SummaryDespite extensive genetic, biochemical and structural studies on Escherichia coli RNA polymerase (RNAP), little is known about its location and distribution in response to environmental changes. To visualize the RNAP by fluorescence microscopy in E. coli under different physiological conditions, we constructed a functional rpoC-gfp gene fusion on the chromosome. We show that, although RNAP is located in the nucleoid and at its periphery, the distribution of RNAP is dynamic and dramatically influenced by cell growth conditions, nutrient starvation and overall transcription activity inside the cell. Moreover, mutational analysis suggests that the stable RNA synthesis plays an important role in nucleoid condensation.

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...

In Escherichia coli the genome must be compacted ϳ1,000-fold to be contained in a cellular structure termed the nucleoid. It is proposed that the structure of the nucleoid is determined by a balance of multiple compaction forces and one major expansion force. The latter is mediated by transertion, a coupling of transcription, translation, and translocation of nascent membrane proteins and/or exported proteins. In supporting this notion, it has been shown consistently that inhibition of transertion by the translation inhibitor chloramphenicol results in nucleoid condensation due to the compaction forces that remain active in the cell. Our previous study showed that during optimal growth, RNA polymerase is concentrated into transcription foci or "factories," analogous to the eukaryotic nucleolus, indicating that transcription and RNA polymerase distribution affect the nucleoid structure. However, the interpretation of the role of transcription in the structure of the nucleoid is complicated by the fact that transcription is implicated in both compacting forces and the expansion force. In this work, we used a new approach to further examine the effect of transcription, specifically from rRNA operons, on the structure of the nucleoid, when the major expansion force was eliminated. Our results showed that transcription is necessary for the chloramphenicol-induced nucleoid compaction. Further, an active transcription from multiple rRNA operons in chromosome is critical for the compaction of nucleoid induced by inhibition of translation. All together, our data demonstrated that transcription of rRNA operons is a key mechanism affecting genome compaction and nucleoid structure.An Escherichia coli cell is small, measuring approximately 2 to 4 m in length and 1 m in diameter. The bacterial genome is 4.6 million bp, which would be approximately 1.5 mm in length if stretched fully. In a rapidly growing cell, there are multiple genome equivalents. Thus, the genome must be compressed at least 1,000-fold to fit into the cell. The bacterial chromosome forms a cellular structure named the nucleoid (25, 42). Normally the E. coli nucleoid shows a characteristic "flexible doublet" shape (49) and is membrane associated (2, 46). Despite great advances being made in understanding the biochemistry and molecular biology of E. coli, the structure of the bacterial nucleoid remains poorly defined.Woldringh et al. proposed that the structure of the nucleoid is determined by a balance of expansion and compaction forces (44). Suggested compaction forces include (i) DNA binding proteins (9, 17), (ii) DNA supercoiling (29,35,38), (iii) macromolecular crowding (20,23,51), and (iv) entropy-driven depletion attraction (18). One of the proposed forces that significantly contributes to expansion of the nucleoid is called transertion. During this process, coupled transcription and translation of membrane proteins and/or periplasmic exported proteins pull and anchor the transcribed bacterial nucleoid onto the cytoplasmic membrane (3, 43). In addition,...