Microarray-based analysis of the transcriptional profiles of the genetically distinct Staphylococcus aureus strains COL, GP268, and Newman indicate that a total of 251 open reading frames (ORFs) are influenced by B activity. While B was found to positively control 198 genes by a factor of >2 in at least two of the three genetic lineages analyzed, 53 ORFs were repressed in the presence of B . Gene products that were found to be influenced by B are putatively involved in all manner of cellular processes, including cell envelope biosynthesis and turnover, intermediary metabolism, and signaling pathways. Most of the genes and/or operons identified as upregulated by B were preceded by a nucleotide sequence that resembled the B consensus promoter sequence of Bacillus subtilis. A conspicuous number of virulence-associated genes were identified as regulated by B activity, with many adhesins upregulated and prominently represented in this group, while transcription of various exoproteins and toxins were repressed. The data presented here suggest that the B of S. aureus controls a large regulon and is an important modulator of virulence gene expression that is likely to act conversely to RNAIII, the effector molecule of the agr locus. We propose that this alternative transcription factor may be of importance for the invading pathogen to fine-tune its virulence factor production in response to changing host environments.Transcription of DNA into RNA is catalyzed by RNA polymerase. In bacteria, one RNA polymerase generates nearly all cellular RNAs, including ribosomal, transfer, and mRNA. This enzyme consists of six subunits, ␣ 2 ␤␤Ј, with ␣ 2 ␤␤Ј forming the catalytically competent RNA polymerase core enzyme (E). The core is capable of elongation and termination of transcription, but it is unable to initiate transcription at specific promoter sequences. The subunit, which when bound to E forms the holoenzyme (E-), directs the multisubunit complex to specific promoter elements and allows efficient initiation of transcription (reviewed in references 5 and 6). Therefore, factors provide an elegant mechanism in eubacteria to allow simultaneous transcription of a variety of genetically unlinked genes, provided all of these genes share the same promoter specificities.In addition to the housekeeping sigma subunit, 70 or A , most bacteria produce one or more additional subunits, termed alternative factors, which direct the respective Ecomplex to distinct classes of promoters that contain alternative factor-specific sequences. Alternative factors have been shown in various bacteria to be of importance for survival under extreme conditions (7,14,23,31,38,44,49,60,68,73,78,79,80) and to influence virulence and pathogenicity (8,13,32,35,37,42,51,57,61,71,75,78,81).At least six alternative factors are produced by the enteric bacterium Escherichia coli (reviewed in reference 6). Genomic sequence analysis suggests that many alternative factors also exist in a number of other pathogenic species such as Treponema palladium (4 alternative f...

Bacterial pathogens regulate virulence factor expression at both the level of transcription initiation and mRNA processing/turnover. Within Staphylococcus aureus, virulence factor transcript synthesis is regulated by a number of two-component regulatory systems, the DNA binding protein SarA, and the SarA family of homologues. However, little is known about the factors that modulate mRNA stability or influence transcript degradation within the organism. As our entree to characterizing these processes, S. aureus GeneChips were used to simultaneously determine the mRNA half-lives of all transcripts produced during log-phase growth. It was found that the majority of log-phase transcripts (90%) have a short half-life (<5 min), whereas others are more stable, suggesting that cis-and/or trans-acting factors influence S. aureus mRNA stability. In support of this, it was found that two virulence factor transcripts, cna and spa, were stabilized in a sarA-dependent manner. These results were validated by complementation and real-time PCR and suggest that SarA may regulate target gene expression in a previously unrecognized manner by posttranscriptionally modulating mRNA turnover. Additionally, it was found that S. aureus produces a set of stable RNA molecules with no predicted open reading frame. Based on the importance of the S. aureus agr RNA molecule, RNAIII, and small stable RNA molecules within other pathogens, it is possible that these RNA molecules influence biological processes within the organism.

-Studies described here utilize high-density oligonucleotide arrays to characterize changes in global mRNA expression patterns during proliferation, cell cycle withdrawal, and terminal differentiation in mouse C2C12 myoblasts. Statistical analyses revealed 629 sequences differentially regulated between proliferating and differentiating myoblasts. These genes were clustered using self-organizing maps to identify sets of coregulated genes and were assigned to functional categories that were analyzed for distribution across expression clusters. Clusters were identified with statistically significant enrichment of functional categories including muscle contraction, cell adhesion, extracellular matrix function, cellular metabolism, mitochondrial transport, DNA replication, cell cycle control, mRNA transcription, and unexpectedly, immune regulation. In addition, functional category enrichment data can be used to predict gene function for numerous differentially regulated expressed sequence tags. The results provide new insight into how genes involved in these cellular processes may play a role in skeletal muscle growth and differentiation. C2C12 cells; oligonucleotide array; functional category enrichment SKELETAL MUSCLE DIFFERENTIATION is a highly ordered process requiring myocyte proliferation, expression of muscle-specific regulatory factors, cell cycle withdrawal, and the synthesis of muscle contractile proteins, resulting in the fusion of mononucleated myoblasts into terminally differentiated multinucleated myotubes (1). Myocyte differentiation is regulated by four myogenic regulatory factors (MRFs): MyoD, Myf5, myogenin, and MRF4 (Myf6) (28, 39). These musclespecific basic helix-loop-helix (bHLH) transcription factors cooperate with the MEF2 family of MADS box transcription factors to activate transcription of muscle structural genes through E-box and MEF2 promoter sites, respectively (5). Negative regulators of muscle gene transcription include the Id dominant-negative HLH proteins, which sequester bHLH proteins into complexes incapable of binding DNA, and the bHLH protein twist (reviewed in Ref. 2).The myogenic program consists of two temporally separated processes: myoblast proliferation and differentiation. Proliferating mononucleate myoblasts expressing MyoD and Myf5 are committed to the muscle lineage and will continue to proliferate in the presence of mitogens under high-serum conditions in vitro. Upon serum deprivation, myoblasts activate transcription of myogenin and undergo irreversible cell cycle arrest following transcription of the cyclin-dependent kinase (Cdk) inhibitor, p21, and dephosphorylation of pRb (1, 40). Skeletal muscle differentiation then proceeds through the induction of muscle-specific gene expression and fusion of myoblasts into myotubes (1,13,14,29,41).Here, we have used high-density oligonucleotide arrays to investigate transcriptional changes occurring during myoblast proliferation and differentiation in C2C12 cells, a well-characterized in vitro model of mouse skeletal muscle cell...

This article is available online at http://www.jlr.org Supplementary key words cynomolgus monkey • dyslipidemia • fi broblast growth factor 19 • hypertriglyceridemiaAtherosclerosis is the major cause of cardiovascular disease and its incidence is on the rise due to its tight relationship to obesity and diabetes. Therapeutic interventions targeted at reducing elevated plasma low-density lipoprotein cholesterol (LDLc), the primary risk factor for development of atherosclerosis, do not eliminate cardiovascular risk particularly in several high-risk subpopulations. The statin class of drugs achieve dramatic reductions in LDLc yet reduce heart attack risk only 33% per 1.5 mmol/L reduction in LDL ( 1 ). As statins primarily limit disease progression through the inhibition of endogenous cholesterol synthesis, newer treatment modalities directed at reversing established atherosclerotic plaque are likely to provide additional benefi t and can have important clinical implications for disease management. This is exemplifi ed by the exploratory clinical studies targeting the enhancement of high-density lipoprotein ( 2 ). In this study, intravenous

Articular cartilage expresses a substantial number of NRs, and a large proportion of the expressed NRs are dysregulated in OA. In particular, LXR signaling in OA articular cartilage is impaired, and stimulation of LXR transcriptional activity can counteract the catabolic effects of IL-1. We conclude that LXR agonism may be a possible therapeutic option for OA.