Ig. 1J) while 6863 of cells expressing the negative control construct Myc-Sec61b had ER whorls (Fig. 1J). This was as expected for full rescue by the wild type HA-Yip1A transgene. For ease of comparison across experiments, we present the data from hereon in terms of rescue efficiency (calculated as detailed in MaterialsConstructsThe siRNAs used against Yip1A were described previously (10) and synthesized by Ambion (Austin, TX). The myc-tagged Sec61b was purchase CAL 120 subcloned from GFP-Sec61b (kindly provided by Dr. Tom Rapoport, Harvard Medical School, Boston, MA) into the EcoRI and XbaI sites of the pCS2-MT vector. The myc-tagged Yif1A construct was cloned by PCR amplification from HeLa cDNA (Qiagen, Hilden, Germany) and inserting the PCR product into the pCS2-MT vector using EcoRI and XbaI sites. The HA-Yip1A rescue construct was created by replacing the FLAG epitope from the FLAG-Yip1A construct [10] with the HA epitope (YPYDVPDYA) using a PCR-based loop-out/loop-in modification of the QuikChange protocol (Stratagene, 
La Jolla, CA) and was the parent construct for all further HA-Yip1A mutations. The HAYip1AN/Sec61b TM was created by first using a PCR-based loop-out technique (Stratagene) to remove the TM domain region (AA 126?57) of the Yip1A construct and the TM domain from Myc- Sec61b (AA 61?7) was subcloned into the XbaI site at 
theMutational Analysis of Yip1AFigure 2. Only a few highly conserved residues in the Yip1A cytoplasmic domain are required for function. Cells co-transfected with Yip1A siRNA and HA-Yip1A D1-83 were fixed after 72 h and co-stained with antibodies against HA (A) and calnexin (B). The asterisk (A and B) marks an expressing cell that did not exhibit ER whorls. Scale bar, 10 mm. (C) Quantification of the 15481974 efficiency of rescue by HA-Yip1A D1?3, HA-Yip1A D1?18 and the negative control Myc-Sec61b. Data were from 3 independent experiments (.100 cells per experiment), 6SD. (D) An alignment of the cytoplasmic domains of human Yip1A with yeast Yip1p. Residues 83?18 are bracketed, with the highly conserved block highlighted in bold. (E)Mutational Analysis of Yip1ABolded residues (in D) were mutated as indicated and tested for rescue. Data from 3 independent experiments (.100 cells per experiment) 6SD are quantified. Yellow bars indicate residues that were partially functional when mutated to alanine. Red bars indicate those same residues showing a more significant loss of function when mutated to a charged residue. Single asterisk, p-value ,0.001; 15755315 double asterisk, p,0.05 (Student’s t-test). The open circle and purple bar indicate the previously identified nonfunctional variant E95K [10]. doi:10.1371/journal.pone.ML-281 0054413.gFigure 3. Regions of the Yip1A TM domain required for ER structuring. (A) Quantification of rescue in cells that were co-transfected with Yip1A siRNA and mutated HA-Yip1A constructs. Data were from 3 independent experiments (.100 cells per experiment), 6SD. Red bars indicate regions that were nonfunctional when mutated to Ala/Leu. (B) A schematic representation of the predicted topology of Yip1A. The results from (A) are represented on the schematic. Residues highlighted in blue were functional and red were nonfunctional when stretches of amino acids were replaced with Ala/Leu. Residues highlighted in yellow were nonfunctional when individual amino acids were replaced with Ala/Leu. Precise substitutions are detailed in Table S1. doi:10.1371/journal.pone.0054413.gMutational Analysis of Yip1AFigure 4. Two residues w.Ig. 1J) while 6863 of cells expressing the negative control construct Myc-Sec61b had ER whorls (Fig. 1J). This was as expected for full rescue by the wild type HA-Yip1A transgene. For ease of comparison across experiments, we present the data from hereon in terms of rescue efficiency (calculated as detailed in MaterialsConstructsThe siRNAs used against Yip1A were described previously (10) and synthesized by Ambion (Austin, TX). The myc-tagged Sec61b was subcloned from GFP-Sec61b (kindly provided by Dr. Tom Rapoport, Harvard Medical School, Boston, MA) into the EcoRI and XbaI sites of the pCS2-MT vector. The myc-tagged Yif1A construct was cloned by PCR amplification from HeLa cDNA (Qiagen, Hilden, Germany) and inserting the PCR product into the pCS2-MT vector using EcoRI and XbaI sites. The HA-Yip1A rescue construct was created by replacing the FLAG epitope from the FLAG-Yip1A construct [10] with the HA epitope (YPYDVPDYA) using a PCR-based loop-out/loop-in modification of the QuikChange protocol (Stratagene, La Jolla, CA) and was the parent construct for all further HA-Yip1A mutations. The HAYip1AN/Sec61b TM was created by first using a PCR-based loop-out technique (Stratagene) to remove the TM domain region (AA 126?57) of the Yip1A construct and the TM domain from Myc- Sec61b (AA 61?7) was subcloned into the XbaI site at theMutational Analysis of Yip1AFigure 2. Only a few highly conserved residues in the Yip1A cytoplasmic domain are required for function. Cells co-transfected with Yip1A siRNA and HA-Yip1A D1-83 were fixed after 72 h and co-stained with antibodies against HA (A) and calnexin (B). The asterisk (A and B) marks an expressing cell that did not exhibit ER whorls. Scale bar, 10 mm. (C) Quantification of the 15481974 efficiency of rescue by HA-Yip1A D1?3, HA-Yip1A D1?18 and the negative control Myc-Sec61b. Data were from 3 independent experiments (.100 cells per experiment), 6SD. (D) An alignment of the cytoplasmic domains of human Yip1A with yeast Yip1p. Residues 83?18 are bracketed, with the highly conserved block highlighted in bold. (E)Mutational Analysis of Yip1ABolded residues (in D) were mutated as indicated and tested for rescue. Data from 3 independent experiments (.100 cells per experiment) 6SD are quantified. Yellow bars indicate residues that were partially functional when mutated to alanine. Red bars indicate those same residues showing a more significant loss of function when mutated to a charged residue. Single asterisk, p-value ,0.001; 15755315 double asterisk, p,0.05 (Student’s t-test). The open circle and purple bar indicate the previously identified nonfunctional variant E95K [10]. doi:10.1371/journal.pone.0054413.gFigure 3. Regions of the Yip1A TM domain required for ER structuring. (A) Quantification of rescue in cells that were co-transfected with Yip1A siRNA and mutated HA-Yip1A constructs. Data were from 3 independent experiments (.100 cells per experiment), 6SD. Red bars indicate regions that were nonfunctional when mutated to Ala/Leu. (B) A schematic representation of the predicted topology of Yip1A. The results from (A) are represented on the schematic. Residues highlighted in blue were functional and red were nonfunctional when stretches of amino acids were replaced with Ala/Leu. Residues highlighted in yellow were nonfunctional when individual amino acids were replaced with Ala/Leu. Precise substitutions are detailed in Table S1. doi:10.1371/journal.pone.0054413.gMutational Analysis of Yip1AFigure 4. Two residues w.