Rhomboid homologs in mycobacteria: insights from phylogeny and genomic analysisReport as inadecuate

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BMC Microbiology

, 10:272

First Online: 29 October 2010Received: 25 June 2010Accepted: 29 October 2010


BackgroundRhomboids are ubiquitous proteins with diverse functions in all life kingdoms, and are emerging as important factors in the biology of some pathogenic apicomplexa and Providencia stuartii. Although prokaryotic genomes contain one rhomboid, actinobacteria can have two or more copies whose sequences have not been analyzed for the presence putative rhomboid catalytic signatures. We report detailed phylogenetic and genomic analyses devoted to prokaryotic rhomboids of an important genus, Mycobacterium.

ResultsMany mycobacterial genomes contained two phylogenetically distinct active rhomboids orthologous to Rv0110 rhomboid protease 1 and Rv1337 rhomboid protease 2 of Mycobacterium tuberculosis H37Rv, which were acquired independently. There was a genome-wide conservation and organization of the orthologs of Rv1337 arranged in proximity with glutamate racemase mur1, while the orthologs of Rv0110 appeared evolutionary unstable and were lost in Mycobacterium leprae and the Mycobacterium avium complex. The orthologs of Rv0110 clustered with eukaryotic rhomboids and contained eukaryotic motifs, suggesting a possible common lineage. A novel nonsense mutation at the Trp73 codon split the rhomboid of Mycobacterium avium subsp. Paratuberculosis into two hypothetical proteins MAP2425c and MAP2426c that are identical to MAV 1554 of Mycobacterium avium. Mycobacterial rhomboids contain putative rhomboid catalytic signatures, with the protease active site stabilized by Phenylalanine. The topology and transmembrane helices of the Rv0110 orthologs were similar to those of eukaryotic secretase rhomboids, while those of Rv1337 orthologs were unique. Transcription assays indicated that both mycobacterial rhomboids are possibly expressed.

ConclusionsMycobacterial rhomboids are active rhomboid proteases with different evolutionary history. The Rv0110 rhomboid protease 1 orthologs represent prokaryotic rhomboids whose progenitor may be the ancestors of eukaryotic rhomboids. The Rv1337 rhomboid protease 2 orthologs appear more stable and are conserved nearly in all mycobacteria, possibly alluding to their importance in mycobacteria. MAP2425c and MAP2426c provide the first evidence for a split homologous rhomboid, contrasting whole orthologs of genetically related species. Although valuable insights to the roles of rhomboids are provided, the data herein only lays a foundation for future investigations for the roles of rhomboids in mycobacteria.

AbbreviationsBLASTBasic Local Alignment Search Tool

GIB-DDBJGenome information Broker-DNA Data Bank of Japan

ESAT-6Early Secreted Antigenic Target 6 kDa protein

iRhomsinactive rhomboids

KEGGKyoto Encyclopedia of Genes and Genomes

LBLuria Bertani

MACMycobacterium avium Complex

MAPMycobacterium avium subspecies Paratuberculosis

MTCMycobacterium tuberculosis Complex

MUSCLEMultiple Sequence Comparison by Log-Expectation

NTMNone-tuberculous mycobacteria

ORFOpen Reading Frame

PARLPresenilin-associated rhomboid-like

PDIMPhthiocerol Dimycocerosate

RT-PCRReverse Transcriptase Polymerase Chain Reaction

SNPSingle Nucleotide Polymorphism

TraSHTransposon Site Hybridization

TMHTransmembrane helice

Electronic supplementary materialThe online version of this article doi:10.1186-1471-2180-10-272 contains supplementary material, which is available to authorized users.

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Author: David P Kateete - Moses Okee - Fred A Katabazi - Alfred Okeng - Jeniffer Asiimwe - Henry W Boom - Kathleen D Eisenach -

Source: https://link.springer.com/article/10.1186/1471-2180-10-272

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