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Exploration of DUF285 Motif Distribution and Similarity Across Mycoplasma and Related Species

This study investigates the DUF285 motif, a 25-amino acid peptide found in various mycoplasmal proteins, particularly in Mycoplasma species. We analyze its occurrence across phylogenetic domains, focusing on its conservation, functional clues gleaned from protein features, and distribution among different taxa. Additionally, we address questions of horizontal gene transfer and sequence diversity among representative open reading frames (ORFs). The research findings contribute to our understanding of the evolutionary relationships and biological significance of this motif.

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Exploration of DUF285 Motif Distribution and Similarity Across Mycoplasma and Related Species

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  1. LP-Signal W D T S N I V S M S S M F Q Q A R N F N Q V L S N W N T E N V T D M N Y M F D G A T K F N S D L S S W K T A N V K T M R S M F S D T K Q F N Q D I S S W N V S N V K N M K N M F Y R A E K F N K S L S D W N L K N I Q E L D H M F F G A S E F N S D I F K W D V S K V V N M D S M F N G A H D F N Q N I T N W N V S N V K T M R S M F S D T K Q F N Q D I K N W R V D N V T D M D R M F Q N A L S F N K D I S S W x x x x V x x M x x M F x x x x x F N x x I x x I L L Q-motif - background First description of a 25 amino acid peptide motif: LppQ Lipoprotein from M. mycoides subsp. mycoides SC E-M. Abdo, J. Nicolet, and J. Frey, Clin. and Diagn. Lab. Imm. (2000)

  2. Publicly accessible motifs that describe the repeating sequence DUF 285: “mycoplasmal protein…” TIGR 02167: “26 AA repeat/mycoplasma”

  3. M. pnemoniae clade M. hominisclade Mycoplasma subgroups Spirolasma-M.mycoidesclade Phytoplasma asteris OY strain 16S rRNA phylogeny vs whole genome phylogeny

  4. M. pnemoniae clade M. hominisclade Mycoplasma subgroups Spirolasma-M.mycoidesclade Phytoplasma asteris OY strain 16S rRNA phylogeny vs whole genome phylogeny DUF285 occurs in some taxa on these branches

  5. Questions arising from initial observations Evidence for HGT? How widely dispersed among species? Degree of similarity among disparate seq? Seq diversity of reps within/between ORFs? Clues to function by protein features?

  6. Distribution of DUF285 • (NCBI search for the DUF) • Includes Eukayote Minimal Green Alga Ostreococcus CAL57751 • Also includes an Archeae Salinibacter (plasmid) YP446962 • GOALS: • Compare prototype ORFs from each of 3 phylogenetic domains

  7. Mycoplasma Lipoprotein Q Salinibacter transmembrane protein Ostreococcus transmembrane protein Location of DUF 285 motifs

  8. Alignment of tandemly arranged “regions” of representative Ostreococcus ORF designated “DUF285” (Workbench ClustalW)

  9. Sample Blast Analysis • TIGR2167_motif vs. Ostreococcus • Length = 26 • Score = 26.6 bits (57), Expect = 5e-04 Identities = 12/26 (46%), Positives = 20/26 (76%), Gaps = 1/26 (3%) • 1024 MFSNSTAFNQ--DISNWNTASVTNMAS 1048 • MFS ++ D+SN++ T++ VTNM+S • 1 MFSGCSSLTSLDVSNFDTSNVTNMSS 26

  10. Tree of BLAST best hits (query=Salinibacter YP446962) (0.75)

  11. Tree of BLAST best hits (query=Salinibacter YP446962) (0.65)

  12. Salinibacter DUF285 ORF topology features

  13. Ostreococcus DUF285 ORF topology features

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