Evolution of the gonadotropin-releasing hormone (GnRH) gene family in relation to vertebrate tetraploidizations

The neuropeptide gonadotropin-releasing hormone (GnRH) plays an important role in the control of reproductive functions. Vertebrates possess multiple GnRH isoforms that are classified into three main groups, namely GnRH1, GnRH2 and GnRH3. In the present study, we show that the chromosomal organization of the three GnRH loci is very well conserved among gnathostome species. We analyzed genes belonging to several other multigenic families that are present in the vicinity of GnRH genes. Five of them were seen to occur in four chromosomal regions that clearly form a paralogon. Moreover, we show that the homologous regions in the amphioxus genome are present on a single locus. Taken together, these observations indicate that GnRH1, GnRH2 and GnRH3 genes represent three paralogous genes that resulted from the two rounds of tetraploidization that took place early in vertebrate evolution. They confirm that the GnRH3 gene which is currently known only in teleost has most likely been lost in the tetrapod lineage. Finally, they suggest the existence of a fourth GnRH gene, named GnRH4. Whether the GnRH4 gene still exists in extant vertebrates is currently unknown. A search for this putative gene would be particularly useful in basal groups such as agnathans and cartilaginous fish.     

Organization of the prolamin gene family provides insight into the evolution of the maize genome and gene duplications in grass species

Zea mays, commonly known as corn, is perhaps the most greatly produced crop in terms of tonnage and a major food, feed, and biofuel resource. Here we analyzed its prolamin gene family, encoding the major seed storage proteins, as a model for gene evolution by syntenic alignments with sorghum and rice, two genomes that have been sequenced recently. Because a high-density gene map has been constructed for maize inbred B73, all prolamin gene copies can be identified in their chromosomal context. Alignment of respective chromosomal regions of these species via conserved genes allow us to identify the pedigree of prolamin gene copies in space and time. Its youngest and largest gene family, the alpha prolamins, arose about 22–26 million years ago (Mya) after the split of the Panicoideae (including maize, sorghum, and millet) from the Pooideae (including wheat, barley, and oats) and Oryzoideae (rice). The first dispersal of alpha prolamin gene copies occurred before the split of the progenitors of maize and sorghum about 11.9 Mya. One of the two progenitors of maize gained a new alpha zein locus, absent in the other lineage, to form a nonduplicated locus in maize after allotetraplodization about 4.8 Mya. But dispersed copies gave rise to tandem duplications through uneven expansion and gene silencing of this gene family in maize and sorghum, possibly because of maize's greater recombination and mutation rates resulting from its diploidization process. Interestingly, new gene loci in maize represent junctions of ancestral chromosome fragments and sites of new centromeres in sorghum and rice.     

日本血吸虫组蛋白基因家族分子进化分析

目的从日本血吸虫(Schistosoma japonicum)组蛋白的基因家族进化方面入手,对其基因家族的分子系统发育、共线性关系和基因倍增模式进行分析。方法下载3种主要致病血吸虫的全基因组序列数据及外源物种基因序列,经Blastp软件比对找出组蛋白各家族基因序列,经多序列比对构建系统进化树,计算选择压力指数(Ka/Ks)。使用基因序列与基因组比对并定位,分析同源基因的共线性关系。结果日本血吸虫基因组共包含组蛋白基因38条,分为5个子家族,分布在25个scaffold上。通过进化树分析共检测到基因倍增事件34次,推定基因丢失事件17次,其中H3和H4的倍增早在血吸虫物种形成之前已经完成。日本血吸虫组蛋白的倍增机制主要是DNA复制性转座,使得组蛋白在进化保守的同时还出现了更特异性的分化,从而携带更多组蛋白密码或其他修饰信息以应对较复杂的生命周期。结论日本血吸虫的组蛋白各子家族多数倍增事件发生在从血吸虫亚洲起源后到进入非洲分化出曼氏血吸虫之前的这段时间内,表明基因倍增是血吸虫应对环境压力的重要手段。日本血吸虫的组蛋白倍增完全来自于DNA序列的复制性转座,且净化选择占主导因素,表明增强适应性的功能分化是基因进化最主要的驱动力。     

B-type natriuretic peptide (BNP), not ANP, is the principal cardiac natriuretic peptide in vertebrates as revealed by comparative studies

The natriuretic peptide (NP) family consists of at least seven members; cardiac ANP, BNP and VNP and brain CNPs (CNP1-4). Phylogenetic and comparative genomic analyses showed that CNP4 is the ancestral molecule of the family, from which CNP3 and CNP1/2 were duplicated in this order, and that the three cardiac NPs were generated from CNP3 by tandem duplication. Seven members existed at the divergence of ray-finned fishes and lobe-finned fishes (tetrapods), but some of the NP genes have disappeared during the course of evolution. In ray-finned fishes, all three cardiac NPs exist in chondrostei and some migratory teleost species, but VNP is generally absent and ANP is absent in a group of teleosts (Beloniformes). In tetrapods, ANP and BNP are present in mammals and amphibians, but ANP is usually absent in reptiles and birds. Thus, BNP is a ubiquitous cardiac NP in bony fishes and tetrapods though elasmobranchs and cyclostomes have only CNP3/4 as a cardiac NP.Functional studies indicate that cardiac NPs are essential Na⁺-extruding hormones throughout vertebrates; they play critical roles in seawater (SW) adaptation in teleosts, while they are important volume-depleting hormones in mammals as water and Na⁺ are regulated in parallel in terrestrial animals. In mammals, cardiac NPs become prominent in pathological conditions such as heart failure where they are used in diagnosis and treatment. Although the functional role of BNP has not yet been fully elucidated compared with ANP in non-mammalian vertebrates, it appears that BNP plays pivotal roles in the cardiovascular and body fluid regulation as shown in mammals. ANP has previously been recognized as the principal cardiac NP in mammals and teleosts, but comparative studies have revealed that BNP is the only cardiac NP that exists in all tetrapods and teleosts. This is an excellent example showing that comparative studies have created new insights into the molecular and functional evolution of a hormone family.     

New insight into the evolution of the vertebrate respiratory system and the discovery of unidirectional airflow in iguana lungs

The generally accepted framework for the evolution of a key feature of the avian respiratory system, unidirectional airflow, is that it is an adaptation for efficiency of gas exchange and expanded aerobic capacities, and therefore it has historically been viewed as important to the ability of birds to fly and to maintain an endothermic metabolism. This pattern of flow has been presumed to arise from specific features of the respiratory system, such as an enclosed intrapulmonary bronchus and parabronchi. Here we show unidirectional airflow in the green iguana, a lizard with a strikingly different natural history from that of birds and lacking these anatomical features. This discovery indicates a paradigm shift is needed. The selective drivers of the trait, its date of origin, and the fundamental aerodynamic mechanisms by which unidirectional flow arises must be reassessed to be congruent with the natural history of this lineage. Unidirectional flow may serve functions other than expanded aerobic capacity; it may have been present in the ancestral diapsid; and it can occur in structurally simple lungs.Energetically demanding forms of locomotion, such as powered flight, require a great capacity for gas exchange and selection for aerobic stamina may underlie many unique features of the avian respiratory system (1, 2). The avian respiratory system consists of highly vascularized lungs and avascular air sacs, which are membranous structures that effect ventilation and, in some species, extend between the muscles and even enter the bones (3). The topography of the conducting airways is complex; they form a circular system of tubes, analogous to the loop formed by the blood circulatory system in which arteries connect to veins through numerous small diameter vessels, the capillaries. Likewise, the avian conducting airways connect to each other through numerous tubules, the parabronchi, to form a circular path for respiratory gases (3). Gases flow through most of the parabronchi in the same direction during both inhalation and exhalation (unidirectional flow). This is due to the presence of aerodynamic valves (4–10). In contrast, the mammalian conducting airways arborize with the branch tips ending in blind sacs, there are no valves, and gases travel in the opposite direction along the conducting airways during expiration from the direction followed during inspiration (tidal flow). The presence of aerodynamic valves and unidirectional flow has generally been thought to be a highly derived feature found, among extant animals, only in birds and having evolved either in the crown group with flight or somewhere along the saurischian lineage leading to birds (11), perhaps as a mechanism to meet the high energetic demands of endothermy.The discovery of unidirectional flow in the lungs of alligators (12, 13) and the savannah monitor lizard (14) indicates that we do not understand the distribution of this phenomenon among different lineages of vertebrates and raises questions about its underlying value. It is possible that unidirectional flow evolved convergently in crocodilians and monitor lizards and serves to expand aerobic capacity. Although monitor lizards are ectotherms, their lifestyles are largely convergent with small predatory mammals (15) and they have high aerobic capacities compared with other lizards (16). In contrast, extant alligators have limited aerobic stamina (17) but their common ancestor with birds may have had a great aerobic capacity (18) or may have been endothermic (19, 20). Crocodilians and monitor lizards also share a suite of features of their pulmonary and cardiac anatomy that have been purported to give rise to, or coevolve with, birdlike patterns of flow. These features are: (i) a bronchus that has grown deep into the lung as a mesobronchium, (ii) partitioning of the respiratory system into a mechanical part that functions in ventilation and a gas-exchanging region, (iii) intercameral perforations, and (iv) separation of the heart into right and left sides (1, 21). Crocodilians and monitors are also derived in having evolved mechanisms to supplement costal ventilation while exercising (18, 22, 23). Thus, unidirectional flow in these lineages may be one of many derived traits underpinning exceptionally high rates of oxygen consumption during activity.It is also possible, however, that this pattern of flow evolved before the split of Diapsida into the Lepidosauromorpha (tuatara, lizards, snakes) and Archosauromorpha (crocodilians and birds) in an ectothermic ancestor lacking expanded aerobic capacities and living as long ago as the Permian Period. Unidirectional flow has been purported to serve ectotherms by harnessing the heart as a pump for air during periods of breath-holding (apnea) (12). Light can be shed on this pattern of evolution with observations of more squamates (snakes, lizards), which are the most diverse and largest (∼9,000 species) group of living reptiles (24).To test the hypothesis that unidirectional flow is present in squamates other than varanid lizards; to better understand anatomical features that give rise to these patterns of flow; and to gain insight into the underlying value of this pattern of flow, green iguanas (Iguana iguana) were studied. Green iguanas differ from monitors because they are herbivores and because they have structurally simple lungs that lack an enclosed intrapulmonary bronchus. Iguanas lack septation of the cardiac ventricle and have poor locomotor stamina. The poor stamina is due in part from an impairment during running in their blood and air circulatory systems (19, 25, 26).     

Estradiol reduces pituitary responsiveness to somatostatin (SRIF-14) and down-regulates the expression of somatostatin sst2 receptors in female goldfish pituitary

Sex steroid hormones have been shown to regulate somatostatin (SRIF) gene expression in goldfish brain, which in turn influences the regulation of GH secretion. In this study, the influences of sex steroids on pituitary responsiveness to SRIF-14 and the pituitary expression of a type two SRIF receptor (sst(2)) were examined. Results from in vitro perifusion of pituitary fragments show that pituitaries from estradiol-primed sexually regressed female fish have significantly lower GH release responsiveness to pulse exposure to SRIF-14 than pituitaries from control or testosterone-treated sexually regressed females. Results from in vitro static culture show that pituitaries from sexually mature female fish have lower GH release responsiveness to SRIF-14 than those from sexually regressed females. In addition, the sst(2) receptor mRNA levels in pituitaries from mature and recrudescent female fish are significantly lower than in sexually regressed female fish. Our results indicate that estradiol acts at the level of the pituitary to regulate GH secretion by influencing the responsiveness to SRIF-14. The underlying mechanism includes, in part, reduction of the expression of sst(2) receptors, presumably leading to the lower number of the receptors available for SRIF binding.     

比较基因组学在蓝氏贾第鞭毛虫进化研究中的应用新进展

蓝氏贾第鞭毛虫(简称贾第虫)作为一种古老的真核生物,在生物进化过程中的地位举足轻重。比较基因组学能够在基因组水平上深入认识贾第虫的进化关系,进一步明确贾第虫在生物进化中的地位。本文对比较基因组学的主要研究方法进行综述,同时介绍比较基因组学在贾第虫生物进化研究中的应用,对贾第虫比较基因组学的发展进行展望。     

中国卫氏并殖吸虫分子鉴定和遗传进化的研究概况

卫氏并殖吸虫病是我国重要的食源性寄生虫病之一,其病原体通过蝲蛄、溪蟹传播,可寄生于人体及多种哺乳动物组织、脏器内,引起肺吸虫病。我国是重要的卫氏并殖吸虫分布国度,有25个省(市、自治区)有分布卫氏并殖吸虫的报告。在卫氏并殖吸虫分类地位的研究中,仅靠形态学技术很难全面揭示该虫种的分子多样性。近些年来,随着分子生物学技术的发展,采用各种分子方法对卫氏并殖吸虫进行分类和鉴定的技术展现出很大的优势。分子遗传技术的应用也为阐明卫氏并殖吸虫的生物学、流行病学和遗传学特性提供了有效的手段和方法。但是,这些分子方法的敏感性和特异性以及其检测时间和花费又有着明显的差异,需要根据不同的研究场合使用相应的方法。分子方法的应用能更好地揭示卫氏并殖吸虫的流行病学和进化的特性,并能为该虫引起的疾病提供更为有效的诊断方法和防控手段。因此,该文概述了我国用于卫氏并殖吸虫分子鉴定和遗传进化的分子手段和方法。     

Unique scorpion toxin with a putative ancestral fold provides insight into evolution of the inhibitor cystine knot motif

The three-disulfide inhibitor cystine knot (ICK) motif is a fold common to venom peptides from spiders, scorpions, and aquatic cone snails. Over a decade ago it was proposed that the ICK motif is an elaboration of an ancestral two-disulfide fold coined the disulfide-directed β-hairpin (DDH). Here we report the isolation, characterization, and structure of a novel toxin [U(1)-liotoxin-Lw1a (U(1)-LITX-Lw1a)] from the venom of the scorpion Liocheles waigiensis that is the first example of a native peptide that adopts the DDH fold. U(1)-LITX-Lw1a not only represents the discovery of a missing link in venom protein evolution, it is the first member of a fourth structural fold to be adopted by scorpion-venom peptides. Additionally, we show that U(1)-LITX-Lw1a has potent insecticidal activity across a broad range of insect pest species, thereby providing a unique structural scaffold for bioinsecticide development.     

Accelerated protein evolution analysis reveals genes and pathways associated with the evolution of mammalian longevity

The genetic basis of the large species differences in longevity and aging remains a mystery. Thanks to recent large-scale genome sequencing efforts, the genomes of multiple species have been sequenced and can be used for cross-species comparisons to study species divergence in longevity. By analyzing proteins under accelerated evolution in several mammalian lineages where maximum lifespan increased, we identified genes and processes that are candidate targets of selection when longevity evolves. We identified several proteins with longevity-specific selection patterns, including COL3A1 that has previously been related to aging and proteins related to DNA damage repair and response such as DDB1 and CAPNS1. Moreover, we found that processes such as lipid metabolism and cholesterol catabolism show such patterns of selection and suggest a link between the evolution of lipid metabolism, cholesterol catabolism, and the evolution of longevity. Lastly, we found evidence that the proteasome–ubiquitin system is under selection specific to lineages where longevity increased and suggest that its selection had a role in the evolution of longevity. These results provide evidence that natural selection acts on species when longevity evolves, give insights into adaptive genetic changes associated with the evolution of longevity in mammals, and provide evidence that at least some repair systems are selected for when longevity increases.     

The next step in gene delivery: molecular engineering of adeno-associated virus serotypes

Delivery is at the heart of gene therapy. Viral DNA delivery systems are asked to avoid the immune system, transduce specific target cell types while avoiding other cell types, infect dividing and non-dividing cells, insert their cargo within the host genome without mutagenesis or to remain episomal, and efficiently express transgenes for a substantial portion of a lifespan. These sought-after features cannot be associated with a single delivery system, or can they? The Adeno-associated virus family of gene delivery vehicles has proven to be highly malleable. Pseudotyping, using AAV serotype 2 terminal repeats to generate designer shells capable of transducing selected cell types, enables the packaging of common genomes into multiple serotypes virions to directly compare gene expression and tropism. In this review the ability to manipulate this virus will be examined from the inside out. The influence of host cell factors and organism biology including the immune response on the molecular fate of the viral genome will be discussed as well as differences in cellular trafficking patterns and uncoating properties that influence serotype transduction. Re-engineering the prototype vector AAV2 using epitope insertion, chemical modification, and molecular evolution not only demonstrated the flexibility of the best-studied serotype, but now also expanded the tool kit for molecular modification of all AAV serotypes. Current AAV research has changed its focus from examination of wild-type AAV biology to the feedback of host cell/organism on the design and development of a new generation of recombinant AAV delivery vehicles. This article is part of a Special Section entitled “Special Section: Cardiovascular Gene Therapy”.     

Evolution of the neuropeptide Y family: new genes by chromosome duplications in early vertebrates and in teleost fishes

Despite sequence information from many vertebrates the evolution of the neuropeptide Y (NPY) family of peptides has been difficult to resolve, particularly among ray-finned fishes. We have used chromosomal location and sequence analyses to identify orthologs and gene duplicates in teleost fish genomes. Our analyses support origin of NPY and peptide YY (PYY) from a common ancestor in early vertebrate evolution through a chromosome duplication. We report here that the teleost tetraploidization generated duplicates of both NPY and PYY and that all four genes are still present in the two sequenced pufferfish genomes Tetraodon nigroviridis and Takifugu rubripes as well as three-spined stickleback, Gasterosteus aculeatus. The zebrafish Danio rerio NPYb gene has probably been lost whereas medaka, Oryzias latipes seems to lack PYYb. Some of the previously published PYY sequences were misidentified and actually constitute NPYb. Our analyses confirm that the peptide previously named PY in some fish species is a duplicate of the PYY gene and hence should be called PYYb. The NPYa and NPYb genes in Takifugu rubripes are predominantly expressed in brain, as detected by RT-PCR, whereas PYYa and PYYb are expressed in several organs including brain, intestine and gonads. Thus, also the resemblance in expression pattern supports the fish gene duplication scenario. Our study shows that when sequence comparisons give ambiguous results, chromosomal location can serve as a useful criterion to identify orthologs. This strategy may help to resolve relationships in several families of short peptides.     

Crustacean neuropeptide genes of the CHH/MIH/GIH family: implications from molecular studies

The crustacean eyestalk CHH/MIH/GIH gene family represents a unique group of neuropeptide originally identified in crustaceans. These neuropeptides shared a high degree of amino acid identity, and the conservation of cysteine residues at the same relative positions. Based on their biological, biochemical, and molecular properties, they can be divided into the CHH and MIH subtypes with two major members in each subtype. In the shrimp, the CHH-subtypes can be divided into two forms (CHH-A and CHH-B). The CHH-A gene also comprises several isoforms which shared a high overall sequence identity. Although the MIH subtypes are postulated to have evolved from the CHH subtypes, the number of major MIH subtypes in each species has yet to be confirmed. While most of the genes consist of the basic plan of three exons and two introns, other alternative spliced variants have recently been described. Moreover, these alternative forms are usually expressed in non-eyestalk tissues. These findings suggest that these neuropeptides may have a broader spectrum of functions in crustaceans. The results from phylogenetic analysis suggest that the evolution of this group of neuropeptides occurs in a manner similar is to the gene duplication and mutation events hypothesized for the origin of the prolactin and growth hormone gene family of the vertebrate pituitary system.     

The evolution of courtship behaviors through the origination of a new gene in Drosophila

New genes can originate by the combination of sequences from unrelated genes or their duplicates to form a chimeric structure. These chimeric genes often evolve rapidly, suggesting that they undergo adaptive evolution and may therefore be involved in novel phenotypes. Their functions, however, are rarely known. Here, we describe the phenotypic effects of a chimeric gene, sphinx, that has recently evolved in Drosophila melanogaster. We show that a knockout of this gene leads to increased male-male courtship in D. melanogaster, although it leaves other aspects of mating behavior unchanged. Comparative studies of courtship behavior in other closely related Drosophila species suggest that this mutant phenotype of male-male courtship is the ancestral condition because these related species show much higher levels of male-male courtship than D. melanogaster. D. melanogaster therefore seems to have evolved in its courtship behaviors by the recruitment of a new chimeric gene.     

Structural insight into the reaction mechanism and evolution of cytokinin biosynthesis

The phytohormone cytokinin regulates plant growth and development. This hormone is also synthesized by some phytopathogenic bacteria, such as Agrobacterium tumefaciens, and is as a key factor in the formation of plant tumors. The rate-limiting step of cytokinin biosynthesis is catalyzed by adenosine phosphate-isopentenyltransferase (IPT). Agrobacterium IPT has a unique substrate specificity that enables it to increase trans-zeatin production by recruiting a metabolic intermediate of the host plant's biosynthetic pathway. Here, we show the crystal structures of Tzs, an IPT from A. tumefaciens, complexed with AMP and a prenyl-donor analogue, dimethylallyl S-thiodiphosphate. The structures reveal that the carbon-nitrogen-based prenylation proceeds by the SN2-reaction mechanism. Site-directed mutagenesis was used to determine the amino acid residues, Asp-173 and His-214, which are responsible for differences in prenyl-donor substrate specificity between plant and bacterial IPTs. IPT and the p loop-containing nucleoside triphosphate hydrolases likely evolved from a common ancestral protein. Despite structural similarities, IPT has evolved a distinct role in which the p loop transfers a prenyl moiety in cytokinin biosynthesis.     

Effect of somatostatin analogue octreotide injected into the third cerebral ventricle on pentagastrin-induced gastric acid secretion in rats

AIM: To investigate the effect of long-lasting somatostatin analogue octreotide (Oct) injected into the third cerebral ventricle (TCV) on gastric acid secretion in rats. METHODS: TCVs were cannulated in male Wistar rats anesthetized with sodium pentobarbital. One week later acute gastric lumen perfusion was carried out and gastric acid was continuously washed with 37℃saline by a perfusion pump. Gastric perfusion samples were collected every 10 min and titrated by 0.01 moL/L NaOH to neutral. On the basis of subcutaneous (sc) injection of pentagastrin (G-5, 160μg/kg), Oct (0.025μg, 0.05μg, 0.1μg, n = 12 in each group) or vehicle (pyrogen-free physiological saline, n = 10) was injected into the TCV. Before and after the TCV injection, 1 h total acid output (TAO) was determined and experimental data were expressed in change rate (%) of TAO. RESULTS: Oct (0.025, 0.05 and 0.1μg) injected into the TCV resulted in change rate of 1.56% (P>0.05), 20.21% (P< 0.01) and 37.82% of TAO (P< 0.001), respectively. Moreover, comparison in change rate of TAO among these 3 doses showed P< 0.05 between 0.025μg and 0.05μg, P< 0.01 between 0.025μg and 0.1μg, and P< 0.05 between 0.05μg and 0.1μg. However, sc injection of 0.05μg Oct had no effect on G-5 stimulated gastric acid secretion. CONCLUSION: Octreotide injected into the third cerebral ventricle inhibits gastrin-induced gastric acid se cretion in a dose-dependent manner.     

Whole-genome comparison of disease and carriage strains provides insights into virulence evolution in Neisseria meningitidis

Neisseria meningitidis is a leading cause of infectious childhood mortality worldwide. Most research efforts have hitherto focused on disease isolates belonging to only a few hypervirulent clonal lineages. However, up to 10% of the healthy human population is temporarily colonized by genetically diverse strains mostly with little or no pathogenic potential. Currently, little is known about the biology of carriage strains and their evolutionary relationship with disease isolates. The expression of a polysaccharide capsule is the only trait that has been convincingly linked to the pathogenic potential of N. meningitidis. To gain insight into the evolution of virulence traits in this species, whole-genome sequences of three meningococcal carriage isolates were obtained. Gene content comparisons with the available genome sequences from three disease isolates indicate that there is no core pathogenome in N. meningitidis. A comparison of the chromosome structure suggests that a filamentous prophage has mediated large chromosomal rearrangements and the translocation of some candidate virulence genes. Interspecific comparison of the available Neisseria genome sequences and dot blot hybridizations further indicate that the insertion sequence IS1655 is restricted only to N. meningitidis; its low sequence diversity is an indicator of an evolutionarily recent population bottleneck. A genome-based phylogenetic reconstruction provides evidence that N. meningitidis has emerged as an unencapsulated human commensal from a common ancestor with Neisseria gonorrhoeae and Neisseria lactamica and consecutively acquired the genes responsible for capsule synthesis via horizontal gene transfer.     

Phylogeny of endocytic components yields insight into the process of nonendosymbiotic organelle evolution

The process by which some eukaryotic organelles, for example the endomembrane system, evolved without endosymbiotic input remains poorly understood. This problem largely arises because many major cellular systems predate the last common eukaryotic ancestor (LCEA) and thus do not provide examples of organellogenesis in progress. A model is emerging whereby gene duplication and divergence of multiple "specificity-" or "identity-" encoding proteins for the various endomembranous organelles produced the diversity of nonendosymbiotically derived cellular compartments present in modern eukaryotes. To address this possibility, we analyzed three molecular components of the endocytic membrane-trafficking machinery. Phylogenetic analyses of the endocytic syntaxins, Rab 5, and the beta-adaptins each reveal a pattern of ancestral, undifferentiated endocytic homologues in the LCEA. Subsequently, these undifferentiated progenitors independently duplicated in widely divergent lineages, convergently producing components with similar endocytic roles, e.g., beta1 and beta2-adaptin. In contrast, beta3, beta4, and all other adaptin complex subunits, as well as paralogues of the syntaxins and Rabs specific for the other membrane-trafficking organelles, all evolved before the LCEA. Thus, the process giving rise to the differentiated organelles of the endocytic system appears to have been interrupted by the major speciation event that produced the extant eukaryotic lineages. These results suggest that although many endocytic components evolved before the LCEA, other major features evolved independently and convergently after diversification into the primary eukaryotic supergroups. This finding provides an example of a basic cellular system that was simpler in the LCEA than in many extant eukaryotes and yields insight into nonendosymbiotic organelle evolution.     

A korarchaeal genome reveals insights into the evolution of the Archaea

The candidate division Korarchaeota comprises a group of uncultivated microorganisms that, by their small subunit rRNA phylogeny, may have diverged early from the major archaeal phyla Crenarchaeota and Euryarchaeota. Here, we report the initial characterization of a member of the Korarchaeota with the proposed name, "Candidatus Korarchaeum cryptofilum," which exhibits an ultrathin filamentous morphology. To investigate possible ancestral relationships between deep-branching Korarchaeota and other phyla, we used whole-genome shotgun sequencing to construct a complete composite korarchaeal genome from enriched cells. The genome was assembled into a single contig 1.59 Mb in length with a G + C content of 49%. Of the 1,617 predicted protein-coding genes, 1,382 (85%) could be assigned to a revised set of archaeal Clusters of Orthologous Groups (COGs). The predicted gene functions suggest that the organism relies on a simple mode of peptide fermentation for carbon and energy and lacks the ability to synthesize de novo purines, CoA, and several other cofactors. Phylogenetic analyses based on conserved single genes and concatenated protein sequences positioned the korarchaeote as a deep archaeal lineage with an apparent affinity to the Crenarchaeota. However, the predicted gene content revealed that several conserved cellular systems, such as cell division, DNA replication, and tRNA maturation, resemble the counterparts in the Euryarchaeota. In light of the known composition of archaeal genomes, the Korarchaeota might have retained a set of cellular features that represents the ancestral archaeal form.