1
|
Panigrahi M, Rajawat D, Nayak SS, Jain K, Vaidhya A, Prakash R, Sharma A, Parida S, Bhushan B, Dutt T. Genomic insights into key genes and QTLs involved in cattle reproduction. Gene 2024; 917:148465. [PMID: 38621496 DOI: 10.1016/j.gene.2024.148465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Revised: 04/05/2024] [Accepted: 04/10/2024] [Indexed: 04/17/2024]
Abstract
From an economic standpoint, reproductive characteristics are fundamental for sustainable production, particularly for monotocous livestock like cattle. A longer inter-calving interval is indicative of low reproductive capacity. This issue changes the dynamics of current and future lactations since it necessitates more inseminations, veterinary care, and hormone interventions. Various reproductive phenotypes, including ovulation, mating, fertility, pregnancy, embryonic growth, and calving-related traits, are observed in dairy cattle, and these traits have been associated with several QTLs. Calving ease, age at puberty, scrotal circumference, and inseminations per conception have been associated with 4437, 10623, 10498, and 2476 Quantitative Trait Loci (QTLs), respectively. This data offers valuable insights into enhancing and comprehending reproductive traits in livestock breeding. Studying QTLs associated with reproductive traits has far-reaching implications across various fields, from agriculture and animal husbandry to human health, evolutionary biology, and conservation. It provides the foundation for informed breeding practices, advances in biotechnology, and a deeper understanding of the genetic underpinnings of reproduction.
Collapse
Affiliation(s)
- Manjit Panigrahi
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India.
| | - Divya Rajawat
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Sonali Sonejita Nayak
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Karan Jain
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Ayushi Vaidhya
- Division of Pharmacology & Toxicology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Ravi Prakash
- Division of Pharmacology & Toxicology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Anurodh Sharma
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Subhashree Parida
- Division of Pharmacology & Toxicology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Bharat Bhushan
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Triveni Dutt
- Livestock Production and Management Section, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| |
Collapse
|
2
|
Carrick BH, Crittenden SL, Chen F, Linsley M, Woodworth J, Kroll-Conner P, Ferdous AS, Keleş S, Wickens M, Kimble J. PUF partner interactions at a conserved interface shape the RNA-binding landscape and cell fate in Caenorhabditis elegans. Dev Cell 2024; 59:661-675.e7. [PMID: 38290520 PMCID: PMC11253550 DOI: 10.1016/j.devcel.2024.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 11/10/2023] [Accepted: 01/08/2024] [Indexed: 02/01/2024]
Abstract
Protein-RNA regulatory networks underpin much of biology. C. elegans FBF-2, a PUF-RNA-binding protein, binds over 1,000 RNAs to govern stem cells and differentiation. FBF-2 interacts with multiple protein partners via a key tyrosine, Y479. Here, we investigate the in vivo significance of partnerships using a Y479A mutant. Occupancy of the Y479A mutant protein increases or decreases at specific sites across the transcriptome, varying with RNAs. Germline development also changes in a specific fashion: Y479A abolishes one FBF-2 function-the sperm-to-oocyte cell fate switch. Y479A's effects on the regulation of one mRNA, gld-1, are critical to this fate change, though other network changes are also important. FBF-2 switches from repression to activation of gld-1 RNA, likely by distinct FBF-2 partnerships. The role of RNA-binding protein partnerships in governing RNA regulatory networks will likely extend broadly, as such partnerships pervade RNA controls in virtually all metazoan tissues and species.
Collapse
Affiliation(s)
- Brian H Carrick
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
| | - Sarah L Crittenden
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Fan Chen
- Department of Statistics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - MaryGrace Linsley
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jennifer Woodworth
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Peggy Kroll-Conner
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Ahlan S Ferdous
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Sündüz Keleş
- Department of Statistics, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Marvin Wickens
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
| | - Judith Kimble
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
| |
Collapse
|
3
|
Qiu C, Zhang Z, Wine RN, Campbell ZT, Zhang J, Hall TMT. Intra- and inter-molecular regulation by intrinsically-disordered regions governs PUF protein RNA binding. Nat Commun 2023; 14:7323. [PMID: 37953271 PMCID: PMC10641069 DOI: 10.1038/s41467-023-43098-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 10/30/2023] [Indexed: 11/14/2023] Open
Abstract
PUF proteins are characterized by globular RNA-binding domains. They also interact with partner proteins that modulate their RNA-binding activities. Caenorhabditis elegans PUF protein fem-3 binding factor-2 (FBF-2) partners with intrinsically disordered Lateral Signaling Target-1 (LST-1) to regulate target mRNAs in germline stem cells. Here, we report that an intrinsically disordered region (IDR) at the C-terminus of FBF-2 autoinhibits its RNA-binding affinity by increasing the off rate for RNA binding. Moreover, the FBF-2 C-terminal region interacts with its globular RNA-binding domain at the same site where LST-1 binds. This intramolecular interaction restrains an electronegative cluster of amino acid residues near the 5' end of the bound RNA to inhibit RNA binding. LST-1 binding in place of the FBF-2 C-terminus therefore releases autoinhibition and increases RNA-binding affinity. This regulatory mechanism, driven by IDRs, provides a biochemical and biophysical explanation for the interdependence of FBF-2 and LST-1 in germline stem cell self-renewal.
Collapse
Affiliation(s)
- Chen Qiu
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Zihan Zhang
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Robert N Wine
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Zachary T Campbell
- Department of Anesthesiology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Jun Zhang
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Traci M Tanaka Hall
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA.
| |
Collapse
|
4
|
Rouhana L, Edgar A, Hugosson F, Dountcheva V, Martindale MQ, Ryan JF. Cytoplasmic Polyadenylation Is an Ancestral Hallmark of Early Development in Animals. Mol Biol Evol 2023; 40:msad137. [PMID: 37288606 PMCID: PMC10284499 DOI: 10.1093/molbev/msad137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 04/18/2023] [Accepted: 06/05/2023] [Indexed: 06/09/2023] Open
Abstract
Differential regulation of gene expression has produced the astonishing diversity of life on Earth. Understanding the origin and evolution of mechanistic innovations for control of gene expression is therefore integral to evolutionary and developmental biology. Cytoplasmic polyadenylation is the biochemical extension of polyadenosine at the 3'-end of cytoplasmic mRNAs. This process regulates the translation of specific maternal transcripts and is mediated by the Cytoplasmic Polyadenylation Element-Binding Protein family (CPEBs). Genes that code for CPEBs are amongst a very few that are present in animals but missing in nonanimal lineages. Whether cytoplasmic polyadenylation is present in non-bilaterian animals (i.e., sponges, ctenophores, placozoans, and cnidarians) remains unknown. We have conducted phylogenetic analyses of CPEBs, and our results show that CPEB1 and CPEB2 subfamilies originated in the animal stem lineage. Our assessment of expression in the sea anemone, Nematostella vectensis (Cnidaria), and the comb jelly, Mnemiopsis leidyi (Ctenophora), demonstrates that maternal expression of CPEB1 and the catalytic subunit of the cytoplasmic polyadenylation machinery (GLD2) is an ancient feature that is conserved across animals. Furthermore, our measurements of poly(A)-tail elongation reveal that key targets of cytoplasmic polyadenylation are shared between vertebrates, cnidarians, and ctenophores, indicating that this mechanism orchestrates a regulatory network that is conserved throughout animal evolution. We postulate that cytoplasmic polyadenylation through CPEBs was a fundamental innovation that contributed to animal evolution from unicellular life.
Collapse
Affiliation(s)
- Labib Rouhana
- Department of Biology, University of Massachusetts Boston, Boston, MA, USA
| | - Allison Edgar
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, USA
| | - Fredrik Hugosson
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, USA
| | - Valeria Dountcheva
- Department of Biology, University of Massachusetts Boston, Boston, MA, USA
| | - Mark Q Martindale
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, USA
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, USA
- Department of Biology, University of Florida, Gainesville, FL, USA
| |
Collapse
|
5
|
Davis GM, Hipwell H, Boag PR. Oogenesis in Caenorhabditis elegans. Sex Dev 2023; 17:73-83. [PMID: 37232019 PMCID: PMC10659005 DOI: 10.1159/000531019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 05/01/2023] [Indexed: 05/27/2023] Open
Abstract
BACKGROUND The nematode, Caenorhabditis elegans has proven itself as a valuable model for investigating metazoan biology. C. elegans have a transparent body, an invariant cell lineage, and a high level of genetic conservation which makes it a desirable model organism. Although used to elucidate many aspects of somatic biology, a distinct advantage of C. elegans is its well annotated germline which allows all aspects of oogenesis to be observed in real time within a single animal. C. elegans hermaphrodites have two U-shaped gonad arms which produce their own sperm that is later stored to fertilise their own oocytes. These two germlines take up much of the internal space of each animal and germ cells are therefore the most abundant cell present within each animal. This feature and the genetic phenotypes observed for mutant worm gonads have allowed many novel findings that established our early understanding of germ cell dynamics. The mutant phenotypes also allowed key features of meiosis and germ cell maturation to be unveiled. SUMMARY This review will focus on the key aspects that make C. elegans an outstanding model for exploring each feature of oogenesis. This will include the fundamental steps associated with germline function and germ cell maturation and will be of use for those interested in exploring reproductive metazoan biology. KEY MESSAGES Since germ cell biology is highly conserved in animals, much can be gained from study of a simple metazoan like C. elegans. Past findings have enhanced understanding on topics that would be more laborious or challenging in more complex animal models.
Collapse
Affiliation(s)
- Gregory M. Davis
- Institute of Innovation, Science and Sustainability, Federation University, Churchill, VIC, Australia
| | - Hayleigh Hipwell
- Department of Biochemistry and Molecular Biology, Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, VIC, Australia
| | - Peter R. Boag
- Department of Biochemistry and Molecular Biology, Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, VIC, Australia
| |
Collapse
|
6
|
Velayudhan SS, Ellis RE. Functional divergence of orthologous temperature-sensitive mutations in C. elegans and C. briggsae. MICROPUBLICATION BIOLOGY 2022; 2022:10.17912/micropub.biology.000705. [PMID: 36575738 PMCID: PMC9790080 DOI: 10.17912/micropub.biology.000705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 01/01/1970] [Accepted: 12/09/2022] [Indexed: 12/29/2022]
Abstract
To learn if orthologous mutations are temperature-sensitive in related species, we studied four C. briggsae mutations orthologous to alleles of important C. elegans genes. Both Cel-glp-4(bn2) and Cbr-glp-4(v473) are temperature-sensitive, causing sterility at 25°C. By contrast, Cel-fog-1 ( q253) is strongly ts , but its ortholog Cbr-fog-1(v442) causes a loss-of-function at all temperatures. Finally, the C. elegans glp-1 alleles bn18 and e2141 are ts sterile. However, their C. briggsae orthologs, Cbr-glp-1(v429) and Cbr-glp-1(v438) respectively, are wild-type at all temperatures. Thus, a ts mutation in one species provides clues about how to design ts alleles in another, but all theoretical outcomes are possible.
Collapse
Affiliation(s)
| | - Ronald E Ellis
- Rowan University SOM
,
Correspondence to: Ronald E Ellis (
)
| |
Collapse
|
7
|
Yang Y, Zhou T, Liu Y, Tian C, Bao L, Wang W, Zhang Y, Liu S, Shi H, Tan S, Gao D, Dunham RA, Liu Z. Identification of an Epigenetically Marked Locus within the Sex Determination Region of Channel Catfish. Int J Mol Sci 2022; 23:ijms23105471. [PMID: 35628283 PMCID: PMC9171582 DOI: 10.3390/ijms23105471] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/06/2022] [Accepted: 05/11/2022] [Indexed: 02/01/2023] Open
Abstract
Channel catfish has an XY sex determination system. However, the X and Y chromosomes harbor an identical gene content of 950 genes each. In this study, we conducted comparative analyses of methylome and transcriptome of genetic males and genetic females before gonadal differentiation to provide insights into the mechanisms of sex determination. Differentially methylated CpG sites (DMCs) were predominantly identified on the sex chromosome, most notably within the sex determination region (SDR), although the overall methylation profiles across the entire genome were similar between genetic males and females. The drastic differences in methylation were located within the SDR at nucleotide position 14.0–20.3 Mb of the sex chromosome, making this region an epigenetically marked locus within the sex determination region. Most of the differentially methylated CpG sites were hypermethylated in females and hypomethylated in males, suggesting potential involvement of methylation modification in sex determination in channel catfish. Along with the differential methylation in the SDR, a number of differentially expressed genes within the SDR were also identified between genetic males and females, making them potential candidate genes for sex determination and differentiation in channel catfish.
Collapse
Affiliation(s)
- Yujia Yang
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA; (Y.Y.); (T.Z.); (Y.L.); (C.T.); (L.B.); (W.W.); (Y.Z.); (S.L.); (H.S.); (S.T.); (R.A.D.)
| | - Tao Zhou
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA; (Y.Y.); (T.Z.); (Y.L.); (C.T.); (L.B.); (W.W.); (Y.Z.); (S.L.); (H.S.); (S.T.); (R.A.D.)
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Yang Liu
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA; (Y.Y.); (T.Z.); (Y.L.); (C.T.); (L.B.); (W.W.); (Y.Z.); (S.L.); (H.S.); (S.T.); (R.A.D.)
| | - Changxu Tian
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA; (Y.Y.); (T.Z.); (Y.L.); (C.T.); (L.B.); (W.W.); (Y.Z.); (S.L.); (H.S.); (S.T.); (R.A.D.)
| | - Lisui Bao
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA; (Y.Y.); (T.Z.); (Y.L.); (C.T.); (L.B.); (W.W.); (Y.Z.); (S.L.); (H.S.); (S.T.); (R.A.D.)
| | - Wenwen Wang
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA; (Y.Y.); (T.Z.); (Y.L.); (C.T.); (L.B.); (W.W.); (Y.Z.); (S.L.); (H.S.); (S.T.); (R.A.D.)
| | - Yu Zhang
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA; (Y.Y.); (T.Z.); (Y.L.); (C.T.); (L.B.); (W.W.); (Y.Z.); (S.L.); (H.S.); (S.T.); (R.A.D.)
| | - Shikai Liu
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA; (Y.Y.); (T.Z.); (Y.L.); (C.T.); (L.B.); (W.W.); (Y.Z.); (S.L.); (H.S.); (S.T.); (R.A.D.)
| | - Huitong Shi
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA; (Y.Y.); (T.Z.); (Y.L.); (C.T.); (L.B.); (W.W.); (Y.Z.); (S.L.); (H.S.); (S.T.); (R.A.D.)
| | - Suxu Tan
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA; (Y.Y.); (T.Z.); (Y.L.); (C.T.); (L.B.); (W.W.); (Y.Z.); (S.L.); (H.S.); (S.T.); (R.A.D.)
| | - Dongya Gao
- Department of Biology, College of Arts and Sciences, Syracuse University, Syracuse, NY 13244, USA; (D.G.); (Z.L.)
| | - Rex A. Dunham
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA; (Y.Y.); (T.Z.); (Y.L.); (C.T.); (L.B.); (W.W.); (Y.Z.); (S.L.); (H.S.); (S.T.); (R.A.D.)
| | - Zhanjiang Liu
- Department of Biology, College of Arts and Sciences, Syracuse University, Syracuse, NY 13244, USA; (D.G.); (Z.L.)
- Correspondence:
| |
Collapse
|
8
|
Joshi M, Andrabi SW, Singh V, Bansal SK, Makker GC, Mishra G, Gupta G, Rajender S. Coding and regulatory transcriptome comparisons between fertile and infertile spermatozoa identify RNA signatures of male infertility. Andrologia 2022; 54:e14437. [PMID: 35437806 DOI: 10.1111/and.14437] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 02/07/2022] [Accepted: 03/24/2022] [Indexed: 12/12/2022] Open
Abstract
The aim of the present study was to identify RNA-based signatures of male infertility by sperm transcriptome analysis. In this study, deep sequencing analyses of coding (mRNA) and regulatory (miRNA) transcriptomes were performed by pooling 15 oligo/oligoasthenozoospermic infertile sperm and 9 normozoospermic fertile sperm samples. Furthermore, interesting candidates were selected for validation by real-time PCR. The comparison of miRNAs between cases and controls identified 94 differentially expressed miRNAs, of which at least 38 have known functions in spermatogenesis. In transcriptome (mRNA) data, a total of 60,505 transcripts were obtained. The comparison of coding RNAs between cases and controls revealed 11,688 differentially expressed genes. miRNA-mRNA paired analysis revealed that 94 differentially expressed miRNAs could potentially target 13,573 genes, of which 6419 transcripts were actually differentially expressed in our data. Out of these, 3303 transcripts showed inverse correlation with their corresponding regulatory miRNAs. Moreover, we found that most of the genes of miRNA-mRNA pairs were involved in male germ cell differentiation, apoptosis, meiosis, spermiogenesis and male infertility. In conclusion, we found that a number of sperm transcripts (miRNAs and mRNAs) have a very high potential of serving as infertility/sperm quality markers.
Collapse
Affiliation(s)
- Meghali Joshi
- Division of Endocrinology, Central Drug Research Institute, Lucknow, India
| | - Syed Waseem Andrabi
- Department of Zoology, Lucknow University, Lucknow, India.,Makker Infertility Clinic, Lucknow, India
| | - Vertika Singh
- Division of Endocrinology, Central Drug Research Institute, Lucknow, India
| | | | | | | | - Gopal Gupta
- Division of Endocrinology, Central Drug Research Institute, Lucknow, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Singh Rajender
- Division of Endocrinology, Central Drug Research Institute, Lucknow, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| |
Collapse
|
9
|
Ellis RE. Sex Determination in Nematode Germ Cells. Sex Dev 2022:1-18. [PMID: 35172320 PMCID: PMC9378769 DOI: 10.1159/000520872] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 11/02/2021] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Animal germ cells differentiate as sperm or as oocytes. These sexual fates are controlled by complex regulatory pathways to ensure that the proper gametes are made at the appropriate times. SUMMARY Nematodes like Caenorhabditis elegans and its close relatives are ideal models for studying how this regulation works, because the XX animals are self-fertile hermaphrodites that produce both sperm and oocytes. In these worms, germ cells use the same signal transduction pathway that functions in somatic cells. This pathway determines the activity of the transcription factor TRA-1, a Gli protein that can repress male genes. However, the pathway is extensively modified in germ cells, largely by the action of translational regulators like the PUF proteins. Many of these modifications play critical roles in allowing the XX hermaphrodites to make sperm in an otherwise female body. Finally, TRA-1 cooperates with chromatin regulators in the germ line to control the activity of fog-1 and fog-3, which are essential for spermatogenesis. FOG-1 and FOG-3 work together to determine germ cell fates by blocking the translation of oogenic transcripts. Key Messages: Although there is great diversity in how germ cell fates are controlled in other animals, many of the key nematode genes are conserved, and the critical role of translational regulators may be universal.
Collapse
Affiliation(s)
- Ronald E Ellis
- Department of Molecular Biology, Rowan University SOM, Stratford, New Jersey, USA
| |
Collapse
|
10
|
Qiu C, Wine RN, Campbell ZT, Hall T. Bipartite interaction sites differentially modulate RNA-binding affinity of a protein complex essential for germline stem cell self-renewal. Nucleic Acids Res 2022; 50:536-548. [PMID: 34908132 PMCID: PMC8754657 DOI: 10.1093/nar/gkab1220] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/23/2021] [Accepted: 12/08/2021] [Indexed: 01/09/2023] Open
Abstract
In C. elegans, PUF proteins promote germline stem cell self-renewal. Their functions hinge on partnerships with two proteins that are redundantly required for stem cell maintenance. Here we focus on understanding how the essential partner protein, LST-1, modulates mRNA regulation by the PUF protein, FBF-2. LST-1 contains two nonidentical sites of interaction with FBF-2, LST-1 A and B. Our crystal structures of complexes of FBF-2, LST-1 A, and RNA visualize how FBF-2 associates with LST-1 A versus LST-1 B. One commonality is that FBF-2 contacts the conserved lysine and leucine side chains in the KxxL motifs in LST-1 A and B. A key difference is that FBF-2 forms unique contacts with regions N- and C-terminal to the KxxL motif. Consequently, LST-1 A does not modulate the RNA-binding affinity of FBF-2, whereas LST-1 B decreases RNA-binding affinity of FBF-2. The N-terminal region of LST-1 B, which binds near the 5' end of RNA elements, is essential to modulate FBF-2 RNA-binding affinity, while the C-terminal residues of LST-1 B contribute strong binding affinity to FBF-2. We conclude that LST-1 has the potential to impact which mRNAs are regulated depending on the precise nature of engagement through its functionally distinct FBF binding sites.
Collapse
Affiliation(s)
- Chen Qiu
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Robert N Wine
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Zachary T Campbell
- Department of Biological Sciences, University of Texas at Dallas, Richardson, TX 75025, USA
| | - Traci M Tanaka Hall
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| |
Collapse
|
11
|
Kulkarni A, Lopez DH, Extavour CG. Shared Cell Biological Functions May Underlie Pleiotropy of Molecular Interactions in the Germ Lines and Nervous Systems of Animals. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00215] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
|
12
|
Huggins HP, Subash JS, Stoffel H, Henderson MA, Hoffman JL, Buckner DS, Sengupta MS, Boag PR, Lee MH, Keiper BD. Distinct roles of two eIF4E isoforms in the germline of Caenorhabditis elegans. J Cell Sci 2020; 133:jcs237990. [PMID: 32079657 PMCID: PMC7132772 DOI: 10.1242/jcs.237990] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 02/10/2020] [Indexed: 01/15/2023] Open
Abstract
Germ cells use both positive and negative mRNA translational control to regulate gene expression that drives their differentiation into gametes. mRNA translational control is mediated by RNA-binding proteins, miRNAs and translation initiation factors. We have uncovered the discrete roles of two translation initiation factor eIF4E isoforms (IFE-1, IFE-3) that bind 7-methylguanosine (m7G) mRNA caps during Caenorhabditiselegans germline development. IFE-3 plays important roles in germline sex determination (GSD), where it promotes oocyte cell fate and is dispensable for spermatogenesis. IFE-3 is expressed throughout the germline and localizes to germ granules, but is distinct from IFE-1 and PGL-1, and facilitates oocyte growth and viability. This contrasts with the robust expression in spermatocytes of IFE-1, the isoform that resides within P granules in spermatocytes and oocytes, and promotes late spermatogenesis. Each eIF4E is localized by its cognate eIF4E-binding protein (IFE-1:PGL-1 and IFE-3:IFET-1). IFE-3 and IFET-1 regulate translation of several GSD mRNAs, but not those under control of IFE-1. Distinct mutant phenotypes, in vivo localization and differential mRNA translation suggest independent dormant and active periods for each eIF4E isoform in the germline.
Collapse
Affiliation(s)
- Hayden P Huggins
- Department of Biochemistry and Molecular Biology, Brody School of Medicine at East Carolina University, Greenville, NC 27834, USA
| | - Jacob S Subash
- Department of Biochemistry and Molecular Biology, Brody School of Medicine at East Carolina University, Greenville, NC 27834, USA
| | - Hamilton Stoffel
- Department of Biochemistry and Molecular Biology, Brody School of Medicine at East Carolina University, Greenville, NC 27834, USA
| | - Melissa A Henderson
- Department of Molecular Sciences, DeBusk College of Osteopathic Medicine, Lincoln Memorial University, Harrogate, TN 37752, USA
| | - Jenna L Hoffman
- Department of Biochemistry and Molecular Biology, Brody School of Medicine at East Carolina University, Greenville, NC 27834, USA
| | - David S Buckner
- Department of Biochemistry and Molecular Biology, Brody School of Medicine at East Carolina University, Greenville, NC 27834, USA
| | - Madhu S Sengupta
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
| | - Peter R Boag
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
| | - Myon-Hee Lee
- Department of Internal Medicine, Brody School of Medicine at East Carolina University, Greenville, NC 27834, USA
| | - Brett D Keiper
- Department of Biochemistry and Molecular Biology, Brody School of Medicine at East Carolina University, Greenville, NC 27834, USA
| |
Collapse
|
13
|
Olesnicky EC, Killian DJ. The cytoplasmic polyadenylation element binding protein (CPEB), Orb, is important for dendrite development and neuron fate specification in Drosophila melanogaster. Gene 2020; 738:144473. [PMID: 32057929 DOI: 10.1016/j.gene.2020.144473] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 02/05/2020] [Accepted: 02/11/2020] [Indexed: 12/14/2022]
Abstract
Cytoplasmic polyadenylation element binding proteins (CPEBs) are widely conserved proteins that regulate the length of poly(A) tails in the cytoplasm, regulate translation, and regulate mRNA transport. While CPEBs are best known for regulating maternal messages in oocytes, CPEBs also have roles in many other cell types including neurons. Here we extend our knowledge of the roles of CPEBs in neurons by showing that the Drosophila CPEB-encoding gene, orb, is required for proper dendrite development in larval sensory dendritic arborization neurons. Furthermore, we provide evidence that orb is important for neuron cell fate specification.
Collapse
Affiliation(s)
- Eugenia C Olesnicky
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO, 80918, United States.
| | - Darrell J Killian
- Department of Molecular Biology, Colorado College, Colorado Springs, CO 80903, United States
| |
Collapse
|
14
|
Wang X, Voronina E. Diverse Roles of PUF Proteins in Germline Stem and Progenitor Cell Development in C. elegans. Front Cell Dev Biol 2020; 8:29. [PMID: 32117964 PMCID: PMC7015873 DOI: 10.3389/fcell.2020.00029] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 01/14/2020] [Indexed: 01/05/2023] Open
Abstract
Stem cell development depends on post-transcriptional regulation mediated by RNA-binding proteins (RBPs) (Zhang et al., 1997; Forbes and Lehmann, 1998; Okano et al., 2005; Ratti et al., 2006; Kwon et al., 2013). Pumilio and FBF (PUF) family RBPs are highly conserved post-transcriptional regulators that are critical for stem cell maintenance (Wickens et al., 2002; Quenault et al., 2011). The RNA-binding domains of PUF proteins recognize a family of related sequence motifs in the target mRNAs, yet individual PUF proteins have clearly distinct biological functions (Lu et al., 2009; Wang et al., 2018). The C. elegans germline is a simple and powerful model system for analyzing regulation of stem cell development. Studies in C. elegans uncovered specific physiological roles for PUFs expressed in the germline stem cells ranging from control of proliferation and differentiation to regulation of the sperm/oocyte decision. Importantly, recent studies started to illuminate the mechanisms behind PUF functional divergence. This review summarizes the many roles of PUF-8, FBF-1, and FBF-2 in germline stem and progenitor cells (SPCs) and discusses the factors accounting for their distinct biological functions. PUF proteins are conserved in evolution, and insights into PUF-mediated regulation provided by the C. elegans model system are likely relevant for other organisms.
Collapse
Affiliation(s)
- Xiaobo Wang
- Division of Biological Sciences, University of Montana, Missoula, MT, United States
| | - Ekaterina Voronina
- Division of Biological Sciences, University of Montana, Missoula, MT, United States
| |
Collapse
|
15
|
Rivera-Tarazona LK, Bhat VD, Kim H, Campbell ZT, Ware TH. Shape-morphing living composites. SCIENCE ADVANCES 2020; 6:eaax8582. [PMID: 32010767 PMCID: PMC6968942 DOI: 10.1126/sciadv.aax8582] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 11/11/2019] [Indexed: 05/31/2023]
Abstract
This work establishes a means to exploit genetic networks to create living synthetic composites that change shape in response to specific biochemical or physical stimuli. Baker's yeast embedded in a hydrogel forms a responsive material where cellular proliferation leads to a controllable increase in the composite volume of up to 400%. Genetic manipulation of the yeast enables composites where volume change on exposure to l-histidine is 14× higher than volume change when exposed to d-histidine or other amino acids. By encoding an optogenetic switch into the yeast, spatiotemporally controlled shape change is induced with pulses of dim blue light (2.7 mW/cm2). These living, shape-changing materials may enable sensors or medical devices that respond to highly specific cues found within a biological milieu.
Collapse
Affiliation(s)
- L. K. Rivera-Tarazona
- Department of Bioengineering, The University of Texas at Dallas, Richardson, TX, USA
| | - V. D. Bhat
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, TX, USA
| | - H. Kim
- Department of Bioengineering, The University of Texas at Dallas, Richardson, TX, USA
| | - Z. T. Campbell
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, TX, USA
| | - T. H. Ware
- Department of Bioengineering, The University of Texas at Dallas, Richardson, TX, USA
| |
Collapse
|
16
|
Aoki ST, Porter DF, Prasad A, Wickens M, Bingman CA, Kimble J. An RNA-Binding Multimer Specifies Nematode Sperm Fate. Cell Rep 2019; 23:3769-3775. [PMID: 29949762 PMCID: PMC6066285 DOI: 10.1016/j.celrep.2018.05.095] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 04/26/2018] [Accepted: 05/30/2018] [Indexed: 11/27/2022] Open
Abstract
FOG-3 is a master regulator of sperm fate in Caenorhabditis elegans and homologous to Tob/BTG proteins, which in mammals are monomeric adaptors that recruit enzymes to RNA binding proteins. Here, we determine the FOG-3 crystal structure and in vitro demonstrate that FOG-3 forms dimers that can multi-merize. The FOG-3 multimeric structure has a basic surface potential, suggestive of binding nucleic acid. Consistent with that prediction, FOG-3 binds directly to nearly 1,000 RNAs in nematode spermatogenic germ cells. Most binding is to the 3′ UTR, and most targets (94%) are oogenic mRNAs, even though assayed in spermatogenic cells. When tethered to a reporter mRNA, FOG-3 represses its expression. Together these findings elucidate the molecular mechanism of sperm fate specification and reveal the evolution of a protein from monomeric to multimeric form with acquisition of a distinct mode of mRNA repression. The mechanism of the sperm or oocyte fate decision has been elusive. Aoki et al. report that nematode FOG-3, a Tob/BTG protein driving sperm fate, has evolved from monomeric to multimeric form with acquisition of a divergent Tob/BTG mechanism for mRNA repression.
Collapse
Affiliation(s)
- Scott T Aoki
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Douglas F Porter
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Aman Prasad
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Marvin Wickens
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Craig A Bingman
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Judith Kimble
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, WI 53706, USA.
| |
Collapse
|
17
|
Bezler A, Braukmann F, West SM, Duplan A, Conconi R, Schütz F, Gönczy P, Piano F, Gunsalus K, Miska EA, Keller L. Tissue- and sex-specific small RNAomes reveal sex differences in response to the environment. PLoS Genet 2019; 15:e1007905. [PMID: 30735500 PMCID: PMC6383947 DOI: 10.1371/journal.pgen.1007905] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 02/21/2019] [Accepted: 12/17/2018] [Indexed: 11/19/2022] Open
Abstract
RNA interference (RNAi) related pathways are essential for germline development and fertility in metazoa and can contribute to inter- and trans-generational inheritance. In the nematode Caenorhabditis elegans, environmental double-stranded RNA provided by feeding can lead to heritable changes in phenotype and gene expression. Notably, transmission efficiency differs between the male and female germline, yet the underlying mechanisms remain elusive. Here we use high-throughput sequencing of dissected gonads to quantify sex-specific endogenous piRNAs, miRNAs and siRNAs in the C. elegans germline and the somatic gonad. We identify genes with exceptionally high levels of secondary 22G RNAs that are associated with low mRNA expression, a signature compatible with silencing. We further demonstrate that contrary to the hermaphrodite germline, the male germline, but not male soma, is resistant to environmental RNAi triggers provided by feeding, in line with previous work. This sex-difference in silencing efficacy is associated with lower levels of gonadal RNAi amplification products. Moreover, this tissue- and sex-specific RNAi resistance is regulated by the germline, since mutant males with a feminized germline are RNAi sensitive. This study provides important sex- and tissue-specific expression data of miRNA, piRNA and siRNA as well as mechanistic insights into sex-differences of gene regulation in response to environmental cues.
Collapse
Affiliation(s)
- Alexandra Bezler
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Fabian Braukmann
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
| | - Sean M. West
- Center for Genomics & Systems Biology, New York University, New York, New York, United States of America
| | - Arthur Duplan
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Raffaella Conconi
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Frédéric Schütz
- Bioinformatics Core Facility; SIB Swiss Institute of Bioinformatics and Centre for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Pierre Gönczy
- Swiss Institute for Experimental Cancer Research (ISREC), Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | - Fabio Piano
- Center for Genomics & Systems Biology, New York University, New York, New York, United States of America
- Center for Genomics & Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Kristin Gunsalus
- Center for Genomics & Systems Biology, New York University, New York, New York, United States of America
- Center for Genomics & Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Eric A. Miska
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
| | - Laurent Keller
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| |
Collapse
|
18
|
Porter DF, Prasad A, Carrick BH, Kroll-Connor P, Wickens M, Kimble J. Toward Identifying Subnetworks from FBF Binding Landscapes in Caenorhabditis Spermatogenic or Oogenic Germlines. G3 (BETHESDA, MD.) 2019; 9:153-165. [PMID: 30459181 PMCID: PMC6325917 DOI: 10.1534/g3.118.200300] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 11/09/2018] [Indexed: 12/31/2022]
Abstract
Metazoan PUF (Pumilio and FBF) RNA-binding proteins regulate various biological processes, but a common theme across phylogeny is stem cell regulation. In Caenorhabditis elegans, FBF (fem-3 Binding Factor) maintains germline stem cells regardless of which gamete is made, but FBF also functions in the process of spermatogenesis. We have begun to "disentangle" these biological roles by asking which FBF targets are gamete-independent, as expected for stem cells, and which are gamete-specific. Specifically, we compared FBF iCLIP binding profiles in adults making sperm to those making oocytes. Normally, XX adults make oocytes. To generate XX adults making sperm, we used a fem-3(gf) mutant requiring growth at 25°; for comparison, wild-type oogenic hermaphrodites were also raised at 25°. Our FBF iCLIP data revealed FBF binding sites in 1522 RNAs from oogenic adults and 1704 RNAs from spermatogenic adults. More than half of these FBF targets were independent of germline gender. We next clustered RNAs by FBF-RNA complex frequencies and found four distinct blocks. Block I RNAs were enriched in spermatogenic germlines, and included validated target fog-3, while Block II and III RNAs were common to both genders, and Block IV RNAs were enriched in oogenic germlines. Block II (510 RNAs) included almost all validated FBF targets and was enriched for cell cycle regulators. Block III (21 RNAs) was enriched for RNA-binding proteins, including previously validated FBF targets gld-1 and htp-1 We suggest that Block I RNAs belong to the FBF network for spermatogenesis, and that Blocks II and III are associated with stem cell functions.
Collapse
Affiliation(s)
- Douglas F Porter
- Department of Biochemistry, University of Wisconsin-Madison, Wisconsin 53706
| | - Aman Prasad
- Department of Biochemistry, University of Wisconsin-Madison, Wisconsin 53706
| | - Brian H Carrick
- Department of Biochemistry, University of Wisconsin-Madison, Wisconsin 53706
| | - Peggy Kroll-Connor
- Howard Hughes Medical Institute, University of Wisconsin-Madison, Wisconsin 53706
| | - Marvin Wickens
- Department of Biochemistry, University of Wisconsin-Madison, Wisconsin 53706
| | - Judith Kimble
- Department of Biochemistry, University of Wisconsin-Madison, Wisconsin 53706
- Howard Hughes Medical Institute, University of Wisconsin-Madison, Wisconsin 53706
| |
Collapse
|
19
|
Qiu C, Bhat VD, Rajeev S, Zhang C, Lasley AE, Wine RN, Campbell ZT, Hall TMT. A crystal structure of a collaborative RNA regulatory complex reveals mechanisms to refine target specificity. eLife 2019; 8:48968. [PMID: 31397673 PMCID: PMC6697444 DOI: 10.7554/elife.48968] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 08/09/2019] [Indexed: 01/09/2023] Open
Abstract
In the Caenorhabditis elegans germline, fem-3 Binding Factor (FBF) partners with LST-1 to maintain stem cells. A crystal structure of an FBF-2/LST-1/RNA complex revealed that FBF-2 recognizes a short RNA motif different from the characteristic 9-nt FBF binding element, and compact motif recognition coincided with curvature changes in the FBF-2 scaffold. Previously, we engineered FBF-2 to favor recognition of shorter RNA motifs without curvature change (Bhat et al., 2019). In vitro selection of RNAs bound by FBF-2 suggested sequence specificity in the central region of the compact element. This bias, reflected in the crystal structure, was validated in RNA-binding assays. FBF-2 has the intrinsic ability to bind to this shorter motif. LST-1 weakens FBF-2 binding affinity for short and long motifs, which may increase target selectivity. Our findings highlight the role of FBF scaffold flexibility in RNA recognition and suggest a new mechanism by which protein partners refine target site selection.
Collapse
Affiliation(s)
- Chen Qiu
- Epigenetics and Stem Cell Biology LaboratoryNational Institute of Environmental Health Sciences, National Institutes of HealthResearch Triangle ParkUnited States
| | - Vandita D Bhat
- Department of Biological SciencesUniversity of Texas at DallasRichardsonUnited States
| | - Sanjana Rajeev
- Department of Biological SciencesUniversity of Texas at DallasRichardsonUnited States
| | - Chi Zhang
- Department of Biological SciencesUniversity of Texas at DallasRichardsonUnited States
| | - Alexa E Lasley
- Department of Biological SciencesUniversity of Texas at DallasRichardsonUnited States
| | - Robert N Wine
- Epigenetics and Stem Cell Biology LaboratoryNational Institute of Environmental Health Sciences, National Institutes of HealthResearch Triangle ParkUnited States
| | - Zachary T Campbell
- Department of Biological SciencesUniversity of Texas at DallasRichardsonUnited States
| | - Traci M Tanaka Hall
- Epigenetics and Stem Cell Biology LaboratoryNational Institute of Environmental Health Sciences, National Institutes of HealthResearch Triangle ParkUnited States
| |
Collapse
|
20
|
Wang M, Ogé L, Perez-Garcia MD, Hamama L, Sakr S. The PUF Protein Family: Overview on PUF RNA Targets, Biological Functions, and Post Transcriptional Regulation. Int J Mol Sci 2018; 19:ijms19020410. [PMID: 29385744 PMCID: PMC5855632 DOI: 10.3390/ijms19020410] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Revised: 01/23/2018] [Accepted: 01/25/2018] [Indexed: 12/13/2022] Open
Abstract
Post-transcriptional regulation of gene expression plays a crucial role in many processes. In cells, it is mediated by diverse RNA-binding proteins. These proteins can influence mRNA stability, translation, and localization. The PUF protein family (Pumilio and FBF) is composed of RNA-binding proteins highly conserved among most eukaryotic organisms. Previous investigations indicated that they could be involved in many processes by binding corresponding motifs in the 3′UTR or by interacting with other proteins. To date, most of the investigations on PUF proteins have been focused on Caenorhabditis elegans, Drosophila melanogaster, and Saccharomyces cerevisiae, while only a few have been conducted on Arabidopsis thaliana. The present article provides an overview of the PUF protein family. It addresses their RNA-binding motifs, biological functions, and post-transcriptional control mechanisms in Caenorhabditis elegans, Drosophila melanogaster, Saccharomyces cerevisiae, and Arabidopsis thaliana. These items of knowledge open onto new investigations into the relevance of PUF proteins in specific plant developmental processes.
Collapse
Affiliation(s)
- Ming Wang
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QUASAV, F-49045 Angers, France.
| | - Laurent Ogé
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QUASAV, F-49045 Angers, France.
| | | | - Latifa Hamama
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QUASAV, F-49045 Angers, France.
| | - Soulaiman Sakr
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QUASAV, F-49045 Angers, France.
| |
Collapse
|
21
|
Luo D, Zhang M, Liu T, Cao W, Guo J, Mao C, Li Y, Wang J, Huang W, Lu D, Zhang S, Li Z, He J. Long range haplotyping of paired-homologous chromosomes by single-chromosome sequencing of a single cell. Sci Rep 2018; 8:1640. [PMID: 29374225 PMCID: PMC5785984 DOI: 10.1038/s41598-018-20069-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 01/11/2018] [Indexed: 12/29/2022] Open
Abstract
The longest possible haplotype is chromosome haplotype that is a set of co-inherited alleles occurred on a single strand chromosome inherited from one parent. Standard whole-genome shotgun sequencing technologies are limited by the inability to independently study the haplotype of homologous chromosomes due to the short-reads sequencing strategy and disturbance of homologue chromosomes. Here, we investigated several types of chromosomal abnormalities by a dilution-based method to separate an intact copy of homologous chromosome from human metaphase cells, and then single chromosomes were independently amplified by whole-genome amplification methods, converted into barcoded sequencing libraries, and sequenced in multiplexed pools by Illumina sequencers. We analyzed single chromosome derived from single metaphase cells of one patient with balanced chromosomal translocation t(3;5)(q24;q13), one patient with (47, XXY) karyotype and one with (47, XY, 21+) Down syndrome. We determined the translocation region of chromosomes in patient with t(3;5)(q24;q13) balanced chromosomal translocation by shallow whole-genome sequencing, which is helpful to pinpoint the chromosomal break point. We showed that SCS can physically separate and independently sequence three copies of chromosome 21 of Down syndrome patient. SCS has potential applications in personal genomics, single-cell genomics, and clinical diagnosis, particularly in revealing chromosomal level of genetic diseases.
Collapse
Affiliation(s)
- Deng Luo
- Department of Biology, South University of Science and Technology of China, Shenzhen, Guangdong, 518055, China
| | - Meng Zhang
- Department of Biology, South University of Science and Technology of China, Shenzhen, Guangdong, 518055, China
| | - Ting Liu
- Department of Biology, South University of Science and Technology of China, Shenzhen, Guangdong, 518055, China
| | - Wei Cao
- Department of Biology, South University of Science and Technology of China, Shenzhen, Guangdong, 518055, China
| | - Jiajie Guo
- Department of Biology, South University of Science and Technology of China, Shenzhen, Guangdong, 518055, China
| | - Caiping Mao
- Reproductive Medicine Center, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215006, China
| | - Yifan Li
- Central Laboratory, Affiliated Nanshan Hospital, Guangdong Medical College, Shenzhen, Guangdong, 518052, China
| | - Juanmei Wang
- Department of Pediatrics, Hunan Provincial People's Hospital, Changsha, Hunan, 410005, China
| | - Weiren Huang
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, 518035, China
| | - Daru Lu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Science, Fudan University, Shanghai, 200438, China
| | - Shuo Zhang
- Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, 200011, China
| | - Zhoufang Li
- Department of Biology, South University of Science and Technology of China, Shenzhen, Guangdong, 518055, China.
| | - Jiankui He
- Department of Biology, South University of Science and Technology of China, Shenzhen, Guangdong, 518055, China.
| |
Collapse
|
22
|
Shin H, Haupt KA, Kershner AM, Kroll-Conner P, Wickens M, Kimble J. SYGL-1 and LST-1 link niche signaling to PUF RNA repression for stem cell maintenance in Caenorhabditis elegans. PLoS Genet 2017; 13:e1007121. [PMID: 29232700 PMCID: PMC5741267 DOI: 10.1371/journal.pgen.1007121] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 12/22/2017] [Accepted: 11/20/2017] [Indexed: 01/14/2023] Open
Abstract
Central questions in regenerative biology include how stem cells are maintained and how they transition from self-renewal to differentiation. Germline stem cells (GSCs) in Caeno-rhabditis elegans provide a tractable in vivo model to address these questions. In this system, Notch signaling and PUF RNA binding proteins, FBF-1 and FBF-2 (collectively FBF), maintain a pool of GSCs in a naïve state. An open question has been how Notch signaling modulates FBF activity to promote stem cell self-renewal. Here we report that two Notch targets, SYGL-1 and LST-1, link niche signaling to FBF. We find that SYGL-1 and LST-1 proteins are cytoplasmic and normally restricted to the GSC pool region. Increasing the distribution of SYGL-1 expands the pool correspondingly, and vast overexpression of either SYGL-1 or LST-1 generates a germline tumor. Thus, SYGL-1 and LST-1 are each sufficient to drive "stemness" and their spatial restriction prevents tumor formation. Importantly, SYGL-1 and LST-1 can only drive tumor formation when FBF is present. Moreover, both proteins interact physically with FBF, and both are required to repress a signature FBF mRNA target. Together, our results support a model in which SYGL-1 and LST-1 form a repressive complex with FBF that is crucial for stem cell maintenance. We further propose that progression from a naïve stem cell state to a state primed for differentiation relies on loss of SYGL-1 and LST-1, which in turn relieves FBF target RNAs from repression. Broadly, our results provide new insights into the link between niche signaling and a downstream RNA regulatory network and how this circuitry governs the balance between self-renewal and differentiation.
Collapse
Affiliation(s)
- Heaji Shin
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Kimberly A. Haupt
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Aaron M. Kershner
- Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Peggy Kroll-Conner
- Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Marvin Wickens
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Judith Kimble
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| |
Collapse
|
23
|
Singh KD, Zheng X, Milstein S, Keller M, Roschitzki B, Grossmann J, Hengartner MO. Differential regulation of germ line apoptosis and germ cell differentiation by CPEB family members in C. elegans. PLoS One 2017; 12:e0182270. [PMID: 28759574 PMCID: PMC5536308 DOI: 10.1371/journal.pone.0182270] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 07/14/2017] [Indexed: 11/21/2022] Open
Abstract
Cytoplasmic polyadenylation element binding (CPEB) proteins are evolutionary conserved RNA-binding proteins that control mRNA polyadenylation and translation. Orthologs in humans and other vertebrates are mainly involved in oogenesis. This is also the case for the C. elegans CPEB family member CPB-3, whereas two further CPEB proteins (CPB-1 and FOG-1) are involved in spermatogenesis. Here we describe the characterisation of a new missense allele of cpb-3 and show that loss of cpb-3 function leads to an increase in physiological germ cell death. To better understand the interaction and effect of C. elegans CPEB proteins on processes such as physiological apoptosis, germ cell differentiation, and regulation of gene expression, we characterised changes in the transcriptome and proteome of C. elegans CPEB mutants. Our results show that, despite their sequence similarities CPEB family members tend to have distinct overall effects on gene expression (both at the transcript and protein levels). This observation is consistent with the distinct phenotypes observed in the various CPEB family mutants.
Collapse
Affiliation(s)
- Kapil Dev Singh
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- PhD Program in Molecular Life Science, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Xue Zheng
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- PhD Program in Molecular Life Science, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Stuart Milstein
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Martin Keller
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- PhD Program in Molecular Life Science, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Bernd Roschitzki
- Functional Genomics Center Zurich, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Jonas Grossmann
- Functional Genomics Center Zurich, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Michael O. Hengartner
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- * E-mail:
| |
Collapse
|
24
|
Rouhana L, Tasaki J, Saberi A, Newmark PA. Genetic dissection of the planarian reproductive system through characterization of Schmidtea mediterranea CPEB homologs. Dev Biol 2017; 426:43-55. [PMID: 28434803 PMCID: PMC5544531 DOI: 10.1016/j.ydbio.2017.04.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 03/30/2017] [Accepted: 04/18/2017] [Indexed: 01/30/2023]
Abstract
Cytoplasmic polyadenylation is a mechanism of mRNA regulation prevalent in metazoan germ cells; it is largely dependent on Cytoplasmic Polyadenylation Element Binding proteins (CPEBs). Two CPEB homologs were identified in the planarian Schmidtea mediterranea. Smed-CPEB1 is expressed in ovaries and yolk glands of sexually mature planarians, and required for oocyte and yolk gland development. In contrast, Smed-CPEB2 is expressed in the testes and the central nervous system; its function is required for spermatogenesis as well as non-autonomously for development of ovaries and accessory reproductive organs. Transcriptome analysis of CPEB knockdown animals uncovered a comprehensive collection of molecular markers for reproductive structures in S. mediterranea, including ovaries, testes, yolk glands, and the copulatory apparatus. Analysis by RNA interference revealed contributions for a dozen of these genes during oogenesis, spermatogenesis, or capsule formation. We also present evidence suggesting that Smed-CPEB2 promotes translation of Neuropeptide Y-8, a prohormone required for planarian sexual maturation. These findings provide mechanistic insight into potentially conserved processes of germ cell development, as well as events involved in capsule deposition by flatworms.
Collapse
Affiliation(s)
- Labib Rouhana
- Department of Biological Sciences, Wright State University, 3640 Colonel Glenn Highway, Dayton, OH 45435, USA; Howard Hughes Medical Institute and Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601 S. Goodwin Ave., Urbana, IL 61801, USA.
| | - Junichi Tasaki
- Department of Biological Sciences, Wright State University, 3640 Colonel Glenn Highway, Dayton, OH 45435, USA
| | - Amir Saberi
- Howard Hughes Medical Institute and Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601 S. Goodwin Ave., Urbana, IL 61801, USA
| | - Phillip A Newmark
- Howard Hughes Medical Institute and Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601 S. Goodwin Ave., Urbana, IL 61801, USA
| |
Collapse
|
25
|
Revisiting Suppression of Interspecies Hybrid Male Lethality in Caenorhabditis Nematodes. G3-GENES GENOMES GENETICS 2017; 7:1211-1214. [PMID: 28209763 PMCID: PMC5386869 DOI: 10.1534/g3.117.039479] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Within the nematode genus Caenorhabditis, Caenorhabditis briggsae and C. nigoni are among the most closely related species known. They differ in sexual mode, with C. nigoni retaining the ancestral XO male-XX female outcrossing system, while C. briggsae recently evolved self-fertility and an XX-biased sex ratio. Wild-type C. briggsae and C. nigoni can produce fertile hybrid XX female progeny, but XO progeny are either 100% inviable (when C. briggsae is the mother) or viable but sterile (when C. nigoni is the mother). A recent study provided evidence suggesting that loss of the Cbr-him-8 meiotic regulator in C. briggsae hermaphrodites allowed them to produce viable and fertile hybrid XO male progeny when mated to C. nigoni Because such males would be useful for a variety of genetic experiments, we sought to verify this result. Preliminary crosses with wild-type C. briggsae hermaphrodites occasionally produced fertile males, but they could not be confirmed to be interspecies hybrids. Using an RNA interference (RNAi) protocol that eliminates any possibility of self-progeny in Cbr-him-8 hermaphrodites, we found sterile males bearing the C. nigoni X chromosome, but no fertile males bearing the C. briggsae X, as in wild-type crosses. Our results suggest that the apparent rescue of XO hybrid viability and fertility is due to incomplete purging of self-sperm prior to mating.
Collapse
|
26
|
Prasad A, Porter DF, Kroll-Conner PL, Mohanty I, Ryan AR, Crittenden SL, Wickens M, Kimble J. The PUF binding landscape in metazoan germ cells. RNA (NEW YORK, N.Y.) 2016; 22:1026-43. [PMID: 27165521 PMCID: PMC4911911 DOI: 10.1261/rna.055871.116] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2016] [Accepted: 04/14/2016] [Indexed: 05/09/2023]
Abstract
PUF (Pumilio/FBF) proteins are RNA-binding proteins and conserved stem cell regulators. The Caenorhabditis elegans PUF proteins FBF-1 and FBF-2 (collectively FBF) regulate mRNAs in germ cells. Without FBF, adult germlines lose all stem cells. A major gap in our understanding of PUF proteins, including FBF, is a global view of their binding sites in their native context (i.e., their "binding landscape"). To understand the interactions underlying FBF function, we used iCLIP (individual-nucleotide resolution UV crosslinking and immunoprecipitation) to determine binding landscapes of C. elegans FBF-1 and FBF-2 in the germline tissue of intact animals. Multiple iCLIP peak-calling methods were compared to maximize identification of both established FBF binding sites and positive control target mRNAs in our iCLIP data. We discovered that FBF-1 and FBF-2 bind to RNAs through canonical as well as alternate motifs. We also analyzed crosslinking-induced mutations to map binding sites precisely and to identify key nucleotides that may be critical for FBF-RNA interactions. FBF-1 and FBF-2 can bind sites in the 5'UTR, coding region, or 3'UTR, but have a strong bias for the 3' end of transcripts. FBF-1 and FBF-2 have strongly overlapping target profiles, including mRNAs and noncoding RNAs. From a statistically robust list of 1404 common FBF targets, 847 were previously unknown, 154 were related to cell cycle regulation, three were lincRNAs, and 335 were shared with the human PUF protein PUM2.
Collapse
Affiliation(s)
- Aman Prasad
- Department of Biochemistry, and Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Douglas F Porter
- Department of Biochemistry, and Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Peggy L Kroll-Conner
- Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Ipsita Mohanty
- Department of Biochemistry, and Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Anne R Ryan
- Department of Biochemistry, and Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Sarah L Crittenden
- Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Marvin Wickens
- Department of Biochemistry, and Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Judith Kimble
- Department of Biochemistry, and Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| |
Collapse
|
27
|
Ellis RE. "The persistence of memory"-Hermaphroditism in nematodes. Mol Reprod Dev 2016; 84:144-157. [PMID: 27291983 DOI: 10.1002/mrd.22668] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 06/01/2016] [Indexed: 12/13/2022]
Abstract
Self-fertility has evolved many times in nematodes. This transition often produces an androdioecious species, with XX hermaphrodites and XO males. Although these hermaphrodites resemble females in most respects, early germ cells differentiate as sperm, and late ones as oocytes. The sperm then receive an activation signal, populate the spermathecae, and are stored for later use in self-fertilization. These traits are controlled by complex modifications to the sex-determination and sperm activation pathways, which have arisen independently during the evolution of each hermaphroditic species. This transformation in reproductive strategy then promotes other major changes in the development, evolution, and population structure of these animals. Mol. Reprod. Dev. 84: 144-157, 2017. © 2016 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Ronald E Ellis
- Department of Molecular Biology, Rowan University SOM, Stratford, New Jersey
| |
Collapse
|
28
|
Skilandat M, Rowinska-Zyrek M, Sigel RKO. Secondary structure confirmation and localization of Mg2+ ions in the mammalian CPEB3 ribozyme. RNA (NEW YORK, N.Y.) 2016; 22:750-763. [PMID: 26966151 PMCID: PMC4836649 DOI: 10.1261/rna.053843.115] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Accepted: 01/04/2016] [Indexed: 06/05/2023]
Abstract
Most of today's knowledge of the CPEB3 ribozyme, one of the few small self-cleaving ribozymes known to occur in humans, is based on comparative studies with the hepatitis delta virus (HDV) ribozyme, which is highly similar in cleavage mechanism and probably also in structure. Here we present detailed NMR studies of the CPEB3 ribozyme in order to verify the formation of the predicted nested double pseudoknot in solution. In particular, the influence of Mg(2+), the ribozyme's crucial cofactor, on the CPEB3 structure is investigated. NMR titrations, Tb(3+)-induced cleavage, as well as stoichiometry determination by hydroxyquinoline sulfonic acid fluorescence and equilibrium dialysis, are used to evaluate the number, location, and binding mode of Mg(2+)ions. Up to eight Mg(2+)ions interact site-specifically with the ribozyme, four of which are bound with high affinity. The global fold of the CPEB3 ribozyme, encompassing 80%-90% of the predicted base pairs, is formed in the presence of monovalent ions alone. Low millimolar concentrations of Mg(2+)promote a more compact fold and lead to the formation of additional structures in the core of the ribozyme, which contains the inner small pseudoknot and the active site. Several Mg(2+)binding sites, which are important for the functional fold, appear to be located in corresponding locations in the HDV and CPEB3 ribozyme, demonstrating the particular relevance of Mg(2+)for the nested double pseudoknot structure.
Collapse
Affiliation(s)
- Miriam Skilandat
- Department of Chemistry, University of Zurich, CH-8057 Zurich, Switzerland
| | | | - Roland K O Sigel
- Department of Chemistry, University of Zurich, CH-8057 Zurich, Switzerland
| |
Collapse
|
29
|
Silva PAGC, Guerreiro A, Santos JM, Braks JAM, Janse CJ, Mair GR. Translational Control of UIS4 Protein of the Host-Parasite Interface Is Mediated by the RNA Binding Protein Puf2 in Plasmodium berghei Sporozoites. PLoS One 2016; 11:e0147940. [PMID: 26808677 PMCID: PMC4726560 DOI: 10.1371/journal.pone.0147940] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 01/11/2016] [Indexed: 11/19/2022] Open
Abstract
UIS4 is a key protein component of the host-parasite interface in the liver stage of the rodent malaria parasite Plasmodium berghei and required for parasite survival after invasion. In the infectious sporozoite, UIS4 protein has variably been shown to be translated but also been reported to be translationally repressed. Here we show that uis4 mRNA translation is regulated by the P. berghei RNA binding protein Pumilio-2 (PbPuf2 or Puf2 from here on forward) in infectious salivary gland sporozoites in the mosquito vector. Using RNA immunoprecipitation we show that uis4 mRNA is bound by Puf2 in salivary gland sporozoites. In the absence of Puf2, uis4 mRNA translation is de-regulated and UIS4 protein expression upregulated in salivary gland sporozoites. Here, using RNA immunoprecipitation, we reveal the first Puf2-regulated mRNA in this parasite.
Collapse
Affiliation(s)
- Patrícia A. G. C. Silva
- Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Av. Prof. Egas Moniz, 1649–028, Lisbon, Portugal
| | - Ana Guerreiro
- Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Av. Prof. Egas Moniz, 1649–028, Lisbon, Portugal
| | - Jorge M. Santos
- Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Av. Prof. Egas Moniz, 1649–028, Lisbon, Portugal
| | | | | | - Gunnar R. Mair
- Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Av. Prof. Egas Moniz, 1649–028, Lisbon, Portugal
- Parasitology, Department of Infectious Diseases, University of Heidelberg Medical School, Im Neuenheimer Feld 324, 69120, Heidelberg, Germany
- * E-mail:
| |
Collapse
|
30
|
Noble DC, Aoki ST, Ortiz MA, Kim KW, Verheyden JM, Kimble J. Genomic Analyses of Sperm Fate Regulator Targets Reveal a Common Set of Oogenic mRNAs in Caenorhabditis elegans. Genetics 2016; 202:221-34. [PMID: 26564160 PMCID: PMC4701086 DOI: 10.1534/genetics.115.182592] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 11/03/2015] [Indexed: 12/18/2022] Open
Abstract
Germ cell specification as sperm or oocyte is an ancient cell fate decision, but its molecular regulation is poorly understood. In Caenorhabditis elegans, the FOG-1 and FOG-3 proteins behave genetically as terminal regulators of sperm fate specification. Both are homologous to well-established RNA regulators, suggesting that FOG-1 and FOG-3 specify the sperm fate post-transcriptionally. We predicted that FOG-1 and FOG-3, as terminal regulators of the sperm fate, might regulate a battery of gamete-specific differentiation genes. Here we test that prediction by exploring on a genomic scale the messenger RNAs (mRNAs) associated with FOG-1 and FOG-3. Immunoprecipitation of the proteins and their associated mRNAs from spermatogenic germlines identifies 81 FOG-1 and 722 FOG-3 putative targets. Importantly, almost all FOG-1 targets are also FOG-3 targets, and these common targets are strongly biased for oogenic mRNAs. The discovery of common target mRNAs suggested that FOG-1 and FOG-3 work together. Consistent with that idea, we find that FOG-1 and FOG-3 proteins co-immunoprecipitate from both intact nematodes and mammalian tissue culture cells and that they colocalize in germ cells. Taking our results together, we propose a model in which FOG-1 and FOG-3 work in a complex to repress oogenic transcripts and thereby promote the sperm fate.
Collapse
Affiliation(s)
- Daniel C Noble
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - Scott T Aoki
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - Marco A Ortiz
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - Kyung Won Kim
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - Jamie M Verheyden
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - Judith Kimble
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706 Howard Hughes Medical Institute, University of Wisconsin, Madison, Wisconsin 53706
| |
Collapse
|
31
|
Ellis RE, Lin SY. The evolutionary origins and consequences of self-fertility in nematodes. F1000PRIME REPORTS 2014; 6:62. [PMID: 25165561 PMCID: PMC4126538 DOI: 10.12703/p6-62] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Self-fertile hermaphrodites have evolved from male/female ancestors in many nematode species, and this transition occurred on three independent occasions in the genus Caenorhabditis. Genetic analyses in Caenorhabditis show that the origin of hermaphrodites required two types of changes: alterations to the sex-determination pathway that allowed otherwise female animals to make sperm during larval development, and the production of signals from the gonad that caused these sperm to activate and fertilize oocytes. Comparisons of C. elegans and C. briggsae hermaphrodites show that the ancestral sex-determination pathway has been altered in multiple unique ways. Some of these changes must have precipitated the production of sperm in XX animals, and others were modifying mutations that increased the efficiency of hermaphroditic reproduction. Reverse genetic experiments show that XX animals acquired the ability to activate sperm by co-opting one of the two redundant pathways that normally work in males. Finally, the adoption of a hermaphroditic lifestyle had profound effects on ecological and sexual interactions and genomic organization. Thus, nematode mating systems are ideal for elucidating the origin of novel traits, and studying the influence of developmental processes on evolutionary change.
Collapse
|
32
|
Ortiz MA, Noble D, Sorokin EP, Kimble J. A new dataset of spermatogenic vs. oogenic transcriptomes in the nematode Caenorhabditis elegans. G3 (BETHESDA, MD.) 2014; 4:1765-72. [PMID: 25060624 PMCID: PMC4169169 DOI: 10.1534/g3.114.012351] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 07/14/2014] [Indexed: 01/12/2023]
Abstract
The nematode Caenorhabditis elegans is an important model for studies of germ cell biology, including the meiotic cell cycle, gamete specification as sperm or oocyte, and gamete development. Fundamental to those studies is a genome-level knowledge of the germline transcriptome. Here, we use RNA-Seq to identify genes expressed in isolated XX gonads, which are approximately 95% germline and 5% somatic gonadal tissue. We generate data from mutants making either sperm [fem-3(q96)] or oocytes [fog-2(q71)], both grown at 22°. Our dataset identifies a total of 10,754 mRNAs in the polyadenylated transcriptome of XX gonads, with 2748 enriched in spermatogenic gonads, 1732 enriched in oogenic gonads, and the remaining 6274 not enriched in either. These spermatogenic, oogenic, and gender-neutral gene datasets compare well with those of previous studies, but double the number of genes identified. A comparison of the additional genes found in our study with in situ hybridization patterns in the Kohara database suggests that most are expressed in the germline. We also query our RNA-Seq data for differential exon usage and find 351 mRNAs with sex-enriched isoforms. We suggest that this new dataset will prove useful for studies focusing on C. elegans germ cell biology.
Collapse
Affiliation(s)
- Marco A Ortiz
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Daniel Noble
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Elena P Sorokin
- Graduate Program in Cellular and Molecular Biology, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Judith Kimble
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706 Graduate Program in Cellular and Molecular Biology, University of Wisconsin-Madison, Madison, Wisconsin 53706 Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, Wisconsin 53706
| |
Collapse
|
33
|
Ivshina M, Lasko P, Richter JD. Cytoplasmic polyadenylation element binding proteins in development, health, and disease. Annu Rev Cell Dev Biol 2014; 30:393-415. [PMID: 25068488 DOI: 10.1146/annurev-cellbio-101011-155831] [Citation(s) in RCA: 154] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The cytoplasmic polyadenylation element binding (CPEB) proteins are sequence-specific mRNA binding proteins that control translation in development, health, and disease. CPEB1, the founding member of this family, has become an important model for illustrating general principles of translational control by cytoplasmic polyadenylation in gametogenesis, cancer etiology, synaptic plasticity, learning, and memory. Although the biological functions of the other members of this protein family in vertebrates are just beginning to emerge, it is already evident that they, too, mediate important processes, such as cancer etiology and higher cognitive function. In Drosophila, the CPEB proteins Orb and Orb2 play key roles in oogenesis and in neuronal function, as do related proteins in Caenorhabditis elegans and Aplysia. We review the biochemical features of the CPEB proteins, discuss their activities in several biological systems, and illustrate how understanding CPEB activity in model organisms has an important impact on neurological disease.
Collapse
Affiliation(s)
- Maria Ivshina
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605;
| | | | | |
Collapse
|
34
|
Ellis RE, Stanfield GM. The regulation of spermatogenesis and sperm function in nematodes. Semin Cell Dev Biol 2014; 29:17-30. [PMID: 24718317 PMCID: PMC4082717 DOI: 10.1016/j.semcdb.2014.04.005] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 04/01/2014] [Indexed: 12/12/2022]
Abstract
In the nematode C. elegans, both males and self-fertile hermaphrodites produce sperm. As a result, researchers have been able to use a broad range of genetic and genomic techniques to dissect all aspects of sperm development and function. Their results show that the early stages of spermatogenesis are controlled by transcriptional and translational processes, but later stages are dominated by protein kinases and phosphatases. Once spermatids are produced, they participate in many interactions with other cells - signals from the somatic gonad determine when sperm activate and begin to crawl, signals from the female reproductive tissues guide the sperm, and signals from sperm stimulate oocytes to mature and be ovulated. The sperm also show strong competitive interactions with other sperm and oocytes. Some of the molecules that mediate these processes have conserved functions in animal sperm, others are conserved proteins that have been adapted for new roles in nematode sperm, and some are novel proteins that provide insights into evolutionary change. The advent of new techniques should keep this system on the cutting edge of research in cellular and reproductive biology.
Collapse
Affiliation(s)
- Ronald E Ellis
- Department of Molecular Biology, Rowan University SOM, B303 Science Center, 2 Medical Center Drive, Stratford, NJ 08084, United States.
| | - Gillian M Stanfield
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, United States
| |
Collapse
|
35
|
O'Connell ML, Cavallo WC, Firnberg M. The expression of CPEB proteins is sequentially regulated during zebrafish oogenesis and embryogenesis. Mol Reprod Dev 2014; 81:376-87. [DOI: 10.1002/mrd.22306] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Accepted: 01/25/2014] [Indexed: 12/25/2022]
Affiliation(s)
- Marcia L. O'Connell
- The Department of Biology; The College of New Jersey; Ewing New Jersey 08628
| | - William C. Cavallo
- The Department of Biology; The College of New Jersey; Ewing New Jersey 08628
| | - Maytal Firnberg
- The Department of Biology; The College of New Jersey; Ewing New Jersey 08628
| |
Collapse
|
36
|
Charlesworth A, Meijer HA, de Moor CH. Specificity factors in cytoplasmic polyadenylation. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 4:437-61. [PMID: 23776146 PMCID: PMC3736149 DOI: 10.1002/wrna.1171] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Revised: 04/08/2013] [Accepted: 04/09/2013] [Indexed: 12/12/2022]
Abstract
Poly(A) tail elongation after export of an messenger RNA (mRNA) to the cytoplasm is called cytoplasmic polyadenylation. It was first discovered in oocytes and embryos, where it has roles in meiosis and development. In recent years, however, has been implicated in many other processes, including synaptic plasticity and mitosis. This review aims to introduce cytoplasmic polyadenylation with an emphasis on the factors and elements mediating this process for different mRNAs and in different animal species. We will discuss the RNA sequence elements mediating cytoplasmic polyadenylation in the 3' untranslated regions of mRNAs, including the CPE, MBE, TCS, eCPE, and C-CPE. In addition to describing the role of general polyadenylation factors, we discuss the specific RNA binding protein families associated with cytoplasmic polyadenylation elements, including CPEB (CPEB1, CPEB2, CPEB3, and CPEB4), Pumilio (PUM2), Musashi (MSI1, MSI2), zygote arrest (ZAR2), ELAV like proteins (ELAVL1, HuR), poly(C) binding proteins (PCBP2, αCP2, hnRNP-E2), and Bicaudal C (BICC1). Some emerging themes in cytoplasmic polyadenylation will be highlighted. To facilitate understanding for those working in different organisms and fields, particularly those who are analyzing high throughput data, HUGO gene nomenclature for the human orthologs is used throughout. Where human orthologs have not been clearly identified, reference is made to protein families identified in man.
Collapse
Affiliation(s)
- Amanda Charlesworth
- Department of Integrative Biology, University of Colorado Denver, Denver, CO, USA
| | | | | |
Collapse
|
37
|
Zhou C, Zhang J, Ma J, Jiang A, Tang G, Mai M, Zhu L, Bai L, Li M, Li X. Gene expression profiling reveals distinct features of various porcine adipose tissues. Lipids Health Dis 2013; 12:75. [PMID: 23705929 PMCID: PMC3679871 DOI: 10.1186/1476-511x-12-75] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Accepted: 05/22/2013] [Indexed: 12/15/2022] Open
Abstract
Background The excessive accumulation of body fat is a major risk factor to develop a variety of metabolic diseases. To investigate the systematic association between the differences in gene expression profiling and adipose deposition, we used pig as a model, and measured the gene expression profiling of six variant adipose tissues in male and females from three pig breeds which display distinct fat level. Results We identified various differential expressed genes among breeds, tissues and between sexes, and further used a clustering method to identify sets of functionally co-expression genes linked to different obesity-related phenotypes. Our results reveal that the subcutaneous adipose tissues mainly modulate metabolic indicators, nonetheless, the visceral adipose tissues as well as the intermuscular adipose tissue were mainly associated with the impaired inflammatory and immune response. Conclusions The present study provided the evidence of gene expression profiling that the subcutaneous adipose tissues are mainly affected the metabolism process, whereas the visceral and intermuscular adipose tissues should been term as the metabolic risk factors of obesity.
Collapse
Affiliation(s)
- Chaowei Zhou
- Institute of Animal Genetics & Breeding, College of Animal Science & Technology, Sichuan Agricultural University, Ya'an, Sichuan 625000, China
| | | | | | | | | | | | | | | | | | | |
Collapse
|
38
|
Zanetti S, Puoti A. Sex Determination in the Caenorhabditis elegans Germline. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013; 757:41-69. [DOI: 10.1007/978-1-4614-4015-4_3] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
39
|
Hansen D, Schedl T. Stem cell proliferation versus meiotic fate decision in Caenorhabditis elegans. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013; 757:71-99. [PMID: 22872475 PMCID: PMC3786863 DOI: 10.1007/978-1-4614-4015-4_4] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The C. elegans germ line has emerged as an important model for -understanding how a stem cell population is maintained throughout the life of the animal while still producing the gametes necessary for propagation of the species. The stem cell population in the adult hermaphrodite is relatively large, with stem cells giving rise to daughters that appear intrinsically equivalent; however, some of the daughters retain the proliferative fate while others enter meiotic prophase. While machinery exists for cells to progress through the mitotic cell cycle and machinery exists for cells to progress through meiotic prophase, central to understanding germ line development is identifying the genes and regulatory processes that determine whether the mitotic cell cycle or meiotic prophase machinery will be utilized; in other words, the genes that regulate the switch of germ cells from the proliferative stem cell fate to the meiotic development fate. Whether a germ cell self-renews or enters meiotic prophase is largely determined by its proximity to the distal tip cell (DTC), which is the somatic niche cell that caps the distal end of the gonad. Germ cells close to the DTC have high levels of GLP-1 Notch signaling, which promotes the proliferative fate, while cells further from the DTC have high activity levels of the GLD-1 and GLD-2 redundant RNA regulatory pathways, as well as a third uncharacterized pathway, each of which direct cells to enter meiotic prophase. Other factors and pathways modulate this core genetic pathway, or work in parallel to it, presumably to ensure that a tight balance is maintained between proliferation and meiotic entry.
Collapse
Affiliation(s)
- Dave Hansen
- Department of Biological Sciences, 2500 University Drive, University of Calgary, Calgary, Alberta, Canada
| | - Tim Schedl
- Department of Genetics, Campus Box 8232, Washington University School of Medicine, 4566 Scott Ave, St Louis MO
| |
Collapse
|
40
|
Translational control in the Caenorhabditis elegans germ line. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013; 757:205-47. [PMID: 22872479 DOI: 10.1007/978-1-4614-4015-4_8] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Translational control is a prevalent form of gene expression regulation in the Caenorhabditis elegans germ line. Linking the amount of protein synthesis to mRNA quantity and translational accessibility in the cell cytoplasm provides unique advantages over DNA-based controls for developing germ cells. This mode of gene expression is especially exploited in germ cell fate decisions and during oogenesis, when the developing oocytes stockpile hundreds of different mRNAs required for early embryogenesis. Consequently, a dense web of RNA regulators, consisting of diverse RNA-binding proteins and RNA-modifying enzymes, control the translatability of entire mRNA expression programs. These RNA regulatory networks are tightly coupled to germ cell developmental progression and are themselves under translational control. The underlying molecular mechanisms and RNA codes embedded in the mRNA molecules are beginning to be understood. Hence, the C. elegans germ line offers fertile grounds for discovering post-transcriptional mRNA regulatory mechanisms and emerges as great model for a systems level understanding of translational control during development.
Collapse
|
41
|
Voronina E, Paix A, Seydoux G. The P granule component PGL-1 promotes the localization and silencing activity of the PUF protein FBF-2 in germline stem cells. Development 2012; 139:3732-40. [PMID: 22991439 DOI: 10.1242/dev.083980] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In the C. elegans germline, maintenance of undifferentiated stem cells depends on the PUF family RNA-binding proteins FBF-1 and FBF-2. FBF-1 and FBF-2 are 89% identical and are required redundantly to silence the expression of mRNAs that promote meiosis. Here we show that, despite their extensive sequence similarity, FBF-1 and FBF-2 have different effects on target mRNAs. FBF-1 promotes the degradation and/or transport of meiotic mRNAs out of the stem cell region, whereas FBF-2 prevents translation. FBF-2 activity depends on the P granule component PGL-1. PGL-1 is required to localize FBF-2 to perinuclear P granules and for efficient binding of FBF-2 to its mRNA targets. We conclude that multiple regulatory mechanisms converge on meiotic RNAs to ensure silencing in germline stem cells. Our findings also support the view that P granules facilitate mRNA silencing by providing an environment in which translational repressors can encounter their mRNA targets immediately upon exit from the nucleus.
Collapse
Affiliation(s)
- Ekaterina Voronina
- Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | | | | |
Collapse
|
42
|
Xu S, Hafer N, Agunwamba B, Schedl P. The CPEB protein Orb2 has multiple functions during spermatogenesis in Drosophila melanogaster. PLoS Genet 2012; 8:e1003079. [PMID: 23209437 PMCID: PMC3510050 DOI: 10.1371/journal.pgen.1003079] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Accepted: 09/27/2012] [Indexed: 12/02/2022] Open
Abstract
Cytoplasmic Polyadenylation Element Binding (CPEB) proteins are translational regulators that can either activate or repress translation depending on the target mRNA and the specific biological context. There are two CPEB subfamilies and most animals have one or more genes from each. Drosophila has a single CPEB gene, orb and orb2, from each subfamily. orb expression is only detected at high levels in the germline and has critical functions in oogenesis but not spermatogenesis. By contrast, orb2 is broadly expressed in the soma; and previous studies have revealed important functions in asymmetric cell division, viability, motor function, learning, and memory. Here we show that orb2 is also expressed in the adult male germline and that it has essential functions in programming the progression of spermatogenesis from meiosis through differentiation. Like the translational regulators boule (bol) and off-schedule (ofs), orb2 is required for meiosis and orb2 mutant spermatocytes undergo a prolonged arrest during the meiotic G2-M transition. However, orb2 differs from boule and off-schedule in that this arrest occurs at a later step in meiotic progression after the synthesis of the meiotic regulator twine. orb2 is also required for the orderly differentiation of the spermatids after meiosis is complete. The differentiation defects in orb2 mutants include abnormal elongation of the spermatid flagellar axonemes, a failure in individualization and improper post-meiotic gene expression. Amongst the orb2 differentiation targets are orb and two other mRNAs, which are transcribed post-meiotically and localized to the tip of the flagellar axonemes. Additionally, analysis of a partial loss of function orb2 mutant suggests that the orb2 differentiation phenotypes are independent of the earlier arrest in meiosis. Cytoplasmic Polyadenylation Element Binding (CPEB) proteins bind and recognize CPE sequences in the 3′ UTRs of target mRNAs and can activate and/or repress their translation depending on the mRNA species and the biological context. Drosophila has two CPEB family genes, orb and orb2. orb is expressed in the germline of both sexes and has critical functions at multiple steps during oogenesis; however, it plays only a limited role in spermatogenesis. Here we show that the second CPEB family gene orb2 has the opposite sex specificity in germline development. While it appears to be dispensable for oogenesis, orb2 has essential functions during spermatogenesis. It is required for programming the orderly and sequential progression of spermatogenesis from meiosis through differentiation. orb2 mutants fail to execute the meiotic G2-M transition and exhibit a range of defects in the process of sperm differentiation.
Collapse
Affiliation(s)
- Shuwa Xu
- Department of Biology, California Institute of Technology, Pasadena, California, United States of America
| | - Nathaniel Hafer
- UMass Center for Clinical and Translational Science, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Blessing Agunwamba
- Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Paul Schedl
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
- * E-mail:
| |
Collapse
|
43
|
Wu J, Campbell ZT, Menichelli E, Wickens M, Williamson JR. A protein.protein interaction platform involved in recruitment of GLD-3 to the FBF.fem-3 mRNA complex. J Mol Biol 2012; 425:738-54. [PMID: 23159559 DOI: 10.1016/j.jmb.2012.11.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Revised: 11/01/2012] [Accepted: 11/07/2012] [Indexed: 02/03/2023]
Abstract
The Pumilio and FBF (PUF) family of RNA-binding proteins interacts with protein partners to post-transcriptionally regulate mRNAs in eukaryotes. The interaction between PUF family member fem-3 binding factor (FBF) and germline development defective-3 (GLD-3) protein promotes spermatogenesis in Caenorhabditis elegans by increasing expression of the fem-3 mRNA. Defined here in these studies is the molecular basis for this critical interaction. A 10-amino-acid region within GLD-3 is required for FBF binding, while a 7-amino-acid loop in FBF between PUF repeats 7 and 8 is necessary for GLD-3 binding. These short sequences are conserved, as other FBF-binding proteins bear sequences similar to those in GLD-3 and other C. elegans PUF proteins contain sequences similar to those in FBF. The FBF-binding region of GLD-3 forms a ternary complex with FBF on the point mutation element (PME) in the fem-3 3' untranslated region, and formation of this GLD-3⋅FBF complex does not impact the RNA-binding activity of FBF. These data raise the possibility of alternative models involving the formation of a GLD-3⋅FBF⋅RNA complex in the regulation of germline mRNAs.
Collapse
Affiliation(s)
- Joann Wu
- Department of Molecular Biology, Department of Chemistry, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | | | | | | | | |
Collapse
|
44
|
Menichelli E, Wu J, Campbell ZT, Wickens M, Williamson JR. Biochemical characterization of the Caenorhabditis elegans FBF.CPB-1 translational regulation complex identifies conserved protein interaction hotspots. J Mol Biol 2012; 425:725-37. [PMID: 23159558 DOI: 10.1016/j.jmb.2012.11.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Revised: 11/01/2012] [Accepted: 11/07/2012] [Indexed: 10/27/2022]
Abstract
Caenorhabditis elegans CPB-1 (cytoplasmic polyadenylation element binding protein homolog-1) and FBF (fem-3 mRNA binding factor) are evolutionary conserved regulators of mRNA translation that belong to the CPEB (cytoplasmic polyadenylation element binding) and PUF (Pumilio and FBF) protein families, respectively. In hermaphrodite worms, CPB-1 and FBF control key steps during germline development, including stem cell maintenance and sex determination. While CPB-1 and FBF are known to interact, the molecular basis and function of the CPB-1⋅FBF complex are not known. The surface of CPB-1 that interacts with FBF was localized using in vivo and in vitro methods to a 10-residue region at the N-terminus of the protein and these residues are present in the FBF-binding protein GLD-3 (germline development defective-3). PUF proteins are characterized by the presence of eight α-helical repeats (PUF repeats) arranged side by side in an elongated structure. Critical residues for CPB-1 binding are found in the extended loop that connects PUF repeats 7 and 8. The same FBF residues also mediate binding to GLD-3, indicating a conserved binding mode between different protein partners. CPB-1 binding was competitive with GLD-3, suggestive of mutual exclusivity in vivo. RNA binding measurements demonstrated that CPB-1 alters the affinity of FBF for specific RNA sequences, implying a functional model where the coregulatory protein CPB-1 modulates FBF target selection.
Collapse
Affiliation(s)
- Elena Menichelli
- Department of Molecular Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | | | | | | | | |
Collapse
|
45
|
Peñagaricano F, Weigel KA, Khatib H. Genome-wide association study identifies candidate markers for bull fertility in Holstein dairy cattle. Anim Genet 2012; 43 Suppl 1:65-71. [PMID: 22742504 DOI: 10.1111/j.1365-2052.2012.02350.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The decline in the reproductive efficiency of dairy cattle has become a challenging problem worldwide. Female fertility is now taken into account in breeding goals while generally less attention is given to male fertility. The objective of this study was to perform a genome-wide association study in Holstein bulls to identify genetic variants significantly related to sire conception rate (SCR), a new phenotypic evaluation of bull fertility. The analysis included 1755 sires with SCR data and 38,650 single nucleotide polymorphisms (SNPs) spanning the entire bovine genome. Associations between SNPs and SCR were analyzed using a mixed linear model that included a random polygenic effect and SNP genotype either as a linear covariate or as a categorical variable. A multiple testing correction approach was used to account for the correlation between SNPs because of linkage disequilibrium. After genome-wide correction, eight SNPs showed significant association with SCR. Some of these SNPs are located close to or in the middle of genes with functions related to male fertility, such as the sperm acrosome reaction, chromatin remodeling during the spermatogenesis, and the meiotic process during male germ cell maturation. Some SNPs showed marked dominance effects, which provide more evidence for the relevance of non-additive effects in traits closely related to fitness such as fertility. The results could contribute to the identification of genes and pathways associated with male fertility in dairy cattle.
Collapse
Affiliation(s)
- F Peñagaricano
- Department of Animal Sciences, University of Wisconsin-Madison, 1675 Observatory Drive, Madison, WI 53706, USA
| | | | | |
Collapse
|
46
|
Fernández-Miranda G, Méndez R. The CPEB-family of proteins, translational control in senescence and cancer. Ageing Res Rev 2012; 11:460-72. [PMID: 22542725 DOI: 10.1016/j.arr.2012.03.004] [Citation(s) in RCA: 115] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2012] [Revised: 03/14/2012] [Accepted: 03/27/2012] [Indexed: 12/31/2022]
Abstract
Cytoplasmic elongation of the poly(A) tail was originally identified as a mechanism to activate maternal mRNAs, stored as silent transcripts with short poly(A) tails, during meiotic progression. A family of RNA-binding proteins named CPEBs, which recruit the translational repression or cytoplasmic polyadenylation machineries to their target mRNAs, directly mediates cytoplasmic polyadenylation. Recent years have witnessed an explosion of studies showing that CPEBs are not only expressed in a variety of somatic tissues, but have essential functions controlling gene expression in time and space in the adult organism. These "new" functions of the CPEBs include regulating the balance between senescence and proliferation and its pathological manifestation, tumor development. In this review, we summarize current knowledge on the functions of the CPEB-family of proteins in the regulation of cell proliferation, their target mRNAs and the mechanism controlling their activities.
Collapse
|
47
|
Cha DS, Datla US, Hollis SE, Kimble J, Lee MH. The Ras-ERK MAPK regulatory network controls dedifferentiation in Caenorhabditis elegans germline. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2012; 1823:1847-55. [PMID: 22820175 DOI: 10.1016/j.bbamcr.2012.07.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Revised: 07/10/2012] [Accepted: 07/11/2012] [Indexed: 11/19/2022]
Abstract
How a committed cell can be reverted to an undifferentiated state is a central question in stem cell biology. This process, called dedifferentiation, is likely to be important for replacing stem cells as they age or get damaged. Tremendous progress has been made in understanding this fundamental process, but its mechanisms are poorly understood. Here we demonstrate that the aberrant activation of Ras-ERK MAPK signaling promotes cellular dedifferentiation in the Caenorhabditis elegans germline. To activate signaling, we removed two negative regulators, the PUF-8 RNA-binding protein and LIP-1 dual specificity phosphatase. The removal of both of these two regulators caused secondary spermatocytes to dedifferentiate and begin mitotic divisions. Interestingly, reduction of Ras-ERK MAPK signaling, either by mutation or chemical inhibition, blocked the initiation of dedifferentiation. By RNAi screening, we identified RSKN-1/P90(RSK) as a downstream effector of MPK-1/ERK that is critical for dedifferentiation: rskn-1 RNAi suppressed spermatocyte dedifferentiation and instead induced meiotic divisions. These regulators are broadly conserved, suggesting that similar molecular circuitry may control cellular dedifferentiation in other organisms, including humans.
Collapse
Affiliation(s)
- Dong Seok Cha
- Division of Hematology/Oncology, Department of Medicine, Brody School of Medicine, East Carolina University, Greenville, NC 27834, USA
| | | | | | | | | |
Collapse
|
48
|
Abstract
The sperm/oocyte decision in the hermaphrodite germline of Caenorhabditis elegans provides a powerful model for the characterization of stem cell fate specification and differentiation. The germline sex determination program that governs gamete fate has been well studied, but direct mediators of cell-type-specific transcription are largely unknown. We report the identification of spe-44 as a critical regulator of sperm gene expression. Deletion of spe-44 causes sperm-specific defects in cytokinesis, cell cycle progression, and organelle assembly resulting in sterility. Expression of spe-44 correlates precisely with spermatogenesis and is regulated by the germline sex determination pathway. spe-44 is required for the appropriate expression of several hundred sperm-enriched genes. The SPE-44 protein is restricted to the sperm-producing germline, where it localizes to the autosomes (which contain sperm genes) but is excluded from the transcriptionally silent X chromosome (which does not). The orthologous gene in other Caenorhabditis species is similarly expressed in a sex-biased manner, and the protein likewise exhibits autosome-specific localization in developing sperm, strongly suggestive of an evolutionarily conserved role in sperm gene expression. Our analysis represents the first identification of a transcriptional regulator whose primary function is the control of gamete-type-specific transcription in this system. Stem cells give rise to the variety of specialized cell types within an organism. The decision to adopt a particular cell fate, a process known as specification or determination, requires the coordinated expression of all of the genes needed for that specialized cell to develop and function properly. Understanding the mechanisms that govern these patterns of gene expression is critical to our understanding of stem cell fate specification. We study this process in a nematode species that makes both sperm and eggs from the same stem cell population. We have identified a gene, named spe-44, that is required for the proper expression of sperm genes (but not egg genes). Mutation in spe-44 produces sterile sperm with developmental defects. spe-44 is controlled by factors that govern the sperm/egg decision, and its function in controlling sperm gene expression appears to be conserved in other nematode species.
Collapse
|
49
|
Campbell ZT, Menichelli E, Friend K, Wu J, Kimble J, Williamson JR, Wickens M. Identification of a conserved interface between PUF and CPEB proteins. J Biol Chem 2012; 287:18854-62. [PMID: 22496444 DOI: 10.1074/jbc.m112.352815] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Members of the PUF (Pumilio and FBF) and CPEB (cytoplasmic polyadenylation element-binding) protein families collaborate to regulate mRNA expression throughout eukaryotes. Here, we focus on the physical interactions between members of these two families, concentrating on Caenorhabditis elegans FBF-2 and CPB-1. To localize the site of interaction on FBF-2, we identified conserved amino acids within C. elegans PUF proteins. Deletion of an extended loop containing several conserved residues abolished binding to CPB-1. We analyzed alanine substitutions at 13 individual amino acids in FBF-2, each identified via its conservation. Multiple single point mutations disrupted binding to CPB-1 but not to RNA. Position Tyr-479 was particularly critical as multiple substitutions to other amino acids at this position did not restore binding. The complex of FBF-2 and CPB-1 repressed translation of an mRNA containing an FBF binding element. Repression required both proteins and was disrupted by FBF-2 alleles that failed to bind CPB-1 or RNA. The equivalent loop in human PUM2 is required for binding to human CPEB3 in vitro, although the primary sequences of the human and C. elegans PUF proteins have diverged in that region. Our findings define a key region in PUF/CPEB interactions and imply a conserved platform through which PUF proteins interact with their protein partners.
Collapse
Affiliation(s)
- Zachary T Campbell
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
| | | | | | | | | | | | | |
Collapse
|
50
|
Thomas CG, Woodruff GC, Haag ES. Causes and consequences of the evolution of reproductive mode in Caenorhabditis nematodes. Trends Genet 2012; 28:213-20. [PMID: 22480920 DOI: 10.1016/j.tig.2012.02.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2011] [Revised: 02/24/2012] [Accepted: 02/27/2012] [Indexed: 12/12/2022]
Abstract
Reproduction is directly connected to the suite of developmental and physiological mechanisms that enable it, but how it occurs also has consequences for the genetics, ecology and longer term evolutionary potential of a lineage. In the nematode Caenorhabditis elegans, anatomically female XX worms can self-fertilize their eggs. This ability evolved recently and in multiple Caenorhabditis lineages from male-female ancestors, providing a model for examining both the developmental causes and longer term consequences of a novel, convergently evolved reproductive mode. Here, we review recent work that implicates translation control in the evolution of XX spermatogenesis, with different selfing lineages possessing both reproducible and idiosyncratic features. We also discuss the consequences of selfing, which leads to a rapid loss of variation and relaxation of natural and sexual selection on mating-related traits, and may ultimately put selfing lineages at a higher risk of extinction.
Collapse
Affiliation(s)
- Cristel G Thomas
- Department of Biology, University of Maryland, College Park, MD 20742, USA
| | | | | |
Collapse
|