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Li YH, Liu TB. Zinc Finger Proteins in the Human Fungal Pathogen Cryptococcus neoformans. Int J Mol Sci 2020; 21:ijms21041361. [PMID: 32085473 PMCID: PMC7072944 DOI: 10.3390/ijms21041361] [Citation(s) in RCA: 8] [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: 12/01/2019] [Revised: 02/13/2020] [Accepted: 02/13/2020] [Indexed: 12/17/2022] Open
Abstract
Zinc is one of the essential trace elements in eukaryotes and it is a critical structural component of a large number of proteins. Zinc finger proteins (ZNFs) are zinc-finger domain-containing proteins stabilized by bound zinc ions and they form the most abundant proteins, serving extraordinarily diverse biological functions. In recent years, many ZNFs have been identified and characterized in the human fungal pathogen Cryptococcus neoformans, a fungal pathogen causing fatal meningitis mainly in immunocompromised individuals. It has been shown that ZNFs play important roles in the morphological development, differentiation, and virulence of C. neoformans. In this review, we, first, briefly introduce the ZNFs and their classification. Then, we explain the identification and classification of the ZNFs in C. neoformans. Next, we focus on the biological role of the ZNFs functionally characterized so far in the sexual reproduction, virulence factor production, ion homeostasis, pathogenesis, and stress resistance in C. neoformans. We also discuss the perspectives on future function studies of ZNFs in C. neoformans.
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Affiliation(s)
- Yuan-Hong Li
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China
- Chongqing Key Laboratory of Microsporidia Infection and Prevention, Southwest University, Chongqing 400715, China
| | - Tong-Bao Liu
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China
- Chongqing Key Laboratory of Microsporidia Infection and Prevention, Southwest University, Chongqing 400715, China
- Correspondence: ; Tel.: +86-23-6825-1088
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Irie M, Koga A, Kaneko-Ishino T, Ishino F. An LTR Retrotransposon-Derived Gene Displays Lineage-Specific Structural and Putative Species-Specific Functional Variations in Eutherians. Front Chem 2016; 4:26. [PMID: 27446905 PMCID: PMC4917564 DOI: 10.3389/fchem.2016.00026] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2016] [Accepted: 06/01/2016] [Indexed: 11/28/2022] Open
Abstract
Amongst the 11 eutherian-specific genes acquired from a sushi-ichi retrotransposon is the CCHC type zinc-finger protein-encoding gene SIRH11/ZCCHC16. Its contribution to eutherian brain evolution is implied because of its involvement in cognitive function in mice, possibly via the noradrenergic system. Although, the possibility that Sirh11/Zcchc16 functions as a non-coding RNA still remains, dN/dS ratios in pairwise comparisons between its orthologs have provided supportive evidence that it acts as a protein. It became a pseudogene in armadillos (Cingulata) and sloths (Pilosa), the only two extant orders of xenarthra, which prompted us to examine the lineage-specific variations of SIRH11/ZCCHC16 in eutherians. We examined the predicted SIRH11/ZCCHC16 open reading frame (ORF) in 95 eutherian species based on the genomic DNA information in GenBank. A large variation in the SIRH11/ZCCHC16 ORF was detected in several lineages. These include a lack of a CCHC RNA-binding domain in its C-terminus, observed in gibbons (Hylobatidae: Primates) and megabats (Megachiroptera: Chiroptera). A lack of the N-terminal half, on the other hand, was observed in New World monkeys (Platyrrhini: Primates) and species belonging to New World and African Hystricognaths (Caviomorpha and Bathyergidae: Rodents) along with Cetacea and Ruminantia (Cetartiodactyla). Among the hominoids, interestingly, three out of four genera of gibbons have lost normal SIRH11/ZCCHC16 function by deletion or the lack of the CCHC RNA-binding domain. Our extensive dN/dS analysis suggests that such truncated SIRH11/ZCCHC16 ORFs are functionally diversified even within lineages. Combined, our results show that SIRH11/ZCCHC16 may contribute to the diversification of eutherians by lineage-specific structural changes after its domestication in the common eutherian ancestor, followed by putative species-specific functional changes that enhanced fitness and occurred as a consequence of complex natural selection events.
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Affiliation(s)
- Masahito Irie
- Department of Nursing, School of Health Sciences, Tokai UniversityIsehara, Japan; Department of Epigenetics, Medical Research Institute, Tokyo Medical and Dental UniversityTokyo, Japan
| | - Akihiko Koga
- Department of Cellular and Molecular Biology, Primate Research Institute, Kyoto University Inuyama, Japan
| | - Tomoko Kaneko-Ishino
- Department of Nursing, School of Health Sciences, Tokai University Isehara, Japan
| | - Fumitoshi Ishino
- Department of Epigenetics, Medical Research Institute, Tokyo Medical and Dental University Tokyo, Japan
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Iwasaki S, Suzuki S, Pelekanos M, Clark H, Ono R, Shaw G, Renfree MB, Kaneko-Ishino T, Ishino F. Identification of a novel PNMA-MS1 gene in marsupials suggests the LTR retrotransposon-derived PNMA genes evolved differently in marsupials and eutherians. DNA Res 2013; 20:425-36. [PMID: 23704700 PMCID: PMC3789554 DOI: 10.1093/dnares/dst020] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Two major gene families derived from Ty3/Gypsy long terminal repeat (LTR) retrotransposons were recently identified in mammals. The sushi-ichi retrotransposon homologue (SIRH) family comprises 12 genes: 11 in eutherians including Peg10 and Peg11/Rtl1 that have essential roles in the eutherian placenta and 1 that is marsupial specific. Fifteen and 12 genes were reported in the second gene family, para-neoplastic antigen MA (PNMA), in humans and mice, respectively, although their biological functions and evolutionary history remain largely unknown. Here, we identified two novel candidate PNMA genes, PNMA-MS1 and -MS2 in marsupials. Like all eutherian-specific PNMA genes, they exhibit the highest homology to a Gypsy12_DR (DR, Danio rerio) Gag protein. PNMA-MS1 is conserved in both Australian and South American marsupial species, the tammar wallaby and grey short-tailed opossum. However, no PNMA-MS1 orthologue was found in eutherians, monotremes or non-mammalian vertebrates. PNMA-MS1 was expressed in the ovary, mammary gland and brain during development and growth in the tammar, suggesting that PNMA-MS1 may have acquired a marsupial-specific function. However, PNMA-MS2 seems to be a pseudogene. The absence of marsupial orthologues of eutherian PNMA genes suggests that the retrotransposition events of the Gypsy12_DR-related retrotransposons that gave rise to the PNMA family occurred after the divergence of marsupials and eutherians.
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Affiliation(s)
- Sawa Iwasaki
- 1Department of Epigenetics, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
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Barraud P, Schubert M, Allain FHT. A strong 13C chemical shift signature provides the coordination mode of histidines in zinc-binding proteins. JOURNAL OF BIOMOLECULAR NMR 2012; 53:93-101. [PMID: 22528293 DOI: 10.1007/s10858-012-9625-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2012] [Accepted: 03/30/2012] [Indexed: 05/31/2023]
Abstract
Zinc is the second most abundant metal ion incorporated in proteins, and is in many cases a crucial component of protein three-dimensional structures. Zinc ions are frequently coordinated by cysteine and histidine residues. Whereas cysteines bind to zinc via their unique S(γ) atom, histidines can coordinate zinc with two different coordination modes, either N(δ1) or N(ε2) is coordinating the zinc ion. The determination of this coordination mode is crucial for the accurate structure determination of a histidine-containing zinc-binding site by NMR. NMR chemical shifts contain a vast amount of information on local electronic and structural environments and surprisingly their utilization for the determination of the coordination mode of zinc-ligated histidines has been limited so far to (15)N nuclei. In the present report, we observed that the (13)C chemical shifts of aromatic carbons in zinc-ligated histidines represent a reliable signature of their coordination mode. Using a statistical analysis of (13)C chemical shifts, we show that (13)C(δ2) chemical shift is sensitive to the histidine coordination mode and that the chemical shift difference δ{(13)C(ε1)} - δ{(13)C(δ2)} provides a reference-independent marker of this coordination mode. The present approach allows the direct determination of the coordination mode of zinc-ligated histidines even with non-isotopically enriched protein samples and without any prior structural information.
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Affiliation(s)
- Pierre Barraud
- Institute of Molecular Biology and Biophysics, ETH Zurich, Schafmattstrasse 20, 8093 Zurich, Switzerland.
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Guerrerio AL, Berg JM. Design of single-stranded nucleic acid binding peptides based on nucleocapsid CCHC-box zinc-binding domains. J Am Chem Soc 2010; 132:9638-43. [PMID: 20586464 DOI: 10.1021/ja910942v] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The solution structures of nucleocapsid (NC)-like CCHC zinc-binding domains bound to nucleic acid targets have revealed that these domains bind guanosine residues within single-stranded nucleic acids. Here, we have performed initial studies examining the potential use of NC-like CCHC zinc-binding domains as modules to construct single-stranded nucleic acid binding peptides. The affinity for guanosine-containing single-stranded deoxyribooligonucleotides increases with the number of CCHC domains in the peptide. The length of the linker between domains affects the spacing of guanosine residues in oligonucleotides that are preferentially bound. These studies provide a proof of principle that NC-like CCHC zinc-binding domains can be utilized as a basis for designing peptides that bind specific single-stranded nucleic acid sequences.
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Affiliation(s)
- Anthony L Guerrerio
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA
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Hashimoto H, Hara K, Hishiki A, Kawaguchi S, Shichijo N, Nakamura K, Unzai S, Tamaru Y, Shimizu T, Sato M. Crystal structure of zinc-finger domain of Nanos and its functional implications. EMBO Rep 2010; 11:848-53. [PMID: 20948543 DOI: 10.1038/embor.2010.155] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2010] [Revised: 08/29/2010] [Accepted: 09/08/2010] [Indexed: 11/09/2022] Open
Abstract
Nanos is an RNA-binding protein that is involved in the development and maintenance of germ cells. In combination with Pumilio, Nanos binds to the 3' untranslated region of a messenger RNA and represses its translation. Nanos has two conserved Cys-Cys-His-Cys zinc-finger motifs that are indispensable for its function. In this study, we have determined the crystal structure of the zinc-finger domain of zebrafish Nanos, for the first time revealing that Nanos adopts a novel zinc-finger structure. In addition, Nanos has a conserved basic surface that is directly involved in RNA binding. Our results provide the structural basis for further studies to clarify Nanos function.
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Affiliation(s)
- Hiroshi Hashimoto
- Graduate School of Nanobioscience, Yokohama City University, Tsurumi-ku, Yokohama, Kanagawa, Japan.
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Matsui T, Tanaka T, Endoh H, Sato K, Tanaka H, Miyauchi E, Kawashima Y, Nagai-Makabe M, Komatsu H, Kohno T, Maeda T, Kodera Y. The RNA Recognition Mechanism of Human Immunodeficiency Virus (HIV) Type 2 NCp8 Is Different from That of HIV-1 NCp7. Biochemistry 2009; 48:4314-23. [DOI: 10.1021/bi802364b] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Takashi Matsui
- Department of Physics, School of Science, Kitasato University, Sagamihara, Kanagawa 228-8555, Japan
- Mitsubishi Kagaku Institute of Life Sciences (MITILS), Machida, Tokyo 194-8511, Japan
| | - Takeshi Tanaka
- Mitsubishi Kagaku Institute of Life Sciences (MITILS), Machida, Tokyo 194-8511, Japan
| | - Hiroshi Endoh
- Department of Physics, School of Science, Kitasato University, Sagamihara, Kanagawa 228-8555, Japan
| | - Kazuki Sato
- Department of Environmental Science, School of Science, Fukuoka Women’s University, Higashi-ku, Fukuoka 813-8529, Japan
| | - Hidekazu Tanaka
- Department of Physics, School of Science, Kitasato University, Sagamihara, Kanagawa 228-8555, Japan
| | - Emi Miyauchi
- Department of Physics, School of Science, Kitasato University, Sagamihara, Kanagawa 228-8555, Japan
| | - Yusuke Kawashima
- Department of Physics, School of Science, Kitasato University, Sagamihara, Kanagawa 228-8555, Japan
| | - Misa Nagai-Makabe
- Department of Physics, School of Science, Kitasato University, Sagamihara, Kanagawa 228-8555, Japan
| | - Hiroyoshi Komatsu
- Department of Clinical Laboratory Medicine, Faculty of Health Science Technology, Bunkyo Gakuin University, Bunkyo-ku, Tokyo 113-0023, Japan
| | - Toshiyuki Kohno
- Mitsubishi Kagaku Institute of Life Sciences (MITILS), Machida, Tokyo 194-8511, Japan
| | - Tadakazu Maeda
- Department of Physics, School of Science, Kitasato University, Sagamihara, Kanagawa 228-8555, Japan
| | - Yoshio Kodera
- Department of Physics, School of Science, Kitasato University, Sagamihara, Kanagawa 228-8555, Japan
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Matsui T, Kodera Y, Miyauchi E, Tanaka H, Endoh H, Komatsu H, Tanaka T, Kohno T, Maeda T. Structural role of the secondary active domain of HIV-2 NCp8 in multi-functionality. Biochem Biophys Res Commun 2007; 358:673-8. [PMID: 17511966 DOI: 10.1016/j.bbrc.2007.04.141] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2007] [Accepted: 04/16/2007] [Indexed: 10/23/2022]
Abstract
Nucleocapsid protein of HIV, containing two CCHC-type zinc fingers connected by a linker, is a multi-functional protein involved in many critical steps of the HIV life cycle. Several in vitro investigations demonstrated that the reactivities of the first zinc finger flanked by the linker of HIV-1 NCp7 and HIV-2 NCp8 were essential for binding to viral RNA, however, that of the second zinc finger flanked by the linker of NCp7 was very weak and non-specific, whereas the part of NCp8 called NCp8-f2, interacted strongly and specifically with viral RNA. In this study, the three-dimensional structure of NCp8-f2 was determined for the first time. Furthermore, we established that NCp8-f2 specifically binds to the stem-loop SD in viral RNA, and that the hydrophobic cleft and the basic residues close to the cleft were essential for specific binding to SD. We discuss the functional significance of NCp8-f2 for NCp8 being a multi-functional protein.
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Affiliation(s)
- Takashi Matsui
- Department of Physics, School of Science, Kitasato University, 1-15-1 Kitasato, Sagamihara, Kanagawa 228-8555, Japan
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