Group II and group III introns of twintrons: potential relationships with nuclear pre-mRNA introns

Two new and important features of introns have emerged from analysis of the Euglena gracilis chloroplast genome. One is a new class of introns, designated group III, that may be the closest contemporaries to nuclear pre-mRNA introns. The second is introns that are interrupted by other introns termed twintrons.     

Growth decline linked to warming-induced water limitation in hemi-boreal forests

Hemi-boreal forests, which make up the transition from temperate deciduous forests to boreal forests in southern Siberia, have experienced significant warming without any accompanying increase in precipitation during the last 80 years. This climatic change could have a profound impact on tree growth and on the stability of forest ecosystems in this region, but at present evidence for these impacts is lacking. In this study, we report a recent dramatic decline in the growth of hemi-boreal forests, based on ring width measurements from three dominant tree-species (Pinus sylvestris, Larix sibirica and Larix gmelinii), sampled from eight sites in the region. We found that regional tree growth has become increasingly limited by low soil water content in the pre- and early-growing season (from October of the previous year to July of the current year) over the past 80 years. A warming-induced reduction in soil water content has also increased the climate sensitivity of these three tree species. Beginning in the mid-1980s, a clear decline in growth is evident for both the pine forests and the larch forests, although there are increasing trends in the proxy of soil water use efficiencies. Our findings are consistent with those from other parts of the world and provide valuable insights into the regional carbon cycle and vegetation dynamics, and should be useful for devising adaptive forest management strategies.     

The rise and falls of introns

There has been a lively debate over the evolution of eukaryote introns: at what point in the tree of life did they appear and from where, and what has been their subsequent pattern of loss and gain? A diverse range of recent research papers is relevant to this debate, and it is timely to bring them together. The absence of introns that are not self-splicing in prokaryotes and several other lines of evidence suggest an ancient eukaryotic origin for these introns, and the subsequent gain and loss of introns appears to be an ongoing process in many organisms. Some introns are now functionally important and there have been suggestions that invoke natural selection for the ancient and recent gain of introns, but it is also possible that fixation and loss of introns can occur in the absence of positive selection.     

Origin and evolution of spliceosomal introns

ABSTRACT: Evolution of exon-intron structure of eukaryotic genes has been a matter of long-standing, intensive debate. The introns-early concept, later rebranded 'introns first' held that protein-coding genes were interrupted by numerous introns even at the earliest stages of life's evolution and that introns played a major role in the origin of proteins by facilitating recombination of sequences coding for small protein/peptide modules. The introns-late concept held that introns emerged only in eukaryotes and new introns have been accumulating continuously throughout eukaryotic evolution. Analysis of orthologous genes from completely sequenced eukaryotic genomes revealed numerous shared intron positions in orthologous genes from animals and plants and even between animals, plants and protists, suggesting that many ancestral introns have persisted since the last eukaryotic common ancestor (LECA). Reconstructions of intron gain and loss using the growing collection of genomes of diverse eukaryotes and increasingly advanced probabilistic models convincingly show that the LECA and the ancestors of each eukaryotic supergroup had intron-rich genes, with intron densities comparable to those in the most intron-rich modern genomes such as those of vertebrates. The subsequent evolution in most lineages of eukaryotes involved primarily loss of introns, with only a few episodes of substantial intron gain that might have accompanied major evolutionary innovations such as the origin of metazoa. The original invasion of self-splicing Group II introns, presumably originating from the mitochondrial endosymbiont, into the genome of the emerging eukaryote might have been a key factor of eukaryogenesis that in particular triggered the origin of endomembranes and the nucleus. Conversely, splicing errors gave rise to alternative splicing, a major contribution to the biological complexity of multicellular eukaryotes. There is no indication that any prokaryote has ever possessed a spliceosome or introns in protein-coding genes, other than relatively rare mobile self-splicing introns. Thus, the introns-first scenario is not supported by any evidence but exon-intron structure of protein-coding genes appears to have evolved concomitantly with the eukaryotic cell, and introns were a major factor of evolution throughout the history of eukaryotes. This article was reviewed by I. King Jordan, Manuel Irimia (nominated by Anthony Poole), Tobias Mourier (nominated by Anthony Poole), and Fyodor Kondrashov. For the complete reports, see the Reviewers' Reports section.     

Split gene origin and periodic introns

The introns-early view has been challenged for several genes; prominent instances are triose phosphate isomerase (TPI), aldolase, pyruvate kinase (PK), alcohol dehydrogenase (ADH), glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and myosin heavy chain. While some of their introns appear to be phylogenetically ancient and/or to delineate exons corresponding to protein modules, a considerable number seemingly do not. But it is argued here that many of these anomalous introns are periodic, that is, relics of internal sequence repetitions within the ancestral gene. Some of these periodic-intron patterns are shared between related genes, as in the alphabeta -barrels of TPI, aldolase and PK, or the Rossmann nucleotide-binding domain common to PK, ADH and GAPDH. This is further evidence for the ancestral status of these introns. The myosin heavy chain C-terminal rod region is paradoxical in that its sequence is clearly periodic but its intron placements are not; however, they exhibit a remarkable coherence of intron translational phases, suggesting that these introns may also have originally had a periodic arrangement now obscured by intron slipping.     

Computational identification of functional introns: high positional conservation of introns that harbor RNA genes

An appreciable fraction of introns is thought to have some function, but there is no obvious way to predict which specific intron is likely to be functional. We hypothesize that functional introns experience a different selection regime than non-functional ones and will therefore show distinct evolutionary histories. In particular, we expect functional introns to be more resistant to loss, and that this would be reflected in high conservation of their position with respect to the coding sequence. To test this hypothesis, we focused on introns whose function comes about from microRNAs and snoRNAs that are embedded within their sequence. We built a data set of orthologous genes across 28 eukaryotic species, reconstructed the evolutionary histories of their introns and compared functional introns with the rest of the introns. We found that, indeed, the position of microRNA- and snoRNA-bearing introns is significantly more conserved. In addition, we found that both families of RNA genes settled within introns early during metazoan evolution. We identified several easily computable intronic properties that can be used to detect functional introns in general, thereby suggesting a new strategy to pinpoint non-coding cellular functions.     

The recent origins of introns

Accumulating evidence that introns are highly restricted in their phylogenetic distribution strongly supports the view that introns were inserted late in eukaryotic evolution into preformed genes and, hence, that exon-shuffling played no role in the assembly of primordial genes. Potential mechanisms of intron insertion and the possible evolution of nuclear introns and their splicing machinery from self-splicing group II introns are also discussed.     

Periodicities in introns.

The sequence information for the splicing process of introns is found in the consensus sequences at the two splice sites. For long introns, of 300 or more nucleotides, the middle regions may provide additional specificity for splicing which can be investigated by defining an adequate quantitative parameter. This methodology permits to retrieve the coding periodicity in the viral and mitochondrial introns and to identify with a statistical significance, a surprising alternating purine-pyrimidine base sequence -i.e. a modulo 2 periodicity- in the eukaryotic introns, and particularly in the vertebrate introns. This alternating structure suggests that the vertebrate introns do not have the genetic information to code for proteins, they carry structural and regulatory functions.     

In search of lost introns

Many fundamental questions concerning the emergence and subsequent evolution of eukaryotic exon-intron organization are still unsettled. Genome-scale comparative studies, which can shed light on crucial aspects of eukaryotic evolution, require adequate computational tools. We describe novel computational methods for studying spliceosomal intron evolution. Our goal is to give a reliable characterization of the dynamics of intron evolution. Our algorithmic innovations address the identification of orthologous introns, and the likelihood-based analysis of intron data. We discuss a compression method for the evaluation of the likelihood function, which is noteworthy for phylogenetic likelihood problems in general. We prove that after O(n l) preprocessing time, subsequent evaluations take O(n l/log l) time almost surely in the Yule-Harding random model of n-taxon phylogenies, where l is the input sequence length. We illustrate the practicality of our methods by compiling and analyzing a data set involving 18 eukaryotes, which is more than in any other study to date. The study yields the surprising result that ancestral eukaryotes were fairly intron-rich. For example, the bilaterian ancestor is estimated to have had more than 90% as many introns as vertebrates do now. AVAILABILITY: The Java implementations of the algorithms are publicly available from the corresponding author's site http://www.iro.umontreal.ca/~csuros/introns/. Data are available on request.     

The ins and outs of group II introns

Group II introns have attracted considerable attention as ribozymes, mobile genetic elements and possible progenitors of nuclear spliceosomal introns. Major advances in understanding their catalytic structure and dispersal strategies have recently come from several model mitochondrial and bacterial self-splicing introns. In Nature, this family of introns shows wide variation in both features and behaviour, and this review includes a focus on the diversity of evolutionary pathways taken.     

Compartmentalized isozyme genes and the origin of introns

Summary Both the mouse cytosolic malate dehydrogenase gene and its mitochondrial counterpart contain eight introns, of which two are present at identical positions between the isozyme genes. The probability that the two intron positions coincide by chance between the two genes has been shown to be significantly small (=1.3×10^–3), suggesting that the conservation of the intron positions has a biological significance. On the basis of a rooted phylogenetic tree inferred from a comparison of these isozymes and lactate dehydrogenases, we have shown that the origins of the conserved introns are very old, possibly going back to a date before the divergence of eubacteria, archaebacteria, and eukaryotes. In the aspartate aminotransferase isozyme genes, five of the introns are at identical places. The origins of the five conserved introns, however, are not obvious at present. It remains possible that some or all of the conserved introns have evolved after the divergence of eubacteria and eukaryotes.     

The role of introns in evolution

What are the roles of 'classical' introns in the evolution of nuclear genes, and what was the origin of these introns? Exon shuffling has been important in the evolution of cell surface and extracellular proteins, but the evidence for it in respect of intracellular proteins is weak. Intron distributions imply that some introns have been removed while others have been inserted in the course of evolution: ancestral patterns of introns may thus have been obscured. Recent evidence on the self-splicing and reverse-splicing abilities of Group II introns supports the hypothesis that these could have been the ancestors of classical introns.     

Exon size distribution and the origin of introns

Since it was first recognised that eukaryotic genes are fragmented into coding segments (exons) separated by non-coding segments (introns), the reason for this phenomenon has been debated. There are two dominant theories: that the piecewise arrangement of genes allows functional protein domains, represented by exons, to recombine by shuffling to form novel proteins with combinations of functions; or that introns represent parasitic DNA that can infest the eukaryotic genome because it does not interfere grossly with the fitness of its host. Differing distributions of exon lengths are predicted by these two theories. In this paper we examine distributions of exon lengths for six different organisms and find that they offer empirical evidence that both theories may in part be correct.     

Identification of a family of group II introns encoding LAGLIDADG ORFs typical of group I introns

Group I and group II introns are unrelated classes of introns that each encode proteins that facilitate intron splicing and intron mobility. Here we describe a new subfamily of nine introns in fungi that are group II introns but encode LAGLIDADG ORFs typical of group I introns. The introns have fairly standard group IIB1 RNA structures and are inserted into three different sites in SSU and LSU rRNA genes. Therefore, introns should not be assumed to be group I introns based solely on the presence of a LAGLIDADG ORF.     

甘肃、新疆、内蒙苹果蠹蛾成虫消长规律

苹果蠹蛾Cydia pomonella(L.)是我国重要的果树害虫和检疫对象。2005年至2010年,本研究在甘肃、新疆及内蒙古的不同区县选取了16个果园,使用性信息素诱捕器对其中的苹果蠹蛾成虫发生规律进行长期监测。结果表明,苹果蠹蛾在西北地区每年发生2.5个世代;在正常气候条件下,3个成虫发生高峰分别出现在5月上旬、7月中下旬和8月中下旬,但不同地区及同一地区不同果园之间存在较大差异;化学防治、迷向防治等防治措施对苹果蠹蛾成虫捕获量的影响较大,因此生活史研究为主的监测并不适合在上述果园中开展。综合上述研究结果,未对苹果蠹蛾的季节动态进行准确的预测,需要对苹果蠹蛾除成虫外的其他虫态的季节性变化进行详细研究,并建议选择3个以上的果园进行监测,综合各个果园的监测结果并得出结论。