PCR-Based Bioprospecting for Homing Endonucleases in Fungal Mitochondrial rRNA Genes

2014 ◽  
pp. 37-53 ◽  
Author(s):  
Mohamed Hafez ◽  
Tuhin Kumar Guha ◽  
Chen Shen ◽  
Jyothi Sethuraman ◽  
Georg Hausner
Keyword(s):  
Rrna Genes ◽  
Homing Endonucleases ◽  
Mitochondrial Rrna

scholarly journals Comparative analysis of RNA enrichment methods for preparation of Cryptococcus neoformans RNA sequencing libraries

2021 ◽  
Author(s):  
Calla L Telzrow ◽  
Paul J Zwack ◽  
Shannon Esher Righi ◽  
Fred S Dietrich ◽  
Cliburn Chan ◽  
...  
Keyword(s):  
Cryptococcus Neoformans ◽  
Rna Sequencing ◽  
Rnase H ◽  
Rrna Genes ◽  
Rna Seq ◽  
Protein Coding ◽  
Mitochondrial Rrna ◽  
Non Coding Rna ◽  
Rrna Depletion ◽  
Enrichment Methods

Abstract RNA sequencing (RNA-Seq) experiments focused on gene expression involve removal of ribosomal RNA (rRNA) because it is the major RNA constituent of cells. This process, called RNA enrichment, is done primarily to reduce cost: without rRNA removal, deeper sequencing must be performed to compensate for the sequencing reads wasted on rRNA. The ideal RNA enrichment method removes all rRNA without affecting other RNA in the sample. We tested the performance of three RNA enrichment methods on RNA isolated from Cryptococcus neoformans, a fungal pathogen of humans. We find that the RNase H depletion method is more efficient in depleting rRNA and more specific in recapitulating non-rRNA levels present in unenriched controls than the commonly-used Poly(A) isolation method. The RNase H depletion method is also more effective than the Ribo-Zero depletion method as measured by rRNA depletion efficiency and recapitulation of protein-coding RNA levels present in unenriched controls, while the Ribo-Zero depletion method more closely recapitulates annotated non-coding RNA (ncRNA) levels. Finally, we leverage these data to accurately map the C. neoformans mitochondrial rRNA genes, and also demonstrate that RNA-Seq data generated with the RNase H and Ribo-Zero depletion methods can be used to explore novel C. neoformans long non-coding RNA genes.

Organelle origins and ribosomal RNA

1988 ◽  
Vol 66 (5) ◽  
pp. 325-348 ◽  
Author(s):  
Michael W. Gray
Keyword(s):  
Ribosomal Rna ◽  
Phylogenetic Trees ◽  
Purple Bacteria ◽  
Plant Mitochondria ◽  
Rrna Genes ◽  
Rna Sequences ◽  
Sequence Organization ◽  
General Acceptance ◽  
Mitochondrial Rrna ◽  
History Of

As the detailed molecular biology of organelle genomes has unfolded, there has been a general acceptance of the view that plastids and mitochondria are of endosymbiotic, eubacterial origin. Plastid genes are strikingly similar to their eubacterial (particularly cyanobacterial) counterparts in sequence, organization, and mode of expression, and such features strongly support the hypothesis that the plastid and its genome were derived in evolution from a blue-green alga-like endosymbiont. Mitochondria, on the other hand, are problematic: mitochondrial genes are organized and expressed in remarkably diverse ways in the different major groups of eukaryotes, and in no case are these features particularly characteristic of either bacterial or nuclear genomes. There is, however, clear evidence derived from gene sequence supporting the eubacterial ancestry of mitochondria, and some of the most compelling data have come from analyses of mitochondrial ribosomal RNA (rRNA). Plant mitochondrial rRNA genes diverge in sequence at a particularly slow rate, and these genes have proven to be especially supportive of the endosymbiont hypothesis, pointing to an origin of mitochondria from within the α subdivision of the purple bacteria. Ribosomal RNA sequences provide a basis for the construction of global phylogenetic trees that probe the evolutionary history of organelles, and that address the question of whether mitochondria and plastids are monophyletic or polyphyletic in origin. Such studies raise the possibility that the rRNA genes of plant mitochondria originated separately from the mitochondrial rRNA genes of other eukaryotes.

Precise localization and nucleotide sequence of the two mouse mitochondrial rRNA genes and three immediately adjacent novel tRNA genes

Cell ◽  
1980 ◽  
Vol 22 (1) ◽  
pp. 157-170 ◽  
Author(s):  
Richard A. Van Etten ◽  
Mark W. Walberg ◽  
David A. Clayton
Keyword(s):  
Nucleotide Sequence ◽  
Rrna Genes ◽  
Trna Genes ◽  
Precise Localization ◽  
Mitochondrial Rrna

scholarly journals Functional Conservation of Mitochondrial RNA Levels Despite Divergent mtDNA Organization

2020 ◽  
Author(s):  
James P Held ◽  
Maulik R Patel
Keyword(s):  
Mitochondrial Genome ◽  
Digital Pcr ◽  
Rrna Genes ◽  
Mitochondrial Rna ◽  
Protein Coding ◽  
Promoter Sequences ◽  
C Elegans ◽  
Functional Conservation ◽  
Mitochondrial Rrna ◽  
Mrna Ratio

Abstract Objective: Mitochondria-encoded ribosomal RNA (rRNA) genes in humans are expressed at a higher rate than protein coding genes of the mitochondria. The organization of the human mitochondrial genome (mtDNA) is amenable to differential expression of rRNAs as it contains a promoter specific to the transcription of the two rRNAs. However, mtDNA is not organized in the same way as humans in all metazoans. In the nematode, Caenorhabditis elegans, the rRNA genes are on opposite sides of the mtDNA molecule and there are no obvious promoter sequences specific to the rRNA genes. Thus, we asked whether rRNA levels are higher relative to mRNAs in mitochondria of C. elegans as they are in humans.Results: Using droplet digital PCR, we discovered that steady-state mitochondrial rRNA transcript levels are approximately 120 times higher than the levels of mitochondrial mRNAs. These data demonstrate that despite the lack of conservation in mitochondrial genome organization, a high mitochondrial rRNA-to-mRNA ratio is a conserved feature of metazoans.

scholarly journals Species identification of processed sea cucumbers from Malaysian market based on concatenated gene sequences of mitochondrial rRNA genes

2019 ◽  
Vol 1 (2) ◽  
pp. Manuscript
Author(s):  
Kamarul Rahim Kamarudin ◽  
Maryam Mohamed Rehan ◽  
'Aisyah Mohamed Rehan
Keyword(s):  
Species Identification ◽  
Sea Cucumber ◽  
Rrna Genes ◽  
Likelihood Method ◽  
Rrna Gene ◽  
Gene Sequences ◽  
Sea Cucumbers ◽  
Protein Coding ◽  
Parsimony Method ◽  
Mitochondrial Rrna

Species identification of sea cucumbers that have undergone body deformation due to extensive food processing e.g. beche-de-mer is difficult especially with the copresence of cases of unlabelled or mislabelled sea cucumber-based products in the markets.  Therefore, a study was done to determine the species identities of processed sea cucumbers from selected Malaysian markets using concatenated gene sequences of non-protein-coding 12S mitochondrial rRNA gene and non-protein-coding 16S mitochondrial rRNA gene. Phylogenetic analyses based on the distance-based Neighbour Joining method, and the character-based methods i.e. the Maximum Parsimony method, Maximum Likelihood method, and the Bayesian Analysis method of 47 ingroup sequences representing 37 processed sea cucumber specimens, six reference samples, and four additional specimens suggested the presence of three main clusters i.e. gamat family consisting of genus Stichopus and genus Thelenota; and timun laut family comprising family Holothuriidae. A number of three gamat species i.e. Stichopus horrens, Stichopus vastus, and Thelenota anax were recorded. Meanwhile, the specimens of Holothuria (Halodeima) atra, Holothuria (Halodeima) edulis, Holothuria (Metriatyla) lessoni, Holothuria (Mertensiothuria) leucospilota, and Holothuria (Metriatyla) scabra were the five timun laut species that grouped under the family Holothuriidae. The outcomes of this study can be utilised by the enforcement agencies to monitor and overcome the issues of species substitution and product mislabelling of processed sea cucumber products in Malaysian markets.

scholarly journals Molecular Characterization and Postsplicing Fate of Three Introns within the Single rRNA Operon of the Hyperthermophilic ArchaeonAeropyrum pernix K1

1998 ◽  
Vol 180 (14) ◽  
pp. 3635-3643 ◽  
Author(s):  
Norimichi Nomura ◽  
Yoshihiko Sako ◽  
Aritsune Uchida
Keyword(s):  
Sequence Data ◽  
Protein Translation ◽  
Open Reading Frames ◽  
Rrna Operon ◽  
Rrna Genes ◽  
23S Rrna ◽  
Homing Endonucleases ◽  
Two Dimensional Gel Electrophoresis ◽  
E Coli

ABSTRACT The single rRNA operon (arnS-arnL) of the hyperthermophilic archaeon Aeropyrum pernix K1 was sequenced. The DNA sequence data and detailed RNA analyses disclosed an unusual feature: the presence of three introns at hitherto undescribed insertion positions within the rRNA genes. The 699-nucleotide (nt) intron Iα was located at position 908 (Escherichia coli numbering [H. F. Noller, Annu. Rev. Biochem. 53:119–162, 1984]) of the 16S rRNA, while the 202-nt intron Iβ and 575-nt intron Iγ were located at positions 1085 and 1927 (E. coli numbering), respectively, of the 23S rRNA. They were located within highly conserved sites which have been implicated as crucial for rRNA function in E. coli. All three introns were remarkably AT rich (41.5 to 43.1 mol% G+C) compared with the mature rRNAs (67.7 and 69.2 mol% G+C for 16S and 23S rRNAs, respectively). No obvious primary sequence similarities were detected among them. After splicing from rRNA transcripts in vivo, a large quantity of intronic RNAs were stably retained in the linear monomeric form, whereas a trace of topoisomeric RNA molecules also appeared, as characterized by their behavior in two-dimensional gel electrophoresis. Secondary structural models of the Iα-, Iβ-, and Iγ-containing rRNA precursors agree with the bulge-helix-bulge motif. Two of the introns, Iα and Iγ, contained open reading frames whose protein translation exhibited no overall similarity with proteins reported so far. However, both share a LAGLI-DADG motif characteristic of homing endonucleases.

Dissecting the major African snake radiation: a molecular phylogeny of the Lamprophiidae Fitzinger (Serpentes, Caenophidia)

Zootaxa ◽  
2008 ◽  
Vol 1945 (1) ◽  
pp. 51-66 ◽  
Author(s):  
NICOLAS VIDAL ◽  
WILLIAM R. BRANCH ◽  
OLIVIER S. G. PAUWELS ◽  
S. BLAIR HEDGES ◽  
DONALD G. BROADLEY ◽  
...  
Keyword(s):  
Mitochondrial Protein ◽  
Sister Group ◽  
Molecular Data ◽  
Rrna Genes ◽  
Phylogenetic Position ◽  
Data Set ◽  
Protein Coding ◽  
Mitochondrial Rrna ◽  
Protein Coding Genes ◽  
History Of

The Elapoidea includes the Elapidae and a large (~60 genera, 280 sp.) and mostly African (including Madagascar) radiation termed Lamprophiidae by Vidal et al. (2007), that includes at least four major groups: the psammophiines, atractaspidines, lamprophiines and pseudoxyrhophiines. In this work, we reviewed the recent taxonomic history of the lamprophiids, and built a data set including two nuclear protein-coding genes (c-mos and RAG2), two mitochondrial rRNA genes (12S and 16S rRNA) and two mitochondrial protein-coding genes (cytochrome b and ND4) for 85 species belonging to 45 genera (thus representing about 75% of the generic diversity and 30% of the specific diversity of the radiation), in order to clarify the phylogenetic relationships of this large and neglected group at the subfamilial and generic levels. To this aim, 480 new sequences were produced. The vast majority of the investigated genera fall into four main monophyletic clusters, that correspond to the four subfamilies mentioned above, although the content of atractaspidines, lamprophiines and pseudoxyrhophiines is revised. We confirm the polyphyly of the genus Stenophis, and the relegation of the genus name Dromophis to the synonymy of the genus name Psammophis. Gonionotophis brussauxi is nested within Mehelya. The genus Lamprophis Fitzinger, 1843 is paraphyletic with respect to Lycodonomorphus Fitzinger, 1843. Lamprophis swazicus is the sister-group to Hormonotus modestus, and may warrant generic recognition. Molecular data do not support the traditional placement of Micrelaps within the Atractaspidinae, but its phylogenetic position, along with that of Oxyrhabdium (previously considered to belong to the Xenodermatidae), requires additional molecular data and they are both treated as Elapoidea incertae sedis. The interrelationships of Psammophiinae, Atractaspidinae, Lamprophiinae, Pseudoxyrhophiinae, Prosymna (13 sp.), Pseudaspis (1 sp.) and Pythonodipsas (1 sp.), Buhoma (2 species), and Psammodynastes (1 sp.) remain unresolved. Finally, the genus Lycognathophis, endemic to the Seychelles, does not belong to the African radiation, but to the Natricidae.

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