A novel assay provides insight into tRNAPhe retrograde nuclear import and re-export in S. cerevisiae

Abstract In eukaryotes, tRNAs are transcribed in the nucleus and subsequently exported to the cytoplasm where they serve as essential adaptor molecules in translation. However, tRNAs can be returned to the nucleus by the evolutionarily conserved process called tRNA retrograde nuclear import, before relocalization back to the cytoplasm via a nuclear re-export step. Several important functions of these latter two trafficking events have been identified, yet the pathways are largely unknown. Therefore, we developed an assay in Saccharomyces cerevisiae to identify proteins mediating tRNA retrograde nuclear import and re-export using the unique wybutosine modification of mature tRNAPhe. Our hydrochloric acid/aniline assay revealed that the karyopherin Mtr10 mediates retrograde import of tRNAPhe, constitutively and in response to amino acid deprivation, whereas the Hsp70 protein Ssa2 mediates import specifically in the latter. Furthermore, tRNAPhe is re-exported by Crm1 and Mex67, but not by the canonical tRNA exporters Los1 or Msn5. These findings indicate that the re-export process occurs in a tRNA family-specific manner. Together, this assay provides insights into the pathways for tRNAPhe retrograde import and re-export and is a tool that can be used on a genome-wide level to identify additional gene products involved in these tRNA trafficking events.

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Chromatin architectural proteins regulate flowering time by precluding gene looping

Science Advances ◽

10.1126/sciadv.abg3097 ◽

2021 ◽

Vol 7 (24) ◽

pp. eabg3097

Author(s):

Bo Zhao ◽

Yanpeng Xi ◽

Junghyun Kim ◽

Sibum Sung

Keyword(s):

Chromatin Structure ◽

Cellular Processes ◽

Genome Wide ◽

A Genome ◽

Evolutionarily Conserved ◽

Architectural Proteins ◽

Floral Repressor ◽

Flanking Regions ◽

Genome Wide Study

Chromatin structure is critical for gene expression and many other cellular processes. In Arabidopsis thaliana, the floral repressor FLC adopts a self-loop chromatin structure via bridging of its flanking regions. This local gene loop is necessary for active FLC expression. However, the molecular mechanism underlying the formation of this class of gene loops is unknown. Here, we report the characterization of a group of linker histone-like proteins, named the GH1-HMGA family in Arabidopsis, which act as chromatin architecture modulators. We demonstrate that these family members redundantly promote the floral transition through the repression of FLC. A genome-wide study revealed that this family preferentially binds to the 5′ and 3′ ends of gene bodies. The loss of this binding increases FLC expression by stabilizing the FLC 5′ to 3′ gene looping. Our study provides mechanistic insights into how a family of evolutionarily conserved proteins regulates the formation of local gene loops.

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Hoxa1 and TALE proteins display cross-regulatory interactions and form a combinatorial binding code on Hoxa1 targets

10.1101/092296 ◽

2016 ◽

Author(s):

Bony De Kumar ◽

Hugo J. Parker ◽

Ariel Paulson ◽

Mark E. Parrish ◽

Irina Pushel ◽

...

Keyword(s):

Es Cells ◽

Hox Proteins ◽

Binding Motifs ◽

Functional Roles ◽

Regulatory Interactions ◽

Mouse Es Cells ◽

Genome Wide ◽

A Genome ◽

Combinatorial Interactions ◽

Insight Into

AbstractHoxa1 has diverse functional roles in differentiation and development. We have identified and characterized properties of regions bound by Hoxa1 on a genome-wide basis in differentiating mouse ES cells. Hoxa1 bound regions are enriched for clusters of consensus binding motifs for Hox, Pbx and Meis and many display co-occupancy of Pbx and Meis. Pbx and Meis are members of the TALE family and genome-wide analysis of multiple TALE members (Pbx, Meis, TGIF, Prep1 and Prep2) show that nearly all Hoxa1 targets display occupancy of one or more TALE members. The combinatorial binding patterns of TALE proteins defines distinct classes of Hoxa1 targets and indicates a role as cofactors in modulating the specificity of Hox proteins. We also discovered extensive auto- and cross-regulatory interactions among the Hoxa1 and TALE genes. This study provides new insight into a regulatory network involving combinatorial interactions between Hoxa1 and TALE proteins.

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Molecular cloning of RBCS genes in Selaginella and the evolution of the rbcS gene family

Archives of Biological Sciences ◽

10.2298/abs141111005w ◽

2015 ◽

Vol 67 (2) ◽

pp. 373-383

Author(s):

Bo Wang ◽

Su Yingjuan ◽

Ting Wang

Keyword(s):

Gene Family ◽

Physcomitrella Patens ◽

Higher Plants ◽

Genome Wide ◽

A Genome ◽

Rbcs Gene ◽

Rbcs Genes ◽

Selaginella Moellendorffii ◽

Insight Into ◽

Major Domain

Rubisco small subunits (RBCS) are encoded by a nuclear rbcS multigene family in higher plants and green algae. However, owing to the lack of rbcS sequences in lycophytes, the characteristics of rbcS genes in lycophytes is unclear. Recently, the complete genome sequence of the lycophyte Selaginella moellendorffii provided the first insight into the rbcS gene family in lycophytes. To understand further the characteristics of rbcS genes in other Selaginella, the full length of rbcS genes (rbcS1 and rbcS2) from two other Selaginella species were isolated. Both rbcS1 and rbcS2 genes shared more than 97% identity among three Selaginella species. RBCS proteins from Selaginella contained the Pfam RBCS domain F00101, which was a major domain of other plant RBCS proteins. To explore the evolution of the rbcS gene family across Selaginella and other plants, we identified and performed comparative analysis of the rbcS gene family among 16 model plants based on a genome-wide analysis. The results showed that (i) two rbcS genes were obtained in Selaginella, which is the second fewest number of rbcS genes among the 16 representative plants; (ii) an expansion of rbcS genes occurred in the moss Physcomitrella patens; (iii) only RBCS proteins from angiosperms contained the Pfam PF12338 domains, and (iv) a pattern of concerted evolution existed in the rbcS gene family. Our study provides new insights into the evolution of the rbcS gene family in Selaginella and other plants.

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A Comprehensive Survey on the Terpene Synthase Gene Family Provides New Insight into Its Evolutionary Patterns

Genome Biology and Evolution ◽

10.1093/gbe/evz142 ◽

2019 ◽

Vol 11 (8) ◽

pp. 2078-2098 ◽

Cited By ~ 8

Author(s):

Shu-Ye Jiang ◽

Jingjing Jin ◽

Rajani Sarojam ◽

Srinivasan Ramachandran

Keyword(s):

Gene Family ◽

Large Scale ◽

Family Members ◽

Terpene Synthase ◽

Limited Information ◽

Terpene Synthases ◽

Genome Wide ◽

A Genome ◽

Family Expansion ◽

Insight Into

Abstract Terpenes are organic compounds and play important roles in plant growth and development as well as in mediating interactions of plants with the environment. Terpene synthases (TPSs) are the key enzymes responsible for the biosynthesis of terpenes. Although some species were employed for the genome-wide identification and characterization of the TPS family, limited information is available regarding the evolution, expansion, and retention mechanisms occurring in this gene family. We performed a genome-wide identification of the TPS family members in 50 sequenced genomes. Additionally, we also characterized the TPS family from aromatic spearmint and basil plants using RNA-Seq data. No TPSs were identified in algae genomes but the remaining plant species encoded various numbers of the family members ranging from 2 to 79 full-length TPSs. Some species showed lineage-specific expansion of certain subfamilies, which might have contributed toward species or ecotype divergence or environmental adaptation. A large-scale family expansion was observed mainly in dicot and monocot plants, which was accompanied by frequent domain loss. Both tandem and segmental duplication significantly contributed toward family expansion and expression divergence and played important roles in the survival of these expanded genes. Our data provide new insight into the TPS family expansion and evolution and suggest that TPSs might have originated from isoprenyl diphosphate synthase genes.

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Admixture into and within sub-Saharan Africa

eLife ◽

10.7554/elife.15266 ◽

2016 ◽

Vol 5 ◽

Cited By ~ 57

Author(s):

George BJ Busby ◽

Gavin Band ◽

Quang Si Le ◽

Muminatou Jallow ◽

Edith Bougama ◽

...

Keyword(s):

Gene Flow ◽

Geographic Region ◽

Sub Saharan Africa ◽

Genome Wide ◽

A Genome ◽

Depth Analysis ◽

Shared Ancestry ◽

Sub Saharan ◽

Linguistic Groups ◽

Insight Into

Similarity between two individuals in the combination of genetic markers along their chromosomes indicates shared ancestry and can be used to identify historical connections between different population groups due to admixture. We use a genome-wide, haplotype-based, analysis to characterise the structure of genetic diversity and gene-flow in a collection of 48 sub-Saharan African groups. We show that coastal populations experienced an influx of Eurasian haplotypes over the last 7000 years, and that Eastern and Southern Niger-Congo speaking groups share ancestry with Central West Africans as a result of recent population expansions. In fact, most sub-Saharan populations share ancestry with groups from outside of their current geographic region as a result of gene-flow within the last 4000 years. Our in-depth analysis provides insight into haplotype sharing across different ethno-linguistic groups and the recent movement of alleles into new environments, both of which are relevant to studies of genetic epidemiology.

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NUMB regulates the endocytosis and activity of the anaplastic lymphoma kinase in an isoform-specific manner

Journal of Molecular Cell Biology ◽

10.1093/jmcb/mjz003 ◽

2019 ◽

Vol 11 (11) ◽

pp. 994-1005 ◽

Cited By ~ 2

Author(s):

Ran Wei ◽

Xuguang Liu ◽

Courtney Voss ◽

Wentao Qin ◽

Lina Dagnino ◽

...

Keyword(s):

Cell Fate ◽

Receptor Tyrosine Kinase ◽

Anaplastic Lymphoma Kinase ◽

Degradation Pathway ◽

Anaplastic Lymphoma ◽

Mechanistic Insight ◽

Evolutionarily Conserved ◽

Specific Manner ◽

Insight Into

Abstract NUMB is an evolutionarily conserved protein that plays an important role in cell adhesion, migration, polarity, and cell fate determination. It has also been shown to play a role in the pathogenesis of certain cancers, although it remains controversial whether NUMB functions as an oncoprotein or tumor suppressor. Here, we show that NUMB binds to anaplastic lymphoma kinase (ALK), a receptor tyrosine kinase aberrantly activated in several forms of cancer, and this interaction regulates the endocytosis and activity of ALK. Intriguingly, the function of the NUMB–ALK interaction is isoform-dependent. While both p66-NUMB and p72-NUMB isoforms are capable of mediating the endocytosis of ALK, the former directs ALK to the lysosomal degradation pathway, thus decreasing the overall ALK level and the downstream MAP kinase signal. In contrast, the p72-NUMB isoform promotes ALK recycling back to the plasma membrane, thereby maintaining the kinase in its active state. Our work sheds light on the controversial role of different isoforms of NUMB in tumorigenesis and provides mechanistic insight into ALK regulation.

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Evidence of evolutionary selection for cotranslational folding

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1705772114 ◽

2017 ◽

Vol 114 (43) ◽

pp. 11434-11439 ◽

Cited By ~ 48

Author(s):

William M. Jacobs ◽

Eugene I. Shakhnovich

Keyword(s):

Self Assembly ◽

Evolutionary Selection ◽

Fitness Effects ◽

Open Questions ◽

Genome Wide ◽

A Genome ◽

Evolutionarily Conserved ◽

Domain Boundaries ◽

Cotranslational Folding ◽

Selection For

Recent experiments and simulations have demonstrated that proteins can fold on the ribosome. However, the extent and generality of fitness effects resulting from cotranslational folding remain open questions. Here we report a genome-wide analysis that uncovers evidence of evolutionary selection for cotranslational folding. We describe a robust statistical approach to identify loci within genes that are both significantly enriched in slowly translated codons and evolutionarily conserved. Surprisingly, we find that domain boundaries can explain only a small fraction of these conserved loci. Instead, we propose that regions enriched in slowly translated codons are associated with cotranslational folding intermediates, which may be smaller than a single domain. We show that the intermediates predicted by a native-centric model of cotranslational folding account for the majority of these loci across more than 500 Escherichia coli proteins. By making a direct connection to protein folding, this analysis provides strong evidence that many synonymous substitutions have been selected to optimize translation rates at specific locations within genes. More generally, our results indicate that kinetics, and not just thermodynamics, can significantly alter the efficiency of self-assembly in a biological context.

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Dbf4-Dependent Kinase (DDK)-Mediated Proteolysis of CENP-A Prevents Mislocalization of CENP-A in Saccharomyces cerevisiae

G3 Genes|Genome|Genetics ◽

10.1534/g3.120.401131 ◽

2020 ◽

Vol 10 (6) ◽

pp. 2057-2068 ◽

Cited By ~ 3

Author(s):

Jessica R. Eisenstatt ◽

Lars Boeckmann ◽

Wei-Chun Au ◽

Valerie Garcia ◽

Levi Bursch ◽

...

Keyword(s):

Dna Replication ◽

Replication Initiation ◽

Centromeric Chromatin ◽

Dna Replication Initiation ◽

Link Type ◽

Genome Wide ◽

A Genome ◽

Evolutionarily Conserved ◽

Histone H3 Variant

The evolutionarily conserved centromeric histone H3 variant (Cse4 in budding yeast, CENP-A in humans) is essential for faithful chromosome segregation. Mislocalization of CENP-A to non-centromeric chromatin contributes to chromosomal instability (CIN) in yeast, fly, and human cells and CENP-A is highly expressed and mislocalized in cancers. Defining mechanisms that prevent mislocalization of CENP-A is an area of active investigation. Ubiquitin-mediated proteolysis of overexpressed Cse4 (GALCSE4) by E3 ubiquitin ligases such as Psh1 prevents mislocalization of Cse4, and psh1Δ strains display synthetic dosage lethality (SDL) with GALCSE4. We previously performed a genome-wide screen and identified five alleles of CDC7 and DBF4 that encode the Dbf4-dependent kinase (DDK) complex, which regulates DNA replication initiation, among the top twelve hits that displayed SDL with GALCSE4. We determined that cdc7-7 strains exhibit defects in ubiquitin-mediated proteolysis of Cse4 and show mislocalization of Cse4. Mutation of MCM5 (mcm5-bob1) bypasses the requirement of Cdc7 for replication initiation and rescues replication defects in a cdc7-7 strain. We determined that mcm5-bob1 does not rescue the SDL and defects in proteolysis of GALCSE4 in a cdc7-7 strain, suggesting a DNA replication-independent role for Cdc7 in Cse4 proteolysis. The SDL phenotype, defects in ubiquitin-mediated proteolysis, and the mislocalization pattern of Cse4 in a cdc7-7 psh1Δ strain were similar to that of cdc7-7 and psh1Δ strains, suggesting that Cdc7 regulates Cse4 in a pathway that overlaps with Psh1. Our results define a DNA replication initiation-independent role of DDK as a regulator of Psh1-mediated proteolysis of Cse4 to prevent mislocalization of Cse4.

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Evidence of evolutionary selection for co-translational folding

10.1101/121871 ◽

2017 ◽

Author(s):

William M. Jacobs ◽

Eugene I. Shakhnovich

Keyword(s):

Self Assembly ◽

E Coli ◽

Evolutionary Selection ◽

Fitness Effects ◽

Open Questions ◽

Genome Wide ◽

A Genome ◽

Evolutionarily Conserved ◽

Domain Boundaries ◽

Selection For

Recent experiments and simulations have demonstrated that proteins can fold on the ribosome. However, the extent and generality of fitness effects resulting from co-translational folding remain open questions. Here we report a genome-wide analysis that uncovers evidence of evolutionary selection for co-translational folding. We describe a robust statistical approach to identify loci within genes that are both significantly enriched in slowly translated codons and evolutionarily conserved. Surprisingly, we find that domain boundaries can explain only a small fraction of these conserved loci. Instead, we propose that regions enriched in slowly translated codons are associated with co-translational folding intermediates, which may be smaller than a single domain. We show that the intermediates predicted by a native-centric model of co-translational folding account for the majority of these loci across more than 500 E. coli proteins. By making a direct connection to protein folding, this analysis provides strong evidence that many synonymous substitutions have been selected to optimize translation rates at specific locations within genes. More generally, our results indicate that kinetics, and not just thermodynamics, can significantly alter the efficiency of self-assembly in a biological context.

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DETECTION OF SELECTION SIGNALS IN CATTLE POPULATIONS BY PCA

AGROFOR ◽

10.7251/agreng2002090o ◽

2020 ◽

Vol 5 (2) ◽

Author(s):

Barbora OLŠANSKÁ ◽

Radovan KASARDA ◽

Kristína LEHOCKÁ ◽

Nina MORAVČÍKOVÁ

Keyword(s):

Muscle Development ◽

Principal Component ◽

Coat Colour ◽

Genome Wide ◽

A Genome ◽

Somatic Diversification ◽

Close Genetic Relationship ◽

Insight Into ◽

Selection Of ◽

Genome Wide Scan

The presented study provides a genome-wide scan of selection signals in cattle by principal component analysis (PCA). The aim was to identify SNP affected by intensive selection based on package PCAdapt implemented under software R. This analysis provided insight into the association between the SNP frequencies related to population differentiation. The four cattle populations were involved in the analysis (Slovak Spotted cattle, Ayrshire, Swiss Simmental and Holstein) with overall 272 of genotyped individuals. After applying quality control, the final dataset consisted of 35 675 SNPs, with an overall length of 2496.14 Mb and average space between adjacent SNP 70.03 ± 76.1 kb. After performing PCA analysis, the uniqueness of the breeds was revealed. On the other hand, a close genetic relationship and eleven SNPs affected by selection were found, with a position close to 162 genes involved in the various biological processes. The majority of genes were involved in the positive regulation of adenylate cyclase activity, embryo development and somatic diversification of immune receptors via somatic mutation. Several candidate genes for genetic control of the immune system (DNAJB9), muscle development (SEPT7, TRIM32, ROCK1, NRAP, PZDZ8, HSPA12A and FGFR2), milk production (SOCS5, CD46), reproduction (LHCGR, EEPD1, FSHR) and coat colour (KIT) were identified. Our results provide insights into the regions of the genome affected by the intensive selection of analysed cattle populations.

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