scholarly journals Correction to ‘A hypervariable mitochondrial protein coding sequence associated with geographical origin in a cosmopolitan bloom-forming alga, Heterosigma akashiwo ’

2017 ◽  
Vol 13 (6) ◽  
pp. 20170358
Author(s):  
Aiko Higashi ◽  
Satoshi Nagai ◽  
Sergio Seoane ◽  
Shoko Ueki
Keyword(s):  
Geographical Origin ◽  
Mitochondrial Protein ◽  
Heterosigma Akashiwo ◽  
Protein Coding ◽  
Coding Sequence

scholarly journals A hypervariable mitochondrial protein coding sequence associated with geographical origin in a cosmopolitan bloom-forming alga, Heterosigma akashiwo

2017 ◽  
Vol 13 (4) ◽  
pp. 20160976 ◽  
Author(s):  
Aiko Higashi ◽  
Satoshi Nagai ◽  
Sergio Seone ◽  
Shoko Ueki
Keyword(s):  
North American ◽  
Mitochondrial Gene ◽  
Mitochondrial Protein ◽  
Hypothetical Protein ◽  
Heterosigma Akashiwo ◽  
Protein Coding ◽  
Recent Climate ◽  
Phylogeographic History ◽  
History Of ◽  
Reliable Marker

Geographical distributions of phytoplankton species can be defined by events on both evolutionary time and shorter scales, e.g. recent climate changes. Additionally, modern industrial activity, including the transport of live fish and spat for aquaculture and aquatic microorganisms in ship ballast water, may aid the spread of phytoplankton. Obtaining a reliable marker is key to gaining insight into the phylogeographic history of a species. Here, we report a hypervariable mitochondrial gene in the cosmopolitan bloom-forming alga, Heterosigma akashiwo . We compared the entire mitochondrial genome sequences of seven H. akashiwo strains from Japanese and North American coastal waters and identified a hypervariable segment. The region codes for a hypothetical protein with no defined function, and its variations between Japanese and North American isolates were prominent, while the sequences were more conserved among Japanese strains and North American isolates. Comparison of the sequence in isolates obtained from different geographical points in the Northern Hemisphere revealed that the sequence variations largely correlated with latitude and longitude (i.e. Pacific/Atlantic oceans). Our results demonstrate the usefulness of the sequence in determining the phylogeographic history of H. akashiwo .

Polyphyletic Origins of Schizothoracinae Fishes (Cyprinidae) in Respect to Their Mitochondrial Protein-Coding Genes

2019 ◽  
Vol 07 (02) ◽  
Author(s):  
Saira Bibi ◽  
Muhammad Fiaz Khan ◽  
Aqsa Rehman ◽  
Faisal Nouroz
Keyword(s):  
Mitochondrial Protein ◽  
Protein Coding ◽  
Protein Coding Genes

Patterns of Nucleotide Substitution in Mitochondrial Protein Coding Genes of Vertebrates

Genetics ◽  
1996 ◽  
Vol 143 (1) ◽  
pp. 537-548 ◽  
Author(s):  
Sudhir Kumar
Keyword(s):  
Nucleotide Substitution ◽  
Mitochondrial Protein ◽  
Likelihood Estimation ◽  
Nucleotide Composition ◽  
Substitution Rates ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Conserved Genes ◽  
Maximum Likelihood Methods ◽  
Position Data

Abstract Maximum likelihood methods were used to study the differences in substitution rates among the four nucleotides and among different nucleotide sites in mitochondrial protein-coding genes of vertebrates. In the lst+2nd codon position data, the frequency of nucleotide G is negatively correlated with evolutionary rates of genes, substitution rates vary substantially among sites, and the transition / transversion rate bias (R) is two to five times larger than that expected at random. Generally, largest transition biases and greatest differences in substitution rates among sites are found in the highly conserved genes. The 3rd positions in placental mammal genes exhibit strong nucleotide composition biases and the transitional rates exceed transversional rates by one to two orders of magnitude. Tamura-Nei and Hasegawa-Kishino-Yano models with gamma distributed variable rates among sites (gamma parameter, α) adequately describe the nucleotide substitution process in 1st+2nd position data. In these data, ignoring differences in substitution rates among sites leads to largest biases while estimating substitution rates. Kimura's two-parameter model with variable-rates among sites performs satisfactorily in likelihood estimation of R, α, and overall amount of evolution for lst+2nd position data. It can also be used to estimate pairwise distances with appropriate values of α for a majority of genes.

scholarly journals Influence of the Leader protein coding region of foot-and-mouth disease virus on virus replication

2013 ◽  
Vol 94 (7) ◽  
pp. 1486-1495 ◽  
Author(s):  
Graham J. Belsham
Keyword(s):  
Disease Virus ◽  
Foot And Mouth Disease ◽  
Mouth Disease ◽  
Initiation Codon ◽  
Coding Region ◽  
Protein Coding ◽  
Coding Sequence ◽  
Bhk Cells ◽  
Leader Protein ◽  
Mouth Disease Virus

The foot-and-mouth disease virus (FMDV) Leader (L) protein is produced in two forms, Lab and Lb, differing only at their amino-termini, due to the use of separate initiation codons, usually 84 nt apart. It has been shown previously, and confirmed here, that precise deletion of the Lab coding sequence is lethal for the virus, whereas loss of the Lb coding sequence results in a virus that is viable in BHK cells. In addition, it is now shown that deletion of the ‘spacer’ region between these two initiation codons can be tolerated. Growth of the virus precisely lacking just the Lb coding sequence resulted in a previously undetected accumulation of frameshift mutations within the ‘spacer’ region. These mutations block the inappropriate fusion of amino acid sequences to the amino-terminus of the capsid protein precursor. Modification, by site-directed mutagenesis, of the Lab initiation codon, in the context of the virus lacking the Lb coding region, was also tolerated by the virus within BHK cells. However, precise loss of the Lb coding sequence alone blocked FMDV replication in primary bovine thyroid cells. Thus, the requirement for the Leader protein coding sequences is highly dependent on the nature and extent of the residual Leader protein sequences and on the host cell system used. FMDVs precisely lacking Lb and with the Lab initiation codon modified may represent safer seed viruses for vaccine production.

scholarly journals Mitogenome Analysis of Four Lamiinae Species (Coleoptera: Cerambycidae) and Gene Expression Responses by Monochamus alternatus When Infected with the Parasitic Nematode, Bursaphelenchus mucronatus

Insects ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 453
Author(s):  
Zi-Yi Zhang ◽  
Jia-Yin Guan ◽  
Yu-Rou Cao ◽  
Xin-Yi Dai ◽  
Kenneth B. Storey ◽  
...  
Keyword(s):  
Gene Expression ◽  
Phylogenetic Trees ◽  
Mitochondrial Gene ◽  
Mitochondrial Protein ◽  
Pine Wilt Disease ◽  
Bursaphelenchus Xylophilus ◽  
Monochamus Alternatus ◽  
Genome Database ◽  
Protein Coding ◽  
Nd5 Gene

We determined the mitochondrial gene sequence of Monochamus alternatus and three other mitogenomes of Lamiinae (Insect: Coleoptera: Cerambycidae) belonging to three genera (Aulaconotus, Apriona and Paraglenea) to enrich the mitochondrial genome database of Lamiinae and further explore the phylogenetic relationships within the subfamily. Phylogenetic trees of the Lamiinae were built using the Bayesian inference (BI) and maximum likelihood (ML) methods and the monophyly of Monochamus, Anoplophora, and Batocera genera was supported. Anoplophora chinensis, An. glabripennis and Aristobia reticulator were closely related, suggesting they may also be potential vectors for the transmission of the pine wood pathogenic nematode (Bursaphelenchus xylophilus) in addition to M. alternatus, a well-known vector of pine wilt disease. There is a special symbiotic relationship between M. alternatus and Bursaphelenchus xylophilus. As the native sympatric sibling species of B. xylophilus, B. mucronatus also has a specific relationship that is often overlooked. The analysis of mitochondrial gene expression aimed to explore the effect of B. mucronatus on the energy metabolism of the respiratory chain of M. alternatus adults. Using RT-qPCR, we determined and analyzed the expression of eight mitochondrial protein-coding genes (COI, COII, COIII, ND1, ND4, ND5, ATP6, and Cty b) between M. alternatus infected by B. mucronatus and M. alternatus without the nematode. Expression of all the eight mitochondrial genes were up-regulated, particularly the ND4 and ND5 gene, which were up-regulated by 4–5-fold (p < 0.01). Since longicorn beetles have immune responses to nematodes, we believe that their relationship should not be viewed as symbiotic, but classed as parasitic.

Yeast CBP1 mRNA 3' end formation is regulated during the induction of mitochondrial function

1991 ◽  
Vol 11 (2) ◽  
pp. 813-821
Author(s):  
S A Mayer ◽  
C L Dieckmann
Keyword(s):  
Mitochondrial Function ◽  
Developmental Stages ◽  
Single Gene ◽  
Mitochondrial Protein ◽  
Nuclear Gene ◽  
State Level ◽  
Yeast Cells ◽  
Cdna Clones ◽  
Coding Sequence ◽  
Polyadenylation Sites

Alternative mRNA processing is one mechanism for generating two or more polypeptides from a single gene. While many mammalian genes contain multiple mRNA 3' cleavage and polyadenylation signals that change the coding sequence of the mature mRNA when used at different developmental stages or in different tissues, only one yeast gene has been identified with this capacity. The Saccharomyces cerevisiae nuclear gene CPB1 encodes a mitochondrial protein that is required for cytochrome b mRNA stability. This 66-kDa protein is encoded by a 2.2-kb mRNA transcribed from CPB1. Previously we showed that a second 1.2-kb transcript is initiated at the CBP1 promoter but has a 3' end near the middle of the coding sequence. Furthermore, it was shown that the ratio of the steady-state level of 2.2-kb CBP1 message to 1.2-kb message decreases 10-fold during the induction of mitochondrial function, while the combined levels of both messages remain constant. Having proposed that regulation of 3' end formation dictates the amount of each CBP1 transcript, we now show that a 146-bp fragment from the middle of CBP1 is sufficient to direct carbon source-regulated production of two transcripts when inserted into the yeast URA3 gene. This fragment contains seven polyadenylation sites for the wild-type 1.2-kb mRNA, as mapped by sequence analysis of CBP1 cDNA clones. Deletion mutations upstream of the polyadenylation sites abolished formation of the 1.2-kb transcript, whereas deletion of three of the sites only led to a reduction in abundance of the 1.2-kb mRNA. Our results indicate that regulation of the abundance of both CBP1 transcripts is controlled by elements in a short segment of the gene that directs 3' end formation of the 1.2-kb transcript, a unique case in yeast cells.

Polyamine-mediated regulation of mouse ornithine decarboxylase is posttranslational

1989 ◽  
Vol 9 (12) ◽  
pp. 5484-5490
Author(s):  
T van Daalen Wetters ◽  
M Macrae ◽  
M Brabant ◽  
A Sittler ◽  
P Coffino
Keyword(s):  
Ornithine Decarboxylase ◽  
Translational Regulation ◽  
Feedback Inhibition ◽  
Chimeric Protein ◽  
Sequence Information ◽  
Pulse Label ◽  
Protein Coding ◽  
Coding Sequence ◽  
Series Of Experiments ◽  
The Difference

The activity of ornithine decarboxylase (ODC) is negatively regulated by intracellular polyamines, which thereby mediate a form of feedback inhibition of the initial enzyme in the pathway of their synthesis. This phenomenon has been believed to result, at least in part, from translational regulation. To investigate this further, we performed four series of experiments. First, we found that a chimeric protein encoded by an mRNA containing the ODC 5' leader sequence did not exhibit polyamine-dependent regulation. Second, we showed that transcripts containing the protein-coding sequence of ODC, but no other ODC-derived sequence information, exhibited regulation. Third, we found that the association of ODC mRNA with ribosomes was not altered when intracellular polyamine levels were modulated under conditions previously deemed to cause translational regulation. Last, we carried out experiments to measure the incorporation of [35S]methionine into ODC in polyamine-starved and polyamine-replete cells. Differential incorporation diminished progressively as pulse-label times were shortened; at the shortest labeling time used (4 min), the difference in favor of ODC in polyamine-starved cells was less than twofold. These findings suggest that it is necessary to reevaluate the question of whether polyamines cause alterations of translation of ODC mRNA.

Cryptic speciation in a biodiversity hotspot: multilocus molecular data reveal new velvet worm species from Western Australia (Onychophora : Peripatopsidae : Kumbadjena)

2018 ◽  
Vol 32 (6) ◽  
pp. 1249 ◽  
Author(s):  
Shoyo Sato ◽  
Rebecca S. Buckman-Young ◽  
Mark S. Harvey ◽  
Gonzalo Giribet
Keyword(s):  
Western Australia ◽  
18S Rrna ◽  
Mitochondrial Protein ◽  
Molecular Data ◽  
12S Rrna ◽  
Protein Coding ◽  
Complex Morphology ◽  
Velvet Worm ◽  
Three New Species ◽  
Western Australian

There is a yet uncovered multitude of species to be found among Western Australian Onychophora. Kumbadjena, one of the two genera that reside in this region, has been previously suggested to house an extensive species complex. Morphology alone has not been able to elucidate the diversity in this genus and has instead muddled species delineations. Topologies and species delimitation analyses resulting from the sequences of two mitochondrial ribosomal markers (12S rRNA and 16S rRNA), one nuclear ribosomal marker (18S rRNA), and one mitochondrial protein-coding gene (cytochrome c oxidase subunit I) are indicative of several undescribed species. Fixed diagnostic nucleotide changes in the highly conserved sequences of 18S rRNA warrant distinction of three new species of Kumbadjena: K. toolbrunupensis, sp. nov., K. karricola, sp. nov., and K. extrema, sp. nov. The geographic distributions of the proposed species suggest that Kumbadjena is another example of short-range endemism, a common occurrence in the flora and fauna of the region. The extensive biodiversity and endemism in the region necessitates conservation to preserve the species and processes that promote speciation harboured by Western Australia.

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