Comparative genomics study reveals Red Sea Bacillus with characteristics associated with potential microbial cell factories (MCFs)

Recent advancements in the use of microbial cells for scalable production of industrial enzymes encourage exploring new environments for efficient microbial cell factories (MCFs). Here, through a comparison study, ten newly sequenced Bacillus species, isolated from the Rabigh Harbor Lagoon on the Red Sea shoreline, were evaluated for their potential use as MCFs. Phylogenetic analysis of 40 representative genomes with phylogenetic relevance, including the ten Red Sea species, showed that the Red Sea species come from several colonization events and are not the result of a single colonization followed by speciation. Moreover, clustering reactions in reconstruct metabolic networks of these Bacillus species revealed that three metabolic clades do not fit the phylogenetic tree, a sign of convergent evolution of the metabolism of these species in response to special environmental adaptation. We further showed Red Sea strains Bacillus paralicheniformis (Bac48) and B. halosaccharovorans (Bac94) had twice as much secreted proteins than the model strain B. subtilis 168. Also, Bac94 was enriched with genes associated with the Tat and Sec protein secretion system and Bac48 has a hybrid PKS/NRPS cluster that is part of a horizontally transferred genomic region. These properties collectively hint towards the potential use of Red Sea Bacillus as efficient protein secreting microbial hosts, and that this characteristic of these strains may be a consequence of the unique ecological features of the isolation environment.

Phosphorylation of threonine residues on Shc promotes ligand binding and mediates crosstalk between MAPK and Akt pathways in breast cancer cells

Scaffold proteins play important roles in regulating signalling network fidelity, the absence of which is often the basis for diseases such as cancer. In the present work, we show that the prototypical scaffold protein Shc is phosphorylated by the extracellular signal-regulated kinase, Erk. In addition, Shc threonine phosphorylation is specifically up-regulated in two selected triple-negative breast cancer (TNBC) cell lines. To explore how Erk-mediated threonine phosphorylation on Shc might play a role in the dysregulation of signalling events, we investigated how Shc affects pathways downstream of EGF receptor. Using an in vitro model and biophysical analysis, we show that Shc threonine phosphorylation is responsible for elevated Akt and Erk signalling, potentially through the recruitment of the 14-3-3 ζ and Pin-1 proteins.

Clinical genomics expands the morbid genome of intellectual disability and offers a high diagnostic yield

Intellectual disability (ID) is a measurable phenotypic consequence of genetic and environmental factors. In this study, we prospectively assessed the diagnostic yield of genomic tools (molecular karyotyping, multi-gene panel and exome sequencing) in a cohort of 337 ID subjects as a first-tier test and compared it with a standard clinical evaluation performed in parallel. Standard clinical evaluation suggested a diagnosis in 16% of cases (54/337) but only 70% of these (38/54) were subsequently confirmed. On the other hand, the genomic approach revealed a likely diagnosis in 58% (n=196). These included copy number variants in 14% (n=54, 15% are novel), and point mutations revealed by multi-gene panel and exome sequencing in the remaining 43% (1% were found to have Fragile-X). The identified point mutations were mostly recessive (n=117, 81%), consistent with the high consanguinity of the study cohort, but also X-linked (n=8, 6%) and de novo dominant (n=19, 13%). When applied directly on all cases with negative molecular karyotyping, the diagnostic yield of exome sequencing was 60% (77/129). Exome sequencing also identified likely pathogenic variants in three novel candidate genes (DENND5A, NEMF and DNHD1) each of which harbored independent homozygous mutations in patients with overlapping phenotypes. In addition, exome sequencing revealed de novo and recessive variants in 32 genes (MAMDC2, TUBAL3, CPNE6, KLHL24, USP2, PIP5K1A, UBE4A, TP53TG5, ATOH1, C16ORF90, SLC39A14, TRERF1, RGL1, CDH11, SYDE2, HIRA, FEZF2, PROCA1, PIANP, PLK2, QRFPR, AP3B2, NUDT2, UFC1, BTN3A2, TADA1, ARFGEF3, FAM160B1, ZMYM5, SLC45A1, ARHGAP33 and CAPS2), which we highlight as potential candidates on the basis of several lines of evidence, and one of these genes (SLC39A14) was biallelically inactivated in a potentially treatable form of hypermanganesemia and neurodegeneration. Finally, likely causal variants in previously published candidate genes were identified (ASTN1, HELZ, THOC6, WDR45B, ADRA2B and CLIP1), thus supporting their involvement in ID pathogenesis. Our results expand the morbid genome of ID and support the adoption of genomics as a first-tier test for individuals with ID.

S2-7: Mechanisms of Action and Biological Significance of HER2 Mutations in HER2−Overexpressing Breast Cancer

Background: Trastuzumab is the most successful HER2−directed therapy in patients with early-stage and advanced HER2 positive breast cancer. Although trastuzumab improves survival in the adjuvant setting, 15–20% of the patients develop metastasis. Lapatinib is currently the only tyrosine kinase inhibitor approved for the treatment of patients with metastatic breast cancer after trastuzumab progression. However, progression eventually occurs and the disease remains incurable for the majority of patients. Recently, somatic mutations in the HER2 kinase domain have been reported in lung adenocarcinomas which result in constitutive phosphorylation of HER2, EGFR and cellular substrates. Activation of these receptors and pathways in lung cancer was associated with tumor progression and trastuzumab resistance, but tumors remained sensitive to a tyrosine kinase inhibitor. Because there are many different types of breast cancer that respond differently to treatments, more approaches are needed to predict which patients will most likely respond to a given therapy.

Material and Methods: Using gene sequencing on 78 HER2 positive breast tumors, our laboratory identified 4 novel missense variants in the kinase domain of HER2. None of the patients whose tumors carried one of these mutations achieved objective response to trastuzumab. Mutants were created using directed mutagenesis, inserted in a lentiviral expression plasmid and stably expressed in different breast cancer or non-tumorigenic cell lines. An ATP-based assay was used for cell survival studies. Migration studies were performed using Boyden-chambers coated with Matrigel. Anchorage-independent colony formation was assessed in soft-agar. Signaling pathways and phosphorylation status were analyzed by Western blot. Localization results were obtained by immunofluorescence and confocal microscopy followed by deconvolution analysis.

Results: Two of the mutants were dramatically under-phosphorylated and presented an altered cellular localization revealed by immunofluorescence studies in both cell lines and patient surgical samples. Also, cells expressing HER2 mutants showed an increased ability to invade Matrigel and migrate and to form colonies in soft-agar, suggesting the induction of a more aggressive behavior. In particular, one of the mutations was strongly associated with resistance to lapatinib treatment in cell survival and soft-agar assays, and higher doses of lapatinib were necessary to inhibit the ERK and AKT pathways. Computational analysis revealed that the mechanism of lapatinib resistance could be explained by a sterical obstruction of the ATP-binding pocket of the protein kinase domain that would impede the binding of lapatinib.

Conclusion: HER2 mutations confer a more aggressive phenotype. A specific mutation directly interacts with Lapatinib binding to HER2 and predicts resistance to Lapatinib in HER2−overexpressing breast cancer cells. Further characterization of novel HER2 mutations may have a direct implication in the development of novel markers for early diagnostics, patient selection and characterization of more appropriate and personalized treatment.

Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr S2-7.

Molecular basis for the lack of enantioselectivity of human 3-phosphoglycerate kinase

Non-natural l-nucleoside analogues are increasingly used as therapeutic agents to treat cancer and viral infections. To be active, l-nucleosides need to be phosphorylated to their respective triphosphate metabolites. This stepwise phosphorylation relies on human enzymes capable of processing l-nucleoside enantiomers. We used crystallographic analysis to reveal the molecular basis for the low enantioselectivity and the broad specificity of human 3-phosphoglycerate kinase (hPGK), an enzyme responsible for the last step of phosphorylation of many nucleotide derivatives. Based on structures of hPGK in the absence of nucleotides, and bound to l and d forms of MgADP and MgCDP, we show that a non-specific hydrophobic clamp to the nucleotide base, as well as a water-filled cavity behind it, allows high flexibility in the interaction between PGK and the bases. This, combined with the dispensability of hydrogen bonds to the sugar moiety, and ionic interactions with the phosphate groups, results in the positioning of different nucleotides so to expose their diphosphate group in a position competent for catalysis. Since the third phosphorylation step is often rate limiting, our results are expected to alleviate in silico tailoring of l-type prodrugs to assure their efficient metabolic processing.

Dynamic Nef and Nef dynamics: how structure could explain the complex activities of this small HIV protein

The Nef protein of the human immunodeficiency virus is as important for disease progression as it is perplexing in its plethora of target molecules and functions. In this article, it is proposed that the complex biology of Nef is regulated through conformational changes of the protein that are triggered by cellular location and specific interactions as Nef traffics through the infected cell.

The role of the Src homology 3-Src homology 2 interface in the regulation of Src kinases

The regulatory fragment of Src kinases, comprising Src homology (SH) 3 and SH2 domains, is responsible for controlled repression of kinase activity. We have used a multidisciplinary approach involving crystallography, NMR, and isothermal titration calorimetry to study the regulatory fragment of Fyn (FynSH32) and its interaction with a physiological activator: a fragment of focal adhesion kinase that contains both phosphotyrosine and polyproline motifs. Although flexible, the preferred disposition of SH3 and SH2 domains in FynSH32 resembles the inactive forms of Hck and Src, differing significantly from LckSH32. This difference, which results from variation in the SH3-SH2 linker sequences, will affect the potential of the regulatory fragments to repress kinase activity. This surprising result implies that the mechanism of repression of Src family members may vary, explaining functional distinctions between Fyn and Lck. The interaction between FynSH32 and focal adhesion kinase is restricted to the canonical SH3 and SH2 binding sites and does not affect the dynamic independence of the two domains. Consequently, the interaction shows no enhancement by an avidity effect. Such an interaction may have evolved to gain specificity through an extended recognition site while maintaining rapid dissociation after signaling.