Genome-wide characterization of phenylalanine ammonia-lyase gene family in watermelon (Citrullus lanatus)

Phenylalanine ammonia-lyase (PAL), the first enzyme in the phenylpropanoid pathway, plays a critical role in plant growth, development, and adaptation. PAL enzymes are encoded by a gene family in plants. Here, we report a genome-wide search for PAL genes in watermelon. A total of 12 PAL genes, designated ClPAL1-12, are identified . Nine are arranged in tandem in two duplication blocks located on chromosomes 4 and 7, and the other three ClPAL genes are distributed as single copies on chromosomes 2, 3, and 8. Both the cDNA and protein sequences of ClPALs share an overall high identity with each other. A phylogenetic analysis places 11 of the ClPALs into a separate cucurbit subclade, whereas ClPAL2, which belongs to neither monocots nor dicots, may serve as an ancestral PAL in plants. In the cucurbit subclade, seven ClPALs form homologous pairs with their counterparts from cucumber. Expression profiling reveals that 11 of the ClPAL genes are expressed and show preferential expression in the stems and male and female flowers. Six of the 12 ClPALs are moderately or strongly expressed in the fruits, particularly in the pulp, suggesting the potential roles of PAL in the development of fruit color and flavor. A promoter motif analysis of the ClPAL genes implies redundant but distinctive cis-regulatory structures for stress responsiveness. Finally, duplication events during the evolution and expansion of the ClPAL gene family are discussed, and the relationships between the ClPAL genes and their cucumber orthologs are estimated.     

The phenylalanine ammonia-lyase gene family in Arabidopsis thaliana

Phenylpropanoid derivatives are a complex class of secondary metabolites that have many important roles in plants during normal growth and in responses to environmental stress. Phenylalanine ammonialyase (PAL) catalyzes the first step in the biosynthesis of phenylpropanoids, and is usually encoded by a multi-gene family. Genomic clones for three Arabidopsis thaliana PAL genes containing the entire protein-coding region and upstream and downstream sequences have been obtained and completely sequenced. Two A. thaliana PAL genes (PAL1 and PAL2) are structurally similar to PAL genes that have been cloned from other plant species, with a single intron at a conserved position, and a long highly conserved second exon. Previously identified promoter motifs plus several additional sequence motifs were found in the promoter regions of PAL1 and PAL2. Expression of PAL1 and PAL2 is both qualitatively and quantitatively similar in different plant organs and under various inductive conditions. A third A. thaliana PAL gene, PAL3, differs significantly from PAL1 and PAL2 and other sequenced plant PAL genes. PAL3 contains an additional intron, and its deduced amino acid sequence is less homologous to other PAL proteins. The PAL3 promoter region lacks several sequence motifs conserved between A. thaliana PAL1 and PAL2, as well as motifs described in other genes involved in phenylpropanoid metabolism. A. thaliana PAL3 was expressed at very low levels under the conditions examined.     

Genome-wide identification, phylogeny and expression analysis of the lipoxygenase gene family in cucumber

Plant lipoxygenase (LOX) is involved in growth and developmental control processes, through the biosynthesis of regulatory molecules and defense responses to pathogens, wounding and stress. To date, few LOX proteins and little tissue expression profiling have been reported in detail for cucumber (Cucumis sativus L.). Recent completion of the cucumber genome sequence now permits genome-wide analysis of the LOX gene family in cucumber as well as comparison with LOX in Arabidopsis and rice. We identified 23 candidate LOX genes in the cucumber genome; phylogenetic analysis indicated that these LOX members cluster into two groups, designated types 1 and 2, as expected from previous studies. Sequence analysis showed that five binding sites of iron, including two consensus histidines in the LOX domain, are highly conserved in the cucumber LOX proteins. Analysis of chromosomal localization and genome distribution suggested that tandem duplication and/or polyploidal duplication contributed to the expansion of the cucumber LOX gene family. Based on intron/exon structure analysis, only a few of the extant intron patterns existed in the ancestor of monocots and eudicots. Expression data showed widespread distribution of the cucumber LOX gene family within plant tissues, suggesting that they perform different functions in different tissues.     

小拟南芥MKK基因家族全基因组鉴定及进化和表达分析

丝裂原活化蛋白激酶激酶(mitogen-activated protein kinase kinase,MAPKK或MKK)是丝裂原活化蛋白激酶(mitogen-activatedproteinkinase,MAPK)级联的重要组成部分,在植物的生长发育和胁迫应答过程中发挥重要作用。目前,已在多种植物中鉴定了MKK基因家族,但在十字花科植物小拟南芥(Arabidopsis pumila)中MKK基因家族的系统鉴定与分析尚未见报道。为了探索小拟南芥MKK基因家族的进化和功能,本研究通过全基因组分析鉴定了小拟南芥中16个MKK基因,散布于小拟南芥的10条染色体上。基于系统发育分析和多重序列比对,将这些基因分为5个亚族:A亚族(5个)、B亚族(2个)、C亚族(4个)、D亚族(3个)和E亚族(2个)。分子进化和共线性分析表明小拟南芥中存在7对复制基因,分别是ApMKK1-1/1-2、ApMKK2-1/2-2、ApMKK3-1/3-2、ApMKK4-1/4-2、ApMKK5-1/5-2、ApMKK9-1/9-2和ApMKK10-1/10-2,其中ApMKK1-1/1-2在复制事件之后发生了加速进化。结合ApMKKs启动子区的顺式元件分布和ApMKKs在成熟叶片、茎、花和果实以及盐胁迫下的表达模式,结果发现复制基因的表达具有组织特异性和功能多样性。部分复制基因在组织中的表达模式存在差异,但在盐胁迫下的表达模式却基本相同。本研究结果为解析MKK介导的小拟南芥发育过程和非生物胁迫信号转导通路的复杂机制奠定了基础。     

Glutathione peroxidase genes in Arabidopsis are ubiquitous and regulated by abiotic stresses through diverse signaling pathways

Glutathione peroxidases (GPXs) are a group of enzymes that protect cells against oxidative damage generated by reactive oxygen species (ROS). The presence of GPXs in plants has been reported by several groups, but the roles of individual members of this family in a single plant species have not been studied. A family of seven related proteins named AtGPX1- AtGPX7 in Arabidopsis was identified, and the genomic organization of this family was reported. The putative subcellular localizations of the encoded proteins are the cytosol, chloroplast, mitochondria, and endoplasmic reticulum. Expressed sequence tags (ESTs) for all the genes except AtGPX7 were identified. Expression analysis of AtGPX genes in Arabidopsis tissues was performed, and different patterns were detected. Interestingly, several genes were up-regulated coordinately in response to abiotic stresses. AtGPX6, like human phospholipid hydroperoxide GPX (PHGPX), possibly encodes mitochondrial and cytosolic isoforms by alternative initiation. In addition, this gene showed the strongest responses under most abiotic stresses tested. AtGPX6::GUS analysis in transgenic Arabidopsis showed that AtGPX6 is highly expressed throughout development in most tissues, thus supporting an important role for this gene in protection against oxidative damage. The different effects of salicylic acid (SA), jasmonic acid (JA), abscisic acid (ABA), and auxin on the expression of the genes indicate that the AtGPX family is regulated by multiple signaling pathways. Analysis of the upstream region of the AtGPX genes revealed the presence of multiple conserved motifs, and some of them resembled antioxidant-responsive elements found in plant and human promoters. The potential regulatory role of specific sequences is discussed.     

Molecular evolutionary analyses of the Arabidopsis L7 ribosomal protein gene family

Cytoplasmic ribosomal protein (r-protein) genes in Arabidopsis thaliana are encoded by 80 multigene families that contain between two and seven members. Gene family members are typically similar at the protein sequence level, with the most divergent members of any gene family retaining 94% identity, on average. However, three Arabidopsis r-protein families - S15a, L7 and P2 - contain highly divergent family members. Here, we investigated the organization, structure, expression and molecular evolution of the L7 r-protein family. Phylogenetic analyses showed that L7 r-protein gene family members constitute two distinct phylogenetic groups. The first group including RPL7B, RPL7C and RPL7D has homologs in plants, animals and fungi. The second group represented by RPL7A is found in plants but has no orthologs from other fully-sequenced eukaryotic genomes. These two groups may have derived from a duplication event prior to the divergence of animals and plants. All four L7 r-protein genes are expressed and all exhibit a differential expression in inflorescence and flowers. RPL7A and RPL7B are less expressed than the other genes in all tissues analyzed. Molecular characterization of nucleic and protein sequences of L7 r-protein genes and analysis of their codon usage did not indicate any functional divergence. The probable evolution of an extra-ribosomal function of group 2 genes is discussed.     

不同胁迫条件下化感与非化感水稻PAL多基因家族的差异表达

水稻苯丙氨酸解氨酶(PAL)调控酚酸类化感物质的合成代谢。编码PAL的基因是一个基因家族,包含至少11个基因成员,并受不同环境条件的调控。为了明确PAL基因家族中调控水稻化感作用的特定基因成员,本研究运用实时荧光定量PCR技术分析了低氮及稗草胁迫条件下强化感水稻PI312777与非化感水稻Lemont中根系的11个PAL成员基因的表达差异。结果表明,低氮和稗草胁迫条件下,PI312777和Lemont中的 PAL4和PAL10均不表达,其余9个PAL基因成员发生了不同程度的表达变化。其中,PAL11均上调表达,其分别在低氮处理和稗草胁迫的PI312777中上调3.29倍和1.07倍,而在相同处理下的Lemont中上调3.92倍和1.08倍;PAL3和PAL9则仅在低氮和稗草胁迫条件下的PI312777中上调表达,低氮胁迫分别为1.83倍和2.66倍,稗草胁迫为1.46倍和2.65倍;而这两个基因在相同处理下的Lemont中表达下调,低氮胁迫下调1.05和1.24倍,稗草胁迫下调1.14和1.16倍,推测PAL3和PAL9可能与胁迫初期调控水稻化感作用有关。     

Nucleotide sequence and expression of a maize H1 histone cDNA.

The first complete amino acid sequence of a H1 histone of a monocotyledonous plant was deduced from a cDNA isolated from a maize library. The encoded H1 protein is 245 amino acid-long and shows the classical tripartite organization of this class of histones. The central globular region of 76 residues shows 60% sequence homology with H1 proteins from dicots but only 20% with the animal H1 proteins. However, several of the amino acids considered as being important in the structure of the nucleosome are conserved between this protein and its animal counterparts. The N-terminal region contains an equal number of acidic and basic residues which appears as a general feature of plant H1 proteins. The 124 residue long and highly basic C-terminal region contains a 7-fold repeated element KA/PKXA/PAKA/PK. Southern-blot hybridization showed that the H1 protein is encoded by a small multigene family. Highly homologous H1 gene families were also detected in the genomes of several more or less closely related plant species. The general expression pattern of these genes was not significantly different from that of these genes encoding the core-histones neither during germination nor in the different tissues of adult maize.     

Transcriptional divergence of the duplicated oxidative stress-responsive genes in the Arabidopsis genome

Previous studies have indicated that Arabidopsis thaliana experienced a genome-wide duplication event shortly before its divergence from Brassica followed by extensive chromosomal rearrangements and deletions. While a large number of the duplicated genes have significantly diverged or lost their sister genes, we found 4222 pairs that are still highly conserved, and as a result had similar functional assignments during the annotation of the genome sequence. Using whole-genome DNA microarrays, we identified 906 duplicated gene pairs in which at least one member exhibited a significant response to oxidative stress. Among these, only 117 pairs were up- or down-regulated in both pairs and many of these exhibited dissimilar patterns of expression. Examination of the expression patterns of PAL1 and PAL2, ACD1 and ACD2, genes coding for two Hsp20s, various P450s, and electron transfer flavoproteins suggests Arabidopsis evolved a number of distinct oxidative stress response mechanisms using similar gene sets following the duplication of its genome.     

Structure and evolution of mammalian maltase-glucoamylase and sucrase-isomaltase genes

Maltase-glucoamylase and sucrase-isomaltase are two human glycosidases responsible for starch digestion. We have performed a comparative analysis of their amino acid sequences from several species of mammals and their orthologues from other chordates. This allowed us to determine the evolutionary history of the enzymes. Both glycosidases are paralogues and contain GH31 family catalytic domains. The common evolutionary precursor of these genes has arisen by a tandem duplication. As a consequence, sucrase-isomaltase consists of two homologous parts. The maltase-glucoamylase gene was a subject of several additional duplications, which number was not the same in different mammals. The locus, containing this gene, consists of 4-7 tandem repeats. The amino acid sequence, encoded by each of them, is similar to both parts of sucrase-isomaltase.