1
|
Lopatto D, Rosenwald AG, Burgess RC, Silver Key C, Van Stry M, Wawersik M, DiAngelo JR, Hark AT, Skerritt M, Allen AK, Alvarez C, Anderson S, Arrigo C, Arsham A, Barnard D, Bedard JEJ, Bose I, Braverman JM, Burg MG, Croonquist P, Du C, Dubowsky S, Eisler H, Escobar MA, Foulk M, Giarla T, Glaser RL, Goodman AL, Gosser Y, Haberman A, Hauser C, Hays S, Howell CE, Jemc J, Jones CJ, Kadlec L, Kagey JD, Keller KL, Kennell J, Kleinschmit AJ, Kleinschmit M, Kokan NP, Kopp OR, Laakso MM, Leatherman J, Long LJ, Manier M, Martinez-Cruzado JC, Matos LF, McClellan AJ, McNeil G, Merkhofer E, Mingo V, Mistry H, Mitchell E, Mortimer NT, Myka JL, Nagengast A, Overvoorde P, Paetkau D, Paliulis L, Parrish S, Toering Peters S, Preuss ML, Price JV, Pullen NA, Reinke C, Revie D, Robic S, Roecklein-Canfield JA, Rubin MR, Sadikot T, Sanford JS, Santisteban M, Saville K, Schroeder S, Shaffer CD, Sharif KA, Sklensky DE, Small C, Smith S, Spokony R, Sreenivasan A, Stamm J, Sterne-Marr R, Teeter KC, Thackeray J, Thompson JS, Velazquez-Ulloa N, Wolfe C, Youngblom J, Yowler B, Zhou L, Brennan J, Buhler J, Leung W, Elgin SCR, Reed LK. Student Attitudes Contribute to the Effectiveness of a Genomics CURE. J Microbiol Biol Educ 2022; 23:e00208-21. [PMID: 36061313 PMCID: PMC9429879 DOI: 10.1128/jmbe.00208-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 03/28/2022] [Indexed: 06/15/2023]
Abstract
The Genomics Education Partnership (GEP) engages students in a course-based undergraduate research experience (CURE). To better understand the student attributes that support success in this CURE, we asked students about their attitudes using previously published scales that measure epistemic beliefs about work and science, interest in science, and grit. We found, in general, that the attitudes students bring with them into the classroom contribute to two outcome measures, namely, learning as assessed by a pre- and postquiz and perceived self-reported benefits. While the GEP CURE produces positive outcomes overall, the students with more positive attitudes toward science, particularly with respect to epistemic beliefs, showed greater gains. The findings indicate the importance of a student's epistemic beliefs to achieving positive learning outcomes.
Collapse
Affiliation(s)
- David Lopatto
- Center for Teaching, Learning and Assessment, Grinnell College, Grinnell, Iowa, USA
| | | | - Rebecca C. Burgess
- Department of Biological Sciences, Stevenson University, Owings Mills, Maryland, USA
| | - Catherine Silver Key
- Department of Biological and Biomedical Sciences, North Carolina Central University, Durham, North Carolina, USA
| | | | - Matthew Wawersik
- Department of Biology, College of William and Mary, Williamsburg, Virginia, USA
| | | | - Amy T. Hark
- Department of Biology, Muhlenberg College, Allentown, Pennsylvania, USA
| | - Matthew Skerritt
- Department of Science, SUNY Corning Community College, Corning, New York, USA
| | - Anna K. Allen
- Department of Biology, Howard University, Washington, DC, USA
| | - Consuelo Alvarez
- Department of Biology, Longwood University, Farmville, Virginia, USA
| | - Sara Anderson
- Department of Biosciences, Minnesota State University Moorhead, Moorhead, Minnesota, USA
| | - Cindy Arrigo
- Department of Biology, New Jersey City University, Jersey City, New Jersey, USA
| | - Andrew Arsham
- Department of Biology, Bemidji State University, Bemidji, Minnesota, USA
| | - Daron Barnard
- Department of Biology, Worcester State University, Worcester, Massachusetts, USA
| | - James E. J. Bedard
- Department of Biology, University of the Fraser Valley, Abbotsford, British Columbia, Canada
| | - Indrani Bose
- Department of Biology, Western Carolina University, Cullowhee, North Carolina, USA
| | - John M. Braverman
- Department of Biology, Saint Joseph’s University, Philadelphia, Pennsylvania, USA
| | - Martin G. Burg
- Department of Biomedical Sciences, Grand Valley State University, Allendale, Michigan, USA
- Department of Cell & Molecular Biology, Grand Valley State University, Allendale, Michigan, USA
| | - Paula Croonquist
- Department of Biology, Anoka-Ramsey Community College, Coon Rapids, Minnesota, USA
| | - Chunguang Du
- Department of Biology, Montclair State University, Montclair, New Jersey, USA
| | - Sondra Dubowsky
- Department of Biology, McLennan Community College, Waco, Texas, USA
| | - Heather Eisler
- Department of Biology, University of the Cumberlands, Williamsburg, Kentucky, USA
| | - Matthew A. Escobar
- Department of Biological Sciences, California State University San Marcos, San Marcos, California, USA
| | - Michael Foulk
- Department of Biology, Mercyhurst University, Erie, Pennsylvania, USA
| | - Thomas Giarla
- Department of Biology, Siena College, Loudonville, New York, USA
| | - Rivka L. Glaser
- Department of Biological Sciences, Stevenson University, Owings Mills, Maryland, USA
| | - Anya L. Goodman
- Department of Chemistry and Biochemistry, California Polytechnic State University, San Luis Obispo, California, USA
| | - Yuying Gosser
- Student Research and Scholarship, City College CUNY, New York, New York, USA
| | - Adam Haberman
- Department of Biology, University of San Diego, San Diego, California, USA
| | - Charles Hauser
- Department of Biology, St. Edward’s University, Austin, Texas, USA
| | - Shan Hays
- Department of Biology, Western Colorado University, Gunnison, Colorado, USA
| | - Carina E. Howell
- Department of Biological Sciences, Lock Haven University, Lock Haven, Pennsylvania, USA
| | - Jennifer Jemc
- Department of Biology, Loyola University Chicago, Chicago, Illinois, USA
| | - Christopher J. Jones
- Department of Biological Sciences, Moravian University, Bethlehem, Pennsylvania, USA
| | - Lisa Kadlec
- Department of Biology, Wilkes University, Wilkes-Barre, Pennsylvania, USA
| | - Jacob D. Kagey
- Department of Biology, University of Detroit Mercy, Detroit, Michigan, USA
| | | | - Jennifer Kennell
- Department of Biology, Vassar College, Poughkeepsie, New York, USA
| | | | - Melissa Kleinschmit
- Department of Liberal Arts, Science, and Business, Northeast Iowa Community College, Peosta, Iowa, USA
| | - Nighat P. Kokan
- Department of Natural Sciences, Cardinal Stritch University, Milwaukee, Wisconsin, USA
| | - Olga Ruiz Kopp
- Department of Biology, Utah Valley University, Orem, Utah, USA
| | - Meg M. Laakso
- Department of Biology, Eastern University, St. Davids, Pennsylvania, USA
| | - Judith Leatherman
- Department of Biological Sciences, University of Northern Colorado, Greeley, Colorado, USA
| | - Lindsey J. Long
- Department of Biology, Oklahoma Christian University, Oklahoma City, Oklahoma, USA
| | - Mollie Manier
- Department of Biological Sciences, George Washington University, Washington, DC, USA
| | | | - Luis F. Matos
- Department of Biology, Eastern Washington University, Cheney, Washington, USA
| | - Amie Jo McClellan
- Science and Mathematics, Bennington College, Bennington, Vermont, USA
| | - Gerard McNeil
- Department of Biology, York College/CUNY, Jamaica, New York, USA
| | - Evan Merkhofer
- Department of Natural Sciences, Mount Saint Mary College, Newburgh, New York, USA
| | - Vida Mingo
- Department of Biology, Columbia College, Columbia, South Carolina, USA
| | - Hemlata Mistry
- Department of Biology, Widener University, Chester, Pennsylvania, USA
- Department of Biochemistry, Widener University, Chester, Pennsylvania, USA
| | | | - Nathan T. Mortimer
- Department of Biological Sciences, Illinois State University, Normal, Illinois, USA
| | - Jennifer Leigh Myka
- Department of Biology, Gateway Community and Technical College, Covington, Kentucky, USA
| | - Alexis Nagengast
- Department of Biochemistry, Widener University, Chester, Pennsylvania, USA
- Department of Chemistry, Widener University, Chester, Pennsylvania, USA
| | - Paul Overvoorde
- Department of Biology, Macalester College, St. Paul, Minnesota, USA
| | - Don Paetkau
- Department of Biology, Saint Mary’s College, Notre Dame, Indiana, USA
| | - Leocadia Paliulis
- Department of Biology, Bucknell University, Lewisburg, Pennsylvania, USA
| | - Susan Parrish
- Department of Biology, McDaniel College, Westminster, Maryland, USA
| | | | - Mary Lai Preuss
- Department of Biological Sciences, Webster University, St. Louis, Missouri, USA
| | - James V. Price
- Department of Biology, Utah Valley University, Orem, Utah, USA
| | - Nicholas A. Pullen
- Department of Biological Sciences, University of Northern Colorado, Greeley, Colorado, USA
| | - Catherine Reinke
- Department of Biology, Linfield University, McMinnville, Oregon, USA
| | - Dennis Revie
- Department of Biology, California Lutheran University, Thousand Oaks, California, USA
| | - Srebrenka Robic
- Department of Biology, Agnes Scott College, Decatur, Georgia, USA
| | | | - Michael R. Rubin
- Department of Biology, University of Puerto Rico at Cayey, Cayey, Puerto Rico, USA
| | - Takrima Sadikot
- Department of Biology, Washburn University, Topeka, Kansas, USA
| | | | - Maria Santisteban
- Department of Biology, University of North Carolina at Pembroke, Pembroke, North Carolina, USA
| | - Kenneth Saville
- Department of Biology, Albion College, Albion, Michigan, USA
| | - Stephanie Schroeder
- Department of Biological Sciences, Webster University, St. Louis, Missouri, USA
| | | | - Karim A. Sharif
- Department of Biology, Massasoit Community College, Brockton, Massachusetts, USA
| | | | - Chiyedza Small
- Department of Biology, Medgar Evers College, CUNY, Brooklyn, New York, USA
| | - Sheryl Smith
- Department of Biology, Arcadia University, Glenside, Pennsylvania, USA
| | - Rebecca Spokony
- Department of Natural Sciences, Baruch College, CUNY, New York, New York, USA
| | - Aparna Sreenivasan
- Department of Biology, School of Natural Sciences, California State University, Monterey Bay, Seaside, California, USA
| | - Joyce Stamm
- Department of Biology, University of Evansville, Evansville, Indiana, USA
| | | | - Katherine C. Teeter
- Department of Biology, Northern Michigan University, Marquette, Michigan, USA
| | - Justin Thackeray
- Department of Biology, Clark University, Worcester, Massachusetts, USA
| | | | | | - Cindy Wolfe
- Department of Biology, Kentucky Wesleyan College, Owensboro, Kentucky, USA
| | - James Youngblom
- Department of Biological Sciences, California State University Stanislaus, Turlock, California, USA
| | - Brian Yowler
- Department of Biology, Geneva College, Beaver Falls, Pennsylvania, USA
| | - Leming Zhou
- Health Information Management, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Janie Brennan
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Jeremy Buhler
- Department of Computer Science and Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Wilson Leung
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Sarah C. R. Elgin
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Laura K. Reed
- Department of Biological Sciences, University of Alabama, Tuscaloosa, Alabama, USA
| |
Collapse
|
2
|
Lopatto D, Rosenwald AG, DiAngelo JR, Hark AT, Skerritt M, Wawersik M, Allen AK, Alvarez C, Anderson S, Arrigo C, Arsham A, Barnard D, Bazinet C, Bedard JEJ, Bose I, Braverman JM, Burg MG, Burgess RC, Croonquist P, Du C, Dubowsky S, Eisler H, Escobar MA, Foulk M, Furbee E, Giarla T, Glaser RL, Goodman AL, Gosser Y, Haberman A, Hauser C, Hays S, Howell CE, Jemc J, Johnson ML, Jones CJ, Kadlec L, Kagey JD, Keller KL, Kennell J, Key SCS, Kleinschmit AJ, Kleinschmit M, Kokan NP, Kopp OR, Laakso MM, Leatherman J, Long LJ, Manier M, Martinez-Cruzado JC, Matos LF, McClellan AJ, McNeil G, Merkhofer E, Mingo V, Mistry H, Mitchell E, Mortimer NT, Mukhopadhyay D, Myka JL, Nagengast A, Overvoorde P, Paetkau D, Paliulis L, Parrish S, Preuss ML, Price JV, Pullen NA, Reinke C, Revie D, Robic S, Roecklein-Canfield JA, Rubin MR, Sadikot T, Sanford JS, Santisteban M, Saville K, Schroeder S, Shaffer CD, Sharif KA, Sklensky DE, Small C, Smith M, Smith S, Spokony R, Sreenivasan A, Stamm J, Sterne-Marr R, Teeter KC, Thackeray J, Thompson JS, Peters ST, Van Stry M, Velazquez-Ulloa N, Wolfe C, Youngblom J, Yowler B, Zhou L, Brennan J, Buhler J, Leung W, Reed LK, Elgin SCR. Facilitating Growth through Frustration: Using Genomics Research in a Course-Based Undergraduate Research Experience. J Microbiol Biol Educ 2020; 21:jmbe-21-6. [PMID: 32148609 PMCID: PMC7048401 DOI: 10.1128/jmbe.v21i1.2005] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 01/23/2020] [Indexed: 06/10/2023]
Abstract
A hallmark of the research experience is encountering difficulty and working through those challenges to achieve success. This ability is essential to being a successful scientist, but replicating such challenges in a teaching setting can be difficult. The Genomics Education Partnership (GEP) is a consortium of faculty who engage their students in a genomics Course-Based Undergraduate Research Experience (CURE). Students participate in genome annotation, generating gene models using multiple lines of experimental evidence. Our observations suggested that the students' learning experience is continuous and recursive, frequently beginning with frustration but eventually leading to success as they come up with defendable gene models. In order to explore our "formative frustration" hypothesis, we gathered data from faculty via a survey, and from students via both a general survey and a set of student focus groups. Upon analyzing these data, we found that all three datasets mentioned frustration and struggle, as well as learning and better understanding of the scientific process. Bioinformatics projects are particularly well suited to the process of iteration and refinement because iterations can be performed quickly and are inexpensive in both time and money. Based on these findings, we suggest that a dynamic of "formative frustration" is an important aspect for a successful CURE.
Collapse
Affiliation(s)
- David Lopatto
- Center for Teaching, Learning and Assessment, Grinnell College, Grinnell, IA 50112, USA
| | | | | | - Amy T. Hark
- Biology, Muhlenberg College, Allentown, PA 18104, USA
| | | | - Matthew Wawersik
- Biology, College of William and Mary, Williamsburg, VA 23187, USA
| | - Anna K. Allen
- Biology, Howard University, Washington, DC 20059, USA
| | | | - Sara Anderson
- Biosciences, Minnesota State University Moorhead, Moorhead, MN 56563, USA
| | - Cindy Arrigo
- Biology, New Jersey City University, Jersey City, NJ 07305, USA
| | - Andrew Arsham
- Biology, Bemidji State University, Bemidji, MN 56601, USA
| | - Daron Barnard
- Biology, Worcester State University, Worcester, MA 01602, USA
| | | | - James E. J. Bedard
- Biology, University of the Fraser Valley, Abbotsford, BC, V2S 7M8, Canada
| | - Indrani Bose
- Biology, Western Carolina University, Cullowhee, NC 28723, USA
| | | | - Martin G. Burg
- Biomedical Sciences and Cell & Molecular Biology, Grand Valley State University, Allendale, MI 49401, USA
| | | | - Paula Croonquist
- Biology, Anoka-Ramsey Community College, Coon Rapids, MN 55433, USA
| | - Chunguang Du
- Biology, Montclair State University, Montclair, NJ 07043, USA
| | | | - Heather Eisler
- Biology, University of the Cumberlands, Williamsburg, KY 40769, USA
| | - Matthew A. Escobar
- Biological Sciences, California State University San Marcos, CA 92096, USA
| | | | - Emily Furbee
- Biology, Washington and Jefferson College, Washington, PA 15301, USA
| | | | - Rivka L. Glaser
- Biological Sciences, Stevenson University, Owings Mills, MD 21117, USA
| | - Anya L. Goodman
- Chemistry and Biochemistry, California Polytechnic State University, San Luis Obispo, CA 93407, USA
| | - Yuying Gosser
- Student Research and Scholarship, City College CUNY, New York, NY 10031, USA
| | - Adam Haberman
- Biology, University of San Diego, San Diego, CA 92110, USA
| | | | - Shan Hays
- Biology, Western Colorado University, Gunnison, CO 81231, USA
| | - Carina E. Howell
- Biological Sciences, Lock Haven University, Lock Haven, PA 17745, USA
| | - Jennifer Jemc
- Biology, Loyola University Chicago, Chicago, IL 60660, USA
| | | | | | - Lisa Kadlec
- Biology, Wilkes University, Wilkes-Barre, PA 18766, USA
| | - Jacob D. Kagey
- Biology, University of Detroit Mercy, Detroit, MI 48221, USA
| | | | | | - S. Catherine Silver Key
- Biological and Biomedical Sciences, North Carolina Central University, Durham, NC 27707, USA
| | | | | | - Nighat P. Kokan
- Natural Sciences, Cardinal Stritch University, Milwaukee, WI 53217, USA
| | | | - Meg M. Laakso
- Biology, Eastern University, St. Davids, PA 19087, USA
| | - Judith Leatherman
- Biological Sciences, University of Northern Colorado, Greeley, CO 80639, USA
| | - Lindsey J. Long
- Biology, Oklahoma Christian University, Oklahoma City, OK 73136, USA
| | - Mollie Manier
- Biological Sciences, George Washington University, Washington, DC 20052, USA
| | | | - Luis F. Matos
- Biology, Eastern Washington University, Cheney, WA 99004, USA
| | - Amie Jo McClellan
- Science and Mathematics, Bennington College, Bennington, VT 05201, USA
| | - Gerard McNeil
- Biology, York College / CUNY, Jamaica, NY 11451, USA
| | - Evan Merkhofer
- Natural Sciences, Mount Saint Mary College, Newbergh, NY 12550, USA
| | - Vida Mingo
- Biology, Columbia College, Columbia, SC 29203, USA
| | - Hemlata Mistry
- Biology and Biochemistry, Widener University, Chester, PA 19013, USA
| | | | | | - Debaditya Mukhopadhyay
- Molecular Biology, Biochemistry, and Bioinformatics, Towson University, Towson, MD 21252, USA
| | | | - Alexis Nagengast
- Chemistry and Biochemistry, Widener University, Chester, PA 19013, USA
| | | | - Don Paetkau
- Biology, Saint Mary’s College, Notre Dame, IN 46556, USA
| | | | - Susan Parrish
- Biology, McDaniel College, Westminster, MD 21157, USA
| | - Mary Lai Preuss
- Biological Sciences, Webster University, St. Louis, MO 63119, USA
| | | | - Nicholas A. Pullen
- Biological Sciences, University of Northern Colorado, Greeley, CO 80639, USA
| | | | - Dennis Revie
- Biology, California Lutheran University, Thousand Oaks, CA 91360, USA
| | | | | | - Michael R. Rubin
- Biology, University of Puerto Rico at Cayey, Cayey, PR 00736, USA
| | | | | | - Maria Santisteban
- Biology, University of North Carolina at Pembroke, Pembroke, NC 28372, USA
| | | | | | | | - Karim A. Sharif
- Biology, Massasoit Community College, Brockton, MA 02302, USA
| | | | - Chiyedza Small
- Biology, Medgar Evers College, CUNY, Brooklyn, NY 11225, USA
| | - Mary Smith
- Biology, North Carolina A & T State University, Greensboro, NC 27411, USA
| | - Sheryl Smith
- Biology, Arcadia, University, Glenside, PA 19038, USA
| | - Rebecca Spokony
- Natural Sciences, Baruch College, CUNY, New York, NY 10010, USA
| | - Aparna Sreenivasan
- Biology, School of Natural Sciences, California State University, Monterey Bay, Seaside, CA 93950, USA
| | - Joyce Stamm
- Biology, University of Evansville, Evansville, IN 47722, USA
| | | | | | | | | | | | | | | | - Cindy Wolfe
- Biology, Kentucky Wesleyan College, Owensboro, KY 42301, USA
| | - James Youngblom
- Biological Sciences, California State University Stanislaus, Turlock, CA 95382, USA
| | - Brian Yowler
- Biology, Grove City College, Grove City, PA 16127, USA
| | - Leming Zhou
- Health Information Management, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Janie Brennan
- Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Jeremy Buhler
- Computer Science and Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Wilson Leung
- Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Laura K. Reed
- Biological Sciences, University of Alabama Tuscaloosa, AL 35487, USA
| | - Sarah C. R. Elgin
- Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| |
Collapse
|
3
|
Del Bel LM, Griffiths N, Wilk R, Wei HC, Blagoveshchenskaya A, Burgess J, Polevoy G, Price JV, Mayinger P, Brill JA. The phosphoinositide phosphatase Sac1 regulates cell shape and microtubule stability in the developing Drosophila eye. Development 2018; 145:dev.151571. [PMID: 29752385 DOI: 10.1242/dev.151571] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 04/30/2018] [Indexed: 12/15/2022]
Abstract
Epithelial patterning in the developing Drosophila melanogaster eye requires the Neph1 homolog Roughest (Rst), an immunoglobulin family cell surface adhesion molecule expressed in interommatidial cells (IOCs). Here, using a novel temperature-sensitive (ts) allele, we show that the phosphoinositide phosphatase Sac1 is also required for IOC patterning. Sac1ts mutants have rough eyes and retinal patterning defects that resemble rst mutants. Sac1ts retinas exhibit elevated levels of phosphatidylinositol 4-phosphate (PI4P), consistent with the role of Sac1 as a PI4P phosphatase. Indeed, genetic rescue and interaction experiments reveal that restriction of PI4P levels by Sac1 is crucial for normal eye development. Rst is delivered to the cell surface in Sac1ts mutants. However, Sac1ts mutant IOCs exhibit severe defects in microtubule organization, associated with accumulation of Rst and the exocyst subunit Sec8 in enlarged intracellular vesicles upon cold fixation ex vivo Together, our data reveal a novel requirement for Sac1 in promoting microtubule stability and suggest that Rst trafficking occurs in a microtubule- and exocyst-dependent manner.
Collapse
Affiliation(s)
- Lauren M Del Bel
- Cell Biology Program, The Hospital for Sick Children, PGCRL Building, 686 Bay Street, Toronto, Ontario, M5G 0A4, Canada.,Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada
| | - Nigel Griffiths
- Cell Biology Program, The Hospital for Sick Children, PGCRL Building, 686 Bay Street, Toronto, Ontario, M5G 0A4, Canada.,Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada
| | - Ronit Wilk
- Cell Biology Program, The Hospital for Sick Children, PGCRL Building, 686 Bay Street, Toronto, Ontario, M5G 0A4, Canada
| | - Ho-Chun Wei
- Cell Biology Program, The Hospital for Sick Children, PGCRL Building, 686 Bay Street, Toronto, Ontario, M5G 0A4, Canada.,Department of Molecular Biology and Biochemistry, Simon Fraser University, South Sciences Building Room 8166, 8888 University Drive, Burnaby, British Columbia, V5A 1S6, Canada
| | - Anastasia Blagoveshchenskaya
- Division of Nephrology & Hypertension, Oregon Health & Science University, 3181 S.W. Sam Jackson Park Rd., Portland, Oregon 97239-3098, USA
| | - Jason Burgess
- Cell Biology Program, The Hospital for Sick Children, PGCRL Building, 686 Bay Street, Toronto, Ontario, M5G 0A4, Canada.,Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada
| | - Gordon Polevoy
- Cell Biology Program, The Hospital for Sick Children, PGCRL Building, 686 Bay Street, Toronto, Ontario, M5G 0A4, Canada
| | - James V Price
- Department of Molecular Biology and Biochemistry, Simon Fraser University, South Sciences Building Room 8166, 8888 University Drive, Burnaby, British Columbia, V5A 1S6, Canada
| | - Peter Mayinger
- Division of Nephrology & Hypertension, Oregon Health & Science University, 3181 S.W. Sam Jackson Park Rd., Portland, Oregon 97239-3098, USA
| | - Julie A Brill
- Cell Biology Program, The Hospital for Sick Children, PGCRL Building, 686 Bay Street, Toronto, Ontario, M5G 0A4, Canada .,Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada
| |
Collapse
|
4
|
Bonomo J, Lynch MD, Warnecke T, Price JV, Gill RT. Genome-scale analysis of anti-metabolite directed strain engineering. Metab Eng 2007; 10:109-20. [PMID: 18093856 DOI: 10.1016/j.ymben.2007.10.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2007] [Revised: 08/17/2007] [Accepted: 10/05/2007] [Indexed: 11/28/2022]
Abstract
Classic strain engineering methods have previously been limited by the low-throughput of conventional sequencing technology. Here, we applied a new genomics technology, scalar analysis of library enrichments (SCALEs), to measure >3 million Escherichia coli genomic library clone enrichment patterns resulting from growth selections employing three aspartic-acid anti-metabolites. Our objective was to assess the extent to which access to genome-scale enrichment patterns would provide strain-engineering insights not reasonably accessible through the use of conventional sequencing. We determined that the SCALEs method identified a surprisingly large range of anti-metabolite tolerance regions (423, 865, or 909 regions for each of the three anti-metabolites) when compared to the number of regions (1-3 regions) indicated by conventional sequencing. Genome-scale methods uniquely enable the calculation of clone fitness values by providing concentration data for all clones within a genomic library before and after a period of selection. We observed that clone fitness values differ substantially from clone concentration values and that this is due to differences in overall clone fitness distributions for each selection. Finally, we show that many of the clones of highest fitness overlapped across all selections, suggesting that inhibition of aspartate metabolism, as opposed to specific inhibited enzymes, dominated each selection. Our follow up studies confirmed our observed growth phenotypes and showed that intracellular amino-acid levels were also altered in several of the identified clones. These results demonstrate that genome-scale methods, such as SCALEs, can be used to dramatically improve understanding of classic strain engineering approaches.
Collapse
Affiliation(s)
- Jeanne Bonomo
- Department of Chemical and Biological Engineering, University of Colorado, UCB 424 Boulder, CO 80309, USA
| | | | | | | | | |
Collapse
|
5
|
Abstract
Assigning functional significance to completed genome sequences is one of the next challenges in biological science. Conventional genetic tools such as deficiency chromosomes help assign essential complementation groups to their corresponding genes. We describe an F2genetic screen to identify lethal mutations within cytogenetic region 61D-61F of the third chromosome of Drosophila melanogaster. One hundred sixteen mutations were identified by their failure to complement both Df(3L)bab-PG and Df(3L)3C7. These alleles were assigned to 14 complementation groups and 9 deficiency intervals. Complementation groups were ordered using existing deficiencies, as well as new deficiencies generated in this study. With the aid of the genomic sequence, genetic and physical maps in the region were correlated by use of PCR to localize the breakpoints of deficiencies within a 268-kb genomic contig (GenBank accession No. AC005847). Six essential complementation groups were assigned to specific genes, including genes encoding a porphobilinogen deaminase and a Sac1-like protein.Key words: Drosophila, functional genomics, porphobilinogen deaminase, synaptojanin.
Collapse
Affiliation(s)
- Ho-Chun Wei
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | | | | |
Collapse
|
6
|
Wei HC, Sanny J, Shu H, Baillie DL, Brill JA, Price JV, Harden N. The Sac1 Lipid Phosphatase Regulates Cell Shape Change and the JNK Cascade during Dorsal Closure in Drosophila. Curr Biol 2003; 13:1882-7. [PMID: 14588244 DOI: 10.1016/j.cub.2003.09.056] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The Sac1 lipid phosphatase dephosphorylates several phosphatidylinositol (PtdIns) phosphates and, in yeast, regulates a diverse range of cellular processes including organization of the actin cytoskeleton and secretion. We have identified mutations in the gene encoding Drosophila Sac1. sac1 mutants die as embryos with defects in dorsal closure (DC). DC involves the migration of the epidermis to close a hole in the dorsal surface of the embryo occupied by the amnioserosa. It requires cell shape change in both the epidermis and amnioserosa and activation of a Jun N-terminal kinase (JNK) MAPK cascade in the leading edge cells of the epidermis [2]. Loss of Sac1 leads to the improper activation of two key events in DC: cell shape change in the amnioserosa and JNK signaling. sac1 interacts genetically with other participants in these two events, and our data suggest that loss of Sac1 leads to upregulation of one or more signals controlling DC. This study is the first report of a role for Sac1 in the development of a multicellular organism.
Collapse
Affiliation(s)
- Ho-Chun Wei
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | | | | | | | | | | | | |
Collapse
|
7
|
Hati S, Bhattacharyya S, Price JV, Tracey AS. Comparative modeling of the phosphatase and kinase domains of protein tyrosine phosphatase and insulin receptor kinase from Drosophila melanogaster (DPTP61fm), and a computational study of their mutual interactions. Biochem Cell Biol 2002; 80:225-39. [PMID: 11989718 DOI: 10.1139/o02-001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The components and functions of the insulin receptor kinase signaling pathway have been conserved in a broad range of Metazoa ranging from mammals to insects and nematodes. There is a high degree of sequence homology and functional similarity between the human insulin receptor kinase (IRK) and the drosophila (Drosophila melanogaster) form (DIRK) of this enzyme. Similarly, a high degree of homology exists between human protein tyrosine phosphatase 1B (PTP1B) (which directly regulates IRK) and its drosophila counterpart DPTP61F (DPTP). However, genetic and biochemical studies have yet to demonstrate that DPTP61F acts in the DIRK pathway. Comparative structural modeling techniques using the known structures of human IRK and PTP1B as templates have yielded structures for the drosophila enzymes. The derived structures confirm that there is a high level of structural conservation at the tertiary level. Association of the DIRK and DPTP enzymes with each other was then investigated with a view to ascertaining whether DIRK might be a substrate of the DPTP. Evaluation of the interaction surfaces, including hydrophobic patch, shape, hydrogen bonding, and electrostatic compatibility, strongly suggested that the drosophila insulin receptor is a substrate of the DPTP. The interaction surfaces of the human and drosophila enzymes are structurally similar, although changes in critical residues modify possible electrostatic and hydrogen-bonding interactions. This suggests that in the mixed systems, DPTP-IRK or PTP1B-DIRK, the kinase domain will be a comparatively poor substrate for phosphatase activity when compared with the native systems.
Collapse
Affiliation(s)
- Sanchita Hati
- Department of Chemistry, Simon Fraser University, Burnaby, BC, Canada
| | | | | | | |
Collapse
|
8
|
Price JV, Savenye ED, Lum D, Breitkreutz A. Dominant enhancers of Egfr in Drosophila melanogaster: genetic links between the Notch and Egfr signaling pathways. Genetics 1997; 147:1139-53. [PMID: 9383058 PMCID: PMC1208239 DOI: 10.1093/genetics/147.3.1139] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The Drosophila epidermal growth factor receptor (EGFR) is a key component of a complex signaling pathway that participates in multiple developmental processes. We have performed an F1 screen for mutations that cause dominant enhancement of wing vein phenotypes associated with mutations in Egfr. With this screen, we have recovered mutations in Hairless (H), vein, groucho (gro), and three apparently novel loci. All of the E(Egfr)s we have identified show dominant interactions in transheterozygous combinations with each other and with alleles of N or Su(H), suggesting that they are involved in cross-talk between the N and EGFR signaling pathways. Further examination of the phenotypic interactions between Egfr, H, and gro revealed that reductions in Egfr activity enhanced both the bristle loss associated with H mutations, and the bristle hyperplasia and ocellar hypertrophy associated with gro mutations. Double mutant combinations of Egfr and gro hypomorphic alleles led to the formation of ectopic compound eyes in a dosage sensitive manner. Our findings suggest that these E(Egfr)s represent links between the Egfr and Notch signaling pathways, and that Egfr activity can either promote or suppress Notch signaling, depending on its developmental context.
Collapse
Affiliation(s)
- J V Price
- Institute of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada.
| | | | | | | |
Collapse
|
9
|
Ursuliak Z, Clemens JC, Dixon JE, Price JV. Differential accumulation of DPTP61F alternative transcripts: regulation of a protein tyrosine phosphatase by segmentation genes. Mech Dev 1997; 65:19-30. [PMID: 9256342 DOI: 10.1016/s0925-4773(97)00046-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
DPTP61F is a non-receptor protein tyrosine phosphatase that is expressed during Drosophila oogenesis and embryogenesis. DPTP61F transcripts are alternatively spliced to produce two isoforms of the protein which are targeted to different subcellular locations. DPTP61Fn accumulates in the nucleus, and DPTP61Fm associates with the membranes of the reticular network and the mitochondria. We have examined the spatial and temporal expression of the two alternative transcripts of dptp61F during Drosophila embryogenesis. Our observations indicate that the two isoforms are expressed in distinct patterns. The DPTP61Fn transcript is expressed in the mesoderm and neuroblast layer during germband extension and later in the gut epithelia. In comparison, the transcript encoding DPTP61Fm accumulates in 16 segmentally repeated stripes in the ectoderm during germband extension. These stripes are flanked by, and adjacent to, the domains of engrailed and wingless gene expression in the anterior/posterior axis. In stage 10 embryos, the domains of DPTP61Fm transcript accumulation are wedge shaped and roughly coincide with the area lateral to the denticle belts that will give rise to naked cuticle. The DPTP61Fm transcript is also expressed later in embryogenesis in the central nervous system. The segmental modulation of DPTP61Fm transcript accumulation in the A/P axis of the germband is regulated by the pair-rule genes, and the intrasegmental pattern of transcript accumulation is regulated by the segment polarity genes.
Collapse
Affiliation(s)
- Z Ursuliak
- Institute of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | | | | | | |
Collapse
|
10
|
Clemens JC, Ursuliak Z, Clemens KK, Price JV, Dixon JE. A Drosophila protein-tyrosine phosphatase associates with an adapter protein required for axonal guidance. J Biol Chem 1996; 271:17002-5. [PMID: 8663600 DOI: 10.1074/jbc.271.29.17002] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
We have used the yeast two-hybrid system to isolate a novel Drosophila adapter protein, which interacts with the Drosophila protein-tyrosine phosphatase (PTP) dPTP61F. Absence of this protein in Drosophila causes the mutant photoreceptor axon phenotype dreadlocks (dock) (Garrity, P. A., Rao, Y., Salecker, I., and Zipursky, S. L.(1996) Cell 85, 639-650). Dock is similar to the mammalian oncoprotein Nck and contains three Src homology 3 (SH3) domains and one Src homology 2 (SH2) domain. The interaction of dPTP61F with Dock was confirmed in vivo by immune precipitation experiments. A sequence containing five PXXP motifs from the non-catalytic domain of the PTP is sufficient for interaction with Dock. This suggests that binding to the PTP is mediated by one or more of the SH3 domains of Dock. Immune precipitations of Dock also co-precipitate two tyrosine-phosphorylated proteins having molecular masses of 190 and 145 kDa. Interactions between Dock and these tyrosine-phosphorylated proteins are likely mediated by the Dock SH2 domain. These findings identify potential signal-transducing partners of Dock and propose a role for dPTP61F and the unidentified phosphoproteins in axonal guidance.
Collapse
Affiliation(s)
- J C Clemens
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | | | | | | | | |
Collapse
|
11
|
Abstract
The spatial and temporal expression of seven Drosophila protein tyrosine phosphatase genes during oogenesis was examined by whole mount in-situ hybridization of antisense RNA probes to ovaries. Our observations indicate diverse expression patterns consistent with multiple roles for protein tyrosine phosphatases in the ovary. DPTP99A and corkscrew transcripts are expressed in follicle cells, consistent with possible roles in the EGF receptor signaling pathway. Transcripts from corkscrew and DPTP10D are detected in the germline during oogenesis and localized to the oocyte during egg chamber development. Localization of the two transcripts is disrupted by mutations in egalitarian and Bicaudal D. DLAR and DPTP4E transcripts are found in the germline during the same developmental stages as DPTP10D transcripts, but their transcripts are not localized to the oocyte. DPTP61F transcription is detected only after stage 6 of oogenesis. After stage 10B these transcripts are transported to the oocyte; thus ovarian transcription of DPTP61F may reflect a maternal contribution of the mRNA for later use during embryogenesis. DPTP69D transcripts are sequestered in the nucleus from stage 7 to stage 10, and then released to the cytoplasm. Our observations suggest that the export of DPTP69D mRNA from the nucleus is temporally regulated during oogenesis.
Collapse
Affiliation(s)
- K A Fitzpatrick
- Institute of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | | | | | | |
Collapse
|
12
|
Price JV, Clifford RJ, Schüpbach T. The maternal ventralizing locus torpedo is allelic to faint little ball, an embryonic lethal, and encodes the Drosophila EGF receptor homolog. Cell 1989; 56:1085-92. [PMID: 2493993 DOI: 10.1016/0092-8674(89)90641-7] [Citation(s) in RCA: 225] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The torpedo gene of Drosophila melanogaster is involved in the establishment of the dorsoventral pattern of eggshell and embryo. We have isolated new alleles of torpedo and have found that torpedo is allelic to the zygotic embryonic lethal faint little ball. We have shown that torpedo resides in subdivision 57F on the second chromosome--at the same location as the Drosophila homolog of the EGF receptor (DER). Using a cosmid that contains most of the DER coding region as a hybridization probe, we have shown that a cytologically small deficiency that eliminates torpedo activity also removes the DER gene, and that an inversion that was isolated as a strong torpedo allele breaks the coding region of the DER gene. We conclude that torpedo is the DER gene.
Collapse
Affiliation(s)
- J V Price
- Biology Department, Princeton University, New Jersey 08544-1003
| | | | | |
Collapse
|
13
|
Abstract
Tetrahymena preribosomal RNA undergoes self-splicing in vitro. The structural components involved in recognition of the 5' splice site have been identified, but the mechanism by which the 3' splice site is recognized is not established. To identify some components of 3'splice site recognition, we have generated mutations near the 3' splice site and determined their effects on self-splicing. Alteration of the 3'-terminal guanosine of the intervening sequence (IVS), a conserved nucleotide in group I IVSs, almost eliminated 3' splice site activity; the IVS-3' exon splicing intermediate accumulated, and exon ligation was extremely slow. These mutations do not result in recruitment of cryptic 3' splice sites, in contrast to mutations that affect the 5' splice site. Alteration of the cytidine preceding the 3'-terminal guanosine or of the first two nucleotides of the 3' exon had similar but less severe effects on exon ligation. Most of the mutants showed some reduction (less than threefold) in GTP addition at the 5' splice site. A mutation that placed a new guanosine residue just upstream from the 3'-terminal guanosine misspliced to produce ligated exons with one extra nucleotide between the 5' and 3' exons. We conclude that multiple nucleotides, located both at the 3' end of the IVS and in the 3' exon, are required for 3' splice site recognition.
Collapse
Affiliation(s)
- J V Price
- Department of Chemistry and Biochemistry, University of Colorado, Boulder 80309
| | | |
Collapse
|
14
|
Abstract
The exons of the self-splicing pre-ribosomal RNA of Tetrahymena thermophila are joined accurately in vitro, even when only 33 nucleotides of the natural 5' exon and 38 nucleotides of the natural 3' exon remain. RNA fingerprint analysis was used to identify the unique ribonuclease T1 oligonucleotide generated by exon ligation. Secondary digests of the ligation junction oligonucleotide with ribonuclease A confirmed the identity of the fragment and demonstrated that the phosphate group that forms the phosphodiester bond at the ligation junction is derived from the 5' position of a uridine nucleotide in the RNA. This observation supports the prediction that the splice junction phosphate is derived from the 3' splice site. These results emphasize the mechanistic similarities of RNA splicing reactions of the group I introns, group II introns and nuclear pre-mRNA introns.
Collapse
Affiliation(s)
- J V Price
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder 80309
| |
Collapse
|
15
|
Price JV, Engberg J, Cech TR. 5' exon requirement for self-splicing of the Tetrahymena thermophila pre-ribosomal RNA and identification of a cryptic 5' splice site in the 3' exon. J Mol Biol 1987; 196:49-60. [PMID: 2443717 DOI: 10.1016/0022-2836(87)90510-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The intervening sequence (IVS) of the Tetrahymena thermophila ribosomal RNA precursor undergoes accurate self-splicing in vitro. The work presented here examines the requirement for Tetrahymena rRNA sequences in the 5' exon for the accuracy and efficiency of splicing. Three plasmids were constructed with nine, four and two nucleotides of the natural 5' exon sequence, followed by the IVS and 26 nucleotides of the Tetrahymena 3' exon. RNA was transcribed from these plasmids in vitro and tested for self-splicing activity. The efficiency of splicing, as measured by the production of ligated exons, is reduced as the natural 5' exon sequence is replaced with plasmid sequences. Accurate splicing persists even when only four nucleotides of the natural 5' exon sequence remain. When only two nucleotides of the natural exon remain, no ligated exons are observed. As the efficiency of the normal reaction diminishes, novel RNA species are produced in increasing amounts. The novel RNA species were examined and found to be products of aberrant reactions of the precursor RNA. Two of these aberrant reactions involve auto-addition of GTP to sites six nucleotides and 52 nucleotides downstream from the 3' splice site. The former site occurs just after the sequence GGU, and may indicate the existence of a GGU-binding site within the IVS RNA. The latter site follows the sequence CUCU, which is identical with the four nucleotides preceding the 5' splice site. This observation led to a model where where the CUCU sequence in the 3' exon acts as a cryptic 5' splice site. The model predicted the existence of a circular RNA containing the first 52 nucleotides of the 3' exon. A small circular RNA was isolated and partially sequenced and found to support the model. So, a cryptic 5' splice site can function even if it is located downstream from the 3' splice site. Precursor RNA labeled at its 5' end, presumably by a GTP exchange reaction mediated by the IVS, is also described.
Collapse
Affiliation(s)
- J V Price
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder 80309
| | | | | |
Collapse
|
16
|
Been MD, Barfod ET, Burke JM, Price JV, Tanner NK, Zaug AJ, Cech TR. Structures involved in Tetrahymena rRNA self-splicing and RNA enzyme activity. Cold Spring Harb Symp Quant Biol 1987; 52:147-57. [PMID: 3454258 DOI: 10.1101/sqb.1987.052.01.019] [Citation(s) in RCA: 34] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- M D Been
- Department of Chemistry and Biochemistry, University of Colorado, Boulder 80309
| | | | | | | | | | | | | |
Collapse
|
17
|
Abstract
Splicing of the Tetrahymena ribosomal RNA precursor is mediated by the folded structure of the RNA molecule and therefore occurs in the absence of any protein in vitro. The Tetrahymena intervening sequence (IVS) has been inserted into the gene for the alpha-donor fragment of beta-galactosidase in a recombinant plasmid. Production of functional beta-galactosidase is dependent on RNA splicing in vivo in Escherichia coli. Thus RNA self-splicing can occur at a rate sufficient to support gene expression in a prokaryote, despite the likely presence of ribosomes on the nascent RNA. The beta-galactosidase messenger RNA splicing system provides a useful method for screening for splicing-defective mutations, several of which have been characterized.
Collapse
|
18
|
Price JV, Kieft GL, Kent JR, Sievers EL, Cech TR. Sequence requirements for self-splicing of the Tetrahymena thermophila pre-ribosomal RNA. Nucleic Acids Res 1985; 13:1871-89. [PMID: 4000946 PMCID: PMC341122 DOI: 10.1093/nar/13.6.1871] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The sequence requirements for splicing of the Tetrahymena pre-rRNA have been examined by altering the rRNA gene to produce versions that contain insertions and deletions within the intervening sequence (IVS). The altered genes were transcribed and the RNA tested for self-splicing in vitro. A number of insertions (8-54 nucleotides) at three locations had no effect on self-splicing activity. Two of these insertions, located at a site 5 nucleotides preceding the 3'-end of the IVS, did not alter the choice of the 3' splice site. Thus the 3' splice site is not chosen by its distance from a fixed point within the IVS. Analysis of deletions constructed at two sites revealed two structures, a hairpin loop and a stem-loop, that are entirely dispensable for IVS excision in vitro. Three other regions were found to be necessary. The regions that are important for self-splicing are not restricted to the conserved sequence elements that define this class of intervening sequences. The requirement for structures within the IVS for pre-rRNA splicing is in sharp contrast to the very limited role of IVS structure in nuclear pre-mRNA splicing.
Collapse
|