Enhanced Understanding of Molecular Interactions and Function Underlying Pain Processes Through Networks of Transcript Isoforms, Genes, and Gene Families

In order to preserve structure and function, proteins tend to preferentially conserve amino acids at particular sites along the sequence. Because mutations can affect structure and function, the question arises whether the preference of a protein site for a particular amino acid varies between protein homologs, and to what extent that variation depends on sequence divergence. Answering these questions can help in the development of models of sequence evolution, as well as provide insights on the dependence of the fitness effects of mutations on the genetic background of sequences, a phenomenon known as epistasis. Here, I comment on recent computational work providing a systematic analysis of the extent to which the amino acid preferences of proteins depend on the background mutations of protein homologs.

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Exploring the Caenorhabditis elegans and Drosophila melanogaster genomes to understand neuropeptide and peptidase function

Biochemical Society Transactions ◽

10.1042/bst0280464 ◽

2000 ◽

Vol 28 (4) ◽

pp. 464-469 ◽

Cited By ~ 12

Author(s):

D. Coates ◽

R. Siviter ◽

R. E. Isaac

Keyword(s):

Drosophila Melanogaster ◽

Caenorhabditis Elegans ◽

Comparative Studies ◽

Gene Families ◽

Human Condition ◽

Form And Function ◽

And Function ◽

The Human Condition

Comparison of peptidase gene families in the newly released Drosophila melanogaster and Caenorhabditis elegans genomes highlights important differences in peptidase distributions with relevance to the evolution of both form and function in these two organisms and can help to identify the most appropriate model when using comparative studies relevant to the human condition.

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The genome of the water strider Gerris buenoi reveals expansions of gene repertoires associated with adaptations to life on the water

10.1101/242230 ◽

2018 ◽

Cited By ~ 1

Author(s):

David Armisén ◽

Rajendhran Rajakumar ◽

Markus Friedrich ◽

Joshua B Benoit ◽

Hugh M. Robertson ◽

...

Keyword(s):

Insulin Receptors ◽

Gene Families ◽

Developmental Genetics ◽

Manual Annotation ◽

Gene Duplications ◽

Water Strider ◽

Protein Coding ◽

Genomic Changes ◽

Aquatic Bugs ◽

And Function

AbstractThe semi-aquatic bugs conquered water surfaces worldwide and occupy ponds, streams, lakes, mangroves, and even open oceans. As such, they inspired a range of scientific studies from ecology and evolution to developmental genetics and hydrodynamics of fluid locomotion. However, the lack of a representative water strider genome hinders thorough investigations of the mechanisms underlying the processes of adaptation and diversification in this group. Here we report the sequencing and manual annotation of the Gerris buenoi (G. buenoi) genome, the first water strider genome to be sequenced so far. G. buenoi genome is about 1 000Mb and the sequencing effort recovered 20 949 predicted protein-coding genes. Manual annotation uncovered a number of local (tandem and proximal) gene duplications and expansions of gene families known for their importance in a variety of processes associated with morphological and physiological adaptations to water surface lifestyle. These expansions affect key processes such as growth, vision, desiccation resistance, detoxification, olfaction and epigenetic components. Strikingly, the G. buenoi genome contains three Insulin Receptors, a unique case among metazoans, suggesting key changes in the rewiring and function of the insulin pathway. Other genomic changes include wavelength sensitivity shifts in opsin proteins likely in association with the requirements of vision in water habitats. Our findings suggest that local gene duplications might have had an important role during the evolution of water striders. These findings along with the G. buenoi genome open exciting research opportunities to understand adaptation and genome evolution of this unique hemimetabolous insect.

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The R2R3-MYB transcription factor family in Taxus chinensis: identification, characterization, expression profiling and posttranscriptional regulation analysis

PeerJ ◽

10.7717/peerj.8473 ◽

2020 ◽

Vol 8 ◽

pp. e8473

Author(s):

Xinling Hu ◽

Lisha Zhang ◽

Iain Wilson ◽

Fenjuan Shao ◽

Deyou Qiu

Keyword(s):

Transcription Factor ◽

Posttranscriptional Regulation ◽

Gene Families ◽

Myb Transcription Factor ◽

Taxus Chinensis ◽

Transcription Factor Family ◽

Myb Genes ◽

And Function ◽

R2r3 Myb

The MYB transcription factor family is one of the largest gene families playing regulatory roles in plant growth and development. The MYB family has been studied in a variety of plant species but has not been reported in Taxus chinensis. Here we identified 72 putative R2R3-MYB genes in T. chinensis using a comprehensive analysis. Sequence features, conversed domains and motifs were characterized. The phylogenetic analysis showed TcMYBs and AtMYBs were clustered into 36 subgroups, of which 24 subgroups included members from T. chinensis and Arabidopsis thaliana, while 12 subgroups were specific to one species. This suggests the conservation and specificity in structure and function of plant R2R3-MYBs. The expression of TcMYBs in various tissues and different ages of xylem were investigated. Additionally, miRNA-mediated posttranscriptional regulation analysis revealed that TcMYBs were the targets of miR858, miR159 and miR828, suggesting the posttranscriptional regulation of MYBs is highly conserved in plants. The results provide a basis for further study the role of TcMYBs in the regulation of secondary metabolites of T. chinensis.

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Evolution and Function of the Sucrose-Phosphate Synthase Gene Families in Wheat and Other Grasses

PLANT PHYSIOLOGY ◽

10.1104/pp.104.042457 ◽

2004 ◽

Vol 135 (3) ◽

pp. 1753-1764 ◽

Cited By ~ 71

Author(s):

C. Kate Castleden ◽

Naohiro Aoki ◽

Vanessa J. Gillespie ◽

Elspeth A. MacRae ◽

W. Paul Quick ◽

...

Keyword(s):

Sucrose Phosphate Synthase ◽

Gene Families ◽

And Function ◽

Sucrose Phosphate ◽

Phosphate Synthase

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Nematode-Induced Changes of Transporter Gene Expression in Arabidopsis Roots

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-18-1247 ◽

2005 ◽

Vol 18 (12) ◽

pp. 1247-1257 ◽

Cited By ~ 89

Author(s):

Ulrich Z. Hammes ◽

Daniel P. Schachtman ◽

R. Howard Berg ◽

Erik Nielsen ◽

Wolfgang Koch ◽

...

Keyword(s):

Gene Families ◽

Transcript Abundance ◽

Giant Cells ◽

Transport Processes ◽

Transfer Cells ◽

Parasitic Nematodes ◽

Feeding Site ◽

Feeding Sites ◽

The Many ◽

And Function

Root-knot plant-parasitic nematodes (Meloidogyne spp.) account for much of the damage inflicted to plants by nematodes. The feeding sites of these nematodes consist of “giant” cells, which have characteristics of transfer cells found in other parts of plants. Increased transport activity across the plasma membrane is a hallmark of transfer cells, and giant cells provide nutrition for nematodes; therefore, we initiated a study to identify the transport processes that contribute to the development and function of nematode-induced feeding sites. The study was conducted over a 4-week period, during which time the large changes in the development of giant cells were documented. The Arabidopsis ATH1 GeneChip was used to identify the many transporter genes that were regulated by nematode infestation. Expression of 50 transporter genes from 18 different gene families was significantly changed upon nematode infestation. Sixteen transporter genes were studied in more detail using real-time reverse-transcriptase polymerase chain reaction to determine transcript abundance in nematode-induced galls that contain giant cells and uninfested regions of the root. Certain genes were expressed primarily in galls whereas others were expressed primarily in the uninfested regions of the root, and a third group was expressed evenly throughout the root. Multiple transport processes are regulated and these may play important roles in nematode feeding-site establishment and maintenance.

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Evolution of NLR resistance genes with non-canonical N-terminal domains in wild tomato species

10.1101/786194 ◽

2019 ◽

Cited By ~ 1

Author(s):

Kyungyong Seong ◽

Eunyoung Seo ◽

Meng Li ◽

Brian Staskawicz

Keyword(s):

Single Molecule ◽

Evolutionary Dynamics ◽

Plant Immunity ◽

Gene Families ◽

Recent Common Ancestor ◽

Wild Tomato Species ◽

Most Recent Common Ancestor ◽

Tomato Species ◽

Large Gene ◽

And Function

AbstractBackgroundNucleotide-binding and leucine-rich repeat immune receptors (NLRs) are an important component of plant immunity that provides resistance against diverse pathogens. NLRs often exist as large gene families, the members of which display diverse multi-domain architectures (MDAs) and evolve through various mechanisms of duplications and selections.ResultsWe conducted resistance gene enrichment sequencing (RenSeq) with single-molecule real time (SMRT) sequencing of PacBio for 18 accessions in Solanaceae including 15 wild tomatoes. We demonstrate what was previously known as Solanaceae Domain (SD) not only is more diverse in structure and function but also far anciently originated from the most recent common ancestor (MRCA) between Asterids and Amaranthaceae. In tomato, NLRs with the extended N-terminus displayed distinct patterns of evolution based on phylogenetic clades by proliferation, continuous elongation and domain losses.ConclusionsOur study provides high quality gene models of NLRs that can serve as resources for future studies for crop engineering and elucidates greater evolutionary dynamics of the extended NLRs than previously assumed.

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Molecular topography of an entire nervous system

10.1101/2020.12.15.422897 ◽

2020 ◽

Author(s):

Seth R Taylor ◽

Gabriel Santpere ◽

Alexis Weinreb ◽

Alec Barrett ◽

Molly B. Reilly ◽

...

Keyword(s):

Gene Expression ◽

Nervous System ◽

Web Application ◽

Gene Families ◽

Regulatory Elements ◽

Individual Neuron ◽

Specific Gene ◽

C Elegans ◽

Underlying Mechanisms ◽

And Function

SummaryNervous systems are constructed from a deep repertoire of neuron types but the underlying gene expression programs that specify individual neuron identities are poorly understood. To address this deficit, we have produced an expression profile of all 302 neurons of the C. elegans nervous system that matches the single cell resolution of its anatomy and wiring diagram. Our results suggest that individual neuron classes can be solely identified by combinatorial expression of specific gene families. For example, each neuron class expresses unique codes of ∼23 neuropeptide-encoding genes and ∼36 neuropeptide receptors thus pointing to an expansive “wireless” signaling network. To demonstrate the utility of this uniquely comprehensive gene expression catalog, we used computational approaches to (1) identify cis-regulatory elements for neuron-specific gene expression across the nervous system and (2) reveal adhesion proteins with potential roles in synaptic specificity and process placement. These data are available at cengen.org and can be interrogated at the web application CengenApp. We expect that this neuron-specific directory of gene expression will spur investigations of underlying mechanisms that define anatomy, connectivity and function throughout the C. elegans nervous system.

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Multiple Regionalized Genes and Their Putative Networks in the Interpeduncular Nucleus Suggest Complex Mechanisms of Neuron Development and Axon Guidance

Frontiers in Neuroanatomy ◽

10.3389/fnana.2021.643320 ◽

2021 ◽

Vol 15 ◽

Author(s):

Isabel M. García-Guillén ◽

Antonia Alonso ◽

Luis Puelles ◽

Faustino Marín ◽

Pilar Aroca

Keyword(s):

Axon Guidance ◽

Gene Families ◽

Brain Atlas ◽

Limbic Structure ◽

Neuron Development ◽

Interpeduncular Nucleus ◽

Functional Roles ◽

Vertebrate Brain ◽

Developing Mouse Brain ◽

And Function

The interpeduncular nucleus (IPN) is a highly conserved limbic structure in the vertebrate brain, located in the isthmus and rhombomere 1. It is formed by various populations that migrate from different sites to the distinct domains within the IPN: the prodromal, rostral interpeduncular, and caudal interpeduncular nuclei. The aim here was to identify genes that are differentially expressed across these domains, characterizing their putative functional roles and interactions. To this end, we screened the 2,038 genes in the Allen Developing Mouse Brain Atlas database expressed at E18.5 and we identified 135 genes expressed within the IPN. The functional analysis of these genes highlighted an overrepresentation of gene families related to neuron development, cell morphogenesis and axon guidance. The interactome analysis within each IPN domain yielded specific networks that mainly involve members of the ephrin/Eph and Cadherin families, transcription factors and molecules related to synaptic neurotransmission. These results bring to light specific mechanisms that might participate in the formation, molecular regionalization, axon guidance and connectivity of the different IPN domains. This genoarchitectonic model of the IPN enables data on gene expression and interactions to be integrated and interpreted, providing a basis for the further study of the connectivity and function of this poorly understood nuclear complex under both normal and pathological conditions.

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Fish and chips: the origin of human gene families is a predictor of the location of GWAS signals

10.21203/rs.3.rs-905423/v1 ◽

2021 ◽

Author(s):

Sara Victoria Good ◽

Ryan Gotesman ◽

Ilya Kisselev ◽

Andrew D. Paterson

Keyword(s):

Human Gene ◽

Gene Families ◽

Selective Constraint ◽

Variant Prioritization ◽

Gene Level ◽

And Function ◽

Genomic Length ◽

Human Complex ◽

Gwas Catalog ◽

Median Expression

Abstract GWAS have identified thousands of loci associated with human complex diseases and traits. How these loci are distributed through the genome has not been systematically evaluated. We hypothesised that the location of GWAS loci differ between ancestral linkage groups (ALGs) related to the paralogy and function of genes. We used data from the NHGRI-EBI GWAS catalog to determine whether the density of GWAS loci relative to HapMap variants in each ALG differed, and whether ALG’s were enriched for experimental factor ontological (EFO) terms assigned to the GWAS traits. In a gene-level analyses we explored the characteristics of genes linked to GWAS loci and those mapping to the ALG’s. We find that GWAS loci were enriched or deficient in 9 and 7 of the 17 ALG’s respectively, while there was no difference in the number of GWAS loci in regions of the human genome unassigned to an ALG. All but 2 ALG’s were significantly enriched or deficient for one or more EFO terms. Lastly, we find that genes assigned to an ALG are under higher levels of selective constraint, have longer coding sequences and higher median expression in the tissue of highest expression than genes not mapping to an ALG. On the other hand, genes associated with GWAS loci have longer genomic length and exhibit higher levels of selective constraint relative to non-GWAS genes.Collectively, this suggests that understanding the location and ancestral origins of GWAS signals may be informative for the development of tools for variant prioritization and interpretation.

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