Sensory deprivation in Staphylococcus aureus

Bacteria use two-component systems (TCSs) to sense and respond to environmental changes. The core genome of the major human pathogen Staphylococcus aureus encodes 16 TCSs, one of which (WalRK) is essential. Here we show that S. aureus can be deprived of its complete sensorial TCS network and still survive under growth arrest conditions similarly to wild-type bacteria. Under replicating conditions, however, the WalRK system is necessary and sufficient to maintain bacterial growth, indicating that sensing through TCSs is mostly dispensable for living under constant environmental conditions. Characterization of S. aureus derivatives containing individual TCSs reveals that each TCS appears to be autonomous and self-sufficient to sense and respond to specific environmental cues, although some level of cross-regulation between non-cognate sensor-response regulator pairs occurs in vivo. This organization, if confirmed in other bacterial species, may provide a general evolutionarily mechanism for flexible bacterial adaptation to life in new niches

Base Pairing Interaction between 5'- and 3'-UTRs Controls icaR mRNA Translation in Staphylococcus aureus.

The presence of regulatory sequences in the 3' untranslated region (3'-UTR) of eukaryotic mRNAs controlling RNA stability and translation efficiency is widely recognized. In contrast, the relevance of 3'-UTRs in bacterial mRNA functionality has been disregarded. Here, we report evidences showing that around one-third of the mapped mRNAs of the major human pathogen Staphylococcus aureus carry 3'-UTRs longer than 100-nt and thus, potential regulatory functions. We selected the long 3'-UTR of icaR, which codes for the repressor of the main exopolysaccharidic compound of the S. aureus biofilm matrix, to evaluate the role that 3'-UTRs may play in controlling mRNA expression. We showed that base pairing between the 3'-UTR and the Shine-Dalgarno (SD) region of icaR mRNA interferes with the translation initiation complex and generates a double-stranded substrate for RNase III. Deletion or substitution of the motif (UCCCCUG) within icaR 3'-UTR was sufficient to abolish this interaction and resulted in the accumulation of IcaR repressor and inhibition of biofilm development. Our findings provide a singular example of a new potential post-transcriptional regulatory mechanism to modulate bacterial gene expression through the interaction of a 3'-UTR with the 5'-UTR of the same mRNA

CDK11 is required for transcription of replication-dependent histone genes

Replication-dependent histones (RDH) are required for packaging of newly synthetized DNA into nucleosomes during the S phase when their expression is highly upregulated. However, the mechanisms of this upregulation in metazoan cells remain poorly understood. Using iCLIP and ChIP–seq, we found that human cyclin-dependent kinase 11 (CDK11) associates with RNA and chromatin of RDH genes primarily in the S phase. Moreover, its amino-terminal region binds FLASH, an RDH-specific 3′-end processing factor, which keeps the kinase on the chromatin. CDK11 phosphorylates serine 2 (Ser2) of the carboxy-terminal domain of RNA polymerase II (RNAPII), which is initiated when RNAPII reaches the middle of RDH genes and is required for further RNAPII elongation and 3′-end processing. CDK11 depletion leads to decreased number of cells in S phase, likely owing to the function of CDK11 in RDH gene expression. Thus, the reliance of RDH expression on CDK11 could explain why CDK11 is essential for the growth of many cancers

Splicing repression allows the gradual emergence of new Alu-exons in primate evolution

Alu elements are retrotransposons that frequently form new exons during primate evolution. Here, we assess the interplay of splicing repression by hnRNPC and nonsense-mediated mRNA decay (NMD) in the quality control and evolution of new Alu-exons. We identify 3100 new Alu-exons and show that NMD more efficiently recognises transcripts with Alu-exons compared to other exons with premature termination codons. However, some Alu-exons escape NMD, especially when an adjacent intron is retained, highlighting the importance of concerted repression by splicing and NMD. We show that evolutionary progression of 3' splice sites is coupled with longer repressive uridine tracts. Once the 3' splice site at ancient Alu-exons reaches a stable phase, splicing repression by hnRNPC decreases, but the exons generally remain sensitive to NMD. We conclude that repressive motifs are strongest next to cryptic exons and that gradual weakening of these motifs contributes to the evolutionary emergence of new alternative exons

A retained intron in the 3'-UTR of Calm3 mRNA mediates its Staufen2- and activity-dependent localization to neuronal dendrites

Dendritic localization and hence local mRNA translation contributes to synaptic plasticity in neurons. Staufen2 (Stau2) is a well-known neuronal double-stranded RNA-binding protein (dsRBP) that has been implicated in dendritic mRNA localization. The specificity of Stau2 binding to its target mRNAs remains elusive. Using individual-nucleotide resolution CLIP (iCLIP), we identified significantly enriched Stau2 binding to the 3'-UTRs of 356 transcripts. In 28 (7.9%) of those, binding occurred to a retained intron in their 3'-UTR The strongest bound 3'-UTR intron was present in the longest isoform of Calmodulin 3 (Calm3(L)) mRNA Calm3(L) 3'-UTR contains six Stau2 crosslink clusters, four of which are in this retained 3'-UTR intron. The Calm3(L) mRNA localized to neuronal dendrites, while lack of the 3'-UTR intron impaired its dendritic localization. Importantly, Stau2 mediates this dendritic localization via the 3'-UTR intron, without affecting its stability. Also, NMDA-mediated synaptic activity specifically promoted the dendritic mRNA localization of the Calm3(L) isoform, while inhibition of synaptic activity reduced it substantially. Together, our results identify the retained intron as a critical element in recruiting Stau2, which then allows for the localization of Calm3(L) mRNA to distal dendrites

Perfil químico y biológico de aceites esenciales de plantas aromáticas de interés agro-industrial en Castilla-La Mancha (España)

The chemical composition and biological activities of essential oils of <i>Salvia officinalis</i> L., <i>Salvia lavandulifolia</i> Vahl., <i>Lavandula x intermedia</i> Emeric ex Loisel., <i>Lavandula latifolia</i> Medik., <i>Lavandula angustifolia</i> Mill. and <i>Thymus vulgaris</i> L. are presented. The essential oils have been analysed by Gas Chromatography Mass Spectrometry and 61 compounds were identified, 23 of which represented more than 1% of the essential oil. The 1,8 cineole (16-23%) appeared as the main compound of <i>Salvia</i> sp. essential oils. The high content of α-thujone was characteristic in <i>S. officinalis</i> oil. Remarkable concentrations of linalool (30-33%), camphor (5-17%) and linalyl acetate (9-28%) were detected in <i>Lavandula</i> sp. oils while carvacrol (21.6%) and p-cimene (23.7%) were the most abundant compounds in <i>T. vulgaris</i> oil. Biological characterization was based on their bioplaguicide activity. The essential oils studied had strong antifeedant effects against <i>Leptinotarsa decemlineata</i> Say, <i>Spodoptera littoralis</i> Boisd., <i>Myzus persicae</i> Sulzer and <i>Rhopalosiphum padi</i> L., phytotoxic activity against <i>Lactuca sativa</i> L. and <i>Lolium perenne</i> L. and also exhibited high antifungal activity against <i>Fusarium</i> sp. Oils from <i>T. vulgaris</i> and <i>L. latifolia</i> showed the highest levels of bioactivity against all target species. These results provide an added-value to the essential oils of aromatic plants of agro-industrial interest for its potential use in the development of natural agrochemicals.<br><br>En este trabajo se presenta el estudio químico y biológico de los aceites esenciales de <i>Salvia officinalis</i> L., <i>Salvia lavandulifolia</i> Vahl., <i>Lavandula</i> x intermedia Emeric ex Loisel., <i>Lavandula latifolia</i> Medik., <i>Lavandula angustifolia</i> Mill. y <i>Thymus vulgaris</i> L. El estudio químico por cromatografía de gases acoplada a espectrometría de masas de los aceites esenciales permitió la identificación de 61 compuestos, de los cuales 23 presentaron un porcentaje mayor o igual al 1 %. Los aceites esenciales de <i>Salvia</i> sp. se caracterizaron por presentar un alto contenido de 1,8 cineol (16-23%) y, en el caso específico de <i>S. officinalis</i>, una elevada proporción de α-tuyona (15.7%). En <i>Lavandula</i> sp., los compuestos mayoritarios del aceite fueron linalol (30-33%), alcanfor (5-17%) y acetato de linalilo (9-28%); mientras que en <i>T. vulgaris</i> lo fueron carvacrol (21.6%) y p-cimeno (23.7%). La caracterización biológica, desde el punto de vista de la actividad bioplaguicida, mostró que los aceites ensayados disminuyeron significativamente la alimentación de <i>Leptinotarsa decemlineata</i> Say, <i>Spodoptera littoralis</i> Boisd., <i>Myzus persicae</i> Sulzer y <i>Rhopalosiphum padi</i> L., mostraron actividad fitotóxica frente a <i>Lactuca sativa</i> L. y <i>Lolium perenne</i> L. y disminuyeron el crecimiento del micelio del hongo de Fusarium sp. Los aceites de <i>T. vulgaris</i> y <i>L. latifolia</i> fueron los más activos frente a todas las especies empleadas como dianas biológicas. Los resultados obtenidos potencian el valor añadido de los aceites de plantas aromáticas de interés agro-industrial en Castilla- La Mancha como una alternativa interesante en programas de desarrollo de agroquímicos naturales

The regulon of the RNA chaperone CspA and its auto-regulation in Staphylococcus aureus

RNA-binding proteins (RBPs) are essential to fine-tune gene expression. RBPs containing the cold-shock domain are RNA chaperones that have been extensively studied. However, the RNA targets and specific functions for many of them remain elusive. Here, combining comparative proteomics and RBP-immunoprecipitation-microarray profiling, we have determined the regulon of the RNA chaperone CspA of Staphylococcus aureus. Functional analysis revealed that proteins involved in carbohydrate and ribonucleotide metabolism, stress response and virulence gene expression were affected by cspA deletion. Stress-associated phenotypes such as increased bacterial aggregation and diminished resistance to oxidative-stress stood out. Integration of the proteome and targetome showed that CspA post-transcriptionally modulates both positively and negatively the expression of its targets, denoting additional functions to the previously proposed translation enhancement. One of these repressed targets was its own mRNA, indicating the presence of a negative post-transcriptional feedback loop. CspA bound the 5'UTR of its own mRNA disrupting a hairpin, which was previously described as an RNase III target. Thus, deletion of the cspA 5'UTR abrogated mRNA processing and auto-regulation. We propose that CspA interacts through a U-rich motif, which is located at the RNase III cleavage site, portraying CspA as a putative RNase III-antagonist

The regulon of the RNA chaperone CspA and its auto-regulation in Staphylococcus aureus

RNA-binding proteins (RBPs) are essential to fine-tune gene expression. RBPs containing the cold-shock domain are RNA chaperones that have been extensively studied. However, the RNA targets and specific functions for many of them remain elusive. Here, combining comparative proteomics and RBP-immunoprecipitation-microarray profiling, we have determined the regulon of the RNA chaperone CspA of Staphylococcus aureus. Functional analysis revealed that proteins involved in carbohydrate and ribonucleotide metabolism, stress response and virulence gene expression were affected by cspA deletion. Stress-associated phenotypes such as increased bacterial aggregation and diminished resistance to oxidative-stress stood out. Integration of the proteome and targetome showed that CspA post-transcriptionally modulates both positively and negatively the expression of its targets, denoting additional functions to the previously proposed translation enhancement. One of these repressed targets was its own mRNA, indicating the presence of a negative post-transcriptional feedback loop. CspA bound the 5'UTR of its own mRNA disrupting a hairpin, which was previously described as an RNase III target. Thus, deletion of the cspA 5'UTR abrogated mRNA processing and auto-regulation. We propose that CspA interacts through a U-rich motif, which is located at the RNase III cleavage site, portraying CspA as a putative RNase III-antagonist

Nascent RNA antagonizes the interaction of a set of regulatory proteins with chromatin.

A number of regulatory factors are recruited to chromatin by specialized RNAs. Whether RNA has a more general role in regulating the interaction of proteins with chromatin has not been determined. We used proteomics methods to measure the global impact of nascent RNA on chromatin in embryonic stem cells. Surprisingly, we found that nascent RNA primarily antagonized the interaction of chromatin modifiers and transcriptional regulators with chromatin. Transcriptional inhibition and RNA degradation induced recruitment of a set of transcriptional regulators, chromatin modifiers, nucleosome remodelers, and regulators of higher-order structure. RNA directly bound to factors, including BAF, NuRD, EHMT1, and INO80 and inhibited their interaction with nucleosomes. The transcriptional elongation factor P-TEFb directly bound pre-mRNA, and its recruitment to chromatin upon Pol II inhibition was regulated by the 7SK ribonucleoprotein complex. We postulate that by antagonizing the interaction of regulatory proteins with chromatin, nascent RNA links transcriptional output with chromatin composition