1
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Feng L, Wang G, Song Q, Feng X, Su J, Ji G, Li M. Proteomics revealed an association between ribosome-associated proteins and amyloid beta deposition in Alzheimer's disease. Metab Brain Dis 2024; 39:263-282. [PMID: 38019374 DOI: 10.1007/s11011-023-01330-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 11/22/2023] [Indexed: 11/30/2023]
Abstract
Most scholars believe that amyloid-beta (Aβ) has the potential to induce apoptosis, stimulate an inflammatory cascade, promote oxidative stress and exacerbate the pathological progression of Alzheimer's disease (AD). Therefore, it is crucial to investigate the deposition of Aβ in AD. At approximately 6 months of age, APP/PS1 double transgenic mice gradually exhibit the development of plaques, as well as spatial and learning impairment. Notably, the hippocampus is specifically affected in the course of AD. Herein, 6-month-old APP/PS1 double transgenic mice were utilized, and the differentially expressed (DE) proteins in the hippocampus were identified and analyzed using 4D label-free quantitative proteomics technology and parallel reaction monitoring (PRM). Compared to wild-type mice, 29 proteins were upregulated and 25 proteins were downregulated in the AD group. Gene Ontology (GO) enrichment analysis of biological processes (BP) indicated that the DE proteins were mainly involved in 'ribosomal large subunit biogenesis'. Molecular function (MF) analysis results were primarily associated with '5.8S rRNA binding' and 'structural constituent of ribosome'. In terms of cellular components (CC), the DE proteins were mainly found in 'polysomal ribosome', 'cytosolic large ribosomal subunit', 'cytosolic ribosome', and 'large ribosomal subunit', among others. Furthermore, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis demonstrated that the results were mainly enriched in the 'Ribosome signaling pathway'. The key target proteins identified were ribosomal protein (Rp)l18, Rpl17, Rpl19, Rpl24, Rpl35, and Rpl6. The PRM verification results were consistent with the findings of the 4D label-free quantitative proteomics analysis. Overall, these findings suggest that Rpl18, Rpl17, Rpl19, Rpl24, Rpl35, and Rpl6 may have potential therapeutic value for the treatment of AD by targeting Aβ.
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Affiliation(s)
- Lina Feng
- Department of Neurology, the Second Affiliated Hospital of Shandong First Medical University, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, 271000, Shandong, China
| | - Guojun Wang
- Department of Neurosurgery, The Affiliated Taian City Central Hospital of Qingdao University, Taian, 271000, Shandong, China
| | - Qile Song
- Department of Neurology, the Second Affiliated Hospital of Shandong First Medical University, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, 271000, Shandong, China
| | - Xiaotong Feng
- Department of Neurology, the Second Affiliated Hospital of Shandong First Medical University, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, 271000, Shandong, China
| | - Jing Su
- Department of Geriatric Cardiovascular, The Affiliated Taian City Central Hospital of Qingdao University, Longtan Road, Taian, 271000, Shandong, China.
| | - Guangcheng Ji
- Department of Neurology, the Third Affiliated Clinical Hospital of the Changchun University of Chinese Medicine, Boshuo Road, Changchun, 130117, Jilin, China.
| | - Mingquan Li
- Department of Neurology, the Third Affiliated Clinical Hospital of the Changchun University of Chinese Medicine, Boshuo Road, Changchun, 130117, Jilin, China.
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2
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Ochkasova A, Arbuzov G, Malygin A, Graifer D. Two "Edges" in Our Knowledge on the Functions of Ribosomal Proteins: The Revealed Contributions of Their Regions to Translation Mechanisms and the Issues of Their Extracellular Transport by Exosomes. Int J Mol Sci 2023; 24:11458. [PMID: 37511213 PMCID: PMC10380927 DOI: 10.3390/ijms241411458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 07/10/2023] [Accepted: 07/12/2023] [Indexed: 07/30/2023] Open
Abstract
Ribosomal proteins (RPs), the constituents of the ribosome, belong to the most abundant proteins in the cell. A highly coordinated network of interactions implicating RPs and ribosomal RNAs (rRNAs) forms the functionally competent structure of the ribosome, enabling it to perform translation, the synthesis of polypeptide chain on the messenger RNA (mRNA) template. Several RPs contact ribosomal ligands, namely, those with transfer RNAs (tRNAs), mRNA or translation factors in the course of translation, and the contribution of a number of these particular contacts to the translation process has recently been established. Many ribosomal proteins also have various extra-ribosomal functions unrelated to translation. The least-understood and -discussed functions of RPs are those related to their participation in the intercellular communication via extracellular vesicles including exosomes, etc., which often carry RPs as passengers. Recently reported data show that such a kind of communication can reprogram a receptor cell and change its phenotype, which is associated with cancer progression and metastasis. Here, we review the state-of-art ideas on the implications of specific amino acid residues of RPs in the particular stages of the translation process in higher eukaryotes and currently available data on the transport of RPs by extracellular vesicles and its biological effects.
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Affiliation(s)
- Anastasia Ochkasova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Grigory Arbuzov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Alexey Malygin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Dmitri Graifer
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
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3
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Canto-Canché B, Burgos-Canul YY, Chi-Chuc D, Tzec-Simá M, Ku-González A, Brito-Argáez L, Carrillo-Pech M, De Los Santos-Briones C, Canseco-Pérez MÁ, Luna-Moreno D, Beltrán-García MJ, Islas-Flores I. Moonlight-like proteins are actually cell wall components in Pseudocercospora fijiensis. World J Microbiol Biotechnol 2023; 39:232. [PMID: 37349471 DOI: 10.1007/s11274-023-03676-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 06/12/2023] [Indexed: 06/24/2023]
Abstract
The fungal cell wall protects fungi against threats, both biotic and abiotic, and plays a role in pathogenicity by facilitating host adhesion, among other functions. Although carbohydrates (e.g. glucans, chitin) are the most abundant components, the fungal cell wall also harbors ionic proteins, proteins bound by disulfide bridges, alkali-extractable, SDS-extractable, and GPI-anchored proteins, among others; the latter consisting of suitable targets which can be used for fungal pathogen control. Pseudocercospora fijiensis is the causal agent of black Sigatoka disease, the principal threat to banana and plantain worldwide. Here, we report the isolation of the cell wall of this pathogen, followed by extensive washing to eliminate all loosely associated proteins and conserve those integrated to its cell wall. In the HF-pyridine protein fraction, one of the most abundant protein bands was recovered from SDS-PAGE gels, electro-eluted and sequenced. Seven proteins were identified from this band, none of which were GPI-anchored proteins. Instead, atypical (moonlight-like) cell wall proteins were identified, suggesting a new class of atypical proteins, bound to the cell wall by unknown linkages. Western blot and histological analyses of the cell wall fractions support that these proteins are true cell wall proteins, most likely involved in fungal pathogenesis/virulence, since they were found conserved in many fungal pathogens.
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Affiliation(s)
- Blondy Canto-Canché
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Colonia Chuburná de Hidalgo, Calle 43 No. 130 x 32 y 34, Mérida, A.C., Yucatán, C.P. 97205, México
| | - Yamily Yazmin Burgos-Canul
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Colonia Chuburná de Hidalgo, Calle 43 No. 130 x 32 y 34, Mérida, A.C., Yucatán, C.P. 97205, México
| | - Deysi Chi-Chuc
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Colonia Chuburná de Hidalgo, Calle 43 No. 130 x 32 y 34, Mérida, A.C., Yucatán, C.P. 97205, México
- Escuela Telebachillerato Comunitario de Xcunya, Calle 20, Mérida, México
| | - Miguel Tzec-Simá
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Colonia Chuburná de Hidalgo, Calle 43 No. 130 x 32 y 34, Mérida, A.C., Yucatán, C.P. 97205, México
| | - Angela Ku-González
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Colonia Chuburná de Hidalgo, Calle 43 No. 130 x 32 y 34, Mérida, A.C., Yucatán, C.P. 97205, México
| | - Ligia Brito-Argáez
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Colonia Chuburná de Hidalgo, Calle 43 No. 130 x 32 y 34, Mérida, A.C., Yucatán, C.P. 97205, México
| | - Mildred Carrillo-Pech
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Colonia Chuburná de Hidalgo, Calle 43 No. 130 x 32 y 34, Mérida, A.C., Yucatán, C.P. 97205, México
| | - César De Los Santos-Briones
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Colonia Chuburná de Hidalgo, Calle 43 No. 130 x 32 y 34, Mérida, A.C., Yucatán, C.P. 97205, México
| | - Miguel Ángel Canseco-Pérez
- Dirección de Investigación, Evaluación y Posgrado, Universidad Tecnológica de Tlaxcala, Carretera a el Carmen Xalplatlahuaya s/n. El Carmen Xalplatlahuaya, Tlaxcala, Huamantla, C.P. 90500, Mexico
| | - Donato Luna-Moreno
- Centro de Investigaciones en Óptica AC, División de Fotónica, Loma del Bosque 115, Col. Lomas del Campestre, León, Gto, C.P. 37150, México
| | | | - Ignacio Islas-Flores
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Colonia Chuburná de Hidalgo, Calle 43 No. 130 x 32 y 34, Mérida, A.C., Yucatán, C.P. 97205, México.
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4
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Gupta MN, Uversky VN. Moonlighting enzymes: when cellular context defines specificity. Cell Mol Life Sci 2023; 80:130. [PMID: 37093283 PMCID: PMC11073002 DOI: 10.1007/s00018-023-04781-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/13/2023] [Accepted: 04/15/2023] [Indexed: 04/25/2023]
Abstract
It is not often realized that the absolute protein specificity is an exception rather than a rule. Two major kinds of protein multi-specificities are promiscuity and moonlighting. This review discusses the idea of enzyme specificity and then focusses on moonlighting. Some important examples of protein moonlighting, such as crystallins, ceruloplasmin, metallothioniens, macrophage migration inhibitory factor, and enzymes of carbohydrate metabolism are discussed. How protein plasticity and intrinsic disorder enable the removing the distinction between enzymes and other biologically active proteins are outlined. Finally, information on important roles of moonlighting in human diseases is updated.
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Affiliation(s)
- Munishwar Nath Gupta
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Hauz Khas, New Delhi, 110016, India
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd., MDC07, Tampa, FL, 33612-4799, USA.
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5
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Rodríguez-Almonacid CC, Kellogg MK, Karamyshev AL, Karamysheva ZN. Ribosome Specialization in Protozoa Parasites. Int J Mol Sci 2023; 24:ijms24087484. [PMID: 37108644 PMCID: PMC10138883 DOI: 10.3390/ijms24087484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 04/10/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
Ribosomes, in general, are viewed as constitutive macromolecular machines where protein synthesis takes place; however, this view has been recently challenged, supporting the hypothesis of ribosome specialization and opening a completely new field of research. Recent studies have demonstrated that ribosomes are heterogenous in their nature and can provide another layer of gene expression control by regulating translation. Heterogeneities in ribosomal RNA and ribosomal proteins that compose them favor the selective translation of different sub-pools of mRNAs and functional specialization. In recent years, the heterogeneity and specialization of ribosomes have been widely reported in different eukaryotic study models; however, few reports on this topic have been made on protozoa and even less on protozoa parasites of medical importance. This review analyzes heterogeneities of ribosomes in protozoa parasites highlighting the specialization in their functions and their importance in parasitism, in the transition between stages in their life cycle, in the change of host and in response to environmental conditions.
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Affiliation(s)
| | - Morgana K Kellogg
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Andrey L Karamyshev
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
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6
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Ochkasova A, Arbuzov G, Kabilov M, Tupikin A, Karpova G, Graifer D. AP lyase activity of the human ribosomal protein uS3: The DNA cleavage sequence specificity and the location of the enzyme active center. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2023; 1871:140880. [PMID: 36396097 DOI: 10.1016/j.bbapap.2022.140880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/10/2022] [Accepted: 11/11/2022] [Indexed: 11/16/2022]
Abstract
The human protein uS3, a component of the small ribosomal subunit, has a long-known extra-ribosomal activity as an enzyme of base excision DNA repair displayed in its ability to cleave DNA at abasic (AP) sites. It has been found that the efficacy of DNA cleavage by uS3 in vitro depends on the DNA sequence. To clarify the issue on the sequence specificity of uS3 as an AP lyase in general, we applied a combinatorial approach based on the use of a model single-stranded circular DNA with an AP site flanked with random trinucleotides at both sides. The cleavage of this DNA by uS3 under conditions when only its minor portion undergoes the reaction resulted in the formation of the linear DNA with random triplets at the 5' and 3' termini. NGS sequencing of the DNA library derived from this DNA allowed identifying the contexts within which uS3 cleaves DNA the most and the least effectively. Given that the AP lyase reaction occurs via the formation of a covalent intermediate (Schiff base), we determined the region comprising the active center of the uS3 protein. By digesting of uS3 cross-linked to a radiolabeled AP site-containing model DNA with specific proteolytic agents followed by analysis of the resulting modified oligopeptides, the cross-link was mapped to the region 155-192 (likely, to R173/R178). Thus, our results clarified two previously unstudied features of the uS3 AP lyase activity, one related to the recognition of sequences in DNA surrounding the AP site, and the other to the protein region directly contacting this site.
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Affiliation(s)
- Anastasia Ochkasova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Grigory Arbuzov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Marsel Kabilov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Alexey Tupikin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Galina Karpova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Dmitri Graifer
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia.
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7
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Tseng YT, Sung YC, Liu CY, Lo KY. Translation initiation factor eIF4G1 modulates assembly of the polypeptide exit tunnel region in yeast ribosome biogenesis. J Cell Sci 2022; 135:275526. [PMID: 35615984 DOI: 10.1242/jcs.259540] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 05/12/2022] [Indexed: 01/24/2023] Open
Abstract
eIF4G is an important eukaryotic translation initiation factor. In this study, eIF4G1, one of the eIF4G isoforms, was shown to directly participate in biogenesis of the large (60S) ribosomal subunit in Saccharomyces cerevisiae cells. Mutation of eIF4G1 decreased the amount 60S ribosomal subunits significantly. The C-terminal fragment of eIF4G1 could complement the function in 60S biogenesis. Analyses of its purified complex with mass spectrometry indicated that eIF4G1 associated with the pre-60S form directly. Strong genetic and direct protein-protein interactions were observed between eIF4G1 and Ssf1 protein. Upon deletion of eIF4G1, Ssf1, Rrp15, Rrp14 and Mak16 were abnormally retained on the pre-60S complex. This purturbed the loading of Arx1 and eL31 at the polypeptide exit tunnel (PET) site and the transition to a Nog2 complex. Our data indicate that eIF4G1 is important in facilitating PET maturation and 27S processing correctly. This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Yun-Ting Tseng
- Department of Agricultural Chemistry, College of Bioresources and Agriculture, National Taiwan University, Taipei 10617, Taiwan
| | - Yu-Cheng Sung
- Department of Agricultural Chemistry, College of Bioresources and Agriculture, National Taiwan University, Taipei 10617, Taiwan
| | - Ching-Yu Liu
- Department of Agricultural Chemistry, College of Bioresources and Agriculture, National Taiwan University, Taipei 10617, Taiwan
| | - Kai-Yin Lo
- Department of Agricultural Chemistry, College of Bioresources and Agriculture, National Taiwan University, Taipei 10617, Taiwan
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8
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Frenkel-Pinter M, Petrov AS, Matange K, Travisano M, Glass JB, Williams LD. Adaptation and Exaptation: From Small Molecules to Feathers. J Mol Evol 2022; 90:166-175. [PMID: 35246710 PMCID: PMC8975760 DOI: 10.1007/s00239-022-10049-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 01/26/2022] [Indexed: 11/27/2022]
Abstract
Evolution works by adaptation and exaptation. At an organismal level, exaptation and adaptation are seen in the formation of organelles and the advent of multicellularity. At the sub-organismal level, molecular systems such as proteins and RNAs readily undergo adaptation and exaptation. Here we suggest that the concepts of adaptation and exaptation are universal, synergistic, and recursive and apply to small molecules such as metabolites, cofactors, and the building blocks of extant polymers. For example, adenosine has been extensively adapted and exapted throughout biological evolution. Chemical variants of adenosine that are products of adaptation include 2' deoxyadenosine in DNA and a wide array of modified forms in mRNAs, tRNAs, rRNAs, and viral RNAs. Adenosine and its variants have been extensively exapted for various functions, including informational polymers (RNA, DNA), energy storage (ATP), metabolism (e.g., coenzyme A), and signaling (cyclic AMP). According to Gould, Vrba, and Darwin, exaptation imposes a general constraint on interpretation of history and origins; because of exaptation, extant function should not be used to explain evolutionary history. While this notion is accepted in evolutionary biology, it can also guide the study of the chemical origins of life. We propose that (i) evolutionary theory is broadly applicable from the dawn of life to the present time from molecules to organisms, (ii) exaptation and adaptation were important and simultaneous processes, and (iii) robust origin of life models can be constructed without conflating extant utility with historical basis of origins.
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Affiliation(s)
- Moran Frenkel-Pinter
- NASA Center for the Origins of Life, Atlanta, GA, 30332-0400, USA.,NSF-NASA Center of Chemical Evolution, Atlanta, GA, 30332-0400, USA.,Institute of Chemistry, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel
| | - Anton S Petrov
- NASA Center for the Origins of Life, Atlanta, GA, 30332-0400, USA.,NSF-NASA Center of Chemical Evolution, Atlanta, GA, 30332-0400, USA.,School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332-0400, USA
| | - Kavita Matange
- NASA Center for the Origins of Life, Atlanta, GA, 30332-0400, USA.,School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332-0400, USA
| | - Michael Travisano
- Department of Ecology, Evolution and Behavior, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Jennifer B Glass
- NASA Center for the Origins of Life, Atlanta, GA, 30332-0400, USA.,School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, 30332-0400, USA
| | - Loren Dean Williams
- NASA Center for the Origins of Life, Atlanta, GA, 30332-0400, USA. .,NSF-NASA Center of Chemical Evolution, Atlanta, GA, 30332-0400, USA. .,School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332-0400, USA.
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9
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Chen C, Yuan J, Ji G, Zhang S, Gao Z. Amphioxus ribosomal proteins RPS15, RPS18, RPS19 and RPS30-precursor act as immune effectors via killing or agglutinating bacteria. FISH & SHELLFISH IMMUNOLOGY 2021; 118:147-154. [PMID: 34487827 DOI: 10.1016/j.fsi.2021.09.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/31/2021] [Accepted: 09/02/2021] [Indexed: 06/13/2023]
Abstract
Previous studies show that some ribosomal proteins perform immune effector functions via killing bacteria directly. However, it remains largely unknown about other effector functions of ribosomal proteins during a bacterial infection. In this study, we expressed and purified four ribosomal proteins of the amphioxus Branchiostoma japonicum, termed rBjRPS15, rBjRPS18, rBjRPS19 and rBjRPS30-precursor (rBjRPS30P). They all exhibited bactericidal activity against Gram-positive Staphylococcus aureus, and with the exception of rBjRPS19 and rBjRPS30P, were capable of killing Gram-negative Escherichia coli. Importantly, rBjRPS15, rBjRPS19 and rBjRPS30P were able to agglutinate S. aureus in the presence of Mg2+, but none of them could agglutinate E. coli even in the presence of Mg2+ or Ca2+. Moreover, the S. aureus agglutination was achieved by the binding of these three proteins to the peptidoglycan component of the bacterial cell wall. This is the first report showing that some ribosomal proteins possess bacterial agglutinating activity, and these data provide a new angle to the roles of ribosomal proteins in immune defense.
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Affiliation(s)
- Chaoyi Chen
- Institute of Evolution & Marine Biodiversity and Department of Marine Biology, Ocean University of China, Qingdao, 266003, China
| | - Jianrui Yuan
- Institute of Evolution & Marine Biodiversity and Department of Marine Biology, Ocean University of China, Qingdao, 266003, China
| | - Guangdong Ji
- Institute of Evolution & Marine Biodiversity and Department of Marine Biology, Ocean University of China, Qingdao, 266003, China
| | - Shicui Zhang
- Institute of Evolution & Marine Biodiversity and Department of Marine Biology, Ocean University of China, Qingdao, 266003, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266003, China
| | - Zhan Gao
- Institute of Evolution & Marine Biodiversity and Department of Marine Biology, Ocean University of China, Qingdao, 266003, China.
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10
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Gueiderikh A, Maczkowiak-Chartois F, Rosselli F. A new frontier in Fanconi anemia: From DNA repair to ribosome biogenesis. Blood Rev 2021; 52:100904. [PMID: 34750031 DOI: 10.1016/j.blre.2021.100904] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 10/14/2021] [Accepted: 10/26/2021] [Indexed: 12/27/2022]
Abstract
Described by Guido Fanconi almost 100 years ago, Fanconi anemia (FA) is a rare genetic disease characterized by developmental abnormalities, bone marrow failure (BMF) and cancer predisposition. The proteins encoded by FA-mutated genes (FANC proteins) and assembled in the so-called FANC/BRCA pathway have key functions in DNA repair and replication safeguarding, which loss leads to chromosome structural aberrancies. Therefore, since the 1980s, FA has been considered a genomic instability and chromosome fragility syndrome. However, recent findings have demonstrated new and unexpected roles of FANC proteins in nucleolar homeostasis and ribosome biogenesis, the alteration of which impacts cellular proteostasis. Here, we review the different cellular, biochemical and molecular anomalies associated with the loss of function of FANC proteins and discuss how these anomalies contribute to BMF by comparing FA to other major inherited BMF syndromes. Our aim is to determine the extent to which alterations in the DNA damage response in FA contribute to BMF compared to the consequences of the loss of function of the FANC/BRCA pathway on the other roles of the pathway.
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Affiliation(s)
- Anna Gueiderikh
- CNRS - UMR9019, Équipe labellisée "La Ligue contre le Cancer", 94805 Villejuif, France; Gustave Roussy Cancer Center, 94805 Villejuif, France; Université Paris-Saclay - Paris Sud, Orsay, France.
| | - Frédérique Maczkowiak-Chartois
- CNRS - UMR9019, Équipe labellisée "La Ligue contre le Cancer", 94805 Villejuif, France; Gustave Roussy Cancer Center, 94805 Villejuif, France; Université Paris-Saclay - Paris Sud, Orsay, France.
| | - Filippo Rosselli
- CNRS - UMR9019, Équipe labellisée "La Ligue contre le Cancer", 94805 Villejuif, France; Gustave Roussy Cancer Center, 94805 Villejuif, France; Université Paris-Saclay - Paris Sud, Orsay, France.
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11
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Yadid M, Lind JU, Ardoña HAM, Sheehy SP, Dickinson LE, Eweje F, Bastings MMC, Pope B, O'Connor BB, Straubhaar JR, Budnik B, Kleber AG, Parker KK. Endothelial extracellular vesicles contain protective proteins and rescue ischemia-reperfusion injury in a human heart-on-chip. Sci Transl Med 2021; 12:12/565/eaax8005. [PMID: 33055246 DOI: 10.1126/scitranslmed.aax8005] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 09/08/2020] [Indexed: 12/17/2022]
Abstract
Extracellular vesicles (EVs) derived from various stem cell sources induce cardioprotective effects during ischemia-reperfusion injury (IRI). These have been attributed mainly to the antiapoptotic, proangiogenic, microRNA (miRNA) cargo within the stem cell-derived EVs. However, the mechanisms of EV-mediated endothelial signaling to cardiomyocytes, as well as their therapeutic potential toward ischemic myocardial injury, are not clear. EV content beyond miRNA that may contribute to cardioprotection has not been fully illuminated. This study characterized the protein cargo of human vascular endothelial EVs (EEVs) to identify lead cardioactive proteins and assessed the effect of EEVs on human laminar cardiac tissues (hlCTs) exposed to IRI. We mapped the protein content of human vascular EEVs and identified proteins that were previously associated with cellular metabolism, redox state, and calcium handling, among other processes. Analysis of the protein landscape of human cardiomyocytes revealed corresponding modifications induced by EEV treatment. To assess their human-specific cardioprotection in vitro, we developed a human heart-on-a-chip IRI assay using human stem cell-derived, engineered cardiac tissues. We found that EEVs alleviated cardiac cell death as well as the loss in contractile capacity during and after simulated IRI in an uptake- and dose-dependent manner. Moreover, we found that EEVs increased the respiratory capacity of normoxic cardiomyocytes. These results suggest that vascular EEVs rescue hlCTs exposed to IRI possibly by supplementing injured myocytes with cargo that supports multiple metabolic and salvage pathways and therefore may serve as a multitargeted therapy for IRI.
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Affiliation(s)
- Moran Yadid
- Disease Biophysics Group, John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Johan U Lind
- Disease Biophysics Group, John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA.,Department of Health Technology, Technical University of Denmark, Kgs. Lyngby 2800, Denmark
| | - Herdeline Ann M Ardoña
- Disease Biophysics Group, John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Sean P Sheehy
- Disease Biophysics Group, John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Lauren E Dickinson
- Disease Biophysics Group, John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Feyisayo Eweje
- Disease Biophysics Group, John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Maartje M C Bastings
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA.,Ecole Polytechnique Federale Lausanne (EPFL), School of Engineering, Institute of Materials, Programmable Biomaterials Laboratory, Station 12, 1015 Lausanne, Switzerland
| | - Benjamin Pope
- Disease Biophysics Group, John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Blakely B O'Connor
- Disease Biophysics Group, John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
| | | | - Bogdan Budnik
- FAS Division of Science, Harvard University, Cambridge, MA 02138, USA
| | - Andre G Kleber
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - Kevin Kit Parker
- Disease Biophysics Group, John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA. .,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
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12
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Xiong W, Zhang J, Lan T, Kong W, Wang X, Liu L, Chen X, Mo B. High resolution RNA-seq profiling of genes encoding ribosomal proteins across different organs and developmental stages in Arabidopsis thaliana. PLANT DIRECT 2021; 5:e00320. [PMID: 34095740 PMCID: PMC8156134 DOI: 10.1002/pld3.320] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 03/16/2021] [Accepted: 03/18/2021] [Indexed: 05/12/2023]
Abstract
In Arabidopsis thaliana, each ribosomal protein (RP) is encoded by a small gene family consisting of two or more highly homologous paralogues, which results in ribosome heterogeneity. It is largely unknown that how genes from multiple member containing RP families are regulated at transcriptional level to accommodate the needs of different plant organs and developmental stages. In this study, we investigated the transcript accumulation profiles of RP genes and found that the expression levels of RP genes are varied dramatically in different organs and developmental stages. Although most RP genes are found to be ubiquitously transcribed, some are obviously transcribed with spatiotemporal specificity. The hierarchical clustering trees of transcript accumulation intensity of RP genes revealed that different organs and developmental stages have different population of RP gene transcripts. By interrogating of the expression fluctuation trend of RP genes, we found that in spite of the fact that most groups of paralogous RP genes are transcribed in concerted manners, some RPs gene have contrasting expression patterns. When transcripts of paralogous RP genes from the same family are considered together, the expression level of most RP genes are well-matched but some are obviously higher or lower, therefore we speculate that some superfluous RPs may act outside the ribosome and a portion of ribosomes may lack one or even more RP(s). Altogether, our analysis results suggested that functional divergence may exist among heterogeneous ribosomes that resulted from different combination of RP paralogues, and substoichiometry of several RP gene families may lead to another layer of heterogeneous ribosomes which also have divergent functions in plants.
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Affiliation(s)
- Wei Xiong
- Guangdong Provincial Key Laboratory for Plant EpigeneticsLonghua Bioindustry and Innovation Research InstituteCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenChina
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong ProvinceCollege of Optoelectronic EngineeringShenzhen UniversityShenzhenChina
| | - Jiancong Zhang
- Guangdong Provincial Key Laboratory for Plant EpigeneticsLonghua Bioindustry and Innovation Research InstituteCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenChina
| | - Ting Lan
- Guangdong Provincial Key Laboratory for Plant EpigeneticsLonghua Bioindustry and Innovation Research InstituteCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenChina
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong ProvinceCollege of Optoelectronic EngineeringShenzhen UniversityShenzhenChina
| | - Wenwen Kong
- Guangdong Provincial Key Laboratory for Plant EpigeneticsLonghua Bioindustry and Innovation Research InstituteCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenChina
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong ProvinceCollege of Optoelectronic EngineeringShenzhen UniversityShenzhenChina
| | - Xiaoyan Wang
- Guangdong Provincial Key Laboratory for Plant EpigeneticsLonghua Bioindustry and Innovation Research InstituteCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenChina
| | - Lin Liu
- Guangdong Provincial Key Laboratory for Plant EpigeneticsLonghua Bioindustry and Innovation Research InstituteCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenChina
| | - Xuemei Chen
- Department of Botany and Plant SciencesInstitute of Integrative Genome BiologyUniversity of CaliforniaRiversideCAUSA
| | - Beixin Mo
- Guangdong Provincial Key Laboratory for Plant EpigeneticsLonghua Bioindustry and Innovation Research InstituteCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenChina
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13
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Kan G, Wang Z, Sheng C, Chen G, Yao C, Mao Y, Chen S. Dual Inhibition of DKC1 and MEK1/2 Synergistically Restrains the Growth of Colorectal Cancer Cells. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:2004344. [PMID: 34026451 PMCID: PMC8132060 DOI: 10.1002/advs.202004344] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 01/28/2021] [Indexed: 05/09/2023]
Abstract
Colorectal cancer, one of the most commonly diagnosed cancers worldwide, is often accompanied by uncontrolled proliferation of tumor cells. Dyskerin pseudouridine synthase 1 (DKC1), screened using the genome-wide RNAi strategy, is a previously unidentified key regulator that promotes colorectal cancer cell proliferation. Enforced expression of DKC1, but not its catalytically inactive mutant D125A, accelerates cell growth in vitro and in vivo. DKC1 knockdown or its inhibitor pyrazofurin attenuates cell proliferation. Proteomics, RNA immunoprecipitation (RIP)-seq, and RNA decay analyses reveal that DKC1 binds to and stabilizes the mRNA of several ribosomal proteins (RPs), including RPL10A, RPL22L1, RPL34, and RPS3. DKC1 depletion significantly accelerates mRNA decay of these RPs, which mediates the oncogenic function of DKC1. Interestingly, these DKC1-regulated RPs also interact with HRAS and suppress the RAS/RAF/MEK/ERK pathway. Pyrazofurin and trametinib combination synergistically restrains colorectal cancer cell growth in vitro and in vivo. Furthermore, DKC1 is markedly upregulated in colorectal cancer tissues compared to adjacent normal tissues. Colorectal cancer patients with higher DKC1 expression has consistently poorer overall survival and progression-free survival outcomes. Taken together, these data suggest that DKC1 is an essential gene and candidate therapeutic target for colorectal cancer.
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Affiliation(s)
- Guangyan Kan
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineSun Yat‐sen University Cancer CenterGuangzhouGuangdong510060P. R. China
| | - Ziyang Wang
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineSun Yat‐sen University Cancer CenterGuangzhouGuangdong510060P. R. China
| | - Chunjie Sheng
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineSun Yat‐sen University Cancer CenterGuangzhouGuangdong510060P. R. China
| | - Gong Chen
- Department of Colorectal SurgeryState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineSun Yat‐sen University Cancer CenterGuangzhouGuangdong510060P. R. China
| | - Chen Yao
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineSun Yat‐sen University Cancer CenterGuangzhouGuangdong510060P. R. China
| | - Yizhi Mao
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineSun Yat‐sen University Cancer CenterGuangzhouGuangdong510060P. R. China
| | - Shuai Chen
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineSun Yat‐sen University Cancer CenterGuangzhouGuangdong510060P. R. China
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14
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Liu ZL. Reasons for 2-furaldehyde and 5-hydroxymethyl-2-furaldehyde resistance in Saccharomyces cerevisiae: current state of knowledge and perspectives for further improvements. Appl Microbiol Biotechnol 2021; 105:2991-3007. [PMID: 33830300 DOI: 10.1007/s00253-021-11256-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 03/16/2021] [Accepted: 03/23/2021] [Indexed: 11/25/2022]
Abstract
Common toxic compounds 2-furaldehyde (furfural) and 5-hydroxymethyl-2-furaldehyde (HMF) are formed from dehydration of pentose and hexose, respectively, during decomposition of lignocellulosic biomass polymers. Furfural and HMF represent a major class of aldehyde toxic chemicals that inhibit microbial growth and interfere with subsequent fermentation for production of renewable fuels and chemicals. Understanding mechanisms of yeast tolerance aids development of tolerant strains as the most economic means to overcome the toxicity. This review updates current knowledge on yeast resistance to these toxic chemicals obtained from rapid advances in the past few years. Findings are largely exemplified by an adapted strain NRRL Y-50049 compared with its progenitor, the industrial yeast Saccharomyces cerevisiae type strain NRRL Y-12632. Newly characterized molecular phenotypes distinguished acquired resistant components of Y-50049 from innate stress response of its progenitor Y-12632. These findings also raised important questions on how to address more deeply ingrained changes in addition to local renovations for yeast adaptation. An early review on understandings of yeast tolerance to these inhibitory compounds is available and its contents omitted here to avoid redundancy. Controversial and confusing issues on identification of yeast resistance to furfural and HMF are further clarified aiming improved future research. Propositions and perspectives on research understanding molecular mechanisms of yeast resistance and future improvements are also presented. KEY POINTS: • Distinguished adapted resistance from innate stress response in yeast. • Defined pathway-based molecular phenotypes of yeast resistance. • Proposed genomic insight and perspectives on yeast resistance and adaptation.
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Affiliation(s)
- Z Lewis Liu
- National Center for Agricultural Utilization Research, Bioenergy Research Unit, USDA Agricultural Research Service, 1815 N. University Street, Peoria, IL, 61604, USA.
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15
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Finkelshtein A, Khamesa H, Tuan LA, Rabanim M, Chamovitz DA. Overexpression of the ribosomal S30 subunit leads to indole-3-carbinol tolerance in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:668-677. [PMID: 33128319 DOI: 10.1111/tpj.15062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 09/18/2020] [Indexed: 06/11/2023]
Abstract
Indole-3-carbinol (I3C), a hydrolysis product of indole-3-methylglucosinolate, is toxic to herbivorous insects and pathogens. In mammals, I3C is extensively studied for its properties in cancer prevention and treatment. Produced in Brassicaceae, I3C reversibly inhibits root elongation in a concentration-dependent manner. This inhibition is partially explained by the antagonistic action of I3C on auxin signaling through TIR1. To further elucidate the mode of action of I3C in plants, we have identified and characterized a novel Arabidopsis mutant tolerant to I3C, ICT1. This mutant was identified following screening of the Full-length cDNA Over-eXpression library (FOX) seed collection for root growth in the presence of exogenous I3C. ICT1 carries the AT2G19750 gene, which encodes an S30 ribosomal protein. Overexpression, but not knockout, of the S30 gene causes tolerance to I3C. The tolerance is specific to I3C, since ICT1 did not exhibit pronounced tolerance to other indole or benzoxazinoid molecules tested. ICT1 maintains I3C-induced antagonism of auxin signaling, indicating that the tolerance is due to an auxin-independent mechanism. Transcript profiling experiments revealed that ICT1 is transcriptionally primed to respond to I3C treatment.
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Affiliation(s)
- Alin Finkelshtein
- School of Plant Sciences and Food Security, Tel Aviv University, Ramat Aviv, 69978, Israel
| | - Hala Khamesa
- School of Plant Sciences and Food Security, Tel Aviv University, Ramat Aviv, 69978, Israel
| | - Luu Anh Tuan
- School of Plant Sciences and Food Security, Tel Aviv University, Ramat Aviv, 69978, Israel
| | - Manely Rabanim
- School of Plant Sciences and Food Security, Tel Aviv University, Ramat Aviv, 69978, Israel
| | - Daniel A Chamovitz
- School of Plant Sciences and Food Security, Tel Aviv University, Ramat Aviv, 69978, Israel
- The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, 8499000, Israel
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16
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Plant miR171 modulates mTOR pathway in HEK293 cells by targeting GNA12. Mol Biol Rep 2021; 48:435-449. [PMID: 33386590 DOI: 10.1007/s11033-020-06070-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 12/04/2020] [Indexed: 01/07/2023]
Abstract
Plant microRNAs have shown the capacity to regulate mammalian systems. The potential bioactivity of miR171vr, an isoform of the plant miR171, on human embryonic kidney 293 (HEK293) cells was investigated. Bioinformatics simulations revealed that human G protein subunit alpha 12 (GNA12) transcript could represent an excellent target for miR171vr. To confirm this prediction, in vitro experiments were performed using a synthetic microRNA designed on miR171vr sequence. MiR-treated cells showed a significant decrease of GNA12 mRNA and protein levels, confirming the putative cross-kingdom interaction. In addition, miR171vr determined the modulation of GNA12 downstream signaling factors, including mTOR, as expected. Finally, the effect of the plant miRNA on HEK293 cell growth and its stability in presence of several stressors, such as those miming digestive processes and procedures for preparing food, were evaluated. All this preliminary evidence would suggest that miR171vr, introduced by diet or as supplement in gene therapies, could potentially influence human gene expression, especially for treating disorders where GNA12 is over-expressed (i.e. oral cancer, breast and prostate adenocarcinoma) or mTOR kinase is down-regulated (e.g. obesity, type 2 diabetes, neurodegeneration).
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17
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Landry-Voyer AM, Bergeron D, Yague-Sanz C, Baker B, Bachand F. PDCD2 functions as an evolutionarily conserved chaperone dedicated for the 40S ribosomal protein uS5 (RPS2). Nucleic Acids Res 2020; 48:12900-12916. [PMID: 33245768 PMCID: PMC7736825 DOI: 10.1093/nar/gkaa1108] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/23/2020] [Accepted: 10/28/2020] [Indexed: 11/12/2022] Open
Abstract
PDCD2 is an evolutionarily conserved protein with previously characterized homologs in Drosophila (zfrp8) and budding yeast (Tsr4). Although mammalian PDCD2 is essential for cell proliferation and embryonic development, the function of PDCD2 that underlies its fundamental cellular role has remained unclear. Here, we used quantitative proteomics approaches to define the protein-protein interaction network of human PDCD2. Our data revealed that PDCD2 specifically interacts with the 40S ribosomal protein uS5 (RPS2) and that the PDCD2-uS5 complex is assembled co-translationally. Loss of PDCD2 expression leads to defects in the synthesis of the small ribosomal subunit that phenocopy a uS5 deficiency. Notably, we show that PDCD2 is important for the accumulation of soluble uS5 protein as well as its incorporation into 40S ribosomal subunit. Our findings support that the essential molecular function of PDCD2 is to act as a dedicated ribosomal protein chaperone that recognizes uS5 co-translationally in the cytoplasm and accompanies uS5 to ribosome assembly sites in the nucleus. As most dedicated ribosomal protein chaperones have been identified in yeast, our study reveals that similar mechanisms exist in human cells to assist ribosomal proteins coordinate their folding, nuclear import and assembly in pre-ribosomal particles.
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Affiliation(s)
- Anne-Marie Landry-Voyer
- Department of Biochemistry & Functional Genomics, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - Danny Bergeron
- Department of Biochemistry & Functional Genomics, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - Carlo Yague-Sanz
- Department of Biochemistry & Functional Genomics, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - Breac Baker
- Department of Biochemistry & Functional Genomics, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - Francois Bachand
- Department of Biochemistry & Functional Genomics, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
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Abstract
Production and expression of RNA requires the action of multiple RNA-binding proteins (RBPs). New RBPs are most often created by novel combinations of dedicated RNA-binding modules. However, recruiting existing genes to create new RBPs is also an important evolutionary strategy. In this report, we analyzed the eight-member uL18 ribosomal protein family in Arabidopsis uL18 proteins share a short structurally conserved domain that binds the 5S ribosomal RNA (rRNA) and allows its incorporation into ribosomes. Our results indicate that Arabidopsis uL18-Like proteins are targeted to either mitochondria or chloroplasts. While two members of the family are found in organelle ribosomes, we show here that two uL18-type proteins function as factors necessary for the splicing of certain mitochondrial and plastid group II introns. These two proteins do not cosediment with mitochondrial or plastid ribosomes but instead associate with the introns whose splicing they promote. Our study thus reveals that the RNA-binding capacity of uL18 ribosomal proteins has been repurposed to create factors that facilitate the splicing of organellar introns.
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19
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Petibon C, Malik Ghulam M, Catala M, Abou Elela S. Regulation of ribosomal protein genes: An ordered anarchy. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 12:e1632. [PMID: 33038057 PMCID: PMC8047918 DOI: 10.1002/wrna.1632] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 09/08/2020] [Accepted: 09/23/2020] [Indexed: 02/06/2023]
Abstract
Ribosomal protein genes are among the most highly expressed genes in most cell types. Their products are generally essential for ribosome synthesis, which is the cornerstone for cell growth and proliferation. Many cellular resources are dedicated to producing ribosomal proteins and thus this process needs to be regulated in ways that carefully balance the supply of nascent ribosomal proteins with the demand for new ribosomes. Ribosomal protein genes have classically been viewed as a uniform interconnected regulon regulated in eukaryotic cells by target of rapamycin and protein kinase A pathway in response to changes in growth conditions and/or cellular status. However, recent literature depicts a more complex picture in which the amount of ribosomal proteins produced varies between genes in response to two overlapping regulatory circuits. The first includes the classical general ribosome‐producing program and the second is a gene‐specific feature responsible for fine‐tuning the amount of ribosomal proteins produced from each individual ribosomal gene. Unlike the general pathway that is mainly controlled at the level of transcription and translation, this specific regulation of ribosomal protein genes is largely achieved through changes in pre‐mRNA splicing efficiency and mRNA stability. By combining general and specific regulation, the cell can coordinate ribosome production, while allowing functional specialization and diversity. Here we review the many ways ribosomal protein genes are regulated, with special focus on the emerging role of posttranscriptional regulatory events in fine‐tuning the expression of ribosomal protein genes and its role in controlling the potential variation in ribosome functions. This article is categorized under:Translation > Ribosome Biogenesis Translation > Ribosome Structure/Function Translation > Translation Regulation
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Affiliation(s)
- Cyrielle Petibon
- Département de microbiologie et d'infectiologie, Universite de Sherbrooke, Faculté de Médecine et des Sciences de la Santé, Sherbrooke, Quebec, Canada
| | - Mustafa Malik Ghulam
- Département de microbiologie et d'infectiologie, Universite de Sherbrooke, Faculté de Médecine et des Sciences de la Santé, Sherbrooke, Quebec, Canada
| | - Mathieu Catala
- Département de microbiologie et d'infectiologie, Universite de Sherbrooke, Faculté de Médecine et des Sciences de la Santé, Sherbrooke, Quebec, Canada
| | - Sherif Abou Elela
- Département de microbiologie et d'infectiologie, Universite de Sherbrooke, Faculté de Médecine et des Sciences de la Santé, Sherbrooke, Quebec, Canada
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Posttranscriptional Regulation of tnaA by Protein-RNA Interaction Mediated by Ribosomal Protein L4 in Escherichia coli. J Bacteriol 2020; 202:JB.00799-19. [PMID: 32123036 PMCID: PMC7186457 DOI: 10.1128/jb.00799-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 02/13/2020] [Indexed: 11/26/2022] Open
Abstract
Some ribosomal proteins have extraribosomal functions in addition to ribosome translation function. The extraribosomal functions of several r-proteins control operon expression by binding to own-operon transcripts. Previously, we discovered a posttranscriptional, RNase E-dependent regulatory role for r-protein L4 in the stabilization of stress-responsive transcripts. Here, we found an additional extraribosomal function for L4 in regulating the tna operon by L4-intergenic spacer mRNA interactions. L4 binds to the transcribed spacer RNA between tnaC and tnaA and alters the structural conformation of the spacer RNA, thereby reducing the translation of TnaA. Our study establishes a previously unknown L4-mediated mechanism for regulating gene expression, suggesting that bacterial cells have multiple strategies for controlling levels of tryptophanase in response to varied cell growth conditions. Escherichia coli ribosomal protein (r-protein) L4 has extraribosomal biological functions. Previously, we described L4 as inhibiting RNase E activity through protein-protein interactions. Here, we report that from stabilized transcripts regulated by L4-RNase E, mRNA levels of tnaA (encoding tryptophanase from the tnaCAB operon) increased upon ectopic L4 expression, whereas TnaA protein levels decreased. However, at nonpermissive temperatures (to inactivate RNase E), tnaA mRNA and protein levels both increased in an rne temperature-sensitive [rne(Ts)] mutant strain. Thus, L4 protein fine-tunes TnaA protein levels independently of its inhibition of RNase E. We demonstrate that ectopically expressed L4 binds with transcribed spacer RNA between tnaC and tnaA and downregulates TnaA translation. We found that deletion of the 5′ or 3′ half of the spacer compared to the wild type resulted in a similar reduction in TnaA translation in the presence of L4. In vitro binding of L4 to the tnaC-tnaA transcribed spacer RNA results in changes to its secondary structure. We reveal that during early stationary-phase bacterial growth, steady-state levels of tnaA mRNA increased but TnaA protein levels decreased. We further confirm that endogenous L4 binds to tnaC-tnaA transcribed spacer RNA in cells at early stationary phase. Our results reveal the novel function of L4 in fine-tuning TnaA protein levels during cell growth and demonstrate that r-protein L4 acts as a translation regulator outside the ribosome and its own operon. IMPORTANCE Some ribosomal proteins have extraribosomal functions in addition to ribosome translation function. The extraribosomal functions of several r-proteins control operon expression by binding to own-operon transcripts. Previously, we discovered a posttranscriptional, RNase E-dependent regulatory role for r-protein L4 in the stabilization of stress-responsive transcripts. Here, we found an additional extraribosomal function for L4 in regulating the tna operon by L4-intergenic spacer mRNA interactions. L4 binds to the transcribed spacer RNA between tnaC and tnaA and alters the structural conformation of the spacer RNA, thereby reducing the translation of TnaA. Our study establishes a previously unknown L4-mediated mechanism for regulating gene expression, suggesting that bacterial cells have multiple strategies for controlling levels of tryptophanase in response to varied cell growth conditions.
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Ballesteros GI, Torres-Díaz C, Bravo LA, Balboa K, Caruso C, Bertini L, Proietti S, Molina-Montenegro MA. In silico analysis of metatranscriptomic data from the Antarctic vascular plant Colobanthus quitensis: Responses to a global warming scenario through changes in fungal gene expression levels. FUNGAL ECOL 2020. [DOI: 10.1016/j.funeco.2019.100873] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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22
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Ochkasova AS, Kabilov MR, Karpova GG, Graifer DM. Exploring the Interaction of Human Ribosomal Protein uS3 with Single-Stranded DNAs Having Different Sequences. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2020. [DOI: 10.1134/s106816201906030x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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23
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Kompella VPS, Stansfield I, Romano MC, Mancera RL. Definition of the Minimal Contents for the Molecular Simulation of the Yeast Cytoplasm. Front Mol Biosci 2019; 6:97. [PMID: 31632983 PMCID: PMC6783697 DOI: 10.3389/fmolb.2019.00097] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 09/11/2019] [Indexed: 11/13/2022] Open
Abstract
The cytoplasm is a densely packed environment filled with macromolecules with hindered diffusion. Molecular simulation of the diffusion of biomolecules under such macromolecular crowding conditions requires the definition of a simulation cell with a cytoplasmic-like composition. This has been previously done for prokaryote cells (E. coli) but not for eukaryote cells such as yeast as a model organism. Yeast proteomics datasets vary widely in terms of cell growth conditions, the technique used to determine protein composition, the reported relative abundance of proteins, and the units in which abundances are reported. We determined that the gene ontology profiles of the most abundant proteins across these datasets are similar, but their abundances vary greatly. To overcome this problem, we chose five mass spectrometry proteomics datasets that fulfilled the following criteria: high internal consistency, consistency with published experimental data, and freedom from GFP-tagging artifacts. Using these datasets, the contents of a simulation cell containing a single 80S ribosome were defined, such that the macromolecular density and the mass ratio of ribosomal-to-cytoplasmic proteins were consistent with experiment and chosen datasets. Finally, multiple tRNAs were added, consistent with their experimentally-determined number in the yeast cell. The resulting composition can be readily used in molecular simulations representative of yeast cytoplasmic macromolecular crowding conditions to characterize a variety of phenomena, such as protein diffusion, protein-protein interactions and biological processes such as protein translation.
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Affiliation(s)
- Vijay Phanindra Srikanth Kompella
- School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin Institute for Computation, Curtin University, Perth, WA, Australia.,Physics Department, Institute for Complex Systems and Mathematical Biology, University of Aberdeen, Aberdeen, United Kingdom
| | - Ian Stansfield
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Maria Carmen Romano
- Physics Department, Institute for Complex Systems and Mathematical Biology, University of Aberdeen, Aberdeen, United Kingdom.,Institute of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Ricardo L Mancera
- School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin Institute for Computation, Curtin University, Perth, WA, Australia
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Yang HW, Kim HD, Kim J. The DNA repair domain of human rpS3 protects against photoaging by removing cyclobutane pyrimidine dimers. FEBS Lett 2019; 593:2060-2068. [PMID: 31180576 DOI: 10.1002/1873-3468.13479] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 06/04/2019] [Accepted: 06/04/2019] [Indexed: 12/25/2022]
Abstract
Ribosomal protein S3 (rpS3) has endonuclease activity for DNA repair. In particular, rpS3 cleaves the phosphodiester bonds of damaged DNA. In this study, we show that the repair domain of rpS3 spans amino acids 144-189. We fused rpS3 with the transactivator of transcription (TAT) sequence to introduce the rpS3 repair domain into cells. We find that the TAT-rpS3 (aa: 144-189) peptide cleaves UV-induced cyclobutane pyrimidine dimers (CPDs) in cells. We also reveal that the TAT-rpS3 peptide reduces matrix metalloproteinase-1 (MMP-1) induction in UV-irradiated fibroblasts and increases cell migration activity. Taken together, our study suggests that penetration of the rpS3 repair domain into cells can cleave UV-induced CPDs and reduce MMP-1 expression induced by UV.
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Affiliation(s)
- Hee Woong Yang
- Laboratory of Biochemistry, Division of Life Sciences, Korea University, Seoul, Korea
| | - Hag Dong Kim
- HAEL Lab, TechnoComplex Building, Korea University, Seoul, Korea
| | - Joon Kim
- Laboratory of Biochemistry, Division of Life Sciences, Korea University, Seoul, Korea.,HAEL Lab, TechnoComplex Building, Korea University, Seoul, Korea
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25
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Morales-Amparano MB, Ramos-Clamont Montfort G, Baqueiro-Peña I, Robles-Burgueño MDR, Vázquez-Moreno L, Huerta-Ocampo JÁ. Proteomic response of Saccharomyces boulardii to simulated gastrointestinal conditions and encapsulation. Food Sci Biotechnol 2019; 28:831-840. [PMID: 31093441 PMCID: PMC6484100 DOI: 10.1007/s10068-018-0508-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 11/01/2018] [Accepted: 11/04/2018] [Indexed: 12/31/2022] Open
Abstract
Probiotics are live microorganisms conferring health benefits when administered in adequate amounts. However, the passage through the gastrointestinal tract represents a challenge due to pH variations, proteases, and bile salts. This study aimed to evaluate the proteomic response of Saccharomyces boulardii to simulated gastrointestinal digestion and the influence of encapsulation on yeast viability. Different pH values and time periods simulating the passage through different sections of the gastrointestinal tract were applied to unencapsulated and encapsulated yeasts. Encapsulation in 0.5% calcium alginate did not improve yeast survival or induce changes in protein patterns whereas protein extracts from control and digested yeasts showed remarkable differences when separated by SDS-PAGE. Protein bands were analyzed by tandem mass spectrometry. Protein identification revealed unique proteins that changed acutely in abundance after simulated digestion. Carbohydrate metabolism, protein processing, and oxide-reduction were the biological processes most affected by simulated gastrointestinal digestion in S. boulardii.
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Affiliation(s)
- Martha Beatriz Morales-Amparano
- Centro de Investigación en Alimentación y Desarrollo, A.C., Carretera Gustavo Enrique Astiazarán Rosas No. 46, Apartado Postal 1735, 83304 Hermosillo, Sonora Mexico
| | - Gabriela Ramos-Clamont Montfort
- Centro de Investigación en Alimentación y Desarrollo, A.C., Carretera Gustavo Enrique Astiazarán Rosas No. 46, Apartado Postal 1735, 83304 Hermosillo, Sonora Mexico
| | - Itzamná Baqueiro-Peña
- Centro de Investigación en Alimentación y Desarrollo, A.C., Carretera Gustavo Enrique Astiazarán Rosas No. 46, Apartado Postal 1735, 83304 Hermosillo, Sonora Mexico
| | - María del Refugio Robles-Burgueño
- Centro de Investigación en Alimentación y Desarrollo, A.C., Carretera Gustavo Enrique Astiazarán Rosas No. 46, Apartado Postal 1735, 83304 Hermosillo, Sonora Mexico
| | - Luz Vázquez-Moreno
- Centro de Investigación en Alimentación y Desarrollo, A.C., Carretera Gustavo Enrique Astiazarán Rosas No. 46, Apartado Postal 1735, 83304 Hermosillo, Sonora Mexico
| | - José Ángel Huerta-Ocampo
- CONACYT-Centro de Investigación en Alimentación y Desarrollo A.C., Carretera Gustavo Enrique Astiazarán Rosas No. 46, Apartado Postal 1735, 83304 Hermosillo, Sonora Mexico
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26
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Protein expression analysis revealed a fine-tuned mechanism of in situ detoxification pathway for the tolerant industrial yeast Saccharomyces cerevisiae. Appl Microbiol Biotechnol 2019; 103:5781-5796. [PMID: 31139900 DOI: 10.1007/s00253-019-09906-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 05/07/2019] [Accepted: 05/07/2019] [Indexed: 12/18/2022]
Abstract
Inhibitory compounds liberated from lignocellulose pretreatment are representative toxic chemicals that repress microbial growth and metabolism. A tolerant strain of the industrial yeast Saccharomyces cerevisiae is able to detoxify a major class of toxic compounds while producing ethanol. Knowledge on the yeast tolerance was mostly obtained by gene expression analysis and limited protein expression evidence is yet available underlying the yeast adaptation. Here we report a comparative protein expression profiling study on Y-50049, a tolerant strain compared with its parental industrial type strain Y-12632. We found a distinctive protein expression of glucose-6-phosphate dehydrogenase (Zwf1) in Y-50049 but not in Y-12632, in the relatively conserved glycolysis and pentose phosphate pathway (PPP) in response to a combinational challenge of 2-furaldehyde (furfural) and 5-hydroxymethyl-2-furaldehyde (HMF). A group of proteins with aldehyde reduction activity was uniquely induced expressed in Y-50049 but not in Y-12632. Such evidence allowed fine-tuning a mechanism of the renovated in situ detoxification by Y-50049. As the key protein, Zwf1 drove the glucose metabolism in favor of the oxidative branch of the PPP facilitating in situ detoxification of the toxic chemicals by Y-50049. The activated expression of Zwf1 generated the essential cofactor nicotinamide adenine dinucleotide phosphate (NADPH) enabling reduction of furfural and HMF through a group of aldehyde reduction enzymes. In return, the activate aldehyde reductions released desirable feedbacks of NADP+ stimulating continued oxidative activity of Zwf1. Thus, a well-maintained cofactor regeneration cycle was established to restore the cofactor imbalance caused by furfural-HMF. Challenges and perspectives on adaptation of significantly differential expressions of ribosomal proteins and other unique proteins are also discussed.
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Zhang SF, Chen Y, Xie ZX, Zhang H, Lin L, Wang DZ. Unraveling the molecular mechanism of the response to changing ambient phosphorus in the dinoflagellate Alexandrium catenella with quantitative proteomics. J Proteomics 2019; 196:141-149. [PMID: 30414514 DOI: 10.1016/j.jprot.2018.11.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 10/30/2018] [Accepted: 11/05/2018] [Indexed: 10/27/2022]
Abstract
Phosphorus (P) is a key macronutrient limiting cell growth and bloom formation of marine dinoflagellates. Physiological responses to changing ambient P have been investigated in dinoflagellates; however, the molecular mechanisms behind these responses remain limited. Here, we compared the protein expression profiles of a marine dinoflagellate Alexandrium catenella grown in inorganic P-replete, P-deficient, and inorganic- and organic-P resupplied conditions using an iTRAQ-based quantitative proteomic approach. P deficiency inhibited cell growth and enhanced alkaline phosphatase activity (APA) but had no effect on photosynthetic efficiency. After P resupply, the P-deficient cells recovered growth rapidly and APA decreased. Proteins involved in sphingolipid metabolism, organic P utilization, starch and sucrose metabolism, and photosynthesis were up-regulated in the P-deficient cells, while proteins associated with protein synthesis, nutrient assimilation and energy metabolism were down-regulated. The responses of the P-deficient A. catenella to the resupply of organic and inorganic P presented significant differences: more biological processes were enhanced in the organic P-resupplied cells than those in the inorganic P-resupplied cells; A. catenella might directly utilize G-6-P for nucleic acid synthesis through the pentose phosphate pathway. Our results indicate that A. catenella has evolved diverse adaptive strategies to ambient P deficiency and specific mechanisms to utilize dissolved organic P, which might be an important reason resulting in A. catenella bloom in the low inorganic P environment. BIOLOGICAL SIGNIFICANCE: The ability of marine dinoflagellates to utilize different phosphorus (P) species and adapt to ambient P deficiency determines their success in the ocean. In this study, we investigated the response mechanisms of a dinoflagellate Alexandrium catenella to ambient P deficiency, and resupply of inorganic- and organic-P at the proteome level. Our results indicated that A. catenella initiated multiple adaptive strategies to ambient P deficiency, e.g. utilizing nonphospholipids and glycosphingolipids instead of phospholipids, enhancing expression of acid phosphatase to utilize organic P, and reallocating intracellular energy. Proteome responses of the P-deficient A. catenella to resupply of inorganic- and organic-P differed significantly, indicating different utilization pathways of inorganic and organic P, A. catenella might directly utilize low molecular weight organic P, such as G-6-P as both P and carbon sources.
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Affiliation(s)
- Shu-Feng Zhang
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, China
| | - Ying Chen
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, China
| | - Zhang-Xian Xie
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, China
| | - Hao Zhang
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, China
| | - Lin Lin
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, China
| | - Da-Zhi Wang
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, China; Key Laboratory of Marine Ecology & Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China.
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28
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The Ribosome as a Missing Link in Prebiotic Evolution III: Over-Representation of tRNA- and rRNA-Like Sequences and Plieofunctionality of Ribosome-Related Molecules Argues for the Evolution of Primitive Genomes from Ribosomal RNA Modules. Int J Mol Sci 2019; 20:ijms20010140. [PMID: 30609737 PMCID: PMC6337102 DOI: 10.3390/ijms20010140] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 12/21/2018] [Accepted: 12/23/2018] [Indexed: 12/18/2022] Open
Abstract
We propose that ribosomal RNA (rRNA) formed the basis of the first cellular genomes, and provide evidence from a review of relevant literature and proteonomic tests. We have proposed previously that the ribosome may represent the vestige of the first self-replicating entity in which rRNAs also functioned as genes that were transcribed into functional messenger RNAs (mRNAs) encoding ribosomal proteins. rRNAs also encoded polymerases to replicate itself and a full complement of the transfer RNAs (tRNAs) required to translate its genes. We explore here a further prediction of our “ribosome-first” theory: the ribosomal genome provided the basis for the first cellular genomes. Modern genomes should therefore contain an unexpectedly large percentage of tRNA- and rRNA-like modules derived from both sense and antisense reading frames, and these should encode non-ribosomal proteins, as well as ribosomal ones with key cell functions. Ribosomal proteins should also have been co-opted by cellular evolution to play extra-ribosomal functions. We review existing literature supporting these predictions. We provide additional, new data demonstrating that rRNA-like sequences occur at significantly higher frequencies than predicted on the basis of mRNA duplications or randomized RNA sequences. These data support our “ribosome-first” theory of cellular evolution.
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Ochkasova AS, Meschaninova MI, Venyaminova AG, Ivanov AV, Graifer DM, Karpova GG. The human ribosome can interact with the abasic site in mRNA via a specific peptide of the uS3 protein located near the mRNA entry channel. Biochimie 2018; 158:117-125. [PMID: 30594661 DOI: 10.1016/j.biochi.2018.12.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 12/25/2018] [Indexed: 12/12/2022]
Abstract
The small subunit ribosomal protein uS3 is a critically important player in the ribosome-mRNA interactions during translation and has numerous functions not directly related to protein synthesis in eukaryotes. A peculiar feature of the human uS3 protein is the ability of its fragment 55-64 exposed on the 40S subunit surface near the mRNA entry channel to form cross-links with 3'-terminal dialdehyde derivatives of various unstructured RNAs and with abasic sites in single-stranded DNAs. Here we showed that the ability of the above uS3 fragment to cross-link to abasic sites in DNAs is inherent only in mature cytoplasmic 40S subunits, but not nuclear pre-40S particles, which implies that it may be relevant to the ribosome-mRNA interplay. To clarify this issue, we investigated interactions of human ribosomes with synthetic mRNA analogues bearing an abasic site protected by a photocleavable group at the 3'-termini. We found that these mRNA analogues can form specific complexes with 80S ribosomes and 40S subunits, where the undamaged upstream part of the analogue is fixed in the mRNA binding channel by interaction with the P-site tRNA, and the downstream part located outside the ribosome is cross-linked to the uS3 fragment 55-64. The yield of cross-links of the mRNA analogues was rather high when their undamaged parts were bound to the mRNA channel prior to deprotection of the abasic site enabling its covalent attachment to the 40S subunit via the uS3 protein, but not vice versa. Based on our findings, one can assume that abasic sites, which can occur in mRNAs due to oxidative stress and ageing, are able to interact directly with the uS3 fragment exposed on the 40S subunit surface near the mRNA entry channel during translation. Consequently, the 40S subunit can be considered as a potential mRNA quality controller.
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Affiliation(s)
- Anastasia S Ochkasova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, 630090, Russia
| | - Maria I Meschaninova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, 630090, Russia
| | - Aliya G Venyaminova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, 630090, Russia
| | - Anton V Ivanov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, 630090, Russia
| | - Dmitri M Graifer
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, 630090, Russia; Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Galina G Karpova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, 630090, Russia; Novosibirsk State University, Novosibirsk, 630090, Russia.
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30
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Jia L, Gao M, Yan J, Chen S, Sun J, Hua Q, Ding J, Shi Z. Evaluation of the sub-optimal induction strategies for heterologous proteins production by Pichia pastoris Mut+/MutS strains and related transcriptional and metabolic analysis. World J Microbiol Biotechnol 2018; 34:180. [DOI: 10.1007/s11274-018-2562-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 11/19/2018] [Indexed: 12/15/2022]
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31
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Ding W, Zhou Y, Qu Q, Cui W, God'spower BO, Liu Y, Chen X, Chen M, Yang Y, Li Y. Azithromycin Inhibits Biofilm Formation by Staphylococcus xylosus and Affects Histidine Biosynthesis Pathway. Front Pharmacol 2018; 9:740. [PMID: 30042679 PMCID: PMC6048454 DOI: 10.3389/fphar.2018.00740] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2018] [Accepted: 06/18/2018] [Indexed: 11/13/2022] Open
Abstract
Staphylococcus xylosus, a coagulase-negative, non-pathogenic bacterium, responsible for opportunistic infections in humans and bovine mastitis, has the ability to form biofilms, which are responsible for persistent infections and antibiotic resistance. In our study, azithromycin significantly inhibited biofilm formation by altering protein expression. Of the 1764 proteins measured by the isobaric Tag for Relative and Absolute Quantification (iTRAQ) technique, only 148 proteins showed significantly different expression between the azithromycin-treated and untreated cells. Most ribosomal proteins were markedly up-regulated, and the expression of the proteins involved in histidine biosynthesis, which, in turn, influence biofilm formation, was down-regulated, particularly imidazole glycerophosphate dehydratase (IGPD). Previously, we had observed that IGPD plays an important role in biofilm formation by S. xylosus. Therefore, hisB expression was studied by real-time PCR, and the interactions between azithromycin and IGPD were predicted by molecular docking analysis. hisB was found to be significantly down-regulated, and six bond interactions were observed between azithromycin and IGPD. Many active atoms of azithromycin did not interact with the biologically active site of IGPD. Surface plasmon resonance analysis used to further study the relationship between IGPD and azithromycin showed minimum interaction between them. Histidine content in the azithromycin-treated and untreated groups was determined. We noted a slight difference, which was not consistent with the expression of the proteins involved in histidine biosynthesis. Therefore, histidine degradation into glutamate was also studied, and we found that all proteins were down-regulated. This could be the reason why histidine content showed little change between the treated and untreated groups. In summary, we found that azithromycin is a potential inhibitor of S. xylosus biofilm formation, and the underlying mechanism was preliminarily elucidated in this study.
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Affiliation(s)
- Wenya Ding
- Department of Veterinary Medicine, Northeast Agricultural University, Harbin, China.,Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, China
| | - Yonghui Zhou
- Department of Veterinary Medicine, Northeast Agricultural University, Harbin, China.,Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, China
| | - Qianwei Qu
- Department of Veterinary Medicine, Northeast Agricultural University, Harbin, China.,Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, China
| | - Wenqiang Cui
- Department of Veterinary Medicine, Northeast Agricultural University, Harbin, China.,Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, China
| | - Bello Onaghise God'spower
- Department of Veterinary Medicine, Northeast Agricultural University, Harbin, China.,Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, China
| | - Yanyan Liu
- Department of Veterinary Medicine, Northeast Agricultural University, Harbin, China.,Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, China
| | - Xueying Chen
- Department of Veterinary Medicine, Northeast Agricultural University, Harbin, China.,Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, China
| | - Mo Chen
- Department of Veterinary Medicine, Northeast Agricultural University, Harbin, China.,Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, China
| | - Yanbei Yang
- Department of Veterinary Medicine, Northeast Agricultural University, Harbin, China.,Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, China
| | - Yanhua Li
- Department of Veterinary Medicine, Northeast Agricultural University, Harbin, China.,Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, China
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Lu AX, Chong YT, Hsu IS, Strome B, Handfield LF, Kraus O, Andrews BJ, Moses AM. Integrating images from multiple microscopy screens reveals diverse patterns of change in the subcellular localization of proteins. eLife 2018; 7:e31872. [PMID: 29620521 PMCID: PMC5935485 DOI: 10.7554/elife.31872] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Accepted: 03/30/2018] [Indexed: 01/29/2023] Open
Abstract
The evaluation of protein localization changes on a systematic level is a powerful tool for understanding how cells respond to environmental, chemical, or genetic perturbations. To date, work in understanding these proteomic responses through high-throughput imaging has catalogued localization changes independently for each perturbation. To distinguish changes that are targeted responses to the specific perturbation or more generalized programs, we developed a scalable approach to visualize the localization behavior of proteins across multiple experiments as a quantitative pattern. By applying this approach to 24 experimental screens consisting of nearly 400,000 images, we differentiated specific responses from more generalized ones, discovered nuance in the localization behavior of stress-responsive proteins, and formed hypotheses by clustering proteins that have similar patterns. Previous approaches aim to capture all localization changes for a single screen as accurately as possible, whereas our work aims to integrate large amounts of imaging data to find unexpected new cell biology.
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Affiliation(s)
- Alex X Lu
- Department of Computer ScienceUniversity of TorontoTorontoCanada
| | - Yolanda T Chong
- Terrence Donnelly Centre for Cellular and Biomolecular ResearchUniversity of TorontoTorontoCanada
| | - Ian Shen Hsu
- Department of Cell and Systems BiologyUniversity of TorontoTorontoCanada
| | - Bob Strome
- Department of Cell and Systems BiologyUniversity of TorontoTorontoCanada
| | | | - Oren Kraus
- Department of Electrical and Computer EngineeringUniversity of TorontoTorontoCanada
| | - Brenda J Andrews
- Terrence Donnelly Centre for Cellular and Biomolecular ResearchUniversity of TorontoTorontoCanada
- Department of Molecular GeneticsUniversity of TorontoTorontoCanada
| | - Alan M Moses
- Department of Computer ScienceUniversity of TorontoTorontoCanada
- Department of Cell and Systems BiologyUniversity of TorontoTorontoCanada
- Center for Analysis of Genome Evolution and FunctionUniversity of TorontoTorontoCanada
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Saha A, Das S, Moin M, Dutta M, Bakshi A, Madhav MS, Kirti PB. Genome-Wide Identification and Comprehensive Expression Profiling of Ribosomal Protein Small Subunit (RPS) Genes and their Comparative Analysis with the Large Subunit (RPL) Genes in Rice. FRONTIERS IN PLANT SCIENCE 2017; 8:1553. [PMID: 28966624 PMCID: PMC5605565 DOI: 10.3389/fpls.2017.01553] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 08/25/2017] [Indexed: 05/07/2023]
Abstract
Ribosomal proteins (RPs) are indispensable in ribosome biogenesis and protein synthesis, and play a crucial role in diverse developmental processes. Our previous studies on Ribosomal Protein Large subunit (RPL) genes provided insights into their stress responsive roles in rice. In the present study, we have explored the developmental and stress regulated expression patterns of Ribosomal Protein Small (RPS) subunit genes for their differential expression in a spatiotemporal and stress dependent manner. We have also performed an in silico analysis of gene structure, cis-elements in upstream regulatory regions, protein properties and phylogeny. Expression studies of the 34 RPS genes in 13 different tissues of rice covering major growth and developmental stages revealed that their expression was substantially elevated, mostly in shoots and leaves indicating their possible involvement in the development of vegetative organs. The majority of the RPS genes have manifested significant expression under all abiotic stress treatments with ABA, PEG, NaCl, and H2O2. Infection with important rice pathogens, Xanthomonas oryzae pv. oryzae (Xoo) and Rhizoctonia solani also induced the up-regulation of several of the RPS genes. RPS4, 13a, 18a, and 4a have shown higher transcript levels under all the abiotic stresses, whereas, RPS4 is up-regulated in both the biotic stress treatments. The information obtained from the present investigation would be useful in appreciating the possible stress-regulatory attributes of the genes coding for rice ribosomal small subunit proteins apart from their functions as house-keeping proteins. A detailed functional analysis of independent genes is required to study their roles in stress tolerance and generating stress- tolerant crops.
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Affiliation(s)
- Anusree Saha
- Department of Plant Sciences, University of HyderabadHyderabad, India
| | - Shubhajit Das
- Department of Plant Sciences, University of HyderabadHyderabad, India
| | - Mazahar Moin
- Department of Plant Sciences, University of HyderabadHyderabad, India
| | - Mouboni Dutta
- Department of Plant Sciences, University of HyderabadHyderabad, India
| | - Achala Bakshi
- Department of Plant Sciences, University of HyderabadHyderabad, India
| | - M. S. Madhav
- Department of Biotechnology, Indian Institute of Rice ResearchHyderabad, India
| | - P. B. Kirti
- Department of Plant Sciences, University of HyderabadHyderabad, India
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Human PDCD2L Is an Export Substrate of CRM1 That Associates with 40S Ribosomal Subunit Precursors. Mol Cell Biol 2016; 36:3019-3032. [PMID: 27697862 DOI: 10.1128/mcb.00303-16] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 09/15/2016] [Indexed: 01/05/2023] Open
Abstract
Protein arginine methyltransferase 3 (PRMT3) forms a stable complex with 40S ribosomal protein S2 (RPS2) and contributes to ribosome biogenesis. However, the molecular mechanism by which PRMT3 influences ribosome biogenesis and/or function still remains unclear. Using quantitative proteomics, we identified human programmed cell death 2-like (PDCD2L) as a novel PRMT3-associated protein. Our data suggest that RPS2 promotes the formation of a conserved extraribosomal complex with PRMT3 and PDCD2L. We also show that PDCD2L associates with 40S subunit precursors that contain a 3'-extended form of the 18S rRNA (18S-E pre-rRNA) and several pre-40S maturation factors. PDCD2L shuttles between the nucleus and the cytoplasm in a CRM1-dependent manner using a leucine-rich nuclear export signal that is sufficient to direct the export of a reporter protein. Although PDCD2L is not required for the biogenesis and export of 40S ribosomal subunits, we found that PDCD2L-null cells accumulate free 60S ribosomal subunits, which is indicative of a deficiency in 40S subunit availability. Our data also indicate that PDCD2L and its paralog, PDCD2, function redundantly in 40S ribosomal subunit production. Our findings uncover the existence of an extraribosomal complex consisting of PDCD2L, RPS2, and PRMT3 and support a role for PDCD2L in the late maturation of 40S ribosomal subunits.
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Lu H, Xiong J, Shang Q, Jiang Y, Cao Y. Roles of RPS41 in Biofilm Formation, Virulence, and Hydrogen Peroxide Sensitivity in Candida albicans. Curr Microbiol 2016; 72:783-7. [PMID: 26952720 DOI: 10.1007/s00284-016-1019-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 01/28/2016] [Indexed: 11/29/2022]
Abstract
In eukaryotes, loss of cytoplasmic ribosomal proteins (RPs) results in a reduced growth rate and other phenotypic defects. The ability to transition from a unicellular budding yeast to a filamentous form is very important for biofilm formation and virulence in Candida albicans. Our recent study found that loss of the RPS41 (C2_10620W_A) gene but not its paralog RPS42 (C1_01640W_A) resulted in altered growth and filamentation changes in C. albicans, so we hypothesized that the RPS41 gene should play important roles in virulence and biofilm formation in this pathogen. We found that both virulence and the ability to form biofilms were defective due to deletion of the RPS41 gene. We also found that loss of the RPS41 gene increased sensitivity to hydrogen peroxide, and that hydrogen peroxide induced the expression of the RPS41 gene in a wild-type strain. These results suggested that the RPS41 gene plays important roles in C. albicans biofilm formation, virulence, and susceptibility to hydrogen peroxide.
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Affiliation(s)
- Hui Lu
- Key Laboratory of the Plateau of the Environmental Damage Control, Lanzhou General Hospital of Lanzhou Military Command, Lanzhou, China
| | - Juan Xiong
- Key Laboratory of the Plateau of the Environmental Damage Control, Lanzhou General Hospital of Lanzhou Military Command, Lanzhou, China
| | - Qinghua Shang
- Department of Pharmacology, Center for New Drug Research, School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai, 200433, China
| | - Yuanying Jiang
- Department of Pharmacology, Center for New Drug Research, School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai, 200433, China.
| | - Yingying Cao
- Department of Pharmacology, Center for New Drug Research, School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai, 200433, China.
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