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The Dilemma of Phage Taxonomy Illustrated by Comparative Genomics of Sfi21-Like Siphoviridae in Lactic Acid Bacteria. Caroline Proux, 2002.The complete genome sequences of two dairy phages, Streptococcus thermophilus phage 7201 and Lactobacillus casei phage A2, are reported . Comparative genomics reveals that both phages are members of the recently proposed Sfi21-like genus of Siphoviridae, a widely distributed phage type in low-GC-content gram-positive bacteria . Graded relatedness, the hallmark of evolving biological systems, was observed when different Sfi21-like phages were compared . Across the structural module, the graded relatedness was represented by a high level of DNA sequence similarity or protein sequence similarity, or a shared gene map in the absence of sequence relatedness . This varying range of relatedness was found within Sfi21-like phages from a single species as demonstrated by the different prophages harbored by Lactococcus lactis strain IL1403 . A systematic dot plot analysis with 11 complete L . lactis phage genome sequences revealed a clear separation of all temperate phages from two classes of virulent phages . The temperate lactococcal phages share DNA sequence homology in a patchwise fashion over the nonstructural gene cluster . With respect to structural genes, four DNA homology groups could be defined within temperate L . lactis phages . Closely related structural modules for all four DNA homology groups were detected in phages from Streptococcus or Listeria, suggesting that they represent distinct evolutionary lineages that have not uniquely evolved in L . lactis . It seems reasonable to base phage taxonomy on data from comparative genomics . However, the peculiar modular nature of phage evolution creates ambiguities in the definition of phage taxa by comparative genomics . For example, depending on the module on which the classification is based, temperate lactococcal phages can be classified as a single phage species, as four distinct phage species, or as two if not three different phage genera . We propose to base phage taxonomy on comparative genomics of a single structural gene module (head or tail genes) . This partially phylogeny-based taxonomical system still mirrors some aspects of the current International Committee on Taxonomy in Virology classification system . In this system the currently sequenced lactococcal phages would be grouped into five genera: c2-, sk1, Sfi11-, r1t-, and Sfi21-like phages . Requirement of ArcA for Redox Regulation in Escherichia coli under Microaerobic but Not Anaerobic or Aerobic Conditions. Svetlana Alexeeva, 2003.In Escherichia coli, the two-component regulatory ArcAB system functions as a major control system for the regulation of expression of genes encoding enzymes involved in both aerobic and anaerobic catabolic pathways . Previously, we have described the physiological response of wild-type E . coli to changes in oxygen availability through the complete range from anaerobiosis to full aerobiosis (S . Alexeeva, B . de Kort, G . Sawers, K . J . Hellingwerf, and M . J . Teixeira de Mattos, J . Bacteriol . 182:4934-4940, 2000, and S . Alexeeva, K . J . Hellingwerf, and M . J . Teixeira de Mattos, J . Bacteriol . 184:1402-1406, 2002) . Here, we address the question of the contribution of the ArcAB-dependent transcriptional regulation to this response . Wild-type E . coli and a mutant lacking the ArcA regulator were grown in glucose-limited chemostat cultures at controlled levels of oxygen availability ranging from full aerobiosis to complete anaerobiosis . A flux analysis of the distribution of catabolic fluxes over parallel pathways was carried out, and the intracellular redox state (as reflected by the NADH/NAD ratio) was monitored for all steady states . Deletion of ArcA neither significantly altered the in vivo activity of the pyruvate dehydrogenase complex and pyruvate formate lyase nor significantly affected catabolism under fully aerobic and fully anaerobic conditions . In contrast, profound effects of the absence of ArcA were seen under conditions of oxygen-restricted growth: increased respiration, an altered electron flux distribution over the cytochrome o- and d-terminal oxidases, and a significant change in the intracellular redox state were observed . Thus, the ArcA regulator was found to exert major control on flux distribution, and it is concluded that the ArcAB system should be considered a microaerobic redox regulator . Identification of an Uptake Hydrogenase Required for Hydrogen-Dependent Reduction of Fe(III) and Other Electron Acceptors by Geobacter sulfurreducens. Maddalena V. Coppi, 2004.Geobacter sulfurreducens, a representative of the family Geobacteraceae that predominates in Fe(III)-reducing subsurface environments, can grow by coupling the oxidation of hydrogen to the reduction of a variety of electron acceptors, including Fe(III), fumarate, and quinones . An examination of the G . sulfurreducens genome revealed two operons, hya and hyb, which appeared to encode periplasmically oriented respiratory uptake hydrogenases . In order to assess the roles of these two enzymes in hydrogen-dependent growth, Hya- and Hyb-deficient mutants were generated by gene replacement . Hyb was found to be required for hydrogen-dependent reduction of Fe(III), anthraquinone-2,6-disulfonate, and fumarate by resting cell suspensions and to be essential for growth with hydrogen and these three electron acceptors . Hya, in contrast, was not . These findings suggest that Hyb is an essential respiratory hydrogenase in G . sulfurreducens .
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