Current Challenges in Bacterial Transcriptomics

Over the past decade or so, dramatic developments in our ability to experimentally determine the content and function of genomes have taken place. In particular, next-generation sequencing technologies are now inspiring a new understanding of bacterial transcriptomes on a global scale. In bacterial cells, whole-transcriptome studies have not received attention, owing to the general view that bacterial genomes are simple. However, several recent RNA sequencing results are revealing unexpected levels of complexity in bacterial transcriptomes, indicating that the transcribed regions of genomes are much larger and complex than previously anticipated. In particular, these data show a wide array of small RNAs, antisense RNAs, and alternative transcripts. Here, we review how current transcriptomics are now revolutionizing our understanding of the complexity and regulation of bacterial transcriptomes.

Homotypic and Heterotypic Interactions of SatBaMV-encoded P20 Protein / 生物化学与生物物理进展

Satellite RNA ofBaMV (satBaMV), a single-stranded positive-sense RNA of 836 nucleotide [excluding 3′ poly(A) tail]containing a single open reading frame which encodes a nonstructural protein of 20 ku (P20), depends on BaMV for its replication and encapsidation. P20 is a nucleic-acid-binding protein, which facilitates the long distance movement of satBaMV in plants.Protein-protein interactions were analyzed by a bacterial two-hybrid system and pull-down assays to investigate whether P20 could self-associate and/or interact with the helper virus proteins. Self-interaction of P20 was the strongest among the viral protein-protein interactions detected in vivo and in vitro. Significant interactions of P20 with methyltransferase (MET) and capsid protein (CP) of BaMV were evidenced. Interactions among triple gene block protein 1, 2 and 3 (TGBp1, TGBp2 and TGBp3) of BaMV were also significant. BaMV CP also exhibited a strong self-interaction and strong affinity to TGBp1, TGBp2 and TGBp3. By deletion analysis,the minimal region delineated for the self-interaction of P20 was the N-terminal 15 amino acids which include the RNA binding motif of P20. N-terminal deletion resulted in the loss of self-interaction of P20. Deletion analysis also confirmed the importance of β-sheet structure of P20 in the P20-P20 interaction. P20 showed significant interactions with two host (Nicotiana benthamiana) proteins,cytochrome-C reductase and β-tubulins. The homotypic and heterotypic interactions of BaMV proteins and P20 in vivo thus suggest that the protein-protein interactions may directly exert an effect on the BaMV and satBaMV RNA movement as a protein complex in the infected host plants.