The complete genome and proteome of Mycoplasma mobile

Abstract

Although often considered "minimal" organisms, mycoplasmas show a wide range of diversity with respect to host environment, phenotypic traits, and pathogenicity. Here we report the complete genomic sequence and proteogenomic map for the piscine mycoplasma Mycoplasma mobile, noted for its robust gliding motility. For the first time, proteomic data are used in the primary annotation of a new genome, providing validation of expression for many of the predicted proteins. Several novel features were discovered including a long repeating unit of DNA of approximately 2435 bp present in five complete copies that are shown to code for nearly identical yet uniquely expressed proteins. M. mobile has among the lowest DNA GC contents (24.9%) and most reduced set of tRNAs of any organism yet reported (28). Numerous instances of tandem duplication as well as lateral gene transfer are evident in the genome. The multiple available complete genome sequences for other motile and immotile mycoplasmas enabled us to use comparative genomic and phylogenetic methods to suggest several candidate genes that might be involved in motility. The results of these analyses leave open the possibility that gliding motility might have arisen independently more than once in the mycoplasma lineage.

Figure 1

Circular genome plot. Ring definitions, from outermost to innermost: Predicted proteins colored by reading frame on the plus strand (red, green, blue are forward frames); predicted proteins colored by reading frame on the minus strand (cyan, magenta, and yellow are reverse frames); RNA coding features (red: tRNAs; blue: rRNAs; magenta: RNAse P RNA; green: tmRNA; cyan: 4.5S SRP RNA); GC content (calculated using a 5000-bp window sliding 100 bases at a time, see plot for range, height of trace proportional to deviation from 25% GC); cumulative GC-skew (calculated using a 5000-bp window sliding 100 bases at a time, see plot for range, height of trace proportional to deviation from 0) as in Grigoriev (1998).

Figure 2

Genome features and proteogenomic map. (First row) Genome ruler. (Second row) Special genome features including tRNAs (orange), mvsp genes (blue), and other features labeled on the figure. (Third row) Coding DNA sequences (CDS), color coded by COG categories automatically assigned for proteins in COGs, or manually assigned as necessary (color key in lower right corner). CDS not validated by proteomics are marked by an *. (Fourth row) Proteogenomic map showing detected peptides covering the predicted proteins color coded by reading frame, as in Figure 1.

Figure 2

Genome features and proteogenomic map. (First row) Genome ruler. (Second row) Special genome features including tRNAs (orange), mvsp genes (blue), and other features labeled on the figure. (Third row) Coding DNA sequences (CDS), color coded by COG categories automatically assigned for proteins in COGs, or manually assigned as necessary (color key in lower right corner). CDS not validated by proteomics are marked by an *. (Fourth row) Proteogenomic map showing detected peptides covering the predicted proteins color coded by reading frame, as in Figure 1.

Figure 3

Long repeat region. (Top) High-resolution view of the “long repeat region” of the M. mobile genome showing repeat arrangement and the lrp genes. (Bottom) Multiple sequence alignment of the lrp proteins showing all peptides detected by proteogenomic mapping (bold italic sequence) and those peptides that help to establish unique expression of that particular lrp protein (highlighted in color). Multiple alignments performed with CLUSTALX (Thompson et al. 1997).

Figure 4

16S rRNA phylogeny of sequenced mycoplasmas. Motile species are shown in bold. The Onion Yellows Phytoplasma is omitted because it was not used in the comparative genomics analysis targeted toward motility genes. The scale bar represents substitutions per site.