Insights into the Evolution of Spermatogenesis-Related Ubiquitin–Proteasome System Genes in Abdominal Testicular Laurasiatherians

During embryonic development in mammals, the testicles generally descend into the scrotum, making the testicular temperature 2–4 °C lower than the core temperature via heat exchange and clearance, and thus more beneficial for normal spermatogenesis. Failure to descend, known as cryptorchidism, carries a series of risks such as infertility and testicular cancer. However, some mammals have evolved abdominal testes while maintaining healthy reproduction. To explore the underlying molecular mechanism, we conducted comparative genomic analyses and functional assays on the spermatogenesis-related ubiquitin–proteasome system (UPS) genes essential to sperm formation in representative laurasiatherians. Here, positive selection and rapid evolution of spermatogenesis-related UPS genes were identified in the abdominal testicular laurasiatherians. Moreover, potential convergent amino acids were found between distantly related species with similar abdominal testicles and functional analyses showed RNF8 (V437I) in abdominal testicular species (437I) has a stronger ubiquitination ability, which suggests that the mammals with abdominal testes might exhibit enhanced sperm cell histone clearance to maintain sperm formation. This evidence implies that, in response to “cryptorchidism injury”, spermatogenesis-related UPS genes in the abdominal testicular species might have undergone adaptive evolution to stabilize sperm formation. Thus, our study could provide some novel insights into the reproductive adaptation in abdominal testicular mammals.

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Rapid evolution and molecular convergence in cryptorchidism-related genes associated with inherently undescended testes in mammals

BMC Ecology and Evolution ◽

10.1186/s12862-021-01753-5 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Simin Chai ◽

Ran Tian ◽

Juanjuan Bi ◽

Shixia Xu ◽

Guang Yang ◽

...

Keyword(s):

Muscle Development ◽

Rapid Evolution ◽

Genetic Material ◽

Comparative Genomic ◽

Testicular Descent ◽

Ancestral State ◽

Undescended Testes ◽

Genomic Analyses ◽

Genetic Mechanisms ◽

Molecular Convergence

Abstract Background The mammalian testis is an important male exocrine gland and spermatozoa-producing organ that usually lies in extra-abdominal scrotums to provide a cooler environment for spermatogenesis and sperm storage. Testicles sometimes fail to descend, leading to cryptorchidism. However, certain groups of mammals possess inherently ascrotal testes (i.e. testes that do not descend completely or at all) that have the same physiological functions as completely descended scrotal testes. Although several anatomical and hormonal factors involved in testicular descent have been studied, there is still a paucity of comprehensive research on the genetic mechanisms underlying the evolution of testicular descent in mammals and how mammals with ascrotal testes maintain their reproductive health. Results We performed integrative phenotypic and comparative genomic analyses of 380 cryptorchidism-related genes and found that the mammalian ascrotal testes trait is derived from an ancestral scrotal state. Rapidly evolving genes in ascrotal mammals were enriched in the Hedgehog pathway—which regulates Leydig cell differentiation and testosterone secretion—and muscle development. Moreover, some cryptorchidism-related genes in ascrotal mammals had undergone positive selection and contained specific mutations and indels. Genes harboring convergent/parallel amino acid substitutions between ascrotal mammals were enriched in GTPase functions. Conclusions Our results suggest that the scrotal testis is an ancestral state in mammals, and the ascrotal phenotype was derived multiple times in independent lineages. In addition, the adaptive evolution of genes involved in testicular descent and the development of the gubernaculum contributed to the evolution of ascrotal testes. Accurate DNA replication, the proper segregation of genetic material, and appropriate autophagy are the potential mechanisms for maintaining physiological normality during spermatogenesis in ascrotal mammals. Furthermore, the molecular convergence of GTPases is probably a mechanism in the ascrotal testes of different mammals. This study provides novel insights into the evolution of the testis and scrotum in mammals and contributes to a better understanding of the pathogenesis of cryptorchidism in humans.

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Draft Genome Sequence of Dermatophagoides pteronyssinus, the European House Dust Mite

Genome Announcements ◽

10.1128/genomea.00789-17 ◽

2017 ◽

Vol 5 (32) ◽

Cited By ~ 8

Author(s):

Rose Waldron ◽

Jamie McGowan ◽

Natasha Gordon ◽

Charley McCarthy ◽

E. Bruce Mitchell ◽

...

Keyword(s):

Genome Sequence ◽

Gene Prediction ◽

Draft Genome ◽

Dermatophagoides Pteronyssinus ◽

Mite Species ◽

Draft Genome Sequence ◽

Comparative Genomic ◽

Genomic Analyses ◽

Dust Mite ◽

Functional Analyses

ABSTRACT Dermatophagoides pteronyssinus is the European dust mite and a major source of human allergens. Here, we present the first draft genome sequence of the mite, as well as the ab initio gene prediction and functional analyses that will facilitate comparative genomic analyses with other mite species.

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The Sinorhizobium fredii HH103 Genome: A Comparative Analysis With S. fredii Strains Differing in Their Symbiotic Behavior With Soybean

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-12-14-0397-fi ◽

2015 ◽

Vol 28 (7) ◽

pp. 811-824 ◽

Cited By ~ 33

Author(s):

José-María Vinardell ◽

Sebastián Acosta-Jurado ◽

Susanne Zehner ◽

Michael Göttfert ◽

Anke Becker ◽

...

Keyword(s):

Core Genome ◽

Comparative Genomic ◽

Secretion Systems ◽

Sinorhizobium Fredii ◽

The Core ◽

Sensing Systems ◽

Plot Analysis ◽

Genomic Analyses ◽

Surface Polysaccharide ◽

Protein Secretion Systems

Sinorhizobium fredii HH103 is a fast-growing rhizobial strain infecting a broad range of legumes including both American and Asiatic soybeans. In this work, we present the sequencing and annotation of the HH103 genome (7.25 Mb), consisting of one chromosome and six plasmids and representing the structurally most complex sinorhizobial genome sequenced so far. Comparative genomic analyses of S. fredii HH103 with strains USDA257 and NGR234 showed that the core genome of these three strains contains 4,212 genes (61.7% of the HH103 genes). Synteny plot analysis revealed that the much larger chromosome of USDA257 (6.48 Mb) is colinear to the HH103 (4.3 Mb) and NGR324 chromosomes (3.9 Mb). An additional region of the USDA257 chromosome of about 2 Mb displays similarity to plasmid pSfHH103e. Remarkable differences exist between HH103 and NGR234 concerning nod genes, flavonoid effect on surface polysaccharide production, and quorum-sensing systems. Furthermore a number of protein secretion systems have been found. Two genes coding for putative type III–secreted effectors not previously described in S. fredii, nopI and gunA, have been located on the HH103 genome. These differences could be important to understand the different symbiotic behavior of S. fredii strains HH103, USDA257, and NGR234 with soybean.

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Structural insights into the functional cycle of the ATPase module of the 26S proteasome

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1621129114 ◽

2017 ◽

Vol 114 (6) ◽

pp. 1305-1310 ◽

Cited By ~ 88

Author(s):

Marc Wehmer ◽

Till Rudack ◽

Florian Beck ◽

Antje Aufderheide ◽

Günter Pfeifer ◽

...

Keyword(s):

Atp Hydrolysis ◽

Ubiquitin Proteasome System ◽

26S Proteasome ◽

Core Particle ◽

Nucleotide Analogs ◽

The Core ◽

Cryo Electron Microscopy ◽

Intracellular Proteins ◽

Ubiquitin Proteasome ◽

Structural Insights

In eukaryotic cells, the ubiquitin–proteasome system (UPS) is responsible for the regulated degradation of intracellular proteins. The 26S holocomplex comprises the core particle (CP), where proteolysis takes place, and one or two regulatory particles (RPs). The base of the RP is formed by a heterohexameric AAA+ ATPase module, which unfolds and translocates substrates into the CP. Applying single-particle cryo-electron microscopy (cryo-EM) and image classification to samples in the presence of different nucleotides and nucleotide analogs, we were able to observe four distinct conformational states (s1 to s4). The resolution of the four conformers allowed for the construction of atomic models of the AAA+ ATPase module as it progresses through the functional cycle. In a hitherto unobserved state (s4), the gate controlling access to the CP is open. The structures described in this study allow us to put forward a model for the 26S functional cycle driven by ATP hydrolysis.

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Phylogenomic and Molecular Demarcation of the Core Members of the PolyphyleticPasteurellaceaeGeneraActinobacillus,Haemophilus, andPasteurella

International Journal of Genomics ◽

10.1155/2015/198560 ◽

2015 ◽

Vol 2015 ◽

pp. 1-15 ◽

Cited By ~ 12

Author(s):

Sohail Naushad ◽

Mobolaji Adeolu ◽

Nisha Goel ◽

Bijendra Khadka ◽

Aqeel Al-Dahwi ◽

...

Keyword(s):

Phylogenetic Trees ◽

Phylogenetic Analyses ◽

Sensu Stricto ◽

The Other ◽

Comparative Genomic ◽

Molecular Signatures ◽

The Core ◽

Conserved Signature Indels ◽

Genomic Analyses ◽

Large Clusters

The generaActinobacillus, Haemophilus,andPasteurellaexhibit extensive polyphyletic branching in phylogenetic trees and do not represent coherent clusters of species. In this study, we have utilized molecular signatures identified through comparative genomic analyses in conjunction with genome based and multilocus sequence based phylogenetic analyses to clarify the phylogenetic and taxonomic boundary of these genera. We have identified large clusters ofActinobacillus, Haemophilus,andPasteurellaspecies which represent the “sensu stricto” members of these genera. We have identified 3, 7, and 6 conserved signature indels (CSIs), which are specifically shared bysensu strictomembers ofActinobacillus, Haemophilus,andPasteurella, respectively. We have also identified two different sets of CSIs that are unique characteristics of the pathogen containing generaAggregatibacterandMannheimia, respectively. It is now possible to demarcate the generaActinobacillus sensu stricto, Haemophilus sensu stricto,andPasteurella sensu strictoon the basis of discrete molecular signatures. The other members of the generaActinobacillus, Haemophilus,andPasteurellathat do not fall within the “sensu stricto” clades and do not contain these molecular signatures should be reclassified as other genera. The CSIs identified here also provide useful diagnostic targets for the identification of current and novel members of the indicated genera.

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Diversity and Horizontal Transfer of Antarctic Pseudomonas spp. Plasmids

Genes ◽

10.3390/genes10110850 ◽

2019 ◽

Vol 10 (11) ◽

pp. 850 ◽

Cited By ~ 1

Author(s):

Krzysztof Romaniuk ◽

Michal Styczynski ◽

Przemyslaw Decewicz ◽

Oliwia Buraczewska ◽

Witold Uhrynowski ◽

...

Keyword(s):

Transposable Elements ◽

Horizontal Transfer ◽

Comparative Genomic ◽

Narrow Host Range ◽

Antarctic Soils ◽

Pseudomonas Spp ◽

Genomic Analyses ◽

Genes Encoding ◽

Pilin Protein ◽

Functional Analyses

Pseudomonas spp. are widely distributed in various environments around the world. They are also common in the Antarctic regions. To date, almost 200 plasmids of Pseudomonas spp. have been sequenced, but only 12 of them were isolated from psychrotolerant strains. In this study, 15 novel plasmids of cold-active Pseudomonas spp. originating from the King George Island (Antarctica) were characterized using a combined, structural and functional approach, including thorough genomic analyses, functional analyses of selected genetic modules, and identification of active transposable elements localized within the plasmids and comparative genomics. The analyses performed in this study increased the understanding of the horizontal transfer of plasmids found within Pseudomonas populations inhabiting Antarctic soils. It was shown that the majority of the studied plasmids are narrow-host-range replicons, whose transfer across taxonomic boundaries may be limited. Moreover, structural and functional analyses enabled identification and characterization of various accessory genetic modules, including genes encoding major pilin protein (PilA), that enhance biofilm formation, as well as active transposable elements. Furthermore, comparative genomic analyses revealed that the studied plasmids of Antarctic Pseudomonas spp. are unique, as they are highly dissimilar to the other known plasmids of Pseudomonas spp.

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Genomic Analyses of New Genes and Their Phenotypic Effects Reveal Rapid Evolution of Essential Functions in Drosophila Development

10.1101/2020.10.27.357848 ◽

2020 ◽

Author(s):

Shengqian Xia ◽

Nicholas W. VanKuren ◽

Chunyan Chen ◽

Li Zhang ◽

Clause Kemkemer ◽

...

Keyword(s):

Genetic Basis ◽

False Negative ◽

Rapid Evolution ◽

Phenotypic Effect ◽

Gene Effects ◽

New Genes ◽

Developmental Effects ◽

Genomic Analyses ◽

Functional Analyses

ABSTRACTIt is a conventionally held dogma that the genetic basis underlying development is conserved in a long evolutionary time scale. Ample experiments based on mutational, biochemical, functional, and complementary knockdown/knockout approaches have revealed the unexpectedly important role of recently evolved new genes in the development of Drosophila. The recent progress in the analyses of gene effects and improvements in the computational identification of new genes, which has led to large sample sizes of new genes, open the door to investigate the evolution of gene essentiality with a phylogenetically high resolution. These advancements also raised interesting issues related to phenotypic effect analyses of genes, particularly of those that recently originated. Here we reported our analyses of these issues, including the dating of gene ages, the interpretation of RNAi data that may confuse false positive/false negative rates, and the potential confounding impact of compensation and developmental effects that were not considered during previous CRISPR knockout experiments. We further analyzed new data from knockdowns of 702 new genes (~66% of total 1,070 Drosophila melanogaster new genes), revealing a similarly high proportion of essential genes from recent evolution, compared to those found in distant ancestors of D. melanogaster. Knockout of a few young genes detected analogous essentiality. Furthermore, our experimentally determined distribution and comparison of knockdown efficiency in different RNAi libraries provided valuable data for general functional analyses of genes. Taken together, these data, along with an improved understanding of the phenotypic effect analyses of new genes, provide further evidence to the conclusion that new genes in Drosophila quickly evolved essential functions in viability during development.

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The ubiquitin–proteasome system and skeletal muscle wasting

Essays in Biochemistry ◽

10.1042/bse0410173 ◽

2005 ◽

Vol 41 ◽

pp. 173-186 ◽

Cited By ~ 110

Author(s):

Didier Attaix ◽

Sophie Ventadour ◽

Audrey Codran ◽

Daniel Béchet ◽

Daniel Taillandier ◽

...

Keyword(s):

Skeletal Muscle ◽

Muscle Wasting ◽

Proteolytic Enzymes ◽

Cathepsin L ◽

Ubiquitin Proteasome System ◽

Complete Breakdown ◽

Skeletal Muscle Proteins ◽

Ubiquitin Proteasome ◽

Tripeptidyl Peptidase Ii ◽

F Box Protein

The ubiquitin–proteasome system (UPS) is believed to degrade the major contractile skeletal muscle proteins and plays a major role in muscle wasting. Different and multiple events in the ubiquitination, deubiquitination and proteolytic machineries are responsible for the activation of the system and subsequent muscle wasting. However, other proteolytic enzymes act upstream (possibly m-calpain, cathepsin L, and/or caspase 3) and downstream (tripeptidyl-peptidase II and aminopeptidases) of the UPS, for the complete breakdown of the myofibrillar proteins into free amino acids. Recent studies have identified a few critical proteins that seem necessary for muscle wasting {i.e. the MAFbx (muscle atrophy F-box protein, also called atrogin-1) and MuRF-1 [muscle-specific RING (really interesting new gene) finger 1] ubiquitin–protein ligases}. The characterization of their signalling pathways is leading to new pharmacological approaches that can be useful to block or partially prevent muscle wasting in human patients.

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