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Schorr AL, Mejia AF, Miranda MY, Mangone M. An updated C. elegans nuclear body muscle transcriptome for studies in muscle formation and function. Skelet Muscle 2023; 13:4. [PMID: 36859305 PMCID: PMC9979539 DOI: 10.1186/s13395-023-00314-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 02/06/2023] [Indexed: 03/03/2023] Open
Abstract
The body muscle is an important tissue used in organisms for proper viability and locomotion. Although this tissue is generally well studied and characterized, and many pathways have been elucidated throughout the years, we still lack a comprehensive understanding of its transcriptome and how it controls muscle development and function. Here, we have updated a nuclear FACS sorting-based methodology to isolate and sequence a high-quality muscle transcriptome from Caenorhabditis elegans mixed-stage animals. We have identified 2848 muscle-specific protein-coding genes, including 78 transcription factors and 206 protein-coding genes containing an RNA binding domain. We studied their interaction network, performed a detailed promoter analysis, and identified novel muscle-specific cis-acting elements. We have also identified 16 high-quality muscle-specific miRNAs, studied their function in vivo using fluorochrome-based analyses, and developed a high-quality C. elegans miRNA interactome incorporating other muscle-specific datasets produced by our lab and others.Our study expands our understanding of how muscle tissue functions in C. elegans andin turn provides results that can in the future be applied to humans to study muscular-related diseases.
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Affiliation(s)
- Anna L. Schorr
- grid.215654.10000 0001 2151 2636Molecular and Cellular Biology Graduate Program, Arizona State University, Tempe, AZ USA ,grid.215654.10000 0001 2151 2636Virginia G. Piper Center for Personalized Diagnostics, The Biodesign Institute at Arizona State University, 1001 S McAllister Ave, Tempe, AZ USA ,grid.215654.10000 0001 2151 2636School of Life Sciences, Arizona State University, 751 E Lemon Mall, Tempe, AZ 85287 USA
| | - Alejandro Felix Mejia
- grid.215654.10000 0001 2151 2636School of Life Sciences, Arizona State University, 751 E Lemon Mall, Tempe, AZ 85287 USA
| | - Martina Y. Miranda
- grid.250942.80000 0004 0507 3225Helios Scholars at the Translational Genomics Research Institute, 445 N 5th St 4th Floor, Phoenix, AZ 85004 USA
| | - Marco Mangone
- Molecular and Cellular Biology Graduate Program, Arizona State University, Tempe, AZ, USA. .,Virginia G. Piper Center for Personalized Diagnostics, The Biodesign Institute at Arizona State University, 1001 S McAllister Ave, Tempe, AZ, USA. .,School of Life Sciences, Arizona State University, 751 E Lemon Mall, Tempe, AZ, 85287, USA.
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Kondratyeva L, Alekseenko I, Chernov I, Sverdlov E. Data Incompleteness May form a Hard-to-Overcome Barrier to Decoding Life's Mechanism. BIOLOGY 2022; 11:1208. [PMID: 36009835 PMCID: PMC9404739 DOI: 10.3390/biology11081208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 08/03/2022] [Accepted: 08/10/2022] [Indexed: 11/23/2022]
Abstract
In this brief review, we attempt to demonstrate that the incompleteness of data, as well as the intrinsic heterogeneity of biological systems, may form very strong and possibly insurmountable barriers for researchers trying to decipher the mechanisms of the functioning of live systems. We illustrate this challenge using the two most studied organisms: E. coli, with 34.6% genes lacking experimental evidence of function, and C. elegans, with identified proteins for approximately 50% of its genes. Another striking example is an artificial unicellular entity named JCVI-syn3.0, with a minimal set of genes. A total of 31.5% of the genes of JCVI-syn3.0 cannot be ascribed a specific biological function. The human interactome mapping project identified only 5-10% of all protein interactions in humans. In addition, most of the available data are static snapshots, and it is barely possible to generate realistic models of the dynamic processes within cells. Moreover, the existing interactomes reflect the de facto interaction but not its functional result, which is an unpredictable emerging property. Perhaps the completeness of molecular data on any living organism is beyond our reach and represents an unsolvable problem in biology.
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Affiliation(s)
- Liya Kondratyeva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia
| | - Irina Alekseenko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia
- Institute of Molecular Genetics of National Research Centre “Kurchatov Institute”, Moscow 123182, Russia
| | - Igor Chernov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia
| | - Eugene Sverdlov
- Institute of Molecular Genetics of National Research Centre “Kurchatov Institute”, Moscow 123182, Russia
- Kurchatov Center for Genome Research, National Research Center “Kurchatov Institute”, Moscow 123182, Russia
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OUP accepted manuscript. Brief Funct Genomics 2022; 21:243-269. [DOI: 10.1093/bfgp/elac007] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 03/17/2022] [Accepted: 03/18/2022] [Indexed: 11/14/2022] Open
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Abstract
Ras is the most mutated oncoprotein in cancer. Among the three oncogenic effectors of Ras - Raf, PI3 Kinase and RalGEF>Ral - signalling through RalGEF>Ral (Ras-like) is by far the least well understood. A variety of signals and binding partners have been defined for Ral, yet we know little of how Ral functions in vivo. This review focuses on previous research in Drosophila that defined a function for Ral in apoptosis and established indirect relationships among Ral, the CNH-domain MAP4 Kinase misshapen, and the JNK MAP kinase basket. Most of the described signalling components are not essential in C. elegans, facilitating subsequent analysis using developmental patterning of the C. elegans vulval precursor cells (VPCs). The functions of two paralogous CNH-domain MAP4 Kinases were defined relative to Ras>Raf, Notch and Ras>RalGEF>Ral signalling in VPCs. MIG-15, the nematode ortholog of misshapen, antagonizes both the Ral-dependent and Ras>Raf-dependent developmental outcomes. In contrast, paralogous GCK-2, the C. elegans ortholog of Drosophila happyhour, propagates the 2°-promoting signal of Ral. Manipulations via CRISPR of Ral signalling through GCK-2 coupled with genetic epistasis delineated a Ras>RalGEF>Ral>Exo84>GCK-2>MAP3KMLK-1> p38PMK-1 cascade. Thus, genetic analysis using invertebrate experimental organisms defined a cascade from Ras to p38 MAP kinase.
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Affiliation(s)
| | - David J. Reiner
- Texas A&M University, Houston, TX, USA,CONTACT David J. Reiner Institute of Biosciences and Technology, College of Medicine, Texas A&M Health Science Center, Texas A&M University, Houston, TX
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Shaikhulova S, Fakhrullina G, Nigamatzyanova L, Akhatova F, Fakhrullin R. Worms eat oil: Alcanivorax borkumensis hydrocarbonoclastic bacteria colonise Caenorhabditis elegans nematodes intestines as a first step towards oil spills zooremediation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 761:143209. [PMID: 33160671 DOI: 10.1016/j.scitotenv.2020.143209] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 10/09/2020] [Accepted: 10/20/2020] [Indexed: 06/11/2023]
Abstract
The environmental hazards of oil spills cannot be underestimated. Bioremediation holds promise among various approaches to tackle oil spills in soils and sediments. In particular, using oil-degrading bacteria is an efficient and self-regulating way to remove oil spills. Using animals for oil spills remediation is in its infancy, mostly due to the lack of efficient oil-degrading capabilities in eukaryotes. Here we show that Caenorhabditis elegans nematodes survive for extended periods (up to 22 days) on pure crude oil diet. Moreover, we report for the first time the use of Alcanivorax borkumensis hydrocarbonoclastic bacteria for colonisation of C. elegans intestines, which allows for effective digestion of crude oil by the nematodes. The worms fed and colonised by A. borkumensis demonstrated the similar or even better longevity, resistance against oxidative and thermal stress and reproductivity as those animals fed with Escherichia coli bacteria (normal food). Importantly, A. borkumensis-carrying nematodes were able to accumulate oil droplet from oil-contaminated soils. Artificial colonisation of soil invertebrates with oil-degrading bacteria will be an efficient way to distribute microorganisms in polluted soil, thus opening new avenues for oil spills zooremediation.
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Affiliation(s)
- Särbinaz Shaikhulova
- Bionanotechnology Lab, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kreml uramı 18, Kazan 420008, Republic of Tatarstan, Russian Federation
| | - Gӧlnur Fakhrullina
- Bionanotechnology Lab, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kreml uramı 18, Kazan 420008, Republic of Tatarstan, Russian Federation
| | - Läysän Nigamatzyanova
- Bionanotechnology Lab, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kreml uramı 18, Kazan 420008, Republic of Tatarstan, Russian Federation
| | - Farida Akhatova
- Bionanotechnology Lab, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kreml uramı 18, Kazan 420008, Republic of Tatarstan, Russian Federation
| | - Rawil Fakhrullin
- Bionanotechnology Lab, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kreml uramı 18, Kazan 420008, Republic of Tatarstan, Russian Federation.
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Zhang P, Wang J, Zhang X, Wang X, Jiang L, Gu X. Identification of AIDS-Associated Kaposi Sarcoma: A Functional Genomics Approach. Front Genet 2020; 10:1376. [PMID: 32038721 PMCID: PMC6992650 DOI: 10.3389/fgene.2019.01376] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 12/17/2019] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Kaposi sarcoma-associated herpes virus (KSHV) is one of the most common causal agents of Kaposi Sarcoma (KS) in individuals with HIV-infections. The virus has gained attention over the past few decades due to its remarkable pathogenic mechanisms. A group of genes, ORF71, ORF72, and ORF73, are expressed as polycistronic mRNAs and the functions of ORF71 and ORF72 in KSHV are already reported in the literature. However, the function of ORF73 has remained a mystery. The aim of this study is to conduct comprehensive exploratory experiments to clarify the role of ORF73 in KSHV pathology and discover markers of AIDS-associated KSHV-induced KS by bioinformatic approaches. METHODS AND RESULTS We searched for homologues of ORF-73 and attempted to predict protein-protein interactions (PPI) based on GeneCards and UniProtKB, utilizing Position-Specific Iterated BLAST (PSI-BLAST). We applied Gene Ontology (GO) and KEGG pathway analyses to identify highly conserved regions between ORF-73 and p53to help us identify potential markers with predominant hits and interactions in the KEGG pathway associated with host apoptosis and cell arrest. The protein p53 is selected because it is an important tumor suppressor antigen. To identify the potential roles of the candidate markers at the molecular level, we used PSIPRED keeping the conserved domains as the major parameters to predict secondary structures. We based the FUGE interpretation consolidations of the sequence-structure comparisons on distance homology, where the score for the amino acids matching the insertion/deletion (indels) detected were based on structures compared to the FUGE database of structural profiles. We also calculated the compatibility scores of sequence alignments accordingly. Based on the PSI-BLAST homologues, we checked the disordered structures predicted using PSI-Pred and DISO-Pred for developing a hidden Markov model (HMM). We further applied these HMMs models based on the alignment of constructed 3D models between the known structure and the HMM of our sequence. Moreover, stable homology and structurally conserved domains confirmed that ORF-73 maybe an important prognostic marker for AIDS-associated KS. CONCLUSION Collectively, similar variants of ORF-73 markers involved in the immune response may interact with targeted host proteins as predicted by our computational analysis. This work also suggests the existence of potential conformational changes that need to be further explored to help elucidate the role of immune signaling during KS towards the development of therapeutic applications.
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Affiliation(s)
- Peng Zhang
- School of Clinical Medicine, Shanghai University of Medicine & Health Sciences, Shanghai, China
- Department of Public Health, Shanghai General Practice Medical Education and Research Center, Shanghai, China
| | - Jiafeng Wang
- Stem Cell Research and Cellular Therapy Center, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Xiao Zhang
- Department of Implant Dentistry, Ninth People's Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Xiaolan Wang
- College of Nursing and Health Management, Shanghai University of Medicine & Health Sciences, Shanghai, China
| | - Liying Jiang
- Shanghai Key Laboratory of Molecular Imaging, Collaborative Research Center, Shanghai University of Medicine & Health Sciences, Shanghai, China
| | - Xuefeng Gu
- Shanghai Key Laboratory of Molecular Imaging, Collaborative Research Center, Shanghai University of Medicine & Health Sciences, Shanghai, China
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