Comparable Rates of Gene Loss and Functional Divergence after Genome Duplications Early in Vertebrate Evolution

Duplicated genes are an important source of new protein functions and novel developmental and physiological pathways. Whereas most models for fate of duplicated genes show that they tend to be rapidly lost, models for pathway evolution suggest that many duplicated genes rapidly acquire novel functions. Little empirical evidence is available, however, for the relative rates of gene loss vs. divergence to help resolve these contradictory expectations. Gene families resulting from genome duplications provide an opportunity to address this apparent contradiction. With genome duplication, the number of duplicated genes in a gene family is at most 2(n), where n is the number of duplications. The size of each gene family, e.g., 1, 2, 3, . . . , 2(n), reflects the patterns of gene loss vs. functional divergence after duplication. We focused on gene families in humans and mice that arose from genome duplications in early vertebrate evolution and we analyzed the frequency distribution of gene family size, i.e., the number of families with two, three or four members. All the models that we evaluated showed that duplicated genes are almost as likely to acquire a new and essential function as to be lost through acquisition of mutations that compromise protein function. An explanation for the unexpectedly high rate of functional divergence is that duplication allows genes to accumulate more neutral than disadvantageous mutations, thereby providing more opportunities to acquire diversified functions and pathways.     

Lineage-Specific Duplication and Loss of Pepsinogen Genes in Hominoid Evolution

Fourteen different pepsinogen-A cDNAs and one pepsinogen-C cDNA have been cloned from gastric mucosa of the orangutan, Pongo pygmaeus. Encoded pepsinogens A were classified into two groups, i.e., types A1 and A2, which are different in acidic character. The occurrence of 9 and 5 alleles of A1 and A2 genes (at least 5 and 3 loci), respectively was anticipated. Respective orthologous genes are present in the chimpanzee genome although their copy numbers are much smaller than those of the orangutan genes. Only A1 genes are present in the human probably due to the loss of the A2 gene. Molecular phylogenetic analyses showed that A1 and A2 genes diverged before the speciation of great hominoids. Further reduplications of respective genes occurred several times in the orangutan lineage, with much higher frequencies than those occurred in the chimpanzee and human lineages. The rates of non-synonymous substitutions were higher than those of synonymous ones in the lineage of A2 genes, implying the contribution of the positive selection on the encoded enzymes. Several sites of pepsin moieties were indeed found to be under positive selection, and most of them locate on the surface of the molecule, being involved in the conformational flexibility. Deduced from the known genomic structures of pepsinogen-A genes of primates and other mammals, the duplication/loss were frequent during their evolution. The extreme multiplication in the orangutan might be advantageous for digestion of herbaceous foods due to the increase in the level of enzymes in stomach and the diversification of enzyme specificity.     

Gene Orders in Genomes of Alpha-Proteobacteria: Similarity and Evolution

The gene orders in the genomes of nine alpha-proteobacteria were compared using quantitative indices S (the relative number of common pairs of adjacent genes) and L (the mean difference between intergenic distances). A sample of 200 homologous genes, occurring in all 11 strains, was studied. In all of the genomes examined, 20 conserved, “uninterrupted” regions, including in total 63 out of 200 genes, were found. The rate of evolutionary change in the gene order widely varied in different evolutionary lineages. The highest rate (40 to 60 genome rearrangements per 100 Myr) was characteristic of the intercellular parasite Wolbachia (Rickettsiales). Computer simulation has showed that the S to L ratio observed in the sample testified that the probability of large genome rearrangements was somewhat lower than that of small ones.     

Conservatism of the Insulin Signaling System in Evolution of Invertebrate and Vertebrate Animals

The insulin system including hormone insulin and signaling mechanisms realizing a wide spectrum of its regulatory effect is one of the major systems in the animals and human organism. At present the history of origin of this regulatory system in the course of evolution starts to be formed. There are grounds to believe that it appeared in unicellular eukaryotes, developed in multicellular ones, and achieved significant perfection in higher vertebrates. This paper analyzes the structural-functional organization of insulin-like peptides, their receptors, and the corresponding signaling mechanisms in four types of invertebrates (sponges, nematodes, molluscs, arthropods) in comparison with those in higher vertebrates. There is revealed evolutionary conservatism in the common structural-functional organization of insulin-like peptides of invertebrates and insulin of vertebrate animals; receptors of insulin-like peptides of invertebrates and receptors of insulin and insulin-like growth factor 1 of vertebrates that have tyrosine kinase activity; the insulin-like signaling systems including signaling blocks, similar by their primary structure in invertebrate and vertebrate animals (IRS-proteins, G-proteins, adenylyl cyclase, protein kinases A and C, etc.). The point of view is put forward that the conservatism of the functional blocks of the insulin system does not mean the absence of evolutionary changes of this system as a whole. Examples of such evolutionary changes leading to complication of the insulin system organization at supramolecular and cellular levels and to an increase of efficiency of its functioning are presented.     

Evolution of Vertebrate Immunity: Sequence and Functional Analysis of the SEFIR Domain Family Member Act1

SEF/IL-17R/CIKS/ACT1 homology (SEFIR) domain containing proteins, which include the IL-17 receptors and an adaptor protein Act1, have essential roles in vertebrate immunity. However, the molecular mechanisms of Act1 function remain largely unexplored. In this article, we employed an evolutionary analysis to discover novel structural and functional properties of Act1. Firstly, we have found that the previously identified helix-loop-helix and Ufd2-box domains in human Act1 have relatively recent evolutionary origins in higher vertebrates. Zebrafish Act1, which lacks these domains, is unable to induce JNK phosphorylation and activate cytokine expression when expressed in human cells. Secondly, we have established that Act1-like proteins contain DEATH-domains in basal animals, such as Hydra and primitive chordates, but lack this domain in vertebrates. Finally, we have shown that Act1-TRAF6 interactions are conserved throughout vertebrate evolution: Act1 derived from zebrafish can bind to TRAF6 and activate NF-κB in human cells. Moreover, we have identified a novel highly conserved motif at the amino-terminus of Act1, which is critical for binding to TRAF6 and activating NF-κB-dependent gene expression. We propose a model of evolutionary changes in Act1-mediated signalling, which contributes to a better understanding of evolution of the vertebrate immunity.     

Retinoic Acid Induced 1, RAI1: A Dosage Sensitive Gene Related to Neurobehavioral Alterations Including Autistic Behavior

Genomic structural changes, such as gene Copy Number Variations (CNVs) are extremely abundant in the human genome. An enormous effort is currently ongoing to recognize and catalogue human CNVs and their associations with abnormal phenotypic outcomes. Recently, several reports related neuropsychiatric diseases (i.e. autism spectrum disorders, schizophrenia, mental retardation, behavioral problems, epilepsy) with specific CNV. Moreover, for some conditions, both the deletion and duplication of the same genomic segment are related to the phenotype. Syndromes associated with CNVs (microdeletion and microduplication) have long been known to display specific neurobehavioral traits. It is important to note that not every gene is susceptible to gene dosage changes and there are only a few dosage sensitive genes. Smith-Magenis (SMS) and Potocki-Lupski (PTLS) syndromes are associated with a reciprocal microdeletion and microduplication within chromosome 17p11.2. in humans. The dosage sensitive gene responsible for most phenotypes in SMS has been identified: the Retinoic Acid Induced 1 (RAI1). Studies on mouse models and humans suggest that RAI1 is likely the dosage sensitive gene responsible for clinical features in PTLS. In addition, the human RAI1 gene has been implicated in several neurobehavioral traits as spinocerebellar ataxia (SCA2), schizophrenia and non syndromic autism. In this review we discuss the evidence of RAI1 as a dosage sensitive gene, its relationship with different neurobehavioral traits, gene structure and mutations, and what is known about its molecular and cellular function, as a first step in the elucidation of the mechanisms that relate dosage sensitive genes with abnormal neurobehavioral outcomes.     

Evolution of Plant Mitochondrial Intron-Encoded Maturases: Frequent Lineage-Specific Loss and Recurrent Intracellular Transfer to the Nucleus

Among land plants, mitochondrial and plastid group II introns occasionally encode proteins called maturases that are important for splicing. Angiosperm nuclear genomes also encode maturases that are targeted to the organelles, but it is not known whether nucleus-encoded maturases exist in other land plant lineages. To examine the evolutionary diversity and history of this essential gene family, we searched for maturase homologs in recently sequenced nuclear and mitochondrial genomes from diverse land plants. We found that maturase content in mitochondrial genomes is highly lineage specific, such that orthologous maturases are rarely shared among major land plant groups. The presence of numerous mitochondrial pseudogenes in the mitochondrial genomes of several species implies that the sporadic maturase distribution is due to frequent inactivation and eventual loss over time. We also identified multiple maturase paralogs in the nuclear genomes of the lycophyte Selaginella moellendorffii, the moss Physcomitrella patens, and the representative angiosperm Vitis vinifera. Phylogenetic analyses of organelle- and nucleus-encoded maturases revealed that the nuclear maturase genes in angiosperms, lycophytes, and mosses arose by multiple shared and independent transfers of mitochondrial paralogs to the nuclear genome during land plant evolution. These findings indicate that plant mitochondrial maturases have experienced a surprisingly dynamic history due to a complex interaction of multiple evolutionary forces that affect the rates of maturase gain, retention, and loss.     

On the Use of Gene Ontology Annotations to Assess Functional Similarity among Orthologs and Paralogs: A Short Report

A recent paper (Nehrt et al., PLoS Comput. Biol. 7:e1002073, 2011) has proposed a metric for the "functional similarity" between two genes that uses only the Gene Ontology (GO) annotations directly derived from published experimental results. Applying this metric, the authors concluded that paralogous genes within the mouse genome or the human genome are more functionally similar on average than orthologous genes between these genomes, an unexpected result with broad implications if true. We suggest, based on both theoretical and empirical considerations, that this proposed metric should not be interpreted as a functional similarity, and therefore cannot be used to support any conclusions about the "ortholog conjecture" (or, more properly, the "ortholog functional conservation hypothesis"). First, we reexamine the case studies presented by Nehrt et al. as examples of orthologs with divergent functions, and come to a very different conclusion: they actually exemplify how GO annotations for orthologous genes provide complementary information about conserved biological functions. We then show that there is a global ascertainment bias in the experiment-based GO annotations for human and mouse genes: particular types of experiments tend to be performed in different model organisms. We conclude that the reported statistical differences in annotations between pairs of orthologous genes do not reflect differences in biological function, but rather complementarity in experimental approaches. Our results underscore two general considerations for researchers proposing novel types of analysis based on the GO: 1) that GO annotations are often incomplete, potentially in a biased manner, and subject to an "open world assumption" (absence of an annotation does not imply absence of a function), and 2) that conclusions drawn from a novel, large-scale GO analysis should whenever possible be supported by careful, in-depth examination of examples, to help ensure the conclusions have a justifiable biological basis.     

Opossum Aldehyde Dehydrogenases: Evidence for Four ALDH1A1-like Genes on Chromosome 6 and ALDH1A2 and ALDH1A3 Genes on Chromosome 1

Evidence is presented for six opossum ALDH1A genes, including four ALDH1A1-like genes on chromosome 6 and ALDH1A2- and ALDH1A3-like genes on chromosome 1. Predicted structures for the opossum aldehyde dehydrogenase (ALDH) subunits and the intron–exon boundaries for opossum ALDH genes showed a high degree of similarity with other mammalian ALDHs. Phylogenetic analyses supported the proposed designation of these opossum class 1 ALDHs as ALDH1A-like, ALDH1A2-like, and ALDH1A3-like and are therefore likely to play important roles in retinal and peroxidic aldehyde metabolism. Alignments of predicted opossum ALDH1A amino acid sequences with sheep ALDH1A1 and rat ALDH1A2 sequences demonstrated conservation of key residues previously shown to participate in catalysis and coenzyme binding. Amino acid substitution rates observed for family 1A ALDHs during vertebrate evolution indicated that ALDH1A2-like genes are evolving slower than ALDH1A1- and ALDH1A3-like genes. It is proposed that the common ancestor for ALDH1A genes predates the appearance of birds during vertebrate evolution.     

Functional Consequences of Wnt-induced Dishevelled 2 Phosphorylation in Canonical and Noncanonical Wnt Signaling

Dishevelled (Dvl) proteins are intracellular effectors of Wnt signaling that have essential roles in both canonical and noncanonical Wnt pathways. It has long been known that Wnts stimulate Dvl phosphorylation, but relatively little is known about its functional significance. We have previously reported that both Wnt3a and Wnt5a induce Dvl2 phosphorylation that is associated with an electrophoretic mobility shift and loss of recognition by monoclonal antibody 10B5. In the present study, we mapped the 10B5 epitope to a 16-amino acid segment of human Dvl2 (residues 594–609) that contains four Ser/Thr residues. Alanine substitution of these residues (P4m) eliminated the mobility shift induced by either Wnt3a or Wnt5a. The Dvl2 P4m mutant showed a modest increase in canonical Wnt/β-catenin signaling activity relative to wild type. Consistent with this finding, Dvl2 4Pm preferentially localized to cytoplasmic puncta. In contrast to wild-type Dvl2, however, the P4m mutant was unable to rescue Wnt3a-dependent neurite outgrowth in TC-32 cells following suppression of endogenous Dvl2/3. Earlier work has implicated casein kinase 1δ/ϵ as responsible for the Dvl mobility shift, and a CK1δ in vitro kinase assay confirmed that Ser⁵⁹⁴, Thr⁵⁹⁵, and Ser⁵⁹⁷ of Dvl2 are CK1 targets. Alanine substitution of these three residues was sufficient to abrogate the Wnt-dependent mobility shift. Thus, we have identified a cluster of Ser/Thr residues in the C-terminal domain of Dvl2 that are Wnt-induced phosphorylation (WIP) sites. Our results indicate that phosphorylation at the WIP sites reduces Dvl accumulation in puncta and attenuates β-catenin signaling, whereas it enables noncanonical signaling that is required for neurite outgrowth.     

Divergent Evolution of Plant NBS-LRR Resistance Gene Homologues in Dicot and Cereal Genomes

The majority of plant disease resistance genes are members of very large multigene families. They encode structurally related proteins containing nucleotide binding site domains (NBS) and C-terminal leucine rich repeats (LRR). The N-terminal region of some resistance genes contain a short sequence called TIR with homology to the animal innate immunity factors, Toll and interleukin receptor-like genes. Only a few plant resistance genes have been functionally analyzed and the origin and evolution of plant resistance genes remain obscure. We have reconstructed gene phylogeny by exhaustive analysis of available genome and amplified NBS domain sequences. Our study shows that NBS domains faithfully predict whole gene structure and can be divided into two major groups. Group I NBS domains contain group-specific motifs that are always linked with the TIR sequence in the N terminus. Significantly, Group I NBS domains and their associated TIR domains are widely distributed in dicot species but were not detected in cereal databases. Furthermore, Group I specific NBS sequences were readily amplified from dicot genomic DNA but could not be amplified from cereal genomic DNA. In contrast, Group II NBS domains are always associated with putative coiled-coil domains in their N terminus and appear to be present throughout the angiosperms. These results suggest that the two main groups of resistance genes underwent divergent evolution in cereal and dicot genomes and imply that their cognate signaling pathways have diverged as well. Received: 17 May 1999 / Accepted: 25 September 1999     

Multiple Gene Duplication and Rapid Evolution in the groEL Gene: Functional Implications

The chaperonins, GroEL and GroES, are present ubiquitously and provide a paradigm in the understanding of assisted protein folding. Due to its essentiality of function, GroEL exhibits high sequence conservation across species. Complete genome sequencing has shown the occurrence of duplicate or multiple copies of groEL genes in bacteria such as Mycobacterium tuberculosis and Corynebacterium glutamicum. Monophyly of each bacterial clade in the phylogenetic tree generated for the GroEL protein suggests a lineage-specific duplication. The duplicated groEL gene in Actinobacteria is not accompanied by the operonic groES despite the presence of upstream regulatory elements. Our analysis suggests that in these bacteria the duplicated groEL genes have undergone rapid evolution and divergence to function in a GroES-independent manner. Evaluation of multiple sequence alignment demonstrates that the duplicated genes have acquired mutations at functionally significant positions including those involved in substrate binding, ATP binding, and GroES binding and those involved in inter-ring and intra-ring interactions. We propose that the duplicate groEL genes in different bacterial clades have evolved independently to meet specific requirements of each clade. We also propose that the groEL gene, although essential and conserved, accumulates nonconservative substitutions to exhibit structural and functional variations. Electronic Supplementary Material Electronic Supplementary material is available for this article at and accessible for authorised users. [Reviewing Editor: Dr. Debashish Bhattacharya]     

Evolution of the Vertebrate Cytosolic Malate Dehydrogenase Gene Family: Duplication and Divergence in Actinopterygian Fish

Abstract A general correlation between neural expression and negative charge in isozymes suggests charge represents an adaptation to the neural environment. Interestingly, a notable exception exists in teleost fish. Two cytosolic malate dehydrogenase (MDH) isozymes have different spatial expression patterns in certain fishes: one is expressed in all tissues and the second is expressed primarily in the eye and skeletal muscle. While the neural MDH isozyme is negatively charged, the difference in charge between the two isozymes is not as pronounced as that observed in other gene families (e.g., triosephosphate isomerase and lactate dehydrogenase). Most tetrapods express a single cytosolic MDH isozyme, and it has been demonstrated recently that the pair of isozymes found in teleosts results from a gene duplication sometime after the separation of teleosts and tetrapods, although the exact timing of this duplication has not been inferred. Phylogenetic analyses suggest that the duplication of teleost isozymes occurred during the radiation of actinopterygian fish, consistent with the timing of duplication at other loci. Using inferred amino acid sequences, we examine the pattern of change following the duplication and across the rest of the MDH gene tree. Comparison between the MDH gene family and another gene family that shows a larger charge differential among members (triosephosphate isomerase) indicates that the smaller charge difference between MDH isozymes is best explained by greater constraint on amino acid change directly following the duplication, not greater constraint across the entire gene tree. This difference in constraint might result from the wider pattern of expression of the “neural” MDH isozyme.     

巴西橡胶树赤霉素信号转导途径HbRGA1结构和功能分析

DELLA蛋白是赤霉素激素信号负调控因子,具有抑制植物生长发育的作用。解析其家族成员结构与功能将有助于揭示橡胶树DELLA蛋白家族成员调控橡胶树生长发育的机制。本研究从橡胶树热研73397叶片中克隆HbRGA1的cDNA全长序列。该基因长为2136 bp,含1839 bp的ORF,编码613个氨基酸。HbRGA1蛋白序列包含DELLA和GRAS保守结构域,与杨树、木薯和橡胶树DELLA基因相似性高达82.5%。qRT-PCR分析发现HbRGA1在橡胶树叶片中表达量高,在树皮和胶乳中表达量极低。叶片中HbRGA1表达量受喷施赤霉素和脱落酸等诱导显著上调。本研究表明HbRGA1与橡胶树赤霉素等激素信号密切相关,为深入研究其在橡胶树生长发育中的结构和功能打下良好基础。     

维甲酸对SK-N-SH细胞增殖和相关基因表达的影响

目的:研究维甲酸对SK-N-SH细胞的增殖和相关基因表达的影响.方法:通过苔盼蓝排除法绘制细胞生长曲线、流式细胞技术测定细胞周期、HE染色光镜观察细胞形态改变以及SABC免疫细胞化学梁色法观察维甲酸对SK-N-SH相关癌基因、抑癌基因表达的影响.结果:1μmol/LRA处理后,SK-N-SH细胞的增殖活动受到明显的抑制,处理第7天抑制率达36.16%;周期测定显示处理后出现明显的G0/G1期阻滞,由对照组的49.7%增加至62.7%,增加了26.2%;免疫细胞化学染色结果显示,处理后细胞癌基因c-myc、c-fos的表达较对照组明显降低,而抑癌基因p53、p27的表达则有所加强.结论:维甲酸能有效抑制SK-N-SH细胞的增殖活动,其对细胞的增殖抑制作用与RA下调c-myc、c-fos等癌基因以及上调p53、p27等抑癌基因的表达有关.