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Zhang Y, An D, Li C, Zhao Z, Wang W. The complete chloroplast genome of greater duckweed (Spirodela polyrhiza 7498) using PacBio long reads: insights into the chloroplast evolution and transcription regulation. BMC Genomics 2020; 21:76. [PMID: 31992185 PMCID: PMC6986005 DOI: 10.1186/s12864-020-6499-y] [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: 11/07/2019] [Accepted: 01/16/2020] [Indexed: 12/16/2022] Open
Abstract
Background Duckweeds (Lemnaceae) are aquatic plants distributed all over the world. The chloroplast genome, as an efficient solar-powered reactor, is an invaluable resource to study biodiversity and to carry foreign genes. The chloroplast genome sequencing has become routine and less expensive with the delivery of high-throughput sequencing technologies, allowing us to deeply investigate genomics and transcriptomics of duckweed organelles. Results Here, the complete chloroplast genome of Spirodela polyrhiza 7498 (SpV2) is assembled by PacBio sequencing. The length of 168,956 bp circular genome is composed of a pair of inverted repeats of 31,844 bp, a large single copy of 91,210 bp and a small single copy of 14,058 bp. Compared to the previous version (SpV1) assembled from short reads, the integrity and quality of SpV2 are improved, especially with the retrieval of two repeated fragments in ycf2 gene. There are a number of 107 unique genes, including 78 protein-coding genes, 25 tRNA genes and 4 rRNA genes. With the evidence of full-length cDNAs generated from PacBio isoform sequencing, seven genes (ycf3, clpP, atpF, rpoC1, rpl2, rps12 and ndhA) are detected to contain type-II introns. The ndhA intron has 50% more sequence divergence than the species-barcoding marker of atpF-atpH, showing the potential power to discriminate close species. A number of 37 RNA editing sites are recognized to have cytosine (C) to uracil (U) substitutions, eight of which are newly defined including six from the intergenic regions and two from the coding sequences of rpoC2 and ndhA genes. In addition, nine operon classes are identified using transcriptomic data. It is found that the operons contain multiple subunit genes encoding the same functional complexes comprising of ATP synthase, photosynthesis system, ribosomal proteins, et.al., which could be simultaneously transcribed and coordinately translated in response to the cell stimuli. Conclusions The understanding of the chloroplast genomics and the transcriptomics of S.polyrhiza would greatly facilitate the study of phylogenetic evolution and the application of genetically engineering duckweeds.
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Affiliation(s)
- Yating Zhang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Dong An
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Changsheng Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology & Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Zhixuan Zhao
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Wenqin Wang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China.
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2
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Li JZ, Chen X, Gong XL, Hu HY, Shi D, Lu YM, Qiu L, Lu F, Hu ZL, Zhang JP. Identification of a functional nuclear localization signal mediating nuclear import of the zinc finger transcription factor ZNF24. PLoS One 2013; 8:e79910. [PMID: 24224020 PMCID: PMC3815127 DOI: 10.1371/journal.pone.0079910] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Accepted: 09/26/2013] [Indexed: 02/05/2023] Open
Abstract
ZNF24 is a member of the SCAN domain family of Krüppel-like zinc finger (ZF) transcription factors, which plays a critical role in cell proliferation and differentiation. However, how ZNF24 enters the nucleus in order to exert its function remains unclear since its nuclear localization signal(s) (NLS) has not been identified. Here, we generated a series of GFP-tagged deletion and point mutants and assessed their subcellular localization. Our results delimit the NLS to ZF1-2. Deletion of ZF1-2 caused cytoplasmic accumulation of ZNF24. Fusion of the ZF1-2 to green fluorescent protein (GFP) targeted GFP to the nucleus, demonstrating that the ZF1-2 is both necessary and sufficient for nuclear localization. ZNF24 containing histidine to leucine mutations that disrupt the structure of ZF1 or/and ZF2 retains appropriate nuclear localization, indicating that neither the tertiary structure of the zinc fingers nor specific DNA binding are necessary for nuclear localization. K286A and R290A mutation led to partial cytoplasmic accumulation. Co-immunoprecipitation demonstrated that ZNF24 interacted with importin-β and this interaction required the ZF motifs. The β-Catenin (CTNNB1) luciferase assays showed that the ZNF24 mutants defective in nuclear localization could not promote CTNNB1promoter activation as the wild-type ZNF24 did. Taken together, these results suggest that consecutive ZF1-2 is critical for the regulation of ZNF24 nuclear localization and its transactivation function.
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Affiliation(s)
- Jian-Zhong Li
- Department of Biochemical Pharmacy, Second Military Medical University, Shanghai, China
- * E-mail: (JZL); (JPZ)
| | - Xia Chen
- Cancer Institute, Second Military Medical University, Shanghai, China
| | - Xue-Lian Gong
- Department of Biochemical Pharmacy, Second Military Medical University, Shanghai, China
- Department of Health Toxicology, Second Military Medical University, Shanghai, China
| | - Hong-Yuan Hu
- Department of Biochemical Pharmacy, Second Military Medical University, Shanghai, China
| | - Duo Shi
- Department of Biochemical Pharmacy, Second Military Medical University, Shanghai, China
| | - Yi-Ming Lu
- Department of Biochemical Pharmacy, Second Military Medical University, Shanghai, China
| | - Lei Qiu
- Department of Biochemical Pharmacy, Second Military Medical University, Shanghai, China
| | - Fa Lu
- Department of Biochemical Pharmacy, Second Military Medical University, Shanghai, China
| | - Zhen-Lin Hu
- Department of Biochemical Pharmacy, Second Military Medical University, Shanghai, China
| | - Jun-Ping Zhang
- Department of Biochemical Pharmacy, Second Military Medical University, Shanghai, China
- * E-mail: (JZL); (JPZ)
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3
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Davies C, Ramakrishnan V, White SW. Structural evidence for specific S8-RNA and S8-protein interactions within the 30S ribosomal subunit: ribosomal protein S8 from Bacillus stearothermophilus at 1.9 A resolution. Structure 1996; 4:1093-104. [PMID: 8805594 DOI: 10.1016/s0969-2126(96)00115-3] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
BACKGROUND Prokaryotic ribosomal protein S8 is an important RNA-binding protein that occupies a central position within the small ribosomal subunit. It interacts extensively with 16S rRNA and is crucial for the correct folding of the central domain of the rRNA. S8 also controls the synthesis of several ribosomal proteins by binding to mRNA. It binds specifically to very similar sites in the two RNA molecules. RESULTS S8 is divided into two tightly associated domains and contains three regions that are proposed to interact with other ribosomal components: two potential RNA-binding sites, and a hydrophobic patch that may interact with a complementary hydrophobic region of S5. The N-terminal domain fold is found in several proteins including two that bind double-stranded DNA. CONCLUSIONS These multiple RNA-binding sites are consistent with the role of S8 in organizing the central domain and agree with the latest models of the 16S RNA which show that the S8 location coincides with a region of complicated nucleic-acid structure. The presence in a wide variety of proteins of a region homologous to the N-terminal domain supports the idea that ribosomal proteins must represent some of the earliest protein molecules.
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Affiliation(s)
- C Davies
- Department of Microbiology, Duke University Medical Center, Durham, NC 27710, USA
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4
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Baum M, Schön A. Localization and expression of the closely linked cyanelle genes for RNase P RNA and two transfer RNAs. FEBS Lett 1996; 382:60-4. [PMID: 8612765 DOI: 10.1016/0014-5793(96)00148-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The genomic region encoding the RNA subunit of the cyanelle RNase P has been characterized. rnpB, which has no homologue in chloroplasts, is flanked by two tRNA genes on the complementary DNA strand. Transcriptional control elements of all three genes have been experimentally determined. Comparison of the sequenced region with the corresponding loci of chloroplast genomes from vascular plants suggests that major inversions may have led to a possible loss or severe truncation of the RNase P RNA coding region during the course of plastid evolution.
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MESH Headings
- Base Sequence
- Cloning, Molecular
- Endoribonucleases/genetics
- Eukaryota/enzymology
- Eukaryota/genetics
- Gene Expression/physiology
- Molecular Sequence Data
- Nucleic Acid Conformation
- Plastids/enzymology
- Plastids/genetics
- Promoter Regions, Genetic/genetics
- RNA, Catalytic/genetics
- RNA, Transfer, Arg/chemistry
- RNA, Transfer, Arg/genetics
- RNA, Transfer, His/chemistry
- RNA, Transfer, His/genetics
- Ribonuclease P
- Sequence Analysis, DNA
- Transcription, Genetic/genetics
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Affiliation(s)
- M Baum
- Institut für Biochemie, Bayerische Julius-Maximilans-Universität, Würzburg, Germany
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5
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Pan C, Mason TL. Identification of the yeast nuclear gene for the mitochondrial homologue of bacterial ribosomal protein L16. Nucleic Acids Res 1995; 23:3673-7. [PMID: 7478995 PMCID: PMC307264 DOI: 10.1093/nar/23.18.3673] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
An open reading frame encoding a member of the L16 family of ribosomal proteins is adjacent to the URA7 gene on the left arm of chromosome II in Saccharomyces cerevisiae. The predicted L16-like polypeptide is basic (pl 11.12), contains 232 amino acids (26.52 kDa) and has 36% amino acid sequence identity to E. coli L16. Immunoblot analysis with polyclonal antibodies to the L16-like polypeptide showed specific cross-reaction with a 22,000 Mr mitochondrial polypeptide that co-sediments with the large subunit of the mitochondrial ribosome in sucrose density gradients. The levels of the L16 mRNA and protein varied in response to carbon source. In [rho degree] cells lacking mitochondrial rRNA, the L16 mRNA accumulated at normal levels, but the protein was barely detectable, indicating RNA-dependent accumulation of the L16 protein. Gene disruption experiments demonstrated that the yeast mitochondrial L16 is an essential ribosomal protein in vivo.
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Affiliation(s)
- C Pan
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst 01003, USA
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6
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Siebel CW, Admon A, Rio DC. Soma-specific expression and cloning of PSI, a negative regulator of P element pre-mRNA splicing. Genes Dev 1995; 9:269-83. [PMID: 7867926 DOI: 10.1101/gad.9.3.269] [Citation(s) in RCA: 102] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
PSI is an RNA-binding protein involved in repressing splicing of the P element third intron in Drosophila somatic cell extracts. PSI produced in bacteria restores splicing inhibition to an extract relieved of inhibitory activity, indicating that PSI plays a direct role in somatic inhibition. Sequence analysis of cDNAs encoding PSI reveals three KH RNA-binding domains, a conserved motif also found in the yeast splicing regulator MER1. Notably, PSI is expressed highly in somatic embryonic nuclei but is undetectable in germ-line cells. In contrast, hrp48, another protein implicated in somatic inhibition, is found in the nucleus and cytoplasm of both tissues. The splicing inhibitory properties and soma-specific expression of PSI may be sufficient to explain the germ-line-specific transposition of P elements.
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Affiliation(s)
- C W Siebel
- Department of Molecular and Cell Biology, University of California at Berkeley 94720
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7
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Sanangelantoni AM, Bocchetta M, Cammarano P, Tiboni O. Phylogenetic depth of S10 and spc operons: cloning and sequencing of a ribosomal protein gene cluster from the extremely thermophilic bacterium Thermotoga maritima. J Bacteriol 1994; 176:7703-10. [PMID: 8002596 PMCID: PMC197229 DOI: 10.1128/jb.176.24.7703-7710.1994] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
A segment of Thermotoga maritima DNA spanning 6,613 bp downstream from the gene tuf for elongation factor Tu was sequenced by use of a chromosome walking strategy. The sequenced region comprised a string of 14 tightly linked open reading frames (ORFs) starting 50 bp downstream from tuf. The first 11 ORFs were identified as homologs of ribosomal protein genes rps10, rpl3, rpl4, rpl23, rpl2, rps19, rpl22, rps3, rpl16, rpl29, and rps17 (which in Escherichia coli constitute the S10 operon, in that order); the last three ORFs were homologous to genes rpl14, rpl24, and rpl5 (which in E. coli constitute the three promoter-proximal genes of the spectinomycin operon). The 14-gene string was preceded by putative -35 and -10 promoter sequences situated 5' to gene rps10, within the 50-bp spacing between genes tuf and rps10; the same region exhibited a potential transcription termination signal for the upstream gene cluster (having tuf as the last gene) but displayed also the potential for formation of a hairpin loop hindering the terminator; this suggests that transcription of rps10 and downstream genes may start farther upstream. The similar organization of the sequenced rp genes in the deepest-branching bacterial phyla (T. maritima) and among Archaea has been interpreted as indicating that the S10-spc gene arrangement existed in the (last) common ancestor. The phylogenetic depth of the Thermotoga lineage was probed by use of r proteins as marker molecules: in all except one case (S3), Proteobacteria or the gram-positive bacteria, and not the genus Thermotoga, were the deepest-branching lineage; in only two cases, however, was the inferred branching order substantiated by bootstrap analysis.
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Affiliation(s)
- A M Sanangelantoni
- Dipartimento di Genetica e Microbiologia A. Buzzati Traverso, Università di Pavia, Italy
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8
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Asemota O, Breda C, Sallaud C, el Turk J, de Kozak I, Buffard D, Esnault R, Kondorosi A. Cloning and expression of a cDNA encoding a cytoplasmic L5 ribosomal protein from alfalfa (Medicago sativa L.). PLANT MOLECULAR BIOLOGY 1994; 26:1201-1205. [PMID: 7811977 DOI: 10.1007/bf00040700] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
A cDNA encoding a putative cytoplasmic ribosomal protein L5 from alfalfa (MsRL5), the first sequence from higher plants, has been characterized. The derived amino acid sequence of 181 residues contains the L5 signature, is 72.2% identical to yeast ribosomal L5 and shares high identity with other RL5 peptides from eukaryotic origin. The sequence does not contain any signal or transit peptide and therefore might be cytoplasmic. In all alfalfa organs examined MsRL5 transcripts were detected at approximately equal levels.
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Affiliation(s)
- O Asemota
- Institut des Sciences Végétales, CNRS, Gif sur Yvette, France
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9
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Chittum HS, Champney WS. Ribosomal protein gene sequence changes in erythromycin-resistant mutants of Escherichia coli. J Bacteriol 1994; 176:6192-8. [PMID: 7928988 PMCID: PMC196958 DOI: 10.1128/jb.176.20.6192-6198.1994] [Citation(s) in RCA: 116] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The genes for ribosomal proteins L4 and L22 from two erythromycin-resistant mutants of Escherichia coli have been isolated and sequenced. In the L4 mutant, an A-to-G transition in codon 63 predicted a Lys-to-Glu change in the protein. In the L22 strain, a 9-bp deletion removed codons 82 to 84, eliminating the sequence Met-Lys-Arg from the protein. Consistent with these DNA changes, in comparison with wild-type proteins, both mutant proteins had reduced first-dimension mobilities in two-dimensional polyacrylamide gels. Complementation of each mutation by a wild-type gene on a plasmid vector resulted in increased erythromycin sensitivity in the partial-diploid strains. The fraction of ribosomes containing the mutant form of the protein was increased by growth in the presence of erythromycin. Erythromycin binding was increased by the fraction of wild-type protein present in the ribosome population. The strain with the L4 mutation was found to be cold sensitive for growth at 20 degrees C, and 50S-subunit assembly was impaired at this temperature. The mutated sequences are highly conserved in the corresponding proteins from a number of species. The results indicate the participation of these proteins in the interaction of erythromycin with the ribosome.
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Affiliation(s)
- H S Chittum
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee 37232
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10
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Burnette-Vick B, Champney WS, Musich PR. A temperature-sensitive mutant of Escherichia coli with an alteration in ribosomal protein L22. Genetica 1994; 94:17-25. [PMID: 7729693 DOI: 10.1007/bf01429216] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
A temperature-sensitive, protein synthesis-defective mutant of Escherichia coli exhibiting an altered ribosomal protein L22 has been investigated. The temperature-sensitive mutation was mapped to the rplV gene for protein L22. The genes from the wild type and mutant strains were amplified by the polymerase chain reaction and the products were sequenced. A cytosine to thymine transition at position 22 of the coding sequence was found in the mutant DNA, predicting an arginine to cysteine alteration in the protein. A single cysteine residue was found in the isolated mutant protein. This amino acid change accounts for the altered mobility of the mutant protein in two-dimensional gels and during reversed-phase HPLC. The temperature-sensitive phenotype was fully complemented by a plasmid carrying the wild type L22 gene. Ribosomes from the complemented cells showed only wild type protein L22 by two dimensional gel analysis and were as heat-resistant as control ribosomes in a translation assay. The point mutation in the L22 gene is uniquely responsible for the temperature-sensitivity of this strain.
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Affiliation(s)
- B Burnette-Vick
- Department of Biochemistry, College of Medicine, East Tennessee State University, Johnson City 37614
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11
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Löffelhardt W, Bohnert HJ. Structure and function of the cyanelle genome. INTERNATIONAL REVIEW OF CYTOLOGY 1994; 151:29-65. [PMID: 7516928 DOI: 10.1016/s0074-7696(08)62630-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- W Löffelhardt
- Institut für Biochemie und Molekulare Zellbiologie, Universität Wien, Austria
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12
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Liu XQ, Huang C, Xu H. The unusual rps3-like orf712 is functionally essential and structurally conserved in Chlamydomonas. FEBS Lett 1993; 336:225-30. [PMID: 8262234 DOI: 10.1016/0014-5793(93)80808-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The Chlamydomonas reinhardtii chloroplast orf712 is a previously described open reading frame that lacks a detectable transcript but potentially encodes a polypeptide with sequence similarities to ribosomal protein Rps3 only at its N- and C-termini. Here we report that orf712 is an essential gene, as demonstrated through gene disruption by particle gun-mediated chloroplast transformation. We also show that an orf712 is present and structurally conserved in all of the two or three major Chlamydomonas lineages. Our results suggest that orf712 is an unusual rps3 gene that contains a large translated intervening sequence.
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Affiliation(s)
- X Q Liu
- Biochemistry Department, Dalhousie University, Halifax, Nova Scotia, Canada
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13
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Tonkyn JC, Gruissem W. Differential expression of the partially duplicated chloroplast S10 ribosomal protein operon. MOLECULAR & GENERAL GENETICS : MGG 1993; 241:141-52. [PMID: 8232197 DOI: 10.1007/bf00280211] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The chloroplast S10 ribosomal protein operon is partially duplicated in many plants because it initiates within the inverted repeat of the circular chloroplast genome. In spinach, the complete S10 operon (S10B) spans the junction between inverted repeat B (IRB) and the large single-copy (LSC) region. The S10 operon is partially duplicated in the inverted repeat A (IRA), but the sequence of S10A completely diverges from S10B at the junction of S10A and the LSC region. The DNA sequence shared by S10A and S10B includes trnI1, the rpl23 pseudogene (rpl23 psi), the intron-containing rpl2 and rps19, which is truncated in S10A at the S10A/LSC junction (rps19'). Transcription of rps19' from the promoter region of S10A could result in the synthesis of a mutant S19 protein. Analysis of RNA accumulation and run-on transcription from S10A and S10B using unique probes from the S10A/LSC and S10B/LSC junctions reveals that expression of S10A is reduced. The difference in S10A and S10B expression appears to be the result of reduced transcription from S10A, rather than differences in RNA stability. Transcription of S10B can initiate at three distinct promoter regions, P1, P2 and P3, which map closely to transcripts detected by S1 nuclease analysis. P1 is located upstream of trnI1 and has the highest transcription initiation frequency in vitro of the three promoter regions. The DNA sequence of P1 is most similar to the chloroplast promoter consensus DNA sequence. Interference by the highly and convergently transcribed psbA-trnH1 operon is considered as a mechanism to explain the reduced activity of the S10A promoters.
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Affiliation(s)
- J C Tonkyn
- Department of Plant Biology, University of California, Berkeley 94720
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14
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Hallick RB, Hong L, Drager RG, Favreau MR, Monfort A, Orsat B, Spielmann A, Stutz E. Complete sequence of Euglena gracilis chloroplast DNA. Nucleic Acids Res 1993; 21:3537-44. [PMID: 8346031 PMCID: PMC331456 DOI: 10.1093/nar/21.15.3537] [Citation(s) in RCA: 288] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
We report the complete DNA sequence of the Euglena gracilis, Pringsheim strain Z chloroplast genome. This circular DNA is 143,170 bp, counting only one copy of a 54 bp tandem repeat sequence that is present in variable copy number within a single culture. The overall organization of the genome involves a tandem array of three complete and one partial ribosomal RNA operons, and a large single copy region. There are genes for the 16S, 5S, and 23S rRNAs of the 70S chloroplast ribosomes, 27 different tRNA species, 21 ribosomal proteins plus the gene for elongation factor EF-Tu, three RNA polymerase subunits, and 27 known photosynthesis-related polypeptides. Several putative genes of unknown function have also been identified, including five within large introns, and five with amino acid sequence similarity to genes in other organisms. This genome contains at least 149 introns. There are 72 individual group II introns, 46 individual group III introns, 10 group II introns and 18 group III introns that are components of twintrons (introns-within-introns), and three additional introns suspected to be twintrons composed of multiple group II and/or group III introns, but not yet characterized. At least 54,804 bp, or 38.3% of the total DNA content is represented by introns.
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Affiliation(s)
- R B Hallick
- Department of Biochemistry, University of Arizona, Tucson 85721
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15
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SecY, an integral subunit of the bacterial preprotein translocase, is encoded by a plastid genome. J Biol Chem 1993. [DOI: 10.1016/s0021-9258(18)53205-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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16
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Drager RG, Hallick RB. A novel Euglena gracilis chloroplast operon encoding four ATP synthase subunits and two ribosomal proteins contains 17 introns. Curr Genet 1993; 23:271-80. [PMID: 8435857 DOI: 10.1007/bf00351506] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The structure of a Euglena gracilis chloroplast operon encoding four subunits of the chloroplast ATP synthase complex and two ribosomal proteins has been determined. These six genes contain 17 introns. This operon is transcribed as a hexacistronic primary transcript which is subsequently processed to monocistronic mRNAs. The linear order of these genes, 5'-rps2-atpI-atpH-atpF-atpA-rps18-3' , encoding ribosomal protein S2, chloroplast ATP synthase subunits CF0IV, CF0III, CF0I, CF1 alpha and ribosomal protein S18, respectively, is similar to the equivalent operons of prokaryotes, cyanelles and land-plant chloroplasts. This operon differs from those of these other organisms in the co-transcription of rps18 and in intron content.
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Affiliation(s)
- R G Drager
- Department of Molecular and Cellular Biology, University of Arizona, Tucson 85721
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17
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Nakai M, Tanaka A, Omata T, Endo T. Cloning and characterization of the secY gene from the cyanobacterium Synechococcus PCC7942. BIOCHIMICA ET BIOPHYSICA ACTA 1992; 1171:113-6. [PMID: 1420358 DOI: 10.1016/0167-4781(92)90150-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The secY gene product is an essential component of the Escherichia coli cytoplasmic membrane, which mediates the protein translocation across the membrane. We found a gene homologous to secY in the genome of the cyanobacterium Synechococcus PCC7942. The deduced amino acid sequence, 439 amino acids long, shows 43% homology with that of the E. coli secY. The hydrophobic profile suggests that the Synechococcus SecY protein is an integral membrane protein containing ten membrane-spanning segments, which are closely related to the E. coli counterpart. The SecY protein may participate in the protein translocation across the cytoplasmic or thylakoid membrane in Synechococcus PCC7942.
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Affiliation(s)
- M Nakai
- Department of Chemistry, Faculty of Science, Nagoya University, Japan
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18
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Görlich D, Prehn S, Hartmann E, Kalies KU, Rapoport TA. A mammalian homolog of SEC61p and SECYp is associated with ribosomes and nascent polypeptides during translocation. Cell 1992; 71:489-503. [PMID: 1423609 DOI: 10.1016/0092-8674(92)90517-g] [Citation(s) in RCA: 339] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
SEC61p is essential for protein translocation across the endoplasmic reticulum membrane of S. cerevisiae. We have found a mammalian homolog that shows more than 50% sequence identity with the yeast protein. Moreover, several regions of SEC61p have significant similarities with corresponding ones of SecYp of bacteria, indicating a strong evolutionary conservation of the mechanism of protein translocation. Mammalian Sec61p, like the yeast protein, is located in the immediate vicinity of nascent polypeptides during their membrane passage. It is tightly associated with membrane-bound ribosomes, suggesting that the nascent chain passes directly from the ribosome into a protein-conducting channel. These results define Sec61p as a ubiquitous key component of the protein translocation apparatus.
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Affiliation(s)
- D Görlich
- Max Delbrück Center for Molecular Medicine, Berlin-Buch, Germany
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19
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Tschauder S, Driessen AJ, Freudl R. Cloning and molecular characterization of the secY genes from Bacillus licheniformis and Staphylococcus carnosus: comparative analysis of nine members of the SecY family. MOLECULAR & GENERAL GENETICS : MGG 1992; 235:147-52. [PMID: 1435726 DOI: 10.1007/bf00286192] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
SecY is a central component of the export machinery that mediates the translocation of secretory proteins across the plasma membrane of Escherichia coli. We have cloned and sequenced the secY genes from Bacillus licheniformis and Staphylococcus carnosus. The deduced amino acid sequences are highly homologous to those of other known SecY polypeptides, all having the potential to form 10 transmembrane segments. Comparative analysis of 9 SecY polypeptides, derived from different bacteria, revealed that 14 amino acid positions (2.7%) are identical in all SecY proteins and 89 (16.9%) show conservative changes. Clusters of conserved amino acid residues were found in 4 of the 10 transmembrane segments and 2 of the 6 cytoplasmic domains. It is suggested that the conserved regions might be involved in the translocation activity of SecY or might be required for the correct interaction of SecY with other components of the secretion apparatus.
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Affiliation(s)
- S Tschauder
- Institut für Biotechnologie 1, Forschungszentrum Jülich GmbH, FRG
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20
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Scaramuzzi CD, Stokes HW, Hiller RG. Characterisation of a chloroplast-encoded secY homologue and atpH from a chromophytic alga. Evidence for a novel chloroplast genome organisation. FEBS Lett 1992; 304:119-23. [PMID: 1618309 DOI: 10.1016/0014-5793(92)80601-c] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
secY is a prokaryotic gene that encodes the SecY protein, an integral membrane component of the prokaryotic protein translocation apparatus. A chloroplast-encoded secY homologue has been identified in the unicellular, chromophytic alga, Pavlova lutherii. The gene predicts a protein composed of ten membrane-spanning regions, that is approximately 25% homologous and 50% similar to bacterial and plastid SecY proteins. The secY gene from P. lutherii is independent of the ribosomal protein (rp) gene cluster to which it is closely linked in other organisms. In P. lutherii secY is located 5' to atpI and atpH. Since, in higher plants the atpIHFA gene cluster and the rp gene cluster are separated by approximately 50 kb, we conclude, this indicates a novel chloroplast gene arrangement in P. lutherii.
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Affiliation(s)
- C D Scaramuzzi
- School of Biological Sciences, Macquarie University, Sydney, NSW, Australia
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21
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Affiliation(s)
- M W Gray
- Department of Biochemistry, Dalhousie University, Halifax, Nova Scotia, Canada
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22
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Copertino DW, Christopher DA, Hallick RB. A mixed group II/group III twintron in the Euglena gracilis chloroplast ribosomal protein S3 gene: evidence for intron insertion during gene evolution. Nucleic Acids Res 1991; 19:6491-7. [PMID: 1721702 PMCID: PMC329205 DOI: 10.1093/nar/19.23.6491] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The splicing of a 409 nucleotide intron from the Euglena gracilis chloroplast ribosomal protein S3 gene (rps3) was examined by cDNA cloning and sequencing, and northern hybridization. Based on the characterization of a partially spliced pre-mRNA, the intron was characterized as a 'mixed' twintron, composed of a 311 nucleotide group II intron internal to a 98 nucleotide group III intron. Twintron excision is via a 2-step sequential splicing pathway, with removal of the internal group II intron preceding excision of the external group III intron. Based on secondary structural analysis of the twintron, we propose that group III introns may represent highly degenerate versions of group II introns. The existence of twintrons is interpreted as evidence that group II introns were inserted during the evolution of Euglena chloroplast genes from a common ancestor with eubacteria, archaebacteria, cyanobacteria, and other chloroplasts.
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Affiliation(s)
- D W Copertino
- Department of Molecular and Cellular Biology, University of Arizona, Tucson 85721
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23
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Michalowski C, Löffelhardt W, Bohnert H. An ORF323 with homology to crtE, specifying prephytoene pyrophosphate dehydrogenase, is encoded by cyanelle DNA in the eukaryotic alga Cyanophora paradoxa. J Biol Chem 1991. [DOI: 10.1016/s0021-9258(18)99037-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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24
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Neumann-Spallart C, Jakowitsch J, Kraus M, Brandtner M, Bohnert HJ, Löffelhardt W. rps10, unreported for plastid DNAs, is located on the cyanelle genome of Cyanophora paradoxa and is cotranscribed with the str operon genes. Curr Genet 1991; 19:313-5. [PMID: 1907893 DOI: 10.1007/bf00355061] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
rps10, encoding the plastid ribosomal protein S10, is a nuclear gene in higher plants and green algae, and is missing from the large ribosomal protein gene cluster of chlorophyll b-type plastids that contains components of the prokaryotic S10, spc and alpha operons. The cyanelle genome of Cyanophora paradoxa is shown to harbor rps10 as another specific feature of its organization. However, this novel plastid gene is not contiguous with the genes of the "S10" operon, but is adjacent to, and cotranscribed with, the str operon, a trait also found in archaebacteria.
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25
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Bryant DA, Schluchter WM, Stirewalt VL. Ferredoxin and ribosomal protein S10 are encoded on the cyanelle genome of Cyanophora paradoxa. Gene X 1991; 98:169-75. [PMID: 1901820 DOI: 10.1016/0378-1119(91)90170-g] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The petF and rsp10 genes of the cyanellar genome of the taxonomically ambiguous flagellate Cyanophora paradoxa have been cloned, mapped, and sequenced. In higher plants these genes are not encoded in the chloroplast DNA, but are encoded in the nucleus. The C. paradoxa petF gene predicts a protein of 99 amino acids (aa) which is more similar to type-I ferredoxins of diverse cyanobacteria than to those of green algae, dinoflagellates, and higher plants. The rsp10 gene (rspJ) predicts a protein of 105 aa which is about 50% identical and 71% homologous to the proteins of Escherichia coli and Mycoplasma capricolum. The results are discussed within the context of the endosymbiotic origins of chloroplasts from cyanobacteria.
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Affiliation(s)
- D A Bryant
- Department of Molecular and Cell Biology, Pennsylvania State University, University Park 16802
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