A Highly Conserved 310-Helix Within the Kinesin Motor Domain is Critical for Kinesin Function and Human Health

AbstractKIF1A, a kinesin-3 family member, plays critical roles as a long-distance cargo-transporter within neurons. Over 100 known KIF1A mutations in humans result in KIF1A Associated Neurological Disease (KAND), developmental and degenerative neurological conditions for which there is no cure. A de novo missense mutation, P305L, was recently identified in several children diagnosed with KAND, but the underlying molecular basis for the disease phenotype is unknown. Interestingly, this residue is highly conserved in kinesin-family proteins, and together with adjacent conserved residues also implicated in KAND, forms an unusual 310-helical element immediately C-terminal to loop-12 (L12, also known as the K-loop in KIF1A) in the conserved kinesin motor core. In KIF1A, the disordered K-loop contains a highly charged insertion of lysines that is thought to endow the motor with a high microtubule-association rate. Here, we characterize the molecular defects of the P305L mutation in KIF1A using genetic, biochemical, and single-molecule approaches. We find the mutation negatively impacts the velocity, run-length, and force generation of the motor. However, a much more dramatic effect is observed on the microtubule-association rate of the motor, revealing that the presence of an intact K-loop is not sufficient for its function. We hypothesize that an elusive K-loop conformation, mediated by formation of a highly conserved adjacent 310-helix that is modulated via P305, is critically important for the kinesin-microtubule interaction. Importantly, we find that the function of this proline is conserved in the canonical kinesin, KIF5, revealing a fundamental principle of the kinesin motor mechanism.

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A highly conserved 310 helix within the kinesin motor domain is critical for kinesin function and human health

Science Advances ◽

10.1126/sciadv.abf1002 ◽

2021 ◽

Vol 7 (18) ◽

pp. eabf1002

Author(s):

Aileen J. Lam ◽

Lu Rao ◽

Yuzu Anazawa ◽

Kyoko Okada ◽

Kyoko Chiba ◽

...

Keyword(s):

Molecular Basis ◽

Fundamental Principle ◽

Association Rate ◽

Biophysical Parameters ◽

Kinesin Motor ◽

Cargo Transport ◽

The Family ◽

Loop Conformation ◽

Conserved Residue ◽

310 Helix

KIF1A is a critical cargo transport motor within neurons. More than 100 known mutations result in KIF1A-associated neurological disorder (KAND), a degenerative condition for which there is no cure. A missense mutation, P305L, was identified in children diagnosed with KAND, but the molecular basis for the disease is unknown. We find that this conserved residue is part of an unusual 310 helix immediately adjacent to the family-specific K-loop, which facilitates a high microtubule-association rate. We find that the mutation negatively affects several biophysical parameters of the motor. However, the microtubule-association rate of the motor is most markedly affected, revealing that the presence of an intact K-loop is not sufficient for its function. We hypothesize that the 310 helix facilitates a specific K-loop conformation that is critical for its function. We find that the function of this proline is conserved in kinesin-1, revealing a fundamental principle of the kinesin motor mechanism.

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Single molecule, full-length transcript sequencing provides insight into the extreme metabolism of ruby-throated hummingbird Archilochus colubris

10.1101/117218 ◽

2017 ◽

Cited By ~ 4

Author(s):

Rachael E. Workman ◽

Alexander M. Myrka ◽

Elizabeth Tseng ◽

G. William Wong ◽

Kenneth C. Welch ◽

...

Keyword(s):

Single Molecule ◽

De Novo ◽

Sequence Divergence ◽

Gene Families ◽

Full Length ◽

Sequencing Data ◽

Bioinformatics Pipeline ◽

Long Distance ◽

Migratory Flight ◽

Lack Of Information

AbstractHummingbirds can support their high metabolic rates exclusively by oxidizing ingested sugars, which is unsurprising given their sugar-rich nectar diet and use of energetically expensive hovering flight. However, they cannot rely on dietary sugars as a fuel during fasting periods, such as during the night, at first light, or when undertaking long-distance migratory flights, and must instead rely exclusively on onboard lipids. This metabolic flexibility is remarkable both in that the birds can switch between exclusive use of each fuel type within minutes and in that de novo lipogenesis from dietary sugar precursors is the principle way in which fat stores are built, sometimes at exceptionally high rates, such as during the few days prior to a migratory flight. The hummingbird hepatopancreas is the principle location of de novo lipogenesis and likely plays a key role in fuel selection, fuel switching, and glucose homeostasis. Yet understanding how this tissue, and the whole organism, achieves and moderates high rates of energy turnover is hampered by a fundamental lack of information regarding how genes coding for relevant enzymes differ in their sequence, expression, and regulation in these unique animals. To address this knowledge gap, we generated a de novo transcriptome of the hummingbird liver using PacBio full-length cDNA sequencing (Iso-Seq), yielding a total of 8.6Gb of sequencing data, or 2.6M reads from 4 different size fractions. We analyzed data using the SMRTAnalysis v3.1 Iso-Seq pipeline, including classification of reads and clustering of isoforms (ICE) followed by error-correction (Arrow). With COGENT, we clustered different isoforms into gene families to generate de novo gene contigs. We performed orthology analysis to identify closely related sequences between our transcriptome and other avian and human gene sets. We also aligned our transcriptome against the Calypte anna genome where possible. Finally, we closely examined homology of critical lipid metabolic genes between our transcriptome data and avian and human genomes. We confirmed high levels of sequence divergence within hummingbird lipogenic enzymes, suggesting a high probability of adaptive divergent function in the hepatic lipogenic pathways. Our results have leveraged cutting-edge technology and a novel bioinformatics pipeline to provide a compelling first direct look at the transcriptome of this incredible organism.

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Advances in the study of the mechanochemical coupling of kinesin

International Journal of Modern Physics B ◽

10.1142/s0217979218400015 ◽

2018 ◽

Vol 32 (18) ◽

pp. 1840001 ◽

Cited By ~ 1

Author(s):

Ming Li ◽

Zhong-Can Ou-Yang ◽

Yao-Gen Shu

Keyword(s):

Molecular Dynamics ◽

Single Molecule ◽

Intracellular Transport ◽

Coordination Mechanism ◽

Personal Perspective ◽

Long Distance ◽

Future Studies ◽

Mechanochemical Coupling ◽

Dynamics Simulations ◽

Made In

Kinesin is a two-headed linear motor for intracellular transport. It can walk a long distance in a hand-over-hand manner along the track before detaching (i.e., high processivity), and it consumes one ATP molecule for each step (i.e., tight mechanochemical coupling). The mechanisms of the coordination of its two heads and the mechanochemical coupling are the central issues of numerous researches. A few advances have been made in recent decades, thanks to the development of single-molecule technologies and molecular dynamics simulations. In this paper, we review some progress of the studies on the kinematics, energetics, coordination mechanism, mechanochemical mechanism of kinesin. We also present a personal perspective on the future studies of kinesin.

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AStrap: identification of alternative splicing from transcript sequences without a reference genome

Bioinformatics ◽

10.1093/bioinformatics/bty1008 ◽

2018 ◽

Vol 35 (15) ◽

pp. 2654-2656 ◽

Cited By ~ 5

Author(s):

Guoli Ji ◽

Wenbin Ye ◽

Yaru Su ◽

Moliang Chen ◽

Guangzao Huang ◽

...

Keyword(s):

Machine Learning ◽

Alternative Splicing ◽

Single Molecule ◽

Reference Genome ◽

De Novo ◽

Supplementary Information ◽

Model Organisms ◽

Sequencing Data ◽

Extensive Evaluation ◽

Reference Genomes

Abstract Summary Alternative splicing (AS) is a well-established mechanism for increasing transcriptome and proteome diversity, however, detecting AS events and distinguishing among AS types in organisms without available reference genomes remains challenging. We developed a de novo approach called AStrap for AS analysis without using a reference genome. AStrap identifies AS events by extensive pair-wise alignments of transcript sequences and predicts AS types by a machine-learning model integrating more than 500 assembled features. We evaluated AStrap using collected AS events from reference genomes of rice and human as well as single-molecule real-time sequencing data from Amborella trichopoda. Results show that AStrap can identify much more AS events with comparable or higher accuracy than the competing method. AStrap also possesses a unique feature of predicting AS types, which achieves an overall accuracy of ∼0.87 for different species. Extensive evaluation of AStrap using different parameters, sample sizes and machine-learning models on different species also demonstrates the robustness and flexibility of AStrap. AStrap could be a valuable addition to the community for the study of AS in non-model organisms with limited genetic resources. Availability and implementation AStrap is available for download at https://github.com/BMILAB/AStrap. Supplementary information Supplementary data are available at Bioinformatics online.

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New Silver(I) Coordination Polymer with Fe4 Single-Molecule Magnets as Long Spacer

Magnetochemistry ◽

10.3390/magnetochemistry4040043 ◽

2018 ◽

Vol 4 (4) ◽

pp. 43 ◽

Cited By ~ 1

Author(s):

Luca Rigamonti ◽

Manuela Vaccari ◽

Fabrizio Roncaglia ◽

Carlo Baschieri ◽

Alessandra Forni

Keyword(s):

Coordination Polymer ◽

Single Molecule ◽

Building Blocks ◽

Zero Field ◽

Single Molecule Magnets ◽

Long Distance ◽

Linear Arrangement ◽

Thermally Activated ◽

Supramolecular Architectures ◽

Donor Nitrogen

In continuation of our work on supramolecular architectures of single-molecule magnets (SMMs) as a promising strategy in developing their magnetic performance, in this paper we report the synthesis and single crystal X-ray structure of the centered triangular tetrairon(III) SMM, [Fe4(PhpPy)2(dpm)6], Fe4 (Hdpm = dipivaloylmethane, H3PhpPy = 2-(hydroxymethyl)-2-(4-(pyridine-4-yl)phenyl)propane-1,3-diol), and its assembly in the coordination polymer {[Fe4(PhpPy)2(dpm)6Ag](ClO4)}n, Fe4Ag, upon reaction with silver(I) perchlorate. Thanks to the presence of the pyridyl rings on the two tripodal ligands, Fe4 behaves as divergent ditopic linker, and due to the Fe4:AgClO4 1:1 ratio, Fe4Ag probably possesses a linear arrangement in which silver(I) ions are linearly coordinated by two nitrogen atoms, forming 1D chains whose positive charge is balanced by the perchlorate anions. The stabilization of such a polymeric structure can be ascribed to the long distance between the two donor nitrogen atoms (23.4 Å) and their donor power. Fe4Ag shows slow relaxation of the magnetization which follows a thermally activated process with Ueff/kB = 11.17(18) K, τ0 = 2.24(17) 10−7 s in zero field, and Ueff/kB = 14.49(5) K, τ0 = 3.88(8) 10−7 s in 1-kOe applied field, in line with what reported for tetrairon(III) SMMs acting as building blocks in polymeric structures.

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Syncrip/hnRNP Q is required for activity-induced Msp300/Nesprin-1 expression and new synapse formation

The Journal of Cell Biology ◽

10.1083/jcb.201903135 ◽

2020 ◽

Vol 219 (3) ◽

Cited By ~ 4

Author(s):

Joshua Titlow ◽

Francesca Robertson ◽

Aino Järvelin ◽

David Ish-Horowicz ◽

Carlas Smith ◽

...

Keyword(s):

Single Molecule ◽

Posttranscriptional Regulation ◽

Rna Binding ◽

Synapse Formation ◽

Long Distance ◽

Key Factor ◽

Larval Neuromuscular Junction ◽

Rnp Granules ◽

Activity Dependent

Memory and learning involve activity-driven expression of proteins and cytoskeletal reorganization at new synapses, requiring posttranscriptional regulation of localized mRNA a long distance from corresponding nuclei. A key factor expressed early in synapse formation is Msp300/Nesprin-1, which organizes actin filaments around the new synapse. How Msp300 expression is regulated during synaptic plasticity is poorly understood. Here, we show that activity-dependent accumulation of Msp300 in the postsynaptic compartment of the Drosophila larval neuromuscular junction is regulated by the conserved RNA binding protein Syncrip/hnRNP Q. Syncrip (Syp) binds to msp300 transcripts and is essential for plasticity. Single-molecule imaging shows that msp300 is associated with Syp in vivo and forms ribosome-rich granules that contain the translation factor eIF4E. Elevated neural activity alters the dynamics of Syp and the number of msp300:Syp:eIF4E RNP granules at the synapse, suggesting that these particles facilitate translation. These results introduce Syp as an important early acting activity-dependent regulator of a plasticity gene that is strongly associated with human ataxias.

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Genomic Analysis of Sarcomyxa edulis Reveals the Basis of Its Medicinal Properties and Evolutionary Relationships

Frontiers in Microbiology ◽

10.3389/fmicb.2021.652324 ◽

2021 ◽

Vol 12 ◽

Author(s):

Fenghua Tian ◽

Changtian Li ◽

Yu Li

Keyword(s):

Single Molecule ◽

De Novo ◽

Genomic Analysis ◽

Single Copy ◽

Whole Genome Sequence ◽

Type I ◽

Whole Genome ◽

Uridine Diphosphate ◽

Protein Coding ◽

Medicinal Value

Yuanmo [Sarcomyxa edulis (Y.C. Dai, Niemelä & G.F. Qin) T. Saito, Tonouchi & T. Harada] is an important edible and medicinal mushroom endemic to Northeastern China. Here we report the de novo sequencing and assembly of the S. edulis genome using single-molecule real-time sequencing technology. The whole genome was approximately 35.65 Mb, with a G + C content of 48.31%. Genome assembly generated 41 contigs with an N50 length of 1,772,559 bp. The genome comprised 9,364 annotated protein-coding genes, many of which encoded enzymes involved in the modification, biosynthesis, and degradation of glycoconjugates and carbohydrates or enzymes predicted to be involved in the biosynthesis of secondary metabolites such as terpene, type I polyketide, siderophore, and fatty acids, which are responsible for the pharmacodynamic activities of S. edulis. We also identified genes encoding 1,3-β-glucan synthase and endo-1,3(4)-β-glucanase, which are involved in polysaccharide and uridine diphosphate glucose biosynthesis. Phylogenetic and comparative analyses of Basidiomycota fungi based on a single-copy orthologous protein indicated that the Sarcomyxa genus is an independent group that evolved from the Pleurotaceae family. The annotated whole-genome sequence of S. edulis can serve as a reference for investigations of bioactive compounds with medicinal value and the development and commercial production of superior S. edulis varieties.

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Mapping and phasing of structural variation in patient genomes using nanopore sequencing

10.1101/129379 ◽

2017 ◽

Cited By ~ 4

Author(s):

Mircea Cretu Stancu ◽

Markus J. van Roosmalen ◽

Ivo Renkens ◽

Marleen Nieboer ◽

Sjors Middelkamp ◽

...

Keyword(s):

Single Molecule ◽

De Novo ◽

Structural Variants ◽

Human Genetic Disease ◽

Structural Genomic ◽

Short Read ◽

Sequencing Technologies ◽

Genome Wide ◽

Long Read ◽

Complex Structural

AbstractStructural genomic variants form a common type of genetic alteration underlying human genetic disease and phenotypic variation. Despite major improvements in genome sequencing technology and data analysis, the detection of structural variants still poses challenges, particularly when variants are of high complexity. Emerging long-read single-molecule sequencing technologies provide new opportunities for detection of structural variants. Here, we demonstrate sequencing of the genomes of two patients with congenital abnormalities using the ONT MinION at 11x and 16x mean coverage, respectively. We developed a bioinformatic pipeline - NanoSV - to efficiently map genomic structural variants (SVs) from the long-read data. We demonstrate that the nanopore data are superior to corresponding short-read data with regard to detection of de novo rearrangements originating from complex chromothripsis events in the patients. Additionally, genome-wide surveillance of SVs, revealed 3,253 (33%) novel variants that were missed in short-read data of the same sample, the majority of which are duplications < 200bp in size. Long sequencing reads enabled efficient phasing of genetic variations, allowing the construction of genome-wide maps of phased SVs and SNVs. We employed read-based phasing to show that all de novo chromothripsis breakpoints occurred on paternal chromosomes and we resolved the long-range structure of the chromothripsis. This work demonstrates the value of long-read sequencing for screening whole genomes of patients for complex structural variants.

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