracellular matrix evolution: spongin short chain collagen-related proteins are homologous to basement membrane type IV collagens and form a novel family widely distributed in invertebrates

Collagens are thought to represent one of the most important molecular innovations in the metazoan line. Basement membrane type IV collagen is present in all Eumetazoa and was found in Homoscleromorpha, a sponge group with a well-organized epithelium, which may represent the first stage of tissue differentiation during animal evolution. In contrast, spongin seems to be a demosponge-specific collagenous protein, which can totally substitute an inorganic skeleton, such as in the well-known bath sponge. In the freshwater sponge Ephydatia mülleri, we previously characterized a family of short-chain collagens that are likely to be main components of spongins. Using a combination of sequence- and structure-based methods, we present evidence of remote homology between the carboxyl-terminal noncollagenous NC1 domain of spongin short-chain collagens and type IV collagen. Unexpectedly, spongin short-chain collagen-related proteins were retrieved in nonsponge animals, suggesting that a family related to spongin constitutes an evolutionary sister to the type IV collagen family. Formation of the ancestral NC1 domain and divergence of the spongin short-chain collagen-related and type IV collagen families may have occurred before the parazoan-eumetazoan split, the earliest divergence among extant animal phyla. Molecular phylogenetics based on NC1 domain sequences suggest distinct evolutionary histories for spongin short-chain collagen-related and type IV collagen families that include spongin short-chain collagen-related gene loss in the ancestors of Ecdyzosoa and of vertebrates. The fact that a majority of invertebrates encodes spongin short-chain collagen-related proteins raises the important question to the possible function of its members. Considering the importance of collagens for animal structure and substratum attachment, both families may have played crucial roles in animal diversification.     

Genome-Wide Characterization,Evolution, and Expression Analysis of the Ascorbate Peroxidase and Glutathione Peroxidase Gene Families in Response to Cold and Osmotic Stress in Ammopiptanthus nanus

Ascorbate peroxidase (APX) and glutathione peroxidase (GPX) are two families of essential peroxidases that maintain redox balance in cells by catalyzing the reduction of hydrogen peroxide. Ammopiptanthus nanus is a rare broad-leaved evergreen shrub that lives in the temperate desert areas of Central Asia and exhibits strong resistance to low temperature and water stress. GPX and APX family members might contribute to the stress response of A. nanus by participating in reactive oxygen species scavenging. In the present study, APX and GPX family members in A. nanus were identified and their structure, evolution, and expression patterns under stress conditions were investigated. A total of 8 GPX genes, 6 APX genes, and 1 APX-like gene were identified in A. nanus, and these genes were unevenly distributed on 7 chromosomes. These APXs and GPXs showed conservation in amino acid sequence, three-dimensional structure, and intron–exon structure. The GPX gene family in A. nanus expanded in gene number, and the expansions were mainly driven by segmental duplication caused by large-scale duplication events in the evolution of Tribe Sophoreae and might play important roles in the freezing and drought tolerance in A. nanus. Expression profiling based on RNA-seq datasets and qRT-PCR analysis showed that most of the APX and GPX members were differentially expressed under osmotic and cold stress, which is in line with the high copies of stress and hormone response-related cis-acting elements predicted from the promoters of the APX and GPX family genes. The study provided new insight into the evolution of APX and GPX family and promoted the understanding of the molecular mechanism underlying the stress tolerance of A. nanus.

     

Sterol 14α-demethylase cytochrome P450 (CYP51), a P450 in all biological kingdoms

The CYP51 family is an intriguing subject for fundamental P450 structure/function studies and is also an important clinical drug target. This review updates information on the variety of the CYP51 family members, including their physiological roles, natural substrates and substrate preferences, and catalytic properties in vitro. We present experimental support for the notion that specific conserved regions in the P450 sequences represent a CYP51 signature. Two possible roles of CYP51 in P450 evolution are discussed and the major approaches for CYP51 inhibition are summarized.     

Molecular evolution and expression of the CRAL_TRIO protein family in insects

CRAL_TRIO domain proteins are known to bind small lipophilic molecules such as retinal, inositol and Vitamin E and include such gene family members as PINTA, α-tocopherol transfer (ATT) proteins, retinoid binding proteins, and clavesins. In insects, very little is known about either the molecular evolution of this family of proteins or their ligand specificity. Here we characterize insect CRAL_TRIO domain proteins and present the first insect CRAL_TRIO protein phylogeny constructed by performing reciprocal BLAST searches of the reference genomes of Drosophila melanogaster, Anopheles gambiae, Apis mellifera, Tribolium castaneum, Bombyx mori, Manduca sexta and Danaus plexippus. We find several highly conserved amino acid residues in the CRAL_TRIO domain-containing genes across insects and a gene expansion resulting in more than twice as many gene family members in lepidopterans than in other surveyed insect species, but no lepidopteran homolog of the PINTA gene in Drosophila. In addition, we examined the expression pattern of CRAL_TRIO domain genes in Manduca sexta heads using RNA-Seq data. Of the 42 gene family members found in the M. sexta reference genome, we found 30 expressed in the head tissue with similar expression profiles between males and females. Our results suggest this gene family underwent a large expansion in Lepidoptera, making the lepidopteran CRAL_TRIO domain family distinct from other holometabolous insect lineages.     

RHR转录因子家族起源、功能以及进化机制的研究进展

转录因子是一类能够通过与基因特异性序列进行结合,从而调控基因转录与表达的蛋白质,对细胞的生物学活性具有重要的调节作用。RHR (Rel-homology region,RHR)转录因子家族属于IF (immunoglobulin fold)转录因子超家族最主要的成员,其成员含有保守的Rel结构域和IPT (immunoglobulin-like fold)结构域。作为古老的转录因子家族,RHR家族成员随着物种演化,通过基因的复制、突变和沉默,不断分化出新型同源基因的同时也伴随着基因的丢失。自然选择导致了各家族成员不同的进化速率,并且在一些功能结构域上展现出了特殊的进化机制。然而,目前有关RHR家族起源和分化的综述比较少见。本文综述了RHR家族各成员的分布、分类、功能及家族进化等方面的研究成果,以期为研究整个转录因子家族的演化机制和物种之间的进化关系提供参考和新的思路。     

GABARAPL1 (GEC1): Original or copycat?

The GABARAPL1 (GABARAP-LIKE 1) gene was first described as an early estrogen-regulated gene that shares a high sequence homology with GABARAP and is thus a part of the GABARAP family. GABARAPL1, like GABARAP, interacts with the GABA_A receptor and tubulin and promotes tubulin polymerization. The GABARAP family members (GABARAP, GABARAPL1 and GABARAPL2) and their close homologs (LC3 and Atg8) are not only involved in the transport of proteins or vesicles but are also implicated in various mechanisms such as autophagy, cell death, cell proliferation and tumor progression. However, despite these similarities, GABARAPL1 displays a complex regulation that is different from that of other GABARAP family members. Moreover, it presents a regulated tissue expression and is the most highly expressed gene among the family in the central nervous system. In this review article, we will outline the specific functions of this protein and also hypothesize about the roles that GABARAPL1 might have in several important biological processes such as cancer or neurodegenerative diseases.     

The role of decorin in collagen fibrillogenesis and skin homeostasis

Decorin, a prototype member of the growing family of the small leucine-rich proteoglycans (SLRP's), plays significant roles in tissue development and assembly, as well as playing both direct and indirect signaling roles. This review will concentrate on decorin's function in collagen fibrillogenesis as determined through the study of mice with a disrupted decorin gene. The fragile skin and abnormal tendon phenotypes initially observed were found to be due to fundamental alterations in collagen fibers, highlighting the crucial role of proteoglycans in general and SLRP's in particular in collagen fibrillogenesis. The altered fibril formation within tissues in turn leads to observable and quantifiable changes at the organismal level. Research into certain fibrotic processes with concomitant upregulation or reduction of decorin makes interesting comparisons with the collagen malformations seen in Dcn ^–/– mice. Overall, decorin is shown to be a vital player in maintaining skin and tendon integrity at the molecular level, among other functions. Published in 2003.     

Lessons from Yeast on Emerging Roles of the ATAD2 Protein Family in Gene Regulation and Genome Organization

ATAD2, a remarkably conserved, yet poorly characterized factor is found upregulated and associated with poor prognosis in a variety of independent cancers in human. Studies conducted on the yeast Saccharomyces cerevisiae ATAD2 homologue, Yta7, are now indicating that the members of this family may primarily be regulators of chromatin dynamics and that their action on gene expression could only be one facet of their general activity. In this review, we present an overview of the literature on Yta7 and discuss the possibility of translating these findings into other organisms to further define the involvement of ATAD2 and other members of its family in regulating chromatin structure and function both in normal and pathological situations.     

Structure and Evolution of the Actin Gene Family in Arabidopsis Thaliana

Higher plants contain families of actin-encoding genes that are divergent and differentially expressed. Progress in understanding the functions and evolution of plant actins has been hindered by the large size of the actin gene families. In this study, we characterized the structure and evolution of the actin gene family in Arabidopsis thaliana. DNA blot analyses with gene-specific probes suggested that all 10 of the Arabidopsis actin gene family members have been isolated and established that Arabidopsis has a much simpler actin gene family than other plants that have been examined. Phylogenetic analyses suggested that the Arabidopsis gene family contains at least two ancient classes of genes that diverged early in land plant evolution and may have separated vegetative from reproductive actins. Subsequent divergence produced a total of six distinct subclasses of actin, and five showed a distinct pattern of tissue specific expression. The concordance of expression patterns with the phylogenetic structure is discussed. These subclasses appear to be evolving independently, as no evidence of gene conversion was found. The Arabidopsis actin proteins have an unusually large number of nonconservative amino acid substitutions, which mapped to the surface of the actin molecule, and should effect protein-protein interactions.     

植物FLOWERING LOCUS T/TERMINAL FLOWER1基因家族的研究进展

植物FLOWERING LOCUS T/TERMINAL FLOWER1(FT/TFL1)基因家族是一个进化上高度保守的基因家族,它在植物的花发育过程中具有重要作用:其成员FT基因编码的蛋白产物是可以长距离转运的成花激素,在花形成过程中起关键作用;另一成员TFL1基因则在花序的形成和维持过程中起重要作用.本文就近年来国内外对植物FT/TFL1基因家族的结构、成员,以及各个成员在花发育转换过程中的功能等研究现状进行综述,并对该基因家族的研究前景提出展望.     

Diversification of ftsZ During Early Land Plant Evolution

The plastid division proteins FtsZ are encoded by a small nuclear gene family in land plants. Although it has been shown for some of the gene products that they are imported into plastids and function in plastid division, the evolution and function of this gene family and their products remain to be unraveled. Here we present two new ftsZ genes from the moss Physcomitrella patens and compare the genomic structure of members of the two plant ftsZ gene families. Comparison of sequence features and phylogenetic analyses confirm the presence of two clusters of paralogues in land plants and demonstrate that these genes were duplicated before the divergence of mosses, ferns and seed plants.