Effect of exonic splicing regulation on synonymous codon usage in alternatively spliced exons of Dscam

<p>Abstract</p> <p>Background</p> <p>Synonymous codon usage is typically biased towards translationally superior codons in many organisms. In <it>Drosophila</it>, genomic data indicates that translationally optimal codons and splice optimal codons are mostly mutually exclusive, and adaptation to translational efficiency is reduced in the intron-exon boundary regions where potential exonic splicing enhancers (ESEs) reside. In contrast to genomic scale analyses on large datasets, a refined study on a well-controlled set of samples can be effective in demonstrating the effects of particular splice-related factors. <it>Down syndrome cell adhesion molecule </it>(<it>Dscam</it>) has the largest number of alternatively spliced exons (ASEs) known to date, and the splicing frequency of each ASE is accessible from the relative abundance of the transcript. Thus, these ASEs comprise a unique model system for studying the effect of splicing regulation on synonymous codon usage.</p> <p>Results</p> <p>Codon Bias Indices (CBI) in the 3' boundary regions were reduced compared to the rest of the exonic regions among 48 and 33 ASEs of exon 6 and 9 clusters, respectively. These regional differences in CBI were affected by splicing frequency and distance from adjacent exons. Synonymous divergence levels between the 3' boundary region and the remaining exonic region of exon 6 ASEs were similar. Additionally, another sensitive comparison of paralogous exonic regions in recently retrotransposed processed genes and their parental genes revealed that, in the former, the differences in CBI between what were formerly the central regions and the boundary regions gradually became smaller over time.</p> <p>Conclusion</p> <p>Analyses of the multiple ASEs of <it>Dscam </it>allowed direct tests of the effect of splice-related factors on synonymous codon usage and provided clear evidence that synonymous codon usage bias is restricted by exonic splicing signals near the intron-exon boundary. A similar synonymous divergence level between the different exonic regions suggests that the intensity of splice-related selection is generally weak and comparable to that of translational selection. Finally, the leveling off of differences in codon bias over time in retrotransposed genes meets the direct prediction of the tradeoff model that invokes conflict between translational superiority and splicing regulation, and strengthens the conclusions obtained from <it>Dscam</it>.</p

Two functionally distinct manganese clusters formed by introducing a mutation in the carboxyl terminus of a photosystem II reaction center polypeptide, D1, of the green alga Chlamydomonas reinhardtii

AbstractTo study the function of the carboxyl-terminal domain of a photosystem II (PSII) reaction center polypeptide, D1, chloroplast mutants of the green alga Chlamydomonas reinhardtii have been generated in which Leu-343 and Ala-344 have been simultaneously or individually replaced by Phe and Ser, respectively. The mutants carrying these replacements individually, L343F and A344S, showed a wild-type phenotype. In contrast, the double mutant, L343FA344S, evolved O2 at only 20–30% of the wild-type rate and was unable to grow photosynthetically. In this mutant, PSII accumulated to 60% of the wild-type level, indicating that the O2-evolving activity per PSII was reduced to approximately half that of the wild-type. However, the amount of Mn atom detected in the thylakoids suggested that a normal amount of Mn cluster was assembled. An investigation of the kinetics of flash-induced fluorescence yield decay revealed that the electron transfer from Q−A to QB was not affected. When a back electron transfer from Q−A to a donor component was measured in the presence of 3-(3,4-dichlorophenol)-1,1-dimethylurea, a significantly slower component of the Q−A oxidation was detected in addition to the normal component that corresponds to the back electron transfer from the Q−A to the S2-state of the Mn cluster. Thermoluminescence measurements revealed that L343FA344S cells contained two functionally distinct Mn clusters. One was equivalent to that of the wild-type, while the other was incapable of water oxidation and was able to advance the transition from the S1-state to the S2-state. These results suggested that a fraction of the Mn cluster had been impaired by the L343FA344S mutation, leading to decreased O2 evolution. We concluded that the structure of the C-terminus of D1 is critical for the formation of the Mn cluster that is capable of water oxidation, in particular, transition to higher S-states

A generalized linear model for decomposing cis-regulatory, parent-of-origin, and maternal effects on allele-specific gene expression

Joint quantification of genetic and epigenetic effects on gene expression is important for understanding the establishment of complex gene regulation systems in living organisms. In particular, genomic imprinting and maternal effects play important roles in the developmental process of mammals and flowering plants. However, the influence of these effects on gene expression are difficult to quantify because they act simultaneously with cis-regulatory mutations. Here we propose a simple method to decompose cis-regulatory (i.e., allelic genotype, AG), genomic imprinting (i.e., parent-of-origin, PO), and maternal (i.e., maternal genotype, MG) effects on allele-specific gene expression using RNA-seq data obtained from reciprocal crosses. We evaluated the efficiency of method using a simulated dataset and applied the method to whole-body Drosophila and mouse trophoblast stem cell (TSC) and liver RNA-seq data. Consistent with previous studies, we found little evidence of PO and MG effects in adult Drosophila samples. In contrast, we identified dozens and hundreds of mouse genes with significant PO and MG effects, respectively. Interestingly, a similar number of genes with significant PO effect were detect in mouse TSCs and livers, whereas more genes with significant MG effect were observed in livers. Further application of this method will clarify how these three effects influence gene expression levels in different tissues and developmental stages, and provide novel insight into the evolution of gene expression regulation.Comment: 27 pages, 3 figures, 2 tabl

Spectral transitions of an ultraluminous X-ray source, NGC 2403 Source 3

Suzaku observation of an ultraluminous X-ray source, NGC 2403 Source 3, performed on 2006 March 16--17, is reported. The Suzaku XIS spectrum of Source 3 was described with a multi-color black-body-like emission from an optically thick accretion disk. The innermost temperature and radius of the accretion disk was measured to be $T_{\rm in} = 1.08_{-0.03}^{+0.02}$ keV and $R_{\rm in} = 122.1_{-6.8}^{+7.7} \alpha^{1/2}$ km, respectively, where $\alpha = (\cos 60^\circ /\cos i)$ with $i$ being the disk inclination. The bolometric luminosity of the source was estimated to be $L_{\rm bol} = 1.82 \times 10^{39} \alpha$ ergs s$^{-1}$. Archival Chandra and XMM-Newton data of the source were analyzed for long-term spectral variations. In almost all observations, the source showed multi-color black-body-like X-ray spectra with parameters similar to those in the Suzaku observation. In only one Chandra observation, however, Source 3 was found to exhibit a power-law-like spectrum, with a photon index of $\Gamma = 2.37 \pm 0.08$, when it was fainter by about $\sim 15$ than in the Suzaku observation. The spectral behavior is naturally explained in terms of a transition between the slim disk state and the "very high" states, both found in Galactic black hole binaries when their luminosity approach the Eddington limit. These results are utilized to argue that ultraluminous X-ray sources generally have significantly higher black-hole masses than ordinary stellar-mass black holes.Comment: Accepted for PASJ 3nd Suzaku special issu