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Redundancy in Periplasmic Binding Protein-Dependent Transport Systems for Trehalose, Sucrose, and Maltose in Sinorhizobium meliloti. John Beck Jensen, 2002.We have identified a cluster of six genes involved in trehalose transport and utilization (thu) in Sinorhizobium meliloti . Four of these genes, thuE, -F, -G, and -K, were found to encode components of a binding protein-dependent trehalose/maltose/sucrose ABC transporter . Their deduced gene products comprise a trehalose/maltose-binding protein (ThuE), two integral membrane proteins (ThuF and ThuG), and an ATP-binding protein (ThuK) . In addition, a putative regulatory protein (ThuR) was found divergently transcribed from the thuEFGK operon . When the thuE locus was inactivated by gene replacement, the resulting S . meliloti strain was impaired in its ability to grow on trehalose, and a significant retardation in growth was seen on maltose as well . The wild type and the thuE mutant were indistinguishable for growth on glucose and sucrose . This suggested a possible overlap in function of the thuEFGK operon with the aglEFGAK operon, which was identified as a binding protein-dependent ATP-binding transport system for sucrose, maltose, and trehalose . The Kms for trehalose transport were 8 ± 1 nM and 55 ± 5 nM in the uninduced and induced cultures, respectively . Transport and growth experiments using mutants impaired in either or both of these transport systems show that these systems form the major transport systems for trehalose, maltose, and sucrose . By using a thuE'-lacZ fusion, we show that thuE is induced only by trehalose and not by cellobiose, glucose, maltopentaose, maltose, mannitol, or sucrose, suggesting that the thuEFGK system is primarily targeted toward trehalose . The aglEFGAK operon, on the other hand, is induced primarily by sucrose and to a lesser extent by trehalose . Tests for root colonization, nodulation, and nitrogen fixation suggest that uptake of disaccharides can be critical for colonization of alfalfa roots but is not important for nodulation and nitrogen fixation per se . Escherichia coli DegP Protease Cleaves between Paired Hydrophobic Residues in a Natural Substrate: the PapA Pilin. C. Hal Jones, 2002.The DegP protein, a multifunctional chaperone and protease, is essential for clearance of denatured or aggregated proteins from the inner-membrane and periplasmic space in Escherichia coli. To date, four natural targets for DegP have been described: colicin A lysis protein, pilin subunits and MalS from E . coli, and high-molecular-weight adherence proteins from Haemophilus influenzae. In vitro, DegP has shown weak protease activity with casein and several other nonnative substrates . We report here the identification of the major pilin subunit of the Pap pilus, PapA, as a natural DegP substrate and demonstrate binding and proteolysis of this substrate in vitro . Using overlapping peptide arrays, we identified three regions in PapA that are preferentially cleaved by DegP . A 7-mer peptide was found to be a suitable substrate for cleavage by DegP in vitro . In vitro proteolysis of model peptide substrates revealed that cleavage is dependent upon the presence of paired hydrophobic amino acids; moreover, cleavage was found to occur between the hydrophobic residues . Finally, we demonstrate that the conserved carboxyl-terminal sequence in pilin subunits, although not a cleavage substrate for DegP, activates the protease and we propose that the activating peptide is recognized by DegP's PDZ domains . Complete Genome Sequence of the Ammonia-Oxidizing Bacterium and Obligate Chemolithoautotroph Nitrosomonas europaea. Patrick Chain, 2003.Nitrosomonas europaea (ATCC 19718) is a gram-negative obligate chemolithoautotroph that can derive all its energy and reductant for growth from the oxidation of ammonia to nitrite . Nitrosomonas europaea participates in the biogeochemical N cycle in the process of nitrification . Its genome consists of a single circular chromosome of 2,812,094 bp . The GC skew analysis indicates that the genome is divided into two unequal replichores . Genes are distributed evenly around the genome, with  47% transcribed from one strand and
53% transcribed from the complementary strand . A total of 2,460 protein-encoding genes emerged from the modeling effort, averaging 1,011 bp in length, with intergenic regions averaging 117 bp . Genes necessary for the catabolism of ammonia, energy and reductant generation, biosynthesis, and CO2 and NH3 assimilation were identified . In contrast, genes for catabolism of organic compounds are limited . Genes encoding transporters for inorganic ions were plentiful, whereas genes encoding transporters for organic molecules were scant . Complex repetitive elements constitute ca . 5% of the genome . Among these are 85 predicted insertion sequence elements in eight different families . The strategy of N . europaea to accumulate Fe from the environment involves several classes of Fe receptors with more than 20 genes devoted to these receptors . However, genes for the synthesis of only one siderophore, citrate, were identified in the genome . This genome has provided new insights into the growth and metabolism of ammonia-oxidizing bacteria .
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