Small auxin upregulated RNA (SAUR) gene family in maize: Identification,evolution, and its phylogenetic comparison with Arabidopsis,rice, and sorghum

Small auxin-up RNAs(SAURs)are the early auxin-responsive genes represented by a large multigene family in plants.Here,we identified 79 SAUR gene family members from maize(Zea mays subsp.mays)by a reiterative database search and manual annotation.Phylogenetic analysis indicated that the SAUR proteins from Arabidopsis,rice,sorghum,and maize had divided into 16 groups.These genes were non-randomly distributed across the maize chromosomes,and segmental duplication and tandem duplication contributed to the expansion of the maize SAUR gene family.Synteny analysis established orthology relationships and functional linkages between SAUR genes in maize and sorghum genomes.We also found that the auxin-responsive elements were conserved in the upstream sequences of maize SAUR members.Selection analyses identified some significant site-specific constraints acted on most SAUR paralogs.Expression profiles based on microarray data have provided insights into the possible functional divergence among members of the SAUR gene family.Quantitative real-time PCR analysis indicated that some of the 10 randomly selected ZmSAUR genes could be induced at least in maize shoot or root tissue tested.The results reveal a comprehensive overview of the maize SAUR gene family and may pave the way for deciphering their function during plant development.     

Small auxin upregulated RNA （SAUR） gene family in maize： Identification,evolution, and its phylogenetic comparison with Arabidopsis,rice, and sorghum

Small auxin-up RNAs （.SAURs） are the early auxin- responsive genes represented by a large multigene family in plants. Here, we identified 79 SAUR gene family members from maize （Zea mays subsp, mays） by a reiterative database search and manual annotation. Phylogenetic analysis indicated that the SAUR proteins from Arabidopsis, rice, sorghum, and maize had divided into 16 groups. These genes were non-randomly distributed across the maize chromosomes, and segmental duplication and tandem duplication contributed to the expansion of the maize .SAUR gene family. Synteny analysis established ortholos~J relationships and functional linkages between SAUR genes in maize and sorghum genomes. We also found that the auxin-responsive elements were conserved in the upstream sequences of maize SAUR members. Selection analyses identified some significant site-specific constraints acted on most SAUR paralogs. Expression profiles based on microarray data have provided insights into the possible functional divergence among members of the .SAUR gene family. Quantitative real-time PCR analysis indicated that some of the 10 randomly selected ZmSAUR genes could be induced at least in maize shoot or root tissue tested. The results reveal a comprehensive overview of the maize .SAUR gene family and may pave the way for deciphering their function during pJant development.     

葡萄NIP基因家族的鉴定与表达分析

类根瘤菌26膜内在蛋白(nodulin 26 like intrinsic proteins,NIPs)是水通道蛋白的亚类,在植物营养获取和胁迫应答过程中发挥着重要作用。该研究利用多种生物信息学软件,对葡萄NIP家族基因进行分析,并采用RT PCR方法克隆得到4个NIP家族基因,利用qRT PCR方法分析非生物胁迫下NIP基因的表达特征。结果显示：(1)在葡萄基因组中,共鉴定到8个NIP基因,分布于葡萄4条染色体上,主要定位在质膜中;结构上含有6个跨膜结构域和两个典型的保守结构域NPA;氨基酸序列中存在很多个可能的磷酸化位点。(2)进化分析表明葡萄和拟南芥NIP基因具有较高的同源性,基因结构包含外显子数4~6个,保守基序种类和数量相似;基因启动子上游2 kb包含多种应答逆境和激素的顺式调控元件,其数量差异可能与基因本身功能相关。(3)NIP家族基因在不同组织中表达水平差异较大,多数成员在叶中表达水平较高,在茎中较低;成功克隆得到4个葡萄VvNIP基因,其长度分别为789 bp、606 bp、897 bp、789 bp,分别编码262、201、298、293个氨基酸。(4)qRT PCR结果显示,不同胁迫处理下NIP基因在葡萄叶片中的表达水平不同：低温处理下葡萄NIP基因大多呈显著下调表达;盐胁迫下,除VvNIP2 1、VvNIP4 2外其余家族基因均呈下调表达;干旱胁迫下VvNIP4 2显著上调。研究表明,VvNIP基因对多种胁迫均有响应,为葡萄逆境胁迫机制研究提供了参考。     

Identification of the factors that interact with NCBP, an 80 kDa nuclear cap binding protein.

It has been shown that the monomethylated cap structure plays important roles in pre-mRNA splicing and nuclear export of RNA. As a candidate for the factor involved in these nuclear events we have previously purified an 80 kDa nuclear cap binding protein (NCBP) from a HeLa cell nuclear extract and isolated its full-length cDNA. In this report, in order to obtain a clue to the cellular functions of NCBP, we attempted to identify a factor(s) that interacts with NCBP. Using the yeast two-hybrid system we isolated three clones from a HeLa cell cDNA library. We designated the proteins encoded by these clones NIPs (NCBP interacting proteins). NIP1 and NIP2 have an RNP consensus-type RNA binding domain, whereas NIP3 contains a unique domain of Arg-Glu or Lys-Glu dipeptide repeats. We also show that NCBP requires NIP1 for binding to the cap structure. Possible roles of NIPs in cap-dependent nuclear processes are discussed.     

Genes identified by visible mutant phenotypes show increased bias toward one of two subgenomes of maize

Not all genes are created equal. Despite being supported by sequence conservation and expression data, knockout homozygotes of many genes show no visible effects, at least under laboratory conditions. We have identified a set of maize (Zea mays L.) genes which have been the subject of a disproportionate share of publications recorded at MaizeGDB. We manually anchored these "classical" maize genes to gene models in the B73 reference genome, and identified syntenic orthologs in other grass genomes. In addition to proofing the most recent version 2 maize gene models, we show that a subset of these genes, those that were identified by morphological phenotype prior to cloning, are retained at syntenic locations throughout the grasses at much higher levels than the average expressed maize gene, and are preferentially found on the maize1 subgenome even with a duplicate copy is still retained on the opposite subgenome. Maize1 is the subgenome that experienced less gene loss following the whole genome duplication in maize lineage 5-12 million years ago and genes located on this subgenome tend to be expressed at higher levels in modern maize. Links to the web based software that supported our syntenic analyses in the grasses should empower further research and support teaching involving the history of maize genetic research. Our findings exemplify the concept of "grasses as a single genetic system," where what is learned in one grass may be applied to another.     

The evolutionary relationships between the two bacteria Escherichia coli and Haemophilus influenzae and their putative last common ancestor

We have tried to approach the nature of the last common ancestor to Haemophilus influenzae and Escherichia coli and to determine how each bacterium could have diverged from this putative organism. The approach used was exhaustive analysis of the homologous proteins coded by genes present in these bacteria, using as criteria for sequence relatedness an alignment of at least 80 amino acid residues and a PAM distance (number of accepted point mutations per 100 residues separating two sequences) below 250. Evolutionarily significant similarities were found between 1,345 H. influenzae proteins (85% of the total genome) and 3,058 E. coli. proteins (75% of the total genome), many of them belonging to families of various sizes (from 666 doublets to 35 large groups of more than 10 members). Nearly all the genes found by this approach to be duplicated in both bacteria were already duplicated in their last common ancestor. This was deduced from (1) the comparison of the respective distributions of evolutionary distances between orthologs (genes separated only by speciation events) and paralogs (genes duplicated in the same genome) and (2) the analysis of the phylogenetic trees reconstructed for each family of paralogs containing at least two members belonging to each bacterium. The distributions of the different categories of homologs show a significant loss of paralogous genes in H. influenzae (reduction proportional to the genome size), of many sequences which are still present in one copy in E. coli, and of some entire gene families. Phylogenetic trees also confirmed this recent loss of paralogous genes in H. influenzae. Thus, the genome size of the last common ancestor of these two bacteria would have been close to that of present-day E. coli, and the evolution of H. influenzae toward a parasitic life led to an important decrease in its genome size by some mechanism of streamlining. During this recent evolution, the memory of the gene order present in the last common ancestor has been blurred, but a few short conserved chromosomal fragments can still be detected in present-day E. coli and H. influenzae.      

Maize orthologs of rice GS5 and their transregulator are associated with kernel development

Genome information from model species such as rice can assist in the cloning of genes in a complex genome,such as maize.Here,we identified a maize ortholog of rice GS5 that contributes to kernel development in maize.The genomewide association analysis of the expression levels of ZmGS5,and 15 of its 26 paralogs,identified a trans-regulator on chromosome 7,which was a BAKi-like gene.This gene that we named as ZmBAK1-7 could regulate the expression of ZmGS5 and three of the paralogs.Candidate-gene association analyses revealed that these five genes were associated with maize kernel development-related traits.Linkage analyses also detected that ZmGSs and ZmBAK1-7 co-localized with mapped QTLs.A transgenic analysis of ZmGS5 in Arabidopsis thaliana L.showed a significant increase in seed weight and cell number,suggesting that ZmGS5 may have a conserved function among different plant species that affects seed development.     

Functional divergence of the NIP III subgroup proteins involved altered selective constraints and positive selection

Background  

Nod26-like intrinsic proteins (NIPs) that belong to the aquaporin superfamily are unique to plants. According to homology modeling and phylogenetic analysis, the NIP subfamily can be further divided into three subgroups with distinct biological functions (NIP I, NIP II, and NIP III). In some grasses, the NIP III subgroup proteins (NIP2s) were demonstrated to be permeable to solutes with larger diameter, such as silicic acid and arsenous acids. However, to date there is no data-mining or direct experimental evidences for the permeability of such larger solutes for dicot NIP2s, although they exhibit similar three-dimensional structures as those in grasses. It is therefore intriguing to investigate the molecular mechanisms that drive the evolution of plant NIP2s.     

Multiple mechanisms promote the retained expression of gene duplicates in the tetraploid frog Xenopus laevis

Gene duplication provides a window of opportunity for biological variants to persist under the protection of a co-expressed copy with similar or redundant function. Duplication catalyzes innovation (neofunctionalization), subfunction degeneration (subfunctionalization), and genetic buffering (redundancy), and the genetic survival of each paralog is triggered by mechanisms that add, compromise, or do not alter protein function. We tested the applicability of three types of mechanisms for promoting the retained expression of duplicated genes in 290 expressed paralogs of the tetraploid clawed frog, Xenopus laevis. Tests were based on explicit expectations concerning the ka/ks ratio, and the number and location of nonsynonymous substitutions after duplication. Functional constraints on the majority of paralogs are not significantly different from a singleton ortholog. However, we recover strong support that some of them have an asymmetric rate of nonsynonymous substitution: 6% match predictions of the neofunctionalization hypothesis in that (1) each paralog accumulated nonsynonymous substitutions at a significantly different rate and (2) the one that evolves faster has a higher ka/ks ratio than the other paralog and than a singleton ortholog. Fewer paralogs (3%) exhibit a complementary pattern of substitution at the protein level that is predicted by enhancement or degradation of different functional domains, and the remaining 13% have a higher average ka/ks ratio in both paralogs that is consistent with altered functional constraints, diversifying selection, or activity-reducing mutations after duplication. We estimate that these paralogs have been retained since they originated by genome duplication between 21 and 41 million years ago. Multiple mechanisms operate to promote the retained expression of duplicates in the same genome, in genes in the same functional class, over the same period of time following duplication, and sometimes in the same pair of paralogs. None of these paralogs are superfluous; degradation or enhancement of different protein subfunctions and neofunctionalization are plausible hypotheses for the retained expression of some of them. Evolution of most X. laevis paralogs, however, is consistent with retained expression via mechanisms that do not radically alter functional constraints, such as selection to preserve post-duplication stoichiometry or temporal, quantitative, or spatial subfunctionalization.     

Genome size reduction in the chicken has involved massive loss of ancestral protein-coding genes

Both mean genomes size and the variance in genome size among species are smaller on average in birds (class Aves) than in the other tetrapod classes. In order to test whether loss of protein-coding genes has contributed to genome size reduction in birds, we compared the chicken genome and five mammalian genomes. Numbers of members (paralogs) were significantly lower in the chicken gene families than in the corresponding mammalian families. Phylogenetic analyses of chicken, mammal, and fish paralogs supported the hypothesis that chicken-specific loss of paralogs occurred much more frequently than mammal-specific gene duplications. Moreover, the phylogenetic analyses supported the hypothesis that a substantial majority of the paralogs lost in chicken originated from duplications prior to the most recent common ancestor of tetrapods and bony fishes. In addition to loss of paralogs, numerous gene families present in the mammalian genomes were missing in the chicken genome; over 1,000 of these families were found in bony fishes, implying presence of the family in the tetrapod ancestor. In the set of families with more members on average in the mammals than in the chicken, immune system function was associated with a greater degree of gene family size reduction in the chicken, consistent with other evidence that immune system gene families have become particularly compact in birds.     

A systematic map of genetic variation in Plasmodium falciparum

Discovering novel genes involved in immune evasion and drug resistance in the human malaria parasite, Plasmodium falciparum, is of critical importance to global health. Such knowledge may assist in the development of new effective vaccines and in the appropriate use of antimalarial drugs. By performing a full-genome scan of allelic variability in 14 field and laboratory strains of P. falciparum, we comprehensively identified approximately 500 genes evolving at higher than neutral rates. The majority of the most variable genes have paralogs within the P. falciparum genome and may be subject to a different evolutionary clock than those without. The group of 211 variable genes without paralogs contains most known immunogens and a few drug targets, consistent with the idea that the human immune system and drug use is driving parasite evolution. We also reveal gene-amplification events including one surrounding pfmdr1, the P. falciparum multidrug-resistance gene, and a previously uncharacterized amplification centered around the P. falciparum GTP cyclohydrolase gene, the first enzyme in the folate biosynthesis pathway. Although GTP cyclohydrolase is not the known target of any current drugs, downstream members of the pathway are targeted by several widely used antimalarials. We speculate that an amplification of the GTP cyclohydrolase enzyme in the folate biosynthesis pathway may increase flux through this pathway and facilitate parasite resistance to antifolate drugs.