Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Mitochondrial Precursor Proteins01:39

Mitochondrial Precursor Proteins

3.9K
Mitochondrial precursors are partially unfolded or loosely folded polypeptide chains. Newly synthesized precursors are inhibited from spontaneously folding into their native conformation by the cytosolic chaperones, heat shock proteins 70 (Hsp70), and mitochondrial import stimulation factors (MSFs). Precursors bound to MSFs are guided to the TOM70-TOM37 receptors, while precursors bound to Hsp70  chaperones are targetted to TOM20-TOM22 receptor complexes.
Most of the mitochondrial...
3.9K
Mitochondrial Protein Sorting01:39

Mitochondrial Protein Sorting

5.9K
Mitochondria are double-membrane organelles of the eukaryotes involved in cellular metabolism, signaling, ATP synthesis, and programmed cell death.  Each of these processes requires specific proteins and enzymes that must be correctly sorted to the right mitochondrial subcompartment for the proper functioning of the organelle.
Most of these mitochondrial proteins are encoded by the nucleus and imported to the mitochondria as unfolded or loosely folded precursors. Mitochondrial precursors...
5.9K
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

7.1K
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
7.1K
Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes02:16

Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes

17.3K
The present-day mitochondrial and chloroplast genomes have retained some of the characteristics of their ancestral prokaryotes and also have acquired new attributes during their evolution within eukaryotic cells. Like prokaryotic genomes, mitochondrial and chloroplast genomes neither bind with histone-like proteins nor show complex packaging into chromosome-like structures, as observed in eukaryotes. Unlike mitotic cell divisions observed in eukaryotic cells, mitochondria and chloroplasts...
17.3K
Export of Mitochondrial and Chloroplast Genes02:19

Export of Mitochondrial and Chloroplast Genes

4.4K
A eukaryotic cell can have up to three different types of genetic systems: nuclear, mitochondrial, and chloroplast. During evolution, organelles have exported many genes to the nucleus; this transfer is still ongoing in some plant species. Approximately 18% of the Arabidopsis thaliana nuclear genome is thought to be derived from the chloroplast’s cyanobacterial ancestor, and around 75% of the yeast genome derived from the mitochondria’s bacterial ancestor. This export has occurred...
4.4K
Porin Insertion in the Outer Mitochondrial Membrane01:12

Porin Insertion in the Outer Mitochondrial Membrane

5.1K
Porins are beta-barrel proteins translocated to the mitochondrial outer membrane through the TOM complex into the intermembrane space. Porin precursors bind TIM chaperones within the intermembrane space and are guided to the Sorting and Assembly Machinery complex or SAM complex on the outer mitochondrial membrane.
Three models describe the assembly of porins by the SAM complex and their insertion into the outer membrane. Model 1 suggests that porins are assembled outside the SAM channel as the...
5.1K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

A Beetle <i>In Vitro</i>: Establishment of a Short-Term Cell Culture from the Pest <i>Popillia japonica</i>.

Insects·2026
Same author

Darwin wasps (Hymenoptera, Ichneumonidae) of the Nature Reserve of Pantalica (Sicily, Italy).

Biodiversity data journal·2026
Same author

SmithRNAs: A Common Feature among Metazoa.

Genome biology and evolution·2025
Same author

De novo genome assembly of the endemic Italian springtail Orchesella dallaii (Collembola: Orchesellidae).

G3 (Bethesda, Md.)·2025
Same author

The genome sequence of <i>Tethysbaena scabra</i> (Pretus, 1991), the first known in the peracarid crustacean order <i>Thermosbaenacea</i>.

F1000Research·2025
Same author

Whole Genome Resequencing Reveals Origins and Global Invasion Pathways of the Japanese Beetle Popillia japonica.

Molecular ecology·2025

Related Experiment Video

Updated: Mar 12, 2026

An Integrated Approach for Microprotein Identification and Sequence Analysis
09:37

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

4.1K

Integrating Secondary Structure Information Enhances Phylogenetic Signal in Mitochondrial Protein Coding Genes.

Claudio Cucini1,2, Francesco Nardi1,2, Joan Pons3

  • 1Department of Life Sciences, University of Siena. Via Aldo Moro 2, 53100 Siena, Italy.

Systematic Biology
|March 10, 2026
PubMed
Summary

Accurate phylogenetic inference is improved by incorporating protein secondary structure. The TRAMPO pipeline partitions mitochondrial genes by structure, enhancing phylogenetic tree reconstruction and reducing evolutionary heterogeneity.

Keywords:
mitochondrial genomepartitioningphylogeneticssecondary structuretransmembrane regions

More Related Videos

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
08:57

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

16.6K
The ITS2 Database
16:17

The ITS2 Database

Published on: March 12, 2012

32.5K

Related Experiment Videos

Last Updated: Mar 12, 2026

An Integrated Approach for Microprotein Identification and Sequence Analysis
09:37

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

4.1K
Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
08:57

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

16.6K
The ITS2 Database
16:17

The ITS2 Database

Published on: March 12, 2012

32.5K

Area of Science:

  • Evolutionary Biology
  • Bioinformatics
  • Molecular Phylogenetics

Background:

  • Accurate phylogenetic inference relies on evolutionary models that capture molecular evolution heterogeneity.
  • Mitochondrial protein-coding genes show regional variation in composition and function, often missed by standard phylogenetic partitioning.
  • Transmembrane α-helices within these genes have specific structural and compositional constraints.

Purpose of the Study:

  • To introduce TRAMPO (TRAnsMembrane Protein Order), a pipeline for phylogenetic partitioning that integrates predicted secondary structural features.
  • To evaluate the impact of structural information on phylogenetic reconstruction using various partitioning strategies and evolutionary models.
  • To assess how structural partitioning affects model fit, phylogenetic congruence, and computational efficiency.

Main Methods:

  • Development and application of the TRAMPO pipeline to incorporate secondary structure (transmembrane, matrix-facing, intermembrane-facing) into phylogenetic partitioning.
  • Analysis of seven mitochondrial datasets from crustaceans, hexapods, and vertebrates.
  • Evaluation of eight partitioning strategies combining codon position, strand, and secondary structure.
  • Phylogenetic analyses using maximum likelihood, various Markov models, and among-site rate variation models (e.g., FreeRates).
  • Assessment of tree topology congruence using quartet distances.

Main Results:

  • Incorporating structural information consistently improved model fit (lower AIC) and reduced partition heterogeneity.
  • Structurally informed partitioning led to more consistent and topologically congruent phylogenetic trees across most datasets.
  • Transmembrane helices, particularly at second codon positions, exhibited distinct evolutionary constraints (e.g., thymine enrichment, hydrophobic composition).
  • The TRAMPO pipeline reduced computational time compared to standard methods.
  • Benefits of structural partitioning were most evident in intermediate evolutionary depth lineages.

Conclusions:

  • Secondary structural features, especially transmembrane helices, contain significant phylogenetic signal.
  • Integrating structural information into partitioning schemes enhances phylogenetic tree reconstruction and mitigates evolutionary heterogeneity.
  • TRAMPO offers a scalable, open-source solution for improving mitochondrial phylogenetics through structural awareness.