An analysis of the function of region 1.2 of the primary sigma factor, sigma 70, from Escherichia coli

The sigma (σ) subunit of eubacterial RNA polymerase is required for recognition of and transcription initiation from promoter DNA sequences. One family of sigma factors includes those related to the primary sigma factor from E. coli, σ70. Members of the σ70 family have four highly conserved domains, of which regions 2 through 4 are present in all members. Region 1 can be subdivided into regions 1.1 and 1.2. Region 1.1 affects DNA binding by σ 70 alone, as well as transcription initiation by holoenzyme. Region 1.2, present and highly conserved in most sigma factors, has not yet been assigned a putative function, although previous work demonstrated that it is not required for either association with the core subunits of RNA polymerase or promoter specific binding by holoenzyme. This study primarily investigates the functional role of region 1.2 during transcription initiation. In vivo and in vitro characterization of thirty-two single amino acid substitutions targeted to region 1.2 of E. coli σ70 as well as a deletion of region 1.2, revealed that mutations in region 1.2 can affect promoter binding, open complex formation, initiated complex formation, and the transition from abortive transcription to elongation. The relative degree of solvent exposure of several positions in region 1.2 has been determined, with positions 116 and 122 likely to be located near the surface of σ70. ^ During the course of this study, the existence of two “wild type” variants of E. coli σ70 was discovered. The identity of amino acid 149 has been reported variably as either arginine or aspartic acid in published articles and in online databases. In vivo and in vitro characterization of the two reported variations of E. coli σ70 (N149 and D149) has determined that the two variants are functionally equivalent. However, in vivo and in vitro characterization of single amino acid substitutions and a region 1.2 deletion in the context of each variant background revealed that the behavior of some mutations are greatly affected by the identity of amino acid 149. ^

Radiocarbon, isotope, biogenic, and 230Th measurements for sediment core RC10-196

The subarctic North Pacific Ocean holds a large CO2 reservoir that is currently isolated from the atmosphere by a low-salinity layer. It has recently been hypothesized that the reorganization of these high-CO2 waters may have played a crucial role in the degassing of carbon dioxide to the atmosphere during the last deglaciation. This reorganization would leave some imprint on paleo-productivity records. Here we present 230Th-normalized biogenic fluxes from an intermediate depth sediment core in the Northwest Pacific (RC10-196, 54.7°N, 177.1°E, 1007 m) and place them within the context of a synthesis of previously-published biogenic flux data from 49 deep-sea cores north of 20°N, ranging from 420 to 3968 m water depth. The 230Th-normalized opal, carbonate, and organic carbon fluxes from RC10-196 peak approximately 13,000 calendar years BP during the Bølling/Allerød (B/A) period. Our data synthesis suggests that biogenic fluxes were in general lowest during the last glacial period, increased somewhat in the Northwest Pacific during Heinrich Event 1, and reached a maximum across the entire North Pacific during the B/A period. We evaluate several mechanisms as possible drivers of deglacial change in biogenic fluxes in the North Pacific, including changes in preservation, sediment focusing, sea ice extent, iron inputs, stratification, and circulation shifts initiated in the North Atlantic and North Pacific. Our analysis suggests that while micronutrient sources likely contributed to some of the observed changes, the heterogeneity in timing of glaciogenic retreat and sea level make these mechanisms unlikely causes of region-wide contemporaneous peaks in export production. We argue that paleo-observations are most consistent with ventilation increases in both the North Pacific (during H1) and North Atlantic (during B/A) being the primary drivers of increases in biogenic flux during the deglaciation, as respectively they were likely to bring nutrients to the surface via increased vertical mixing and shoaling of the global thermocline.

Contents of 230Th, Fe2O3, MnO and P2O5 in bottom sediments from the Tropical Pacific

Shape of the 230Th vertical distribution curve ideally close to exponential is studied to determine isotopic age of deep-sea sediments. In practice such ideal 230Th vertical distribution curve is rarely occur; secondary maxima and minima often appear on it. It has been shown that oxyhydroxides of Fe, Mn, and also Corg and P are of prime importance for 230Th concentration. A method is offered for normalizing the vertical distribution curve of 230Th based on taking into account content of these elements in sediment.

Down-core sedimentary Sr-Nd isotope records from two Cape Basin sediment cores in the South Atlantic: GeoB3603-2 (Meteor cruise M34/1) and MD02-2594 (Marion Dufresne cruise MD128)

We report down-core sedimentary Nd isotope (epsilon Nd) records from two South Atlantic sediment cores, MD02-2594 and GeoB3603-2, located on the western South African continental margin. The core sites are positioned downstream of the present-day flow path of North Atlantic Deep Water (NADW) and close to the Southern Ocean, which makes them suitable for reconstructing past variability in NADW circulation over the last glacial cycle. The Fe-Mn leachates epsilon Nd records show a coherent decreasing trend from glacial radiogenic values towards less radiogenic values during the Holocene. This trend is confirmed by epsilon Nd in fish debris and mixed planktonic foraminifera, albeit with an offset during the Holocene to lower values relative to the leachates, matching the present-day composition of NADW in the Cape Basin. We interpret the epsilon Nd changes as reflecting the glacial shoaling of Southern Ocean waters to shallower depths combined with the admixing of southward flowing Northern Component Water (NCW). A compilation of Atlantic epsilon Nd records reveals increasing radiogenic isotope signatures towards the south and with increasing depth. This signal is most prominent during the Last Glacial Maximum (LGM) and of similar amplitude across the Atlantic basin, suggesting continuous deep water production in the North Atlantic and export to the South Atlantic and the Southern Ocean. The amplitude of the epsilon Nd change from the LGM to Holocene is largest in the southernmost cores, implying a greater sensitivity to the deglacial strengthening of NADW at these sites. This signal impacted most prominently the South Atlantic deep and bottom water layers that were particularly deprived of NCW during the LGM. The epsilon Nd variations correlate with changes in 231Pa/230Th ratios and benthic d13C across the deglacial transition. Together with the contrasting 231Pa/230Th: epsilon Nd pattern of the North and South Atlantic, this indicates a progressive reorganization of the AMOC to full strength during the Holocene.