Analyzing the genomic variation of microbial cell factories in the era of “New Biotechnology”

The application of genome-scale technologies, both experimental and in silico, to industrial biotechnology has allowed improving the conversion of biomass-derived feedstocks to chemicals, materials and fuels through microbial fermentation. In particular, due to rapidly decreasing costs and its suitability for identifying the genetic determinants of a phenotypic trait of interest, whole genome sequencing is expected to be one of the major driving forces in industrial biotechnology in the coming years. We present some of the recent studies that have successfully applied high-throughput sequencing technologies for finding the underlying molecular mechanisms for (a) improved carbon source utilization, (b) increased product formation, and (c) stress tolerance. We also discuss the strengths and weaknesses of different strategies for mapping industrially relevant genotype-to-phenotype links including exploiting natural diversity in natural isolates or crosses between isolates, classical mutagenesis and evolutionary engineering

A sequence-based survey of the complex structural organization of tumor genomes

Tumors and cancer cell lines were surveyed with end-sequencing profiling, yielding the largest available collection of sequence-ready tumor genome breakpoints and providing evidence that some rearrangements may be recurrent

Evolutionary relationships of Aurora kinases: Implications for model organism studies and the development of anti-cancer drugs

BACKGROUND: As key regulators of mitotic chromosome segregation, the Aurora family of serine/threonine kinases play an important role in cell division. Abnormalities in Aurora kinases have been strongly linked with cancer, which has lead to the recent development of new classes of anti-cancer drugs that specifically target the ATP-binding domain of these kinases. From an evolutionary perspective, the species distribution of the Aurora kinase family is complex. Mammals uniquely have three Aurora kinases, Aurora-A, Aurora-B, and Aurora-C, while for other metazoans, including the frog, fruitfly and nematode, only Aurora-A and Aurora-B kinases are known. The fungi have a single Aurora-like homolog. Based on the tacit assumption of orthology to human counterparts, model organism studies have been central to the functional characterization of Aurora kinases. However, the ortholog and paralog relationships of these kinases across various species have not been rigorously examined. Here, we present comprehensive evolutionary analyses of the Aurora kinase family. RESULTS: Phylogenetic trees suggest that all three vertebrate Auroras evolved from a single urochordate ancestor. Specifically, Aurora-A is an orthologous lineage in cold-blooded vertebrates and mammals, while structurally similar Aurora-B and Aurora-C evolved more recently in mammals from a duplication of an ancestral Aurora-B/C gene found in cold-blooded vertebrates. All so-called Aurora-A and Aurora-B kinases of non-chordates are ancestral to the clade of chordate Auroras and, therefore, are not strictly orthologous to vertebrate counterparts. Comparisons of human Aurora-B and Aurora-C sequences to the resolved 3D structure of human Aurora-A lends further support to the evolutionary scenario that vertebrate Aurora-B and Aurora-C are closely related paralogs. Of the 26 residues lining the ATP-binding active site, only three were variant and all were specific to Aurora-A. CONCLUSIONS: In this study, we found that invertebrate Aurora-A and Aurora-B kinases are highly divergent protein families from their chordate counterparts. Furthermore, while the Aurora-A family is ubiquitous among all vertebrates, the Aurora-B and Aurora-C families in humans arose from a gene duplication event in mammals. These findings show the importance of understanding evolutionary relationships in the interpretation and transference of knowledge from studies of model organism systems to human cellular biology. In addition, given the important role of Aurora kinases in cancer, evolutionary analysis and comparisons of ATP-binding domains suggest a rationale for designing dual action anti-tumor drugs that inhibit both Aurora-B and Aurora-C kinases

Exploring tumour evolution through mutational patterns in bone tumours

Cancer is a continuation of the evolutionary process on a cellular scale. The mutations that define this evolutionary process show a marked variety of complexity, which I have explored in this work. First, I have explored the genomics of osteoblastoma, a rare benign bone tumour. This work, for the first time, demonstrates that osteoblastoma and the related entity, osteoid osteoma, are defined by structural rearrangements in the AP-1 family of genes, FOS and FOSB. This original work is the first report of a FOS mutation in a human bone-forming tumour since its discovery as one of the archetypal proto-oncogenes, forming the basis of a much-needed diagnostic test. Giant cell tumours (GCTs) of bone are characterised by an H3.3 gene mutation. I have explored a group of benign (GCTs), benign metastasising and malignant bone tumours which possess this mutation. Methylation profiling and evolutionary analysis suggest that malignant tumours have transformed from GCTs, acquiring replicative immortality or an additional epigenetic regulatory mutation. In contrast, my analyses show that benign metastatic disease can occur without any additional mutational changes. Finally, I have studied complex mutational events more broadly in cancer and benign neoplastic disease. I reported chromothripsis and chromoplexy in malignant GCTs and osteoblastoma respectively for the first time. I explored the detection, frequency and evolutionary onset of chromoplexy in a collection of 2,626 human tumours. Found across almost all cancer types, the particularly striking and novel finding was the high frequency of chromoplexy in thyroid cancers, creating many of the known driver fusions. Altogether, focusing on primary bone tumours, I have demonstrated how both simple and complex mutational events can define the earliest steps in tumour evolution. The analysis of complex patterns of mutation can also give new insights into the patterns of progression of both malignant and metastatic disease