Length and GC content variability of introns among teleostean genomes in the light of the metabolic rate hypothesis

The systematic codon usage bias has an important effect on genetic adaption in native species

Random mutations increase genetic variety and natural selection enhances adaption over generations. Codon usage biases (CUB) provide clues about the genome adaptation mechanisms of native species and extremophile species. Significant numbers of gene (CDS) of nine classes of endangered, native species, including extremophiles and mesophiles were utilised to compute CUB. Codon usage patterns differ among the lineages of endangered and extremophiles with native species. Polymorphic usage of nucleotides with codon burial suggests parallelism of native species within relatively confined taxonomic groups. Utilizing the deviation pattern of CUB of endangered and native species, I present a calculation parameter to estimate the extinction risk of endangered species. Species diversity and extinction risk are both positively associated with the propensity of random mutation in CDS (Coding DNA sequence). Codon bias tenet profoundly selected and it governs to adaptive evolution of native species.

ErCas12a and T5exo-ErCas12a Mediate Simple and Efficient Genome Editing in Zebrafish

Simple Summary

CRISPR/Cas9 enables efficient mutagenesis and generation of various knockout and knockin alleles in many species including zebrafish. However, the application of the Cas12a nuclease in zebrafish is far from ideal due to demanding experimental conditions, especially the requirements for delivery such as a purified protein and the heatshock of embryos. Here we show that ErCas12a, the only Cas12a reported to be effective when injected as mRNA in zebrafish, is highly efficient for large fragment knockin via either microhomology-mediated or non-homologous end joining pathways with mild heatshock conditions. Moreover, we fused T5 exonuclease to ErCas12a and found that the fusion protein could efficiently induce gene knockout and knockin without heatshock. Therefore, we demonstrated the efficacy of multiple genome-editing applications using ErCas12a and its variant with simplified conditions in zebrafish.

Abstract

In zebrafish, RNA-guided endonucleases such as Cas9 have enabled straightforward gene knockout and the construction of reporter lines or conditional alleles via targeted knockin strategies. However, the performance of another commonly used CRISPR system, Cas12a, is significantly limited due to both the requirement of delivery as purified protein and the necessity of heatshock of injected embryos. To explore the potential of CRISPR/Cas12a-mediated genome editing and simplify its application in zebrafish, we took advantage of the recently reported mRNA-active ErCas12a and investigated its efficacy for the knockin of large DNA fragments, such as fluorescent reporter genes. For knockin via either microhomology-mediated end joining (MMEJ) or non-homologous end joining (NHEJ) pathways, ErCas12a-injected embryos with a brief heatshock displayed comparable knockin efficiency with Cas9 injection. Through the fusion of T5 exonuclease (T5exo) to the N-terminus of ErCas12a (T5exo-ErCas12a), we further demonstrated high efficiency gene knockout and knockin at a normal incubation temperature, eliminating the embryo-damaging heatshock step. In summary, our results demonstrate the feasibility of ErCas12a- and T5exo-ErCas12a-mediated genome manipulation under simplified conditions, and further expand the genome editing toolbox for various applications in zebrafish.

Spliceosomal Introns: Features, Functions, and Evolution

Spliceosomal introns, which have been found in most eukaryotic genes, are non-coding sequences excised from pre-mRNAs by a special complex called spliceosome during mRNA splicing. Introns occur in both protein- and RNA-coding genes and can be found in coding and untranslated gene regions. Because intron sequences vary greatly due to a high rate of polymorphism, the functions of intron had been for a long time associated only with alternative splicing, while intron evolution had been viewed not as an evolution of an individual genomic element, but rather considered within a framework of the evolution of the gene intron-exon structure. Here, we review the theories of intron origin, evolutionary events in the exon-intron structure, such as intron gain, loss, and sliding, intron functions known to date, and mechanisms by which changes in the intron features (length and phase) can affect the regulation of gene-mediated processes.

GC bias lead to increased small amino acids and random coils of proteins in cold-water fishes

BACKGROUND

Temperature adaptation of biological molecules is fundamental in evolutionary studies but remains unsolved. Fishes living in cold water are adapted to low temperatures through adaptive modification of their biological molecules, which enables their functioning in extreme cold. To study nucleotide and amino acid preference in cold-water fishes, we investigated the substitution asymmetry of codons and amino acids in protein-coding DNA sequences between cold-water fishes and tropical fishes., The former includes two Antarctic fishes, Dissostichus mawsoni (Antarctic toothfish), Gymnodraco acuticeps (Antarctic dragonfish), and two temperate fishes, Gadus morhua (Atlantic cod) and Gasterosteus aculeatus (stickleback), and the latter includes three tropical fishes, including Danio rerio (zebrafish), Oreochromis niloticus (Nile tilapia) and Xiphophorus maculatus (Platyfish).

RESULTS

Cold-water fishes showed preference for Guanines and cytosines (GCs) in both synonymous and nonsynonymous codon substitution when compared with tropical fishes. Amino acids coded by GC-rich codons are favored in the temperate fishes, while those coded by AT-rich codons are disfavored. Similar trends were discovered in Antarctic fishes but were statistically weaker. The preference of GC rich codons in nonsynonymous substitution tends to increase ratio of small amino acid in proteins, which was demonstrated by biased small amino acid substitutions in the cold-water species when compared with the tropical species, especially in the temperate species. Prediction and comparison of secondary structure of the proteomes showed that frequency of random coils are significantly larger in the cold-water fish proteomes than those of the tropical fishes.

CONCLUSIONS

Our results suggested that natural selection in cold temperature might favor biased GC content in the coding DNA sequences, which lead to increased frequency of small amino acids and consequently increased random coils in the proteomes of cold-water fishes.

Lifestyle and DNA base composition in polychaetes

A comparative analysis of polychaete species, classified as motile and low-motile forms, highlighted that the former were characterized not only by a higher metabolic rate (MR), but also by a higher genomic GC content. The fluctuation of both variables was not affected by the phylogenetic relationship of the species. Thus, present results further support that a very active lifestyle affects MR and GC at the same time, showing an unexpected similarity between invertebrates and vertebrates. In teleosts, indeed, a similar pattern has been also observed in comparisons of migratory and nonmigratory species. A cause-effect link between MR and GC has not yet been proved, but the fact that the two variables are significantly linked in all the organisms so far analyzed is, most probably, of relevant biological and evolutionary meaning. The present results fit very well within the frame of the metabolic rate hypothesis proposed to explain the DNA base composition variability among organisms. On the contrary, the thermostability hypothesis was not supported. At present, no data about the recombination rate in polychaetes were available to test the biased gene conversion (BGC hypothesis).

On the genome base composition of teleosts: the effect of environment and lifestyle

BACKGROUND

The DNA base composition is well known to be highly variable among organisms. Bio-physic studies on the effect of the GC increments on the DNA structure have shown that GC-richer DNA sequences are more bendable. The result was the keystone of the hypothesis proposing the metabolic rate as the major force driving the GC content variability, since an increased resistance to the torsion stress is mainly required during the transcription process to avoid DNA breakage. Hence, the aim of the present work is to test if both salinity and migration, suggested to affect the metabolic rate of teleostean fishes, affect the average genomic GC content as well. Moreover, since the gill surface has been reported to be a major morphological expression of metabolic rate, this parameter was also analyzed in the light of the above hypothesis.

RESULTS

Teleosts living in different environments (freshwater and seawater) and with different lifestyles (migratory and non-migratory) were analyzed studying three variables: routine metabolic rate, gill area and genomic GC-content, none of them showing a phylogenetic signal among fish species. Routine metabolic rate, specific gill area and average genomic GC were higher in seawater than freshwater species. The same trend was observed comparing migratory versus non-migratory species. Crossing salinity and lifestyle, the active migratory species living in seawater show coincidentally the highest routine metabolic rate, the highest specific gill area and the highest average genomic GC content.

CONCLUSIONS

The results clearly highlight that environmental factors (salinity) and lifestyle (migration) affect not only the physiology (i.e. the routine metabolic rate), and the morphology (i.e. gill area) of teleosts, but also basic genome feature (i.e. the GC content), thus opening to an interesting liaison among the three variables in the light of the metabolic rate hypothesis.