PMC:1069646 / 11219-16357 JSONTXT

{"project":"2_test","denotations":[{"id":"15780005-11244060-84825029","span":{"begin":339,"end":342},"obj":"11244060"},{"id":"15780005-15111095-84825030","span":{"begin":343,"end":346},"obj":"15111095"},{"id":"15780005-9580676-84825031","span":{"begin":485,"end":488},"obj":"9580676"},{"id":"15780005-15236643-84825032","span":{"begin":4955,"end":4958},"obj":"15236643"},{"id":"15780005-14749835-84825033","span":{"begin":4959,"end":4962},"obj":"14749835"},{"id":"T835","span":{"begin":339,"end":342},"obj":"11244060"},{"id":"T64344","span":{"begin":343,"end":346},"obj":"15111095"},{"id":"T86722","span":{"begin":485,"end":488},"obj":"9580676"},{"id":"T74719","span":{"begin":4955,"end":4958},"obj":"15236643"},{"id":"T68147","span":{"begin":4959,"end":4962},"obj":"14749835"}],"text":"Genome Properties and General Comparison with the Genomes of Other Parasites and Endosymbionts\nThe genome of wBm is represented by a single circular chromosome consisting of 1,080,084 nucleotides and is 34% G+C. The size agrees with the 1.1 Mb length previously determined by both pulsed-field gel electrophoresis and restriction mapping [113,114]. The origin of replication (oriC) was tentatively mapped immediately upstream of the hemE gene on the basis of GC- and AT-skew analyses [115] (Figure 1). The genome of wBm has an extremely low density of predicted functional genes compared to all other bacteria, with the exceptions of R. prowazekii (Table 1) and Mycobacterium leprae. Both Wolbachia spp. and Rickettsia spp. have undergone considerable gene loss in many metabolic pathways, relative to other alpha-proteobacteria (Table 2). A comparison of predicted functional genes in wBm and Rickettsia spp. reveals a large core set that is conserved among these genomes, as well as smaller sets unique to each genome (Figure 2). In contrast, nearly all observed pseudogenes are unique to each genome (Figure 2), suggesting substantial independent genome degradation. Wolbachia (wBm) and R. conorii contain, in addition to many demonstrable pseudogenes, a considerable number of short open reading frames (ORFs), which have no detectable orthologs in current protein databases but are recognized as probable genes by gene prediction programs. However, most of these sequences, which comprise approximately 5% of the total predicted gene number in wBm, are likely to be fragmented genes as well (Table 1).\nFigure 1 Genogram of the Complete Circular Genome of wBm\nThe scale indicates coordinates in kilobase pairs (kbp) with the putative origin of replication positioned at 0 kbp. The outermost ring indicates the GC-skew over all bases in the forward strand using a window size of 40 kbp and a step size of 1 kbp. Positive and negative skew are shaded gold and blue, respectively. Features are shown as paired rings separated by a circular baseline. In each pair, the outer and inner rings represent the forward and reverse DNA strands, respectively. Working inward from the scale, the features displayed are as follows: identified genes and their broad functional classification (multihued, as listed); tRNA (blue)/rRNA (red) genes; putative pseudogenes (green); repeated sequences (red) and transposon-related repeats (blue).\nFigure 2 Venn Diagram Showing Comparison of Conserved and Unique Genes and Pseudogenes in wBm (Wolbachia from B. malayi), Rickettsia prowazekii, Rickettsia conorii, and in wBm and wMel (among Those Assigned to COGs)\n(A) Predicted functional protein-coding genes.\n(B) Pseudogenes.\n(C) Combined results for comparison between wBm and wMel.\nG, intact gene; P, pseudogene.\nTable 1 Comparison of Genome Features of Proteobacterial Endosymbionts and Endoparasites a Independent estimates obtained during this work. wBm, Wolbachia from B. malayi; wMel, Wolbachia from Drosophila melanogaster; R. conorii, Rickettsia conorii; R. prowazekii, Rickettsia prowazekii; B. aphidicola, Buchnera aphidicola; B. floridanus, Blochmannia floridanus; W. glossinidia, Wigglesworthia glossinidia. IS, insection element sequence\nTable 2 Gene Loss and Decay in Wolbachia and Rickettsia Gene conservation and loss were determined with respect to the set of 1,177 genes that are represented by confidently identifiable orthologs in all free-living alpha-proteobacteria. For each category, the first number indicates retained genes, the second number indicates lost genes, and the third number indicates pseudogenes. The sum of these numbers equals the total number of genes in this category in the alpha-proteobacterial core set. wBm, Wolbachia from B. malayi; wMel, Wolbachia from Drosophila melanogaster; R. conorii, Rickettsia conorii; R. prowazekii, Rickettsia prowazekii. The wBm genome contains one copy of each of the ribosomal RNA genes (16S, 23S, and 5S), which do not form an operon, as also observed in wMel and Rickettsia but in contrast to most other bacteria, and 34 tRNA genes that include cognates for all amino acids. Probable biological function was assigned to 558 (approximately 70%) of the 806 protein coding genes; a more general prediction of biochemical function was made for an additional 49 ORFs. Most of the predicted genes (617, 76%) could be included in clusters of orthologous groups of proteins (COGs) with orthologs not only in wMel and Rickettsia but also in more distant organisms.\nA lack of flagellar, fimbrial or pili genes indicates that wBm is probably nonmotile (Table 2). However, some intracellular pathogens, including spotted fever group Rickettsia, exploit a different motility mechanism that makes use of the host cell actin polymerization to promote bacterial locomotion. Actin-based motility of Rickettsia depends upon activation of the host Arp2/3 complex by the WASP family protein RickA [116,117]. A gene coding for WASP family protein (Wbm0076) was identified in wBm suggesting that it might be able to employ actin polymerization for locomotion and cell-to-cell spread."}