NORMAL GENOMIC

• Devault A, Banuls AL
• The promastigote surface antigen gene family of the Leishmania parasite:differential evolution by positive selection and recombination.
• BMC Evol Biol. 2008; 8: 292-292
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• BACKGROUND: PSA (promastigote surface antigen) is one of the major classesof membrane proteins present at the surface of the parasitic protozoanLeishmania. While it harbours leucine rich repeats, which are suggestiveof its involvement in parasite-to-host physical interactions, its exactrole is largely unknown. Furthermore, the extent of diversity of this genefamily, both in copy number and sequence has not been established.RESULTS: From the newly available complete genome sequences of L. major,L. infantum and L. braziliensis, we have established the complete list ofPSA genes, based on the conservation of specific domain architecture. Thelatter includes an array of leucine rich repeats of unique signatureflanked by conserved cysteine-rich domains. All PSA genes code either forsecreted or membrane-anchored surface proteins. Besides the few previouslyidentified PSA genes, which are shown here to be part of a relativelylarge subclass of PSA genes located on chromosome 12, this studyidentifies seven other PSA subtypes. The latter, whose genes lie onchromosomes 5, 9, 21 and 31 in all three species, form single gene (twogenes in one instance) subfamilies, which phylogenetically cluster ashighly related orthologs. On the other hand, genes found on chromosome 12generally show high diversification, as reflected in greater sequencedivergence between species, and in an extended set of divergent paralogs.Moreover, we show that the latter genes are submitted to strong positiveselection. We also provide evidence that evolution of these genes isdriven by intra- and intergenic recombination, thereby modulating thenumber of LRRs in protein and generating chimeric genes. CONCLUSION: PSAis a Leishmania family of membrane-bound or secreted proteins, whose mainsignature consists in a specific LRR sequence. All PSA genes found in thegenomes of three sequenced Leishmania species unambiguously distributeinto eight subfamilies of orthologs. Seven of these are evolvingrelatively slowly and could correspond to basic functions related toparasite/host interactions. On the opposite, the other PSA gene class,which include all so far experimentally studied PSA genes, could beinvolved in more specialised adaptative functions.

• Skrzypek E, Myers-Morales T, Whiteheart SW, Straley SC
• Application of a Saccharomyces cerevisiae model to study requirements fortrafficking of Yersinia pestis YopM in eucaryotic cells.
• Infect Immun. 2003; 71: 937-47
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• YopM is a leucine-rich repeat (LRR) virulence protein that is deliveredinto host cells when any of the three human-pathogenic species of Yersiniabinds to mammalian cells. It exhibits heterogeneity of size and sequenceamong the yersiniae, but the functional consequences of this variabilityare not yet known. Yersinia pestis YopM was previously shown to accumulatein the nuclei of infected HeLa cells by a mechanism that requiresvesicular trafficking. In this study, we characterized the trafficking ofY. pestis YopM in a Saccharomyces cerevisiae model previously found tosupport nuclear localization of YopM from an enteropathogenic Yersiniastrain (C. F. Lesser and S. I. Miller, EMBO J. 20:1840-1849, 2001). Y.pestis YopM was N-terminally fused to the yeast enhanced green fluorescentprotein (yEGFP) and inducibly expressed in the cytoplasm. yEGFP-YopMlocalized to the yeast nucleus, showing that this property is conservedfor YopMs so far tested and that infection and the presence of other Yopsare not required for its trafficking. When expressed in S. cerevisiae thatis temperature sensitive for vesicular transport, YopM failed toaccumulate in the nucleus at the nonpermissive temperature but didaccumulate when the permissive temperature was restored. This shows thatvesicular trafficking also is required in yeast for normal localization ofYopM. YopM consists of a 71-residue leader sequence, 15 LRRs, and a32-residue tail. Deletion analysis revealed that the leader sequence ortail is alone insufficient to direct YopM to the nucleus, showing that theLRR structure is required. Both the N-terminal and C-terminal halves ofYopM localized to the nucleus, indicating the possible presence of twonuclear localization signals (NLSs) in YopM or domains in YopM where anNLS-containing protein might bind; this fits with the presence of twohighly conserved regions among Yersinia YopMs. yEGFP-YopM lacking LRRs 4to 7 or 7 to 10 accumulated in the nucleus in yeast, and YopM lackingthese LRRs concentrated normally in the HeLa cell nucleus after deliveryby Yersinia infection, showing that these LRRs are not essential for YopMtrafficking in eucaryotic cells. However, because Y. pestis carryingeither of these YopMs is strongly compromised in virulence in mice, thesefindings revealed that LRRs 4 to 10 map a region of YopM or support aconformation of YopM that is necessary for a pathogenic effect.

• Sisk TJ, Roys S, Chang CH
• Self-association of CIITA and its transactivation potential.
• Mol Cell Biol. 2001; 21: 4919-28
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• The major histocompatibility complex (MHC) class II transactivator (CIITA)regulates the expression of genes involved in the immune response,including MHC class II genes and the interleukin-4 gene. Interactionsbetween CIITA and sequence-specific, DNA-binding proteins are required forCIITA to function as an activator of MHC class II genes. CIITA alsointeracts with the coactivators CBP (also called p300), and thisinteraction leads to synergistic activation of MHC class II promoters.Here, we report that CIITA forms complexes with itself and that a centralregion, including the GTP-binding domain is sufficient forself-association. Additionally, this central region interacts with theC-terminal leucine-rich repeat as well as the N-terminal acidic domain.LXXLL motifs residing in the GTP-binding domain are essential forself-association. Finally, distinct differences exist among various CIITAmutant proteins with regard to activation function, subcellularlocalization, and association with wild-type protein and dominant-negativepotential.

• Matsushima N, Ohyanagi T, Tanaka T, Kretsinger RH
• Super-motifs and evolution of tandem leucine-rich repeats within the smallproteoglycans--biglycan, decorin, lumican, fibromodulin, PRELP, keratocan,osteoadherin, epiphycan, and osteoglycin.
• Proteins. 2000; 38: 210-25
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• Leucine-rich repeats (LRRs) with 20-30 amino acids in unit length arepresent in many proteins from prokaryotes to eukaryotes. TheLRR-containing proteins include a family of nine small proteoglycans,forming three distinct subfamilies: class I contains biglycan/PG-I anddecorin/PG-II; class II: lumican, fibromodulin, PRELP, keratocan, andosteoadherin; and class III: epiphycan/PG-Lb and osteoglycin orosteoinductive factor. Comparative sequence analysis of the 34 availableprotein sequences reveals that these proteoglycans have two types of LRRs,which we call S and T. The type S LRR is 21 residues long and has theconsensus sequence of xxaPzxLPxxLxxLxLxxNxI. The type T LRR has 26residues; its consensus sequence is zzxxaxxxxFxxaxxLxxLxLxxNxL. In both"x" indicates variable residue; "z" is frequently a gap; "a" is Val, Leu,or Ile; and I is Ile or Leu. These type S and TLRRs are ordered into twosuper-motifs--STT with about 73 residues in classes I and II and ST withabout 47 residues in class III. The 12 LRRs in the small proteoglycans ofI and II are best represented as (STT)4; the seven LRRs of class III as(ST)T(ST)2. Our analyses indicate that classes I/II and III evolved alongdifferent paths after the establishment of the precursor ST, and classes Iand II also diverged after the establishment of the precursor (STT)4.

• Harmsen MM, Ruuls RC, Nijman IJ, Niewold TA, Frenken LG, de Geus B
• Llama heavy-chain V regions consist of at least four distinct subfamiliesrevealing novel sequence features.
• Mol Immunol. 2000; 37: 579-90
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• In addition to conventional antibodies (Abs), camelids possess Absconsisting of only heavy chains. The variable domain of such a heavy-chainAb (VHH) is fully capable of antigen (Ag) binding. Earlier analysis of 47VHHs showed sequence features unique to VHH domains. These include thepresence of characteristic amino acid substitutions in positions which, inconventional VH domains are involved in interdomain interactions, and thepresence of a long third complementarity-determining region (CDR3) whichis frequently constrained by an interloop disulphide bond. Here, wedescribe a large (152) set of Lama glama VHH cDNAs. Based on amino acidsequence similarity, these and other published camelid VHHs wereclassified into four subfamilies. Three subfamilies are absent indromedaries, which have been the primary source of VHHs thus far.Comparison of these subfamilies to conventional VH regions reveals newfeatures characteristic of VHHs and shows that many features earlierregarded as characteristic of VHHs in general are actually subfamilyspecific. A long CDR3 with a concomitant putative additional disulphidebond is only observed in two VHH subfamilies. Furthermore, we identifiednew VHH-characteristic residues at positions forming interdomain sites inconventional VH domains. The VHH subfamilies also differ from each otherand conventional VH domains in the canonical structure of CDR1 and CDR2,mean CDR3 length, and amino acid residue variability. Since differentVHH-characteristic residues are observed in all four subfamilies, thesesubfamilies must have evolved independently from classical VH domains.