Azotobacter vinelandii is a soil bacterium related to the Pseudomonas genus that fixes nitrogen under aerobic conditions while simultaneously protecting nitrogenase from oxygen damage. In response to carbon availability, this organism undergoes a simple differentiation process to form cysts that are resistant to drought and other physical and chemical agents. Here we report the complete genome sequence of A. vinelandii DJ, which has a single circular genome of 5,365,318 bp. In order to reconcile an obligate aerobic lifestyle with exquisitely oxygen-sensitive processes, A. vinelandii is specialized in terms of its complement of respiratory proteins. It is able to produce alginate, a polymer that further protects the organism from excess exogenous oxygen, and it has multiple duplications of alginate modification genes, which may alter alginate composition in response to oxygen availability. The genome analysis identified the chromosomal locations of the genes coding for the three known oxygen-sensitive nitrogenases, as well as genes coding for other oxygen-sensitive enzymes, such as carbon monoxide dehydrogenase and formate dehydrogenase. These findings offer new prospects for the wider application of A. vinelandii as a host for the production and characterization of oxygen-sensitive proteins.
SUMMARY Nuclear export of unspliced and singly spliced viral mRNA is a critical step in the HIV life cycle. The structural basis by which the virus selects its own mRNA among more abundant host cellular RNAs for export has been a mystery for more than 25 years. Here, we describe an unusual topological structure that the virus uses to recognize its own mRNA. The viral Rev response element (RRE) adopts an “A”-like structure in which the two legs constitute two tracks of binding sites for the viral Rev protein and position the two primary known Rev-binding sites ~55 Å apart, matching the distance between the two RNA-binding motifs in the Rev dimer. Both the legs of the “A” and the separation between them are required for optimal RRE function. This structure accounts for the specificity of Rev for the RRE and thus the specific recognition of the viral RNA.
Iron-sulfur clusters ([Fe-The in vivo maturation of simple [Fe-S] proteins is proposed to require preassembly of [Fe-S] species on molecular scaffolds. The first [Fe-S] cluster assembly system to be described is the NIF 2 system from Azotobacter vinelandii. This system consists of a cysteine desulfurase, encoded by nifS, which supplies the S for [Fe-S] cluster formation, and a proposed scaffold protein, encoded by nifU (1). The NIF system is specialized for the maturation of [Fe-S] proteins involved in nitrogen fixation.A. vinelandii also contains a second [Fe-S] protein maturation system designated ISC. The ISC system is required for the general maturation of cellular [Fe-S] proteins involved in intermediary metabolism, such as aconitase (2). The ISC system is more complicated than the NIF system as it includes the products of eight contiguous genes : iscR, iscS, iscU, iscA, hscB, hscA, fdx, and iscX (3). Although the NIF and ISC systems exhibit physiological target specificity, each can partially replace the function of the other, when expressed at high levels (4, 5).Even though the NIF and ISC systems are differentiated by their apparent target specificities, they share a number of common structural and functional features. For example, NifS and IscS have similar sequences, and they both exhibit cysteine desulfurase activity (2). IscU also shares considerable sequence identity when compared with the N-terminal domain of NifU, including conservation of three cysteine residues that are likely to provide the nucleation site(s) for [Fe-S] cluster assembly (2, 6).NifU is a modular protein that contains three distinct domains (Fig. 1). The central domain contains a stable redoxactive [2Fe-2S] cluster with an as-yet-unknown function (7). In vitro and in vivo experiments have established that labile [Fe-S] clusters can be assembled on both the N-terminal and C-terminal domains of NifU, and such cluster-loaded forms of NifU can be used for activation of the nitrogenase 9). Thus, NifU contains two different sites upon which labile [Fe-S] clusters can be assembled in vitro, but the functional relationship between these sites is not yet known.There are no genes within the ISC transcriptional unit that encode proteins with sequence similarity to the C-terminal domain of NifU. However, located elsewhere on the A. vinelandii genome is a gene, designated nfuA, whose product encodes a protein having a C-terminal sequence similar to the C-terminal domain of NifU (Fig. 1). The sequence conservation between NifU and NfuA includes two cysteine residues that are required for the in vitro assembly of [Fe-S] clusters within the NifU C-terminal domain. Like NifU, NfuA also appears to be a modular protein because the amino acid sequence within its N-terminal region shares some sequence similarity with another protein involved in [Fe-S] protein maturation designated IscA (Fig. 1). IscA is a nonessential protein encoded within the ISC transcriptional unit, and it has been proposed to serve as an alternative [Fe-S] cluster ass...
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