scholarly journals Novel Expansion of Matrix Metalloproteases in the Laboratory Axolotl (Ambystoma mexicanum) and Other Salamander Species

2021 ◽  
Vol 9 ◽  
Author(s):  
Nour Al Haj Baddar ◽  
Nataliya Timoshevskaya ◽  
Jeramiah J. Smith ◽  
Houfu Guo ◽  
S. Randal Voss
Keyword(s):  
Ambystoma Mexicanum ◽  
Matrix Metalloproteases ◽  
Sequence Information ◽  
The Novel ◽  
Tail Regeneration ◽  
Extracellular Milieu ◽  
Comprehensive Survey ◽  
Protein Components ◽  
Salamander Species ◽  
Mmp Genes

Matrix metalloprotease (MMP) genes encode endopeptidases that cleave protein components of the extracellular matrix (ECM) as well as non-ECM proteins. Here we report the results of a comprehensive survey of MMPs in the laboratory axolotl and other representative salamanders. Surprisingly, 28 MMPs were identified in salamanders and 9 MMP paralogs were identified as unique to the axolotl and other salamander taxa, with several of these presenting atypical amino acid insertions not observed in other tetrapod vertebrates. Furthermore, as assessed by sequence information, all of the novel salamander MMPs are of the secreted type, rather than cell membrane anchored. This suggests that secreted type MMPs expanded uniquely within salamanders to presumably execute catalytic activities in the extracellular milieu. To facilitate future studies of salamander-specific MMPs, we annotated transcriptional information from published studies of limb and tail regeneration. Our analysis sets the stage for comparative studies to understand why MMPs expanded uniquely within salamanders.

Heterotrimeric G-Protein Signaling in Plants: Conserved and Novel Mechanisms

2019 ◽  
Vol 70 (1) ◽  
pp. 213-238 ◽  
Author(s):  
Sona Pandey
Keyword(s):  
G Protein ◽  
G Proteins ◽  
Stress Responses ◽  
Sequence Information ◽  
G Protein Signaling ◽  
Protein Signaling ◽  
Biotic And Abiotic Stress ◽  
Use Efficiency ◽  
Protein Components ◽  
Heterotrimeric G Protein Signaling

Heterotrimeric GTP-binding proteins are key regulators of a multitude of signaling pathways in all eukaryotes. Although the core G-protein components and their basic biochemistries are broadly conserved throughout evolution, the regulatory mechanisms of G proteins seem to have been rewired in plants to meet specific needs. These proteins are currently the focus of intense research in plants due to their involvement in many agronomically important traits, such as seed yield, organ size regulation, biotic and abiotic stress responses, symbiosis, and nitrogen use efficiency. The availability of massive sequence information from a variety of plant species, extensive biochemical data generated over decades, and impressive genetic resources for plant G proteins have made it possible to examine their role, unique properties, and novel regulation. This review focuses on some recent advances in our understanding of the mechanistic details of this critical signaling pathway to enable the precise manipulation and generation of plants to meet future needs.

Skeletal patterns in the autopodium of native and regenerated limbs of the larval axolotl, Ambystoma mexicanum

1991 ◽  
Vol 69 (1) ◽  
pp. 1-6 ◽  
Author(s):  
Steven R. Scadding
Keyword(s):  
Vitamin A ◽  
Significant Variation ◽  
Limb Regeneration ◽  
Ambystoma Mexicanum ◽  
Skeletal Patterning ◽  
Skeletal Pattern ◽  
Limb Pattern ◽  
Salamander Species

The purpose of this investigation was to study the autopodial skeletal patterns that are observed in native (never regenerated) and regenerated limbs of the larval axolotl, Ambystoma mexicanum. The axolotl is used widely in limb regeneration studies, and in the regenerating axolotl limb mesopodial patterns can be modified by such factors as vitamin A administration. It is also known that other salamander species show significant variation in autopodial skeletal patterning. Hence, it seemed important to determine the type and frequency of autopodial variants in both native limbs and those that have regenerated after amputation at either the stylopodial and zeugopodial levels. The results showed that native limbs exhibited a complete skeletal pattern in the majority of cases, but that variants involving loss of a phalange or reduction in the number of carpals or tarsals occurred frequently. Regenerated limb patterns were more variable than those seen in native limbs, and limbs regenerating from zeugopodial level amputations were more variable than those regenerating from stylopodial level amputation. The significance of these observations for the development and regeneration of limb pattern is discussed.

scholarly journals Experimentally Induced Metamorphosis in Axolotl (Ambystoma mexicanum) Under Constant Diet Restructures Microbiota Accompanied by Reduced Limb Regenerative Capacity

2018 ◽  
Author(s):  
Turan Demircan ◽  
Guvanch Ovezmyradov ◽  
Berna Yıldırım ◽  
İlknur Keskin ◽  
Ayse Elif İlhan ◽  
...  
Keyword(s):  
Model Organism ◽  
Fecal Microbiota ◽  
Ambystoma Mexicanum ◽  
Rrna Gene ◽  
Regenerative Capacity ◽  
Experimental Procedure ◽  
Bacterial Microbiota ◽  
Major Transition ◽  
Salamander Species ◽  
Experimentally Induced

AbstractAxolotl (Ambystoma mexicanum) is a critically endangered salamander species and a model organism for regenerative and developmental biology. Despite life-long neoteny in nature and in captive-bred colonies, metamorphosis of these animals can be experimentally induced by administering Thyroid hormones (THs). However, biological consequences of this experimental procedure, such as host microbiota response and implications for regenerative capacity, remain largely unknown. Here, we systematically compared host bacterial microbiota associated with skin, stomach, gut tissues and fecal samples based on 16S rRNA gene sequences, along with limb regenerative capacity, between neotenic and metamorphic Axolotls. Our results show that distinct bacterial communities inhabit individual organs of Axolotl and undergo substantial restructuring through metamorphosis. Drastic restructuring was observed for skin microbiota, highlighted by a major transition from Firmicutes-enriched to Proteobacteria-enriched relative abundance and precipitously decreased diversity. Remarkably, shifts in microbiota was accompanied by a steep reduction in limb regenerative capacity. Fecal microbiota of neotenic and metamorphic Axolotl shared relatively higher similarity, suggesting that diet continues to shape microbiota despite fundamental transformations in the host digestive organs. The results provide novel insights into microbiological and regenerative aspects of Axolotl metamorphosis and will establish a baseline for future in-depth studies.

scholarly journals Identifying structural variants using linked-read sequencing data

2017 ◽  
Author(s):  
Rebecca Elyanow ◽  
Hsin-Ta Wu ◽  
Benjamin J. Raphael
Keyword(s):  
Cancer Cell Line ◽  
Whole Genome Sequencing Data ◽  
Sequence Information ◽  
The Novel ◽  
Cancer Genes ◽  
Structural Variants ◽  
Sequencing Data ◽  
Individual Genome ◽  
Large Deletions ◽  
Cancer Genomes

AbstractStructural variation, including large deletions, duplications, inversions, translocations, and other rearrangements, is common in human and cancer genomes. A number of methods have been developed to identify structural variants from Illumina short-read sequencing data. However, reliable identification of structural variants remains challenging because many variants have breakpoints in repetitive regions of the genome and thus are difficult to identify with short reads. The recently developed linked-read sequencing technology from 10X Genomics combines a novel barcoding strategy with Illumina sequencing. This technology labels all reads that originate from a small number (~5-10) DNA molecules ~50Kbp in length with the same molecular barcode. These barcoded reads contain long-range sequence information that is advantageous for identification of structural variants. We present Novel Adjacency Identification with Barcoded Reads (NAIBR), an algorithm to identify structural variants in linked-read sequencing data. NAIBR predicts novel adjacencies in a individual genome resulting from structural variants using a probabilistic model that combines multiple signals in barcoded reads. We show that NAIBR outperforms several existing methods for structural variant identification – including two recent methods that also analyze linked-reads – on simulated sequencing data and 10X whole-genome sequencing data from the NA12878 human genome and the HCC1954 breast cancer cell line. Several of the novel somatic structural variants identified in HCC1954 overlap known cancer genes.

scholarly journals Touching the Surface: Diverse Roles for the Flagellar Membrane in Kinetoplastid Parasites

2020 ◽  
Vol 84 (2) ◽  
Author(s):  
Felice D. Kelly ◽  
Marco A. Sanchez ◽  
Scott M. Landfear
Keyword(s):  
Extracellular Milieu ◽  
Body Of Knowledge ◽  
Genome Wide ◽  
Internal Structures ◽  
Flagellar Membrane ◽  
Microbe Interactions ◽  
Intracellular Organelles ◽  
Host Microbe Interactions ◽  
Protein Components ◽  
Host Parasite

SUMMARY While flagella have been studied extensively as motility organelles, with a focus on internal structures such as the axoneme, more recent research has illuminated the roles of the flagellar surface in a variety of biological processes. Parasitic protists of the order Kinetoplastida, which include trypanosomes and Leishmania species, provide a paradigm for probing the role of flagella in host-microbe interactions and illustrate that this interface between the flagellar surface and the host is of paramount importance. An increasing body of knowledge indicates that the flagellar membrane serves a multitude of functions at this interface: attachment of parasites to tissues within insect vectors, close interactions with intracellular organelles of vertebrate cells, transactions between flagella from different parasites, junctions between the flagella and the parasite cell body, emergence of nanotubes and exosomes from the parasite directed to either host or microbial targets, immune evasion, and sensing of the extracellular milieu. Recent whole-organelle or genome-wide studies have begun to identify protein components of the flagellar surface that must mediate these diverse host-parasite interactions. The increasing corpus of knowledge on kinetoplastid flagella will likely prove illuminating for other flagellated or ciliated pathogens as well.

Vitamin A inhibits amphibian tail regeneration

1987 ◽  
Vol 65 (2) ◽  
pp. 457-459 ◽  
Author(s):  
Steven R. Scadding
Keyword(s):  
Retinoic Acid ◽  
Vitamin A ◽  
Xenopus Laevis ◽  
Ambystoma Mexicanum ◽  
Complete Inhibition ◽  
Notophthalmus Viridescens ◽  
Tail Regeneration ◽  
Dose Levels ◽  
Dose Dependent

The objective of this investigation was to determine what effect vitamin A had on tail regeneration in Notophthalmus viridescens adults, in Ambystoma mexicanum larvae, and in Xenopus laevis tadpoles. Notophthalmus viridescens and Ambystoma mexicanum had their tails amputated and then were treated with retinol palmitate by immersion in concentrations known to cause proximodistal duplications in regenerating limbs. Xenopus laevis tadpoles had their tails amputated and then were treated with either retinol palmitate by immersion, or with retinoic acid administered by implantation of silastin blocks containing retinoic acid. The results ranged from no effect at all at the lower dose levels used, to complete inhibition of tail regeneration at higher dose levels. The degree of inhibition of tail regeneration appeared to be dose dependent. In no case were any duplicated or accessory structures formed analogous to those observed in regenerating limbs. This result suggests that the morphogenetic processes involved in tail regeneration are at least in some ways different from those occurring in limbs, where a similar vitamin A treatment would cause proximodistal duplication or production of accessory limb structures.

scholarly journals Probing the Modularity of Megasynthases by Rational Engineering of a Fatty Acid Synthase (FAS) Type I

2018 ◽  
Author(s):  
Alexander Rittner ◽  
Karthik S. Paithankar ◽  
David Drexler ◽  
Aaron Himmler ◽  
Martin Grininger
Keyword(s):  
Fatty Acid Synthase ◽  
Fundamental Property ◽  
Catalytic Efficiency ◽  
Sequence Information ◽  
Type I ◽  
The Novel ◽  
Strongly Coupled ◽  
Rational Engineering ◽  
The Family ◽  
Biological Entities

AbstractModularity is an aspect of a decomposable system with a coordinating authority that acts as a glue which holds the loosely held components. These multi-component entities (“modules”) facilitate rewiring into different designs allowing for change. Such modular character is a fundamental property of many biological entities, especially the family of megasynthases such as polyketide synthases (PKSs). The ability of these PKSs to produce diverse product spectra is strongly coupled to their broad architectural modularity. Decoding the molecular basis of modularity, i.e. identifying the folds and domains that comprise the modules as well as understanding constrains of the assembly of modules, is of utmost importance for harnessing megasynthases for the synthesis of designer compounds. In this study, we exploit the close semblance between PKSs and animal FAS to re-engineer animal FAS to probe the modularity of the FAS/PKS family. Guided by structural and sequence information, we truncate and dissect animal FAS into its components, and reassemble them to generate new PKS-like modules as well as bimodular constructs. The novel engineered modules resemble all four common module types of PKSs and demonstrate that this approach can be a powerful tool to create higher catalytic efficiency. Our data exemplify the inherent plasticity and robustness of the overall FAS/PKS fold, and open new avenues to explore FAS-based biosynthetic pathways for custom compound design.

scholarly journals Thousands of novel translated open reading frames in humans inferred by ribosome footprint profiling

2015 ◽  
Author(s):  
Anil Raj ◽  
Sidney H. Wang ◽  
Heejung Shim ◽  
Arbel Harpak ◽  
Yang I. Li ◽  
...  
Keyword(s):  
Significant Negative Correlation ◽  
Selective Constraint ◽  
Open Reading Frames ◽  
Sequence Information ◽  
The Novel ◽  
Protein Coding ◽  
Coding Sequences ◽  
Coding Regions ◽  
Human Lymphoblastoid Cell ◽  
Reading Frames

AbstractAccurate annotation of protein coding regions is essential for understanding how genetic information is translated into biological functions. Here we describe riboHMM, a new method that uses ribosome footprint data along with gene expression and sequence information to accurately infer translated sequences. We applied our method to human lymphoblastoid cell lines and identified 7,273 previously unannotated coding sequences, including 2,442 translated upstream open reading frames. We observed an enrichment of harringtonine-treated ribosome footprints at the inferred initiation sites, validating many of the novel coding sequences. The novel sequences exhibit significant signatures of selective constraint in the reading frames of the inferred proteins, suggesting that many of these are functional. Nearly 40% of bicistronic transcripts showed significant negative correlation in the levels of translation of their two coding sequences, suggesting a key regulatory role for these novel translated sequences. Our work significantly expands the set of known coding regions in humans.

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