Ganoderma lucidum is a widely used medicinal macrofungus in traditional Chinese medicine that creates a diverse set of bioactive compounds. Here we report its 43.3-Mb genome, encoding 16,113 predicted genes, obtained using next-generation sequencing and optical mapping approaches. The sequence analysis reveals an impressive array of genes encoding cytochrome P450s (CYPs), transporters and regulatory proteins that cooperate in secondary metabolism. The genome also encodes one of the richest sets of wood degradation enzymes among all of the sequenced basidiomycetes. In all, 24 physical CYP gene clusters are identified. Moreover, 78 CYP genes are coexpressed with lanosterol synthase, and 16 of these show high similarity to fungal CYPs that specifically hydroxylate testosterone, suggesting their possible roles in triterpenoid biosynthesis. The elucidation of the G. lucidum genome makes this organism a potential model system for the study of secondary metabolic pathways and their regulation in medicinal fungi.

SummaryIscR is an iron-sulphur (Fe-S) cluster-containing transcription factor that represses transcription of the operon containing its own gene and the iscSUAhscBA-fdx genes, whose products are involved in Fe-S cluster biogenesis. In this study, global transcriptional profiling of Escherichia coli IscR + and IscR

A recent analysis by the LHCb collaboration suggests the existence of three narrow pentaquark-like states -the P c (4312), P c (4440) and P c (4457) -instead of just one in the previous analysis (the P c (4450)). The closeness of the P c (4312) to theDΣ c threshold and the P c (4440)/P c (4457) to theD * Σ c one suggests a molecular interpretation of these resonances. We show that these three pentaquark-like resonances can be naturally accommodated in a contact-range effective field theory description that incorporates heavy-quark spin symmetry. This description leads to the prediction of all the seven possible S-wave heavy antimeson-baryon molecules (that is, there should be four additional molecular pentaquarks in addition to the P c (4312), P c (4440) and P c (4457)), providing the first example of a heavy-quark spin symmetry molecular multiplet that is complete. If this is confirmed, it will not only give us an impressive example of the application of heavy-quark symmetries and effective field theories in hadron physics: it will also uncover a clear and powerful ordering principle for the molecular spectrum, reminiscent of the SU(3)-flavor multiplets to which the light hadron spectrum conforms.

By exploring global gene expression of Escherichia coli growing on six different carbon sources, we discovered a striking genome transcription pattern: as carbon substrate quality declines, cells systematically increase the number of genes expressed. Gene induction occurs in a hierarchical manner and includes many factors for uptake and metabolism of better but currently unavailable carbon sources. Concomitantly, cells also increase their motility. Thus, as the growth potential of the environment decreases, cells appear to devote progressively more energy on the mere possibility of improving conditions. This adaptation is not what would be predicated by classic regulatory models alone. We also observe an inverse correlation between gene activation and rRNA synthesis suggesting that reapportioning RNA polymerase (RNAP) contributes to the expanded genome activation. Significant differences in RNAP distribution in vivo, monitored using an RNAP-green fluorescent protein fusion, from energy-rich and energy-poor carbon source cultures support this hypothesis. Together, these findings represent the integration of both substrate-specific and global regulatory systems, and may be a bacterial approximation to metazoan risk-prone foraging behavior.Jacob and Monod originally studied Escherichia coli gene regulation using carbon catabolism as the experimental system (specifically lactose). They elucidated that genes needed to metabolize lactose are specifically induced by that substrate (1). Over the ensuing 40 years this model has been refined and extended to many substrates and it is now generally accepted that virtually all carbohydrate catabolic genes can be regulated by substrate-specific induction (2). This mechanism is attractive because it promotes efficient use of cellular resources, and energy need not be wasted producing enzymes and transporters for substrates unless they are available.In addition to these highly specific mechanisms, cells also have several levels of global regulation. A prime example is carbon catabolite repression, a multifactorial system that blocks expression of alternative carbon utilization pathways when glucose is present (3). Relief from carbon catabolite repression, among other effects, activates the cyclic AMP receptor protein (CRP), 1 a global transcription factor that positively regulates most carbon catabolic pathways including those for glucose (4). Such global mechanisms have the advantage of responding to many different conditions and can potentiate a spectrum of transcriptional outcomes.While much is known about how individual substrate-specific and global systems regulate a limited set of operons under a defined condition, much less is known regarding how the two coordinate genome-wide transcription under a range of conditions. In this paper, we report the findings from a global gene expression study of E. coli growing on a series of six carbon sources. A transcription pattern emerges from these profiles that expands hierarchically as the growth rate declines. Inspection of the u...

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