Piecing together the puzzle of parasitic plant plastome evolution

The importance of photosynthesis as a mode of energy production has put plastid genomes of plants under a constant purifying selection. This has shaped the characteristic features of plastid genomes across the entire spectrum of photosynthetic plants and has led to a highly uniform and conserved plastid genome with respect to structure, size, gene order, intron and editing site positions and coding capacity. Parasitic species that have dropped photosynthesis as the main energy provider share striking deviations from the plastid genome norm: multiple rearrangements within the circular chromosome, pseudogenization and gene deletions, promoter losses, intron losses as well as the extensive loss of mRNA editing competence have been reported. The collective loss of larger sets of functionally related genes like those for the plastid NADH–dehydrogenase complex and concomitant losses of RNA polymerase genes together with their target promoters point to “domino effects” where an initial loss might have triggered others. An example, which will be discussed in more detail, is the concomitant loss of the intron maturase gene matK and all introns that are supposedly subject to MatK-dependent splicing in two Cuscuta species.     

Chromothripsis and human disease: piecing together the shattering process

The unprecedented resolution of high-throughput genomics has enabled the recent discovery of a phenomenon by which specific regions of the genome are shattered and then stitched together via a single devastating event, referred to as chromothripsis. Potential mechanisms governing this process are now emerging, with implications for our understanding of the role of genomic rearrangements in development and disease.     

Catastrophic kinesins: piecing together their mechanism by 3D reconstruction

Kin Is, kinesins with an internal catalytic domain, de-polymerize microtubules from both ends, and the KIF2C crystal structure presented by ([this issue of Cell]) provides provocative evidence to support the theory that the highly conserved sequences are critical structural elements in these catastrophic kinesins.     

Chromosomal mapping of ANTP class homeobox genes in amphioxus: piecing together ancestral genomes

Homeobox genes encode DNA-binding proteins, many of which are implicated in the control of embryonic development. Evolutionarily, most homeobox genes fall into two related clades: the ANTP and the PRD classes. Some genes in ANTP class, notably Hox, ParaHox, and NK genes, have an intriguing arrangement into physical clusters. To investigate the evolutionary history of these gene clusters, we examined homeobox gene chromosomal locations in the cephalochordate amphioxus, Branchiostoma floridae. We deduce that 22 amphioxus ANTP class homeobox genes localize in just three chromosomes. One contains the Hox cluster plus AmphiEn, AmphiMnx, and AmphiDll. The ParaHox cluster resides in another chromosome, whereas a third chromosome contains the NK type homeobox genes, including AmphiMsx and AmphiTlx. By comparative analysis we infer that clustering of ANTP class homeobox genes evolved just once, during a series of extensive cis-duplication events of genes early in animal evolution. A trans-duplication event occurred later to yield the Hox and ParaHox gene clusters on different chromosomes. The results obtained have implications for understanding the origin of homeobox gene clustering, the diversification of the ANTP class of homeobox genes, and the evolution of animal genomes.     

Putting together the psoriasis puzzle: an update on developing targeted therapies

Psoriasis vulgaris is a chronic, debilitating skin disease that affects millions of people worldwide. There is no mouse model that accurately reproduces all facets of the disease, but the accessibility of skin tissue from patients has facilitated the elucidation of many pathways involved in the pathogenesis of psoriasis and highlighted the importance of the immune system in the disease. The pathophysiological relevance of these findings has been supported by genetic studies that identified polymorphisms in genes associated with NFκB activation, IL-23 signaling and T helper 17 (Th17)-cell adaptive immune responses, and in genes associated with the epidermal barrier. Recently developed biologic agents that selectively target specific components of the immune system are highly effective for treating psoriasis. In particular, emerging therapeutics are focused on targeting the IL-23–Th17-cell axis, and several agents that block IL-17 signaling have shown promising results in early-phase clinical trials. This review discusses lessons learned about the pathogenesis of psoriasis from mouse-and patient-based studies, emphasizing how the outcomes of clinical trials with T-cell-targeted and cytokine-blocking therapies have clarified our understanding of the disease.     

Amino acid determinants of alpha-synuclein aggregation: putting together pieces of the puzzle

The centrosome is the major microtubule-organizing center of animal cells. It influences cell shape and polarity and directs the formation of the bipolar mitotic spindle. Numerical and structural centrosome aberrations have been implicated in disease, notably cancer. In dividing cells, centrosomes need to be duplicated and segregated in synchrony with chromosomes. This centrosome cycle requires a series of structural and functional transitions that are regulated by both phosphorylation and proteolysis. Here we summarize recent information on the regulation of the centrosome cycle and its coordination with the chromosomal cell cycle.     

Assembly of the outermost spore layer: pieces of the puzzle are coming together

Certain endospore‐forming soil dwelling bacteria are important human, animal or insect pathogens. These organisms produce spores containing an outer layer, the exosporium. The exosporium is the site of interactions between the spore and the soil environment and between the spore and the infected host during the initial stages of infection. The composition and assembly process of the exosporium are poorly understood. This is partly due to the extreme stability of the exosporium that has proven to be refractive to existing methods to deconstruct the intact structure into its component parts. Although more than 20 proteins have been identified as exosporium‐associated, their abundance, relationship to other proteins and the processes by which they are assembled to create the exosporium are largely unknown. In this issue of Molecular Microbiology, Terry, Jiang, and colleagues in Per Bullough's laboratory show that the ExsY protein is a major structural protein of the exosporium basal layer of B. cereus family spores and that it can self‐assemble into complex structures that possess many of the structural features characteristic of the exosporium basal layer. The authors refined a model for exosporium assembly. Their findings may have implications for exosporium formation in other spore forming bacteria, including Clostridium species.     

Putting together the pieces of polio: how Dorothy Horstmann helped solve the puzzle

Dr. Dorothy Horstmann, epidemiologist, virologist, clinician, and educator, was the first woman appointed as a professor at the Yale School of Medicine. Horstmann made significant contributions to the fields of public health and virology, her most notable being the demonstration that poliovirus reached the central nervous system via the bloodstream, upsetting conventional wisdom and paving the way for polio vaccines. In 1961, she was appointed a professor at Yale School of Medicine, and in 1969, she became the first woman at Yale to receive an endowed chair, which was named in honor of her mentor, Dr. John Rodman Paul. In this review, the major scientific contributions of Dr. Dorothy Horstmann will be highlighted from her more than 50-year tenure at Yale School of Medicine.     

Piecing together the structure-function puzzle: experiences in structure-based functional annotation of hypothetical proteins

The combination of genomic sequencing with structural genomics has provided a wealth of new structures for previously uncharacterized ORFs, more commonly referred to as hypothetical proteins. This rapid growth has been the direct result of high-throughput, automated approaches in both the identification of new ORFs and the determination of high-resolution 3-D protein structures. A significant bottleneck is reached, however, at the stage of functional annotation in that the assignment of function is not readily automatable. It is often the case that the initial structural analysis at best indicates a functional family for a given hypothetical protein, but further identification of a relevant ligand or substrate is impeded by the diversity of function in a particular structural classification of proteins family, a highly selective and specific ligand-binding site, or the identification of a novel protein fold. Our approach to the functional annotation of hypothetical proteins relies on the combination of structural information with additional bioinformatics evidence garnered from operon prediction, loose functional information of additional operon members, conservation of catalytic residues, as well as cocrystallization trials and virtual ligand screening. The synthesis of all available information for each protein has permitted the functional annotation of several hypothetical proteins from Escherichia coli and each assignment has been confirmed through generally accepted biochemical methods.