Parallel evolution of the genetic code in arthropod mitochondrial genomes

The genetic code provides the translation table necessary to transform the information contained in DNA into the language of proteins. In this table, a correspondence between each codon and each amino acid is established: tRNA is the main adaptor that links the two. Although the genetic code is nearly universal, several variants of this code have been described in a wide range of nuclear and organellar systems, especially in metazoan mitochondria. These variants are generally found by searching for conserved positions that consistently code for a specific alternative amino acid in a new species. We have devised an accurate computational method to automate these comparisons, and have tested it with 626 metazoan mitochondrial genomes. Our results indicate that several arthropods have a new genetic code and translate the codon AGG as lysine instead of serine (as in the invertebrate mitochondrial genetic code) or arginine (as in the standard genetic code). We have investigated the evolution of the genetic code in the arthropods and found several events of parallel evolution in which the AGG codon was reassigned between serine and lysine. Our analyses also revealed correlated evolution between the arthropod genetic codes and the tRNA-Lys/-Ser, which show specific point mutations at the anticodons. These rather simple mutations, together with a low usage of the AGG codon, might explain the recurrence of the AGG reassignments.     

Unusual genetic codes and a novel gene structure for tRNA(AGYSer) in starfish mitochondrial DNA

The nucleotide sequence of a 3849-bp fragment of starfish mitochondrial genome was determined. The genes for NADH dehydrogenase subunits 3, 4, 5, and COIII, and three kinds of (tRNA(UCNSer), tRNA(His), and tRNA(AGYSer) were identified by comparing with the genes of other animal mitochondria so far elucidated. The gene arrangement of starfish mitochondrial genome was different from those of vertebrate and insect mitochondrial genomes. Comparison of the protein-encoding nucleotide sequences of starfish mitochondria with those of other animal mitochondria suggested a unique genetic code in starfish mitochondrial genome; both AGA and AGG (arginine in the universal code) code for serine, AUA (isoleucine in the universal code but methionine in most mitochondrial systems) for isoleucine, and AAA (lysine) for asparagine. It was also inferred that these AGA and AGG codons are decoded by serine tRNA(AGYSer) originally corresponding to AGC and AGU codons. This situation is similar to the case of Drosophila mitochondrial genome. Variations in the use of AGA and AGG codons were discussed on the basis of the evolution of animals and decoding capacity of various tRNA(AGYSer) species possessing different sizes of the dihydrouridine (D) arm.     

Evolution of the mitochondrial genetic code IV. AAA as an asparagine codon in some animal mitochondria

Summary Differences in assignments from those in the universal genetic code occur in codes of mitochondria. In this report, the published sequences of the mitochondrial genes for COI and ND1 in a platyhelminth (Fasciola hepatica) are examined and it is concluded that AAA may be a codon for asparagine instead of lysine, whereas AAG is the sole codon for lysine in this species.     

Taurine-containing uridine modifications in tRNA anticodons are required to decipher non-universal genetic codes in ascidian mitochondria

Variations in the genetic code are found frequently in mitochondrial decoding systems. Four non-universal genetic codes are employed in ascidian mitochondria: AUA for Met, UGA for Trp, and AGA/AGG(AGR) for Gly. To clarify the decoding mechanism for the non-universal genetic codes, we isolated and analyzed mitochondrial tRNAs for Trp, Met, and Gly from an ascidian, Halocynthia roretzi. Mass spectrometric analysis identified 5-taurinomethyluridine (τm(5)U) at the anticodon wobble positions of tRNA(Met)(AUR), tRNA(Trp)(UGR), and tRNA(Gly)(AGR), suggesting that τm(5)U plays a critical role in the accurate deciphering of all four non-universal codes by preventing the misreading of pyrimidine-ending near-cognate codons (NNY) in their respective family boxes. Acquisition of the wobble modification appears to be a prerequisite for the genetic code alteration.     

线粒体遗传密码及基因组遗传密码的对称分析

病毒、细菌和真核生物的氨基酸编码都使用相同的遗传密码,表明它们可能有共同的来源。但人和牛的线粒体的遗传密码和基因组的遗传密码相比,出现以下不同;（1）ATA编码甲硫氮酸M而不是异亮氨酸I。（2）TGA不再是终止密码子X而编码色氨酸W。（3）AGA和AGG不再是精氨酸R的密码子而变为终止密码子X。应用高维空间拓扑分析的方法,对线粒体遗传密码和基因组遗传密码的6维编码空间进行对称性分析,得到如下结果：（1）线粒体遗传密码的起始密码子是2个而不是1个。（2）线粒体遗传密码的终止密码子是4个而不是3个。（3）线粒体遗传密码空间只有2、4、6三种偶数简并度而没1、3两种奇数简并度,表明其对称度较高。（4）线粒体遗传密码空间除丝氨酸S分成两个平行的子空间之外,终止密码子X亦分成两个平行的子空间,表明其连通度较低。（5）线粒体遗传密码一基因组遗传密码相比,共有3个简并平面出现变异,即：1001λλ（M和I）,011λ1λ（W和X）,以及1011λλ（S和X或S和R）。（6）基因组遗传密码的1、3两种奇数简并度可能来源于线粒体遗传密码的1001λλ平面和011λ1λ平面的对称性破缺。对线粒体遗传密码变异的生物学意义及遗传密码的起源进行了分析和讨论。     

Amino Acid Exchangeability and the Adaptive Code Hypothesis

Since the genetic code first was determined, many have claimed that it is organized adaptively, so as to assign similar codons to similar amino acids. This claim has proved difficult to establish due to the absence of relevant comparative data on alternative primordial codes and of objective measures of amino acid exchangeability. Here we use a recently developed measure of exchangeability to evaluate a null hypothesis and two alternative hypotheses about the adaptiveness of the genetic code. The null hypothesis that there is no tendency for exchangeable amino acids to be assigned to similar codons can be excluded here as expected from earlier work. The first alternative hypothesis is that any such correlation between codon distance and amino acid distance is due to incremental mechanisms of code evolution, and not to adaptation to reduce deleterious effects of future mutations. More specifically, new codon assignments that occur by ambiguity reduction or by codon capture will tend to give rise to correlations, whether due to the condition of amino acid ambiguity, or to the condition of similarity between a new tRNA synthetase (or tRNA) and its parent. The second alternative hypothesis, the adaptive hypothesis, then may be defined as an excess relative to what may be expected given the incremental nature of evolution, reflecting true adaptation for robustness rather than an incidental effect. The results reported here indicate that most of the nonrandomness in the amino acids to codon assignments can be explained by incremental code evolution, with a small residue of orderliness that may reflect code adaptation.     

The genetic code in bovine mitochondria: sequence of genes for the cytochrome oxidase subunit II and two tRNAs

Bovine-heart mitochondrial DNA from a single animal was isolated and fragments representative of the entire genome cloned into multicopy plasmid vectors to facilitate determination of its complete nucleotide sequence. We present here the sequence of the region covering the gene for cytochrome oxidase subunit II. Comparison of this sequence with the amino acid sequence of the homologous beef-heart protein has enabled the determination of most of the bovine mitochondrial genetic code. The code differs from the "universal" genetic code in that UGA codes for tryptophan and not termination, and AUA codes for methionine and not isoleucine. The only codon family not represented is the AGA/AGG pair normally used for arginine; evidence from other genes suggests that these code for termination in bovine mitochondria. The sequence presented also includes the adjacent tRNAAsp and tRNALys genes. The tRNAAsp gene is separated by one nucleotide from the 5' end of the COII gene and only three bases separate the 3' end of this gene and the adjacent tRNALys gene. This highly compact gene organisation is very similar to that found in the corresponding region of the human mitochondrial genome and the gene arrangement is identical. The structure of the respective bovine and human tRNAs vary primarily the "D-" and "T psi C-loops".     

The role of alternative genetic codes in viral evolution and emergence

Although the ‘universal’ genetic code is widespread among life-forms, a number of diverse lineages have evolved unique codon reassignments. The proteomes of these organisms and organelles must, by necessity, use the same codon assignments. Likewise, for an exogenous genetic element, such as an infecting viral genome, to be accurately and completely expressed with the host's translation system, it must employ the same genetic code. This raises a number of intriguing questions regarding the origin and evolution of viruses. In particular, it is extremely unlikely that viruses of hosts utilizing the universal genetic code would emerge, via cross-species transmission, in hosts utilizing alternative codes, and vice versa. Consequently, more parsimonious scenarios for the origins of such viruses include the prolonged co-evolution of viruses with cellular life, or the escape of genetic material from host genomes. Further, we raise the possibility that emerging viruses provide the selection pressure favoring the use of alternative codes in potential hosts, such that the evolution of a variant genetic code acts as a unique and powerful antiviral strategy. As such, in the face of new emerging viruses, hosts with codon reassignments would have a significant selective advantage compared to hosts utilizing the universal code.     

Yeast as a model organism for studying the evolution of non-standard genetic codes.

During the last 30 years, a number of alterations to the standard genetic code have been uncovered both in prokaryotes and eukaryotic nuclear and mitochondrial genomes. But, the study of the evolutionary pathways and molecular mechanisms of codon identity redefinition has been largely ignored due to the assumption that non-standard genetic codes can only evolve through neutral evolutionary mechanisms and that they have no functional significance. The recent discovery of a genetic code change in the genus Candida that evolved through an ambiguous messenger RNA decoding mechanism is bringing that naive assumption to an abrupt end by showing, in a rather dramatic way, that genetic code changes have profound physiological and evolutionary consequences for the species that redefine codon identity. In this paper, the recent data on the evolution of the Candida genetic code are reviewed and an experimental framework based on forced evolution, molecular genetics and comparative and functional genomics methodologies is put forward for the study of non-standard genetic codes and genetic code ambiguity in general. Additionally, the importance of using Saccharomyces cerevisiae as a model organism for elucidating the evolutionary pathway of the Candida and other genetic code changes is emphasised.     

Evolutionary deviations from the universal genetic code in ciliates

The review surveys the information, including the most recent data, on the evolution of genetic code in ciliates, which is among the few codes deviating from the universal one. We discuss the cases of recurrent, independently arising deviations from the assignments of standard codons of polypeptide chain termination in the mitochondrial and nuclear genomes of ciliates and some other protozoans. Possible molecular mechanisms are considered, which underlie deviations from standard termination code to coding glutamine (codon UAA and UAG) and cystein or tryptophane (codon UGA) in the nuclear genome. Critical analysis of the main hypotheses on the evolution of secondary deviations from the universal code in ciliates is presented.     

Study of the genetic code adaptability by means of a genetic algorithm

We used simulated evolution to study the adaptability level of the canonical genetic code. An adapted genetic algorithm (GA) searches for optimal hypothetical codes. Adaptability is measured as the average variation of the hydrophobicity that the encoded amino acids undergo when errors or mutations are present in the codons of the hypothetical codes. Different types of mutations and point mutation rates that depend on codon base number are considered in this study. Previous works have used statistical approaches based on randomly generated alternative codes or have used local search techniques to determine an optimum value. In this work, we emphasize what can be concluded from the use of simulated evolution considering the results of previous works. The GA provides more information about the difficulty of the evolution of codes, without contradicting previous studies using statistical or engineering approaches. The GA also shows that, within the coevolution theory, the third base clearly improves the adaptability of the current genetic code.     

Time‐lapse camera trapping as an alternative to pitfall trapping for estimating activity of leaf litter arthropods

Pitfall trapping is the standard technique to estimate activity and relative abundance of leaf litter arthropods. Pitfall trapping is not ideal for long‐term sampling because it is lethal, labor‐intensive, and may have taxonomic sampling biases. We test an alternative sampling method that can be left in place for several months at a time: verticallyplaced time‐lapse camera traps that have a short focal distance, enabling identification of small arthropods. We tested the effectiveness of these time‐lapse cameras, and quantified escape and avoidance behavior of arthropod orders encountering pitfall traps by placing cameras programed with a range of sampling intervals above pitfalls, to assess numerical, taxonomic, and body size differences in samples collected by the two methods. Cameras programed with 1‐ or 15‐min intervals recorded around twice as many arthropod taxa per day and a third more individuals per day than pitfall traps. Hymenoptera (ants), Embioptera (webspinners), and Blattodea (cockroaches) frequently escaped from pitfalls so were particularly under‐sampled by them. The time‐lapse camera method effectively samples litter arthropods to collect long‐term data. It is standardized, non‐lethal, and does not alter the substrate or require frequent visits.     

An Analysis of the Metabolic Theory of the Origin of the Genetic Code

A computer program was used to test Wong's coevolution theory of the genetic code. The codon correlations between the codons of biosynthetically related amino acids in the universal genetic code and in randomly generated genetic codes were compared. It was determined that many codon correlations are also present within random genetic codes and that among the random codes there are always several which have many more correlations than that found in the universal code. Although the number of correlations depends on the choice of biosynthetically related amino acids, the probability of choosing a random genetic code with the same or greater number of codon correlations as the universal genetic code was found to vary from 0.1% to 34% (with respect to a fairly complete listing of related amino acids). Thus, Wong's theory that the genetic code arose by coevolution with the biosynthetic pathways of amino acids, based on codon correlations between biosynthetically related amino acids, is statistical in nature. Received: 8 August 1996 / Accepted: 26 December 1996     

eDNA metabarcoding of avocado flowers: ‘Hass’ it got potential to survey arthropods in food production systems?

In the face of global biodiversity declines, surveys of beneficial and antagonistic arthropod diversity as well as the ecological services that they provide are increasingly important in both natural and agro-ecosystems. Conventional survey methods used to monitor these communities often require extensive taxonomic expertise and are time-intensive, potentially limiting their application in industries such as agriculture, where arthropods often play a critical role in productivity (e.g. pollinators, pests and predators). Environmental DNA (eDNA) metabarcoding of a novel substrate, crop flowers, may offer an accurate and high throughput alternative to aid in the detection of these managed and unmanaged taxa. Here, we compared the arthropod communities detected with eDNA metabarcoding of flowers, from an agricultural species (Persea americana—‘Hass’ avocado), with two conventional survey techniques: digital video recording (DVR) devices and pan traps. In total, 80 eDNA flower samples, 96 h of DVRs and 48 pan trap samples were collected. Across the three methods, 49 arthropod families were identified, of which 12 were unique to the eDNA dataset. Environmental DNA metabarcoding from flowers revealed potential arthropod pollinators, as well as plant pests and parasites. Alpha diversity levels did not differ across the three survey methods although taxonomic composition varied significantly, with only 12% of arthropod families found to be common across all three methods. eDNA metabarcoding of flowers has the potential to revolutionize the way arthropod communities are monitored in natural and agro-ecosystems, potentially detecting the response of pollinators and pests to climate change, diseases, habitat loss and other disturbances.     

Comparison of translation loads for standard and alternative genetic codes

Background  

The (almost) universality of the genetic code is one of the most intriguing properties of cellular life. Nevertheless, several variants of the standard genetic code have been observed, which differ in one or several of 64 codon assignments and occur mainly in mitochondrial genomes and in nuclear genomes of some bacterial and eukaryotic parasites. These variants are usually considered to be the result of non-adaptive evolution. It has been shown that the standard genetic code is preferential to randomly assembled codes for its ability to reduce the effects of errors in protein translation.     

Mitochondrial Genetic Codes Evolve to Match Amino Acid Requirements of Proteins

Mitochondria often use genetic codes different from the standard genetic code. Now that many mitochondrial genomes have been sequenced, these variant codes provide the first opportunity to examine empirically the processes that produce new genetic codes. The key question is: Are codon reassignments the sole result of mutation and genetic drift? Or are they the result of natural selection? Here we present an analysis of 24 phylogenetically independent codon reassignments in mitochondria. Although the mutation-drift hypothesis can explain reassignments from stop to an amino acid, we found that it cannot explain reassignments from one amino acid to another. In particular—and contrary to the predictions of the mutation-drift hypothesis—the codon involved in such a reassignment was not rare in the ancestral genome. Instead, such reassignments appear to take place while the codon is in use at an appreciable frequency. Moreover, the comparison of inferred amino acid usage in the ancestral genome with the neutral expectation shows that the amino acid gaining the codon was selectively favored over the amino acid losing the codon. These results are consistent with a simple model of weak selection on the amino acid composition of proteins in which codon reassignments are selected because they compensate for multiple slightly deleterious mutations throughout the mitochondrial genome. We propose that the selection pressure is for reduced protein synthesis cost: most reassignments give amino acids that are less expensive to synthesize. Taken together, our results strongly suggest that mitochondrial genetic codes evolve to match the amino acid requirements of proteins.     

The use of ants and other soil and litter arthropods as bio-indicators of the impacts of rainforest clearing and subsequent land use

The present study investigated the impacts of rainforest clearance, and associated subsequent land␣use for pasture, on assemblages of soil and litter arthropods in eastern subtropical Australia. We assessed the utility of soil and litter arthropods as potential bio-indicators of cleared and forested habitats. Arthropods were sampled from 24 sites (12 sites each in rainforest and pasture) using two methods (extraction from litter, pitfall traps). Responses of taxa were analysed at various levels of taxonomic resolution, including ‘coarse’ arthropods (all arthropods sorted to Order/Class), ant genera and ant species. Multivariate analyses of arthropod composition indicated that an increase in the level of taxonomic resolution did not provide a commensurate increase in the sensitivity of assemblage response. Indicator values (IndVals), computed for each taxon, showed that a number of arthropod taxa may have potential as bio-indicators of habitat change. However the use of many of these, especially many ant species found in our study, may be unreliable because even after extensive numbers of sites were sampled, most species showed patchy distributions. To overcome this problem, we generated ‘composite indices’, by combining information from sets of indicator taxa. The utility of these composite indices is discussed.