Putative cross-kingdom horizontal gene transfer in sponge (Porifera) mitochondria

BACKGROUND: The mitochondrial genome of Metazoa is usually a compact molecule without introns. Exceptions to this rule have been reported only in corals and sea anemones (Cnidaria), in which group I introns have been discovered in the cox1 and nad5 genes. Here we show several lines of evidence demonstrating that introns can also be found in the mitochondria of sponges (Porifera). RESULTS: A 2,349 bp fragment of the mitochondrial cox1 gene was sequenced from the sponge Tetilla sp. (Spirophorida). This fragment suggests the presence of a 1143 bp intron. Similar to all the cnidarian mitochondrial introns, the putative intron has group I intron characteristics. The intron is present in the cox1 gene and encodes a putative homing endonuclease. In order to establish the distribution of this intron in sponges, the cox1 gene was sequenced from several representatives of the demosponge diversity. The intron was found only in the sponge order Spirophorida. A phylogenetic analysis of the COI protein sequence and of the intron open reading frame suggests that the intron may have been transmitted horizontally from a fungus donor. CONCLUSION: Little is known about sponge-associated fungi, although in the last few years the latter have been frequently isolated from sponges. We suggest that the horizontal gene transfer of a mitochondrial intron was facilitated by a symbiotic relationship between fungus and sponge. Ecological relationships are known to have implications at the genomic level. Here, an ecological relationship between sponge and fungus is suggested based on the genomic analysis

Diversity of sponge mitochondrial introns revealed by cox 1 sequences of Tetillidae

<p>Abstract</p> <p>Background</p> <p>Animal mitochondrial introns are rare. In sponges and cnidarians they have been found in the <it>cox 1 </it>gene of some spirophorid and homosclerophorid sponges, as well as in the <it>cox 1 </it>and <it>nad 5 </it>genes of some Hexacorallia. Their sporadic distribution has raised a debate as to whether these mobile elements have been vertically or horizontally transmitted among their hosts. The first sponge found to possess a mitochondrial intron was a spirophorid sponge from the Tetillidae family. To better understand the mode of transmission of mitochondrial introns in sponges, we studied <it>cox 1 </it>intron distribution among representatives of this family.</p> <p>Results</p> <p>Seventeen tetillid <it>cox 1 </it>sequences were examined. Among these sequences only six were found to possess group I introns. Remarkably, three different forms of introns were found, named introns 714, 723 and 870 based on their different positions in the <it>cox 1 </it>alignment. These introns had distinct secondary structures and encoded LAGLIDADG ORFs belonging to three different lineages. Interestingly, sponges harboring the same intron form did not always form monophyletic groups, suggesting that their introns might have been transferred horizontally. To evaluate whether the introns were vertically or horizontally transmitted in sponges and cnidarians we used a host parasite approach. We tested for co-speciation between introns 723 (the introns with the highest number of sponge representatives) and their nesting <it>cox 1 </it>sequences. Reciprocal AU tests indicated that the intron and <it>cox 1 </it>tree are significantly different, while a likelihood ratio test was not significant. A global test of co-phylogeny had significant results; however, when cnidarian sequences were analyzed separately the results were not significant.</p> <p>Conclusions</p> <p>The co-speciation analyses thus suggest that a vertical transmission of introns in the ancestor of sponges and cnidarians, followed by numerous independent losses, cannot solely explain the current distribution of metazoan group I introns. An alternative scenario that includes horizontal gene transfer events appears to be more suitable to explain the incongruence between the intron 723 and the <it>cox 1 </it>topologies. In addition, our results suggest that three different intron forms independently colonized the <it>cox 1 </it>gene of tetillids. Among sponges, the Tetillidae family seems to be experiencing an unusual number of intron insertions.</p

Isometric Scaling in Developing Long Bones Is Achieved by an Optimal Epiphyseal Growth Balance.

One of the major challenges that developing organs face is scaling, that is, the adjustment of physical proportions during the massive increase in size. Although organ scaling is fundamental for development and function, little is known about the mechanisms that regulate it. Bone superstructures are projections that typically serve for tendon and ligament insertion or articulation and, therefore, their position along the bone is crucial for musculoskeletal functionality. As bones are rigid structures that elongate only from their ends, it is unclear how superstructure positions are regulated during growth to end up in the right locations. Here, we document the process of longitudinal scaling in developing mouse long bones and uncover the mechanism that regulates it. To that end, we performed a computational analysis of hundreds of three-dimensional micro-CT images, using a newly developed method for recovering the morphogenetic sequence of developing bones. Strikingly, analysis revealed that the relative position of all superstructures along the bone is highly preserved during more than a 5-fold increase in length, indicating isometric scaling. It has been suggested that during development, bone superstructures are continuously reconstructed and relocated along the shaft, a process known as drift. Surprisingly, our results showed that most superstructures did not drift at all. Instead, we identified a novel mechanism for bone scaling, whereby each bone exhibits a specific and unique balance between proximal and distal growth rates, which accurately maintains the relative position of its superstructures. Moreover, we show mathematically that this mechanism minimizes the cumulative drift of all superstructures, thereby optimizing the scaling process. Our study reveals a general mechanism for the scaling of developing bones. More broadly, these findings suggest an evolutionary mechanism that facilitates variability in bone morphology by controlling the activity of individual epiphyseal plates

Deposition of collagen type I onto skeletal endothelium reveals a new role for blood vessels in regulating bone morphology

\u3cp\u3eRecently, blood vessels have been implicated in the morphogenesis of various organs. The vasculature is also known to be essential for endochondral bone development, yet the underlying mechanism has remained elusive. We show that a unique composition of blood vessels facilitates the role of the endothelium in bone mineralization and morphogenesis. Immunostaining and electron microscopy showed that the endothelium in developing bones lacks basement membrane, which normally isolates the blood vessel from its surroundings. Further analysis revealed the presence of collagen type I on the endothelial wall of these vessels. Because collagen type I is the main component of the osteoid, we hypothesized that the bone vasculature guides the formation of the collagenous template and consequently of the mature bone. Indeed, some of the bone vessels were found to undergo mineralization. Moreover, the vascular pattern at each embryonic stage prefigured the mineral distribution pattern observed one day later. Finally, perturbation of vascular patterning by overexpressing Vegf in osteoblasts resulted in abnormal bone morphology, supporting a role for blood vessels in bone morphogenesis. These data reveal the unique composition of the endothelium in developing bones and indicate that vascular patterning plays a role in determining bone shape by forming a template for deposition of bone matrix.\u3c/p\u3

Deposition of collagen type I onto skeletal endothelium reveals a new role for blood vessels in regulating bone morphology

Recently, blood vessels have been implicated in the morphogenesis of various organs. The vasculature is also known to be essential for endochondral bone development, yet the underlying mechanism has remained elusive. We show that a unique composition of blood vessels facilitates the role of the endothelium in bone mineralization and morphogenesis. Immunostaining and electron microscopy showed that the endothelium in developing bones lacks basement membrane, which normally isolates the blood vessel from its surroundings. Further analysis revealed the presence of collagen type I on the endothelial wall of these vessels. Because collagen type I is the main component of the osteoid, we hypothesized that the bone vasculature guides the formation of the collagenous template and consequently of the mature bone. Indeed, some of the bone vessels were found to undergo mineralization. Moreover, the vascular pattern at each embryonic stage prefigured the mineral distribution pattern observed one day later. Finally, perturbation of vascular patterning by overexpressing Vegf in osteoblasts resulted in abnormal bone morphology, supporting a role for blood vessels in bone morphogenesis. These data reveal the unique composition of the endothelium in developing bones and indicate that vascular patterning plays a role in determining bone shape by forming a template for deposition of bone matrix

Growth balance is optimized for minimum element drifting activity.

<p>Graphs showing the range of relative positions of the FP in which the total drifting activity of symmetry-breaking elements is minimal and the actual relative position of the FP in each bone as a function of total bone length. On the right of each graph is a 3D representation of an adult bone with colored marks of element locations. Throughout the development of all bones, the FP either overlaps or is in high proximity to the range of values that leads to minimal element drifting activity. Data for this figure are provided in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002212#pbio.1002212.s004" target="_blank">S4 Data</a>.</p

Element drift plays a restricted role in long bone isometric scaling.

<p>Graphs showing the physical position of each element throughout development. On the right of each graph is a 3D representation of an adult bone with colored marks of element locations. As indicated by thick gray background, elements remain stationary for periods ranging from several days to most of the developmental process. Data for this figure are provided in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002212#pbio.1002212.s002" target="_blank">S2 Data</a>.</p

The fixed plane model for isometric scaling of long bones.

<p>Illustration of fixed planes formed at the transverse plane where the ratio between the distances from the distal and the proximal ends of the bone is equal to the ratio between the distal and the proximal growth rates. <b>(A)</b> When growth is symmetric, the relative position of an element located at 50% length (rectangle) is maintained, whereas an element located at 75% length (triangle) drifts proximally to maintain its relative position. <b>(B)</b> When distal growth rate is three times higher than proximal growth rate, the location of the FP is at the 75% length. As a result, the relative position of the triangle element is maintained, whereas the rectangle element drifts distally to maintain its relative position.</p

A flowchart of the algorithm for rigid registration of multiple bone images.

<p>The input of the algorithm is <i>N</i> 3D micro-CT images {<i>I</i>^<i>N</i>} and the index of the root image (<i>I</i>^<i>Root</i>; 1 ≤ <i>Root</i> ≤ <i>N</i>) to which all other images will be registered. <b>(A)</b> Preprocessing. For each input image <i>I</i>^<i>N</i>: 1. Zero-out all trabecular regions. 2. Zero-out all background regions. 3. Align bone to axes by applying PCA. 4. Extract cylindrical shape descriptor. <b>(B)</b> Pairwise Registration. For a pair of a source (<i>I</i>^<i>s</i>) and a target (<i>I</i>^<i>t</i>) image: 5. For each of the four basic alignments between the bones (with or without proximal-distal inversion × with or without right-left side inversion), calculate the affinity (<b><i>Ψ</i></b>) between the extracted shape descriptors of <i>I</i>^<i>s</i> and <i>I</i>^<i>t</i> as a function of the rotation angle (<b><i>Θ</i></b>) of <i>I</i>^<i>t</i> about <i>PC1</i>. 6. From each local optimum in the calculated affinity function, perform several volume-based registration steps using NCC as a similarity measure and downhill descent as the optimization method. 7. Identify the path that reached the highest NCC score and optimize it using additional volume-based registration steps until convergence is reached. 8. If NCC <0.7, perform manual validation of the registration. <b>(C)</b> Agglomeration of pairwise to multiple image registration and interpolation. 9. Sort and re-index all bones based on their lengths, from shortest (“1”) to longest (“<i>N</i>”). 10. Register all pairs of bones <i>I</i>^<i>s</i>, <i>I</i>^<i>t</i> (<i>s</i> < <i>t</i>) adhering to either one of the following criteria: <i>I</i>^<i>s</i> and <i>I</i>^<i>t</i> are lengthwise consecutive: <i>t</i> − <i>s</i> = 1 (subdiagonal entries in <i>D</i>; in blue), or <i>t</i> – <i>s</i> > 1 ∧ <i>Length</i>(<i>I</i>^<i>t</i>)/<i>Length</i>(<i>I</i>^<i>s</i>) ≤ 1.2 (non-subdiagonal entries in <i>D</i>; in green). Assign the resulting NCC score in the corresponding cell in <i>D</i>. 11. Calculate the MST of the graph inspired by <i>D</i>, with <i>I</i>^<i>Root</i> being the root of the tree. 12. Infer all final transformations (<i>A</i>^<i>N</i>) based on the MST. 13. Transform/interpolate each image <i>I</i>^<i>N</i> according to its inferred final transformation. The output is <i>N</i> 4 × 4 homogenous transformation matrices </p><p></p><p></p><p></p><p><mo>{</mo></p><p></p><p><mi>A</mi></p><p><mi>f</mi><mi>i</mi><mi>n</mi><mi>a</mi><mi>l</mi></p><mi>N</mi><p></p><p></p><mo>}</mo><p></p><p></p><p></p><p></p>, each aligns the corresponding input image <i>I</i>^<i>N</i> to the root image <i>I</i>^<i>Root</i>, and the <i>N</i> transformed images. For more details, see <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002212#sec011" target="_blank">Materials and Methods</a>.<p></p