Functional divergence of the NIP III subgroup proteins involved altered selective constraints and positive selection

Abstract Background Nod26-like intrinsic proteins (NIPs) that belong to the aquaporin superfamily are unique to plants. According to homology modeling and phylogenetic analysis, the NIP subfamily can be further divided into three subgroups with distinct biological functions (NIP I, NIP II, and NIP III). In some grasses, the NIP III subgroup proteins (NIP2s) were demonstrated to be permeable to solutes with larger diameter, such as silicic acid and arsenous acids. However, to date there is no data-mining or direct experimental evidences for the permeability of such larger solutes for dicot NIP2s, although they exhibit similar three-dimensional structures as those in grasses. It is therefore intriguing to investigate the molecular mechanisms that drive the evolution of plant NIP2s. Results The NIP III subgroup is more ancient with a divergence time that predates the monocot-dicot split. The proliferation of NIP2 genes in modern grass species is primarily attributed to whole genome and segmental chromosomal duplication events. The structure of NIP2 genes is relatively conserved, possessing five exons and four introns. All NIP2s possess an ar/R filter consisting of G, S, G, and R, except for the cucumber CsNIP2;2, where a small G in the H2 is substituted with the bulkier C residue. Our maximum likelihood analysis revealed that NIP2s, especially the loop A (LA) region, have undergone strong selective pressure for adaptive evolution. The analysis at the amino acid level provided strong statistical evidences for the functional divergence between monocot and dicot NIP III subgroup proteins. In addition, several SDPs (Specificity Determining Positions) responsible for functional specificity were predicted. Conclusions The present study provides the first evidences of functional divergence between dicot and monocot NIP2s, and suggests that positive selection, as well as a radical shift of evolutionary rate at some critical amino acid sites is the primary driver. These findings will expand our understanding to evolutionary mechanisms driving the functional diversification of monocot and dicot NIP III subgroup proteins.</p

Divergence in function and expression of the NOD26-like intrinsic proteins in plants

<p>Abstract</p> <p>Background</p> <p>NOD26-like intrinsic proteins (NIPs) that belong to the aquaporin superfamily are plant-specific and exhibit a similar three-dimensional structure. Experimental evidences however revealed that functional divergence should have extensively occurred among NIP genes. It is therefore intriguing to further investigate the evolutionary mechanisms being responsible for the functional diversification of the NIP genes. To better understand this process, a comprehensive analysis including the phylogenetic, positive selection, functional divergence, and transcriptional analysis was carried out.</p> <p>Results</p> <p>The origination of NIPs could be dated back to the primitive land plants, and their diversification would be no younger than the emergence time of the moss <it>P. patens</it>. The rapid proliferation of NIPs in plants may be primarily attributed to the segmental chromosome duplication produced by polyploidy and tandem duplications. The maximum likelihood analysis revealed that <it>NIPs </it>should have experienced strong selective pressure for adaptive evolution after gene duplication and/or speciation, prompting the formation of distinct <it>NIP </it>groups. Functional divergence analysis at the amino acid level has provided strong statistical evidence for shifted evolutionary rate and/or radical change of the physiochemical properties of amino acids after gene duplication, and DIVERGE2 has identified the critical amino acid sites that are thought to be responsible for the divergence for further investigation. The expression of plant NIPs displays a distinct tissue-, cell-type-, and developmental specific pattern, and their responses to various stress treatments are quite different also. The differences in organization of <it>cis</it>-acting regulatory elements in the promoter regions may partially explain their distinction in expression.</p> <p>Conclusion</p> <p>A number of analyses both at the DNA and amino acid sequence levels have provided strong evidences that plant NIPs have suffered a high divergence in function and expression during evolution, which is primarily attributed to the strong positive selection or a rapid change of evolutionary rate and/or physiochemical properties of some critical amino acid sites.</p

Mutational Bias and Translational Selection Shaping the Codon Usage Pattern of Tissue-Specific Genes in Rice

<div><p>The regulatory mechanisms of determining which genes specifically expressed in which tissues are still not fully elucidated, especially in plants. Using internal correspondence analysis, I first establish that tissue-specific genes exhibit significantly different synonymous codon usage in rice, although this effect is weak. The variability of synonymous codon usage between tissues accounts for 5.62% of the total codon usage variability, which has mainly arisen from the neutral evolutionary forces, such as GC content variation among tissues. Moreover, tissue-specific genes are under differential selective constraints, inferring that natural selection also contributes to the codon usage divergence between tissues. These findings may add further evidence in understanding the differentiation and regulation of tissue-specific gene products in plants.</p> </div

Comparison of synonymous <i>d</i>_S (a) and nonsynonymous substitution rates <i>d</i>_N (b) between rice and <i>B. distachyon</i>, and <i>sorghum</i> orthologous gene pairs for tissue-specific and non-tissue-specific classes of genes.

<p>The symbol ** indicates significant difference at the 0.01 level (<i>p</i><0.01).</p

Base composition of coding sequences of tissue- and non-tissue-specific genes in rice.

<p><i>Note</i>: Data are reported as means ± SD. Within a column, mean values followed by different letters (a, b, c, d, e, f, and g) mean significant difference at the 0.05 level (<i>p</i><0.05).</p

Internal correspondence analysis of tissue-specific genes in rice.

<p>The global codon usage variability was decomposed into within-block and between-block variability, consisting of the amino acid usage (between-AA) variability (<i>b</i>, <i>e</i>, <i>h</i>), synonymous codon usage (within-AA) variability (<i>a</i>, <i>d</i>, <i>g</i>), and variability of between- (<i>d</i>, <i>e</i>, <i>f</i>) or within tissues (<i>a</i>, <i>b</i>, <i>c</i>). The decomposition of global variability yields nine elementary analyses (<i>a</i>-<i>i</i>). In each peculiar analysis, the contribution to the total variance is indicated, where only the first 10 eigenvalues are represented to allow for a direct visual comparison.</p

Comparison of ENC, CAI, and CDS length of tissue- and non-tissue-specific genes in rice.

<p><i>Note</i>: Data are reported as means ± SD. Within a column, mean values followed by different letters (a, b, c, d, e, and f) mean significant difference at the 0.05 level (<i>p</i><0.05).</p

Molecular Identification and Analysis of Arsenite Stress-Responsive miRNAs in Rice

Arsenic is highly toxic to living organisms including humans and plants. To investigate the responsive functions of miRNAs under arsenite stress, an <i>indica</i> rice, Minghui 86, has been deeply sequenced, and a total of 67 arsenite-responsive miRNAs were identified in rice seedling roots, of which 5 were further validated experimentally. The potential targets of those differential miRNAs include some transcription factors, protein kinases, and DNA- or metal ion-binding proteins that are associated with cellular and metabolic processes, pigmentation, and stress responses. The regulatory roles of four miRNAs on their targets in response to arsenite were further confirmed by real time RT-PCR. Interestingly, osa-miR6256 was originally characterized as a putative exonic miRNA, supporting the notion that miRNAs may also originate from some exons in plants. The first identification of arsenite-responsive miRNAs at the whole genome-wide level will broaden the current understanding of the molecular mechanisms of arsenite responses in rice