scholarly journals A role for circular code properties in translation

2020 ◽  
Author(s):  
Simone Giannerini ◽  
Alberto Danielli ◽  
Diego Luis Gonzalez ◽  
Greta Goracci
Keyword(s):  
Molecular Mechanisms ◽  
Translation Speed ◽  
Translation Elongation ◽  
Protein Coding ◽  
Coding Sequences ◽  
Initiator Codon ◽  
Circular Codes ◽  
Elongation Process ◽  
Circular Code ◽  
Shed Light

AbstractCircular codes represent a form of coding allowing detection/correction of frameshift errors. Building on recent theoretical advances on circular codes, we provide evidence that protein coding sequences exhibit in-frame circular code marks, that are absent in introns and are intimately linked to the keto-amino transformation of codon bases. These properties strongly correlate with translation speed, codon influence and protein expression levels. Strikingly, circular code marks are absent at the beginning of coding sequences, but stably occur 40 codons after the initiator codon, hinting at the translation elongation process. Finally, we use the lens of circular codes to show that codon influence on translation correlates with the strong-weak dichotomy of the first two bases of the codon. The results provide promising universal tools for sequence indicators and sequence optimization for bioinformatics and biotechnological applications, and can shed light on the molecular mechanisms behind the decoding process.

scholarly journals A role for circular code properties in translation

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Simone Giannerini ◽  
Diego Luis Gonzalez ◽  
Greta Goracci ◽  
Alberto Danielli
Keyword(s):  
Molecular Mechanisms ◽  
Translation Speed ◽  
Translation Elongation ◽  
Protein Coding ◽  
Coding Sequences ◽  
Initiator Codon ◽  
Circular Codes ◽  
Elongation Process ◽  
Circular Code ◽  
Shed Light

AbstractCircular codes represent a form of coding allowing detection/correction of frame-shift errors. Building on recent theoretical advances on circular codes, we provide evidence that protein coding sequences exhibit in-frame circular code marks, that are absent in introns and are intimately linked to the keto-amino transformation of codon bases. These properties strongly correlate with translation speed, codon influence and protein synthesis levels. Strikingly, circular code marks are absent at the beginning of coding sequences, but stably occur 40 codons after the initiator codon, hinting at the translation elongation process. Finally, we use the lens of circular codes to show that codon influence on translation correlates with the strong-weak dichotomy of the first two bases of the codon. The results can lead to defining new universal tools for sequence indicators and sequence optimization for bioinformatics and biotechnological applications, and can shed light on the molecular mechanisms behind the decoding process.

scholarly journals Draft Genome Sequence of Stenotrophomonas sp. Strain SbOxS2, an Antimony-Oxidizing Bacterium Isolated from Stibnite Mine Tailing Soil

2020 ◽  
Vol 9 (49) ◽  
Author(s):  
Natsuko Hamamura ◽  
Nobuyoshi Nakajima ◽  
Shigeki Yamamura
Keyword(s):  
Heavy Metal ◽  
Genome Sequence ◽  
Molecular Mechanisms ◽  
Draft Genome ◽  
Heavy Metal Resistance ◽  
Metal Resistance ◽  
Mine Tailing ◽  
Draft Genome Sequence ◽  
Protein Coding ◽  
Coding Sequences

ABSTRACT The antimony-oxidizing Stenotrophomonas sp. strain SbOxS2 was isolated from stibnite mine tailing soil. The draft genome sequence of strain SbOxS2 comprises 4.76 Mbp with 4,211 predicted protein-coding sequences. This genome will provide useful information for characterizing the molecular mechanisms associated with heavy metal resistance within the genus Stenotrophomonas.

scholarly journals Draft Genome Sequence of Urease-Producing Pseudorhodobacter sp. Strain E13, Isolated from the Yellow Sea in Gunsan, South Korea

2019 ◽  
Vol 8 (23) ◽  
Author(s):  
Si Chul Kim ◽  
Hyo Jung Lee
Keyword(s):  
South Korea ◽  
Genome Sequence ◽  
Yellow Sea ◽  
Draft Genome ◽  
The Yellow Sea ◽  
Draft Genome Sequence ◽  
Protein Coding ◽  
Coding Sequences ◽  
Gram Negative ◽  
Content Type

Here, we report the draft genome sequence of Pseudorhodobacter sp. strain E13, a Gram-negative, aerobic, nonflagellated, and rod-shaped bacterium which was isolated from the Yellow Sea in South Korea. The assembled genome sequence is 3,878,578 bp long with 3,646 protein-coding sequences in 159 contigs.

scholarly journals The Landscape of microRNAs in βCell: Between Phenotype Maintenance and Protection

2021 ◽  
Vol 22 (2) ◽  
pp. 803
Author(s):  
Giuseppina Emanuela Grieco ◽  
Noemi Brusco ◽  
Giada Licata ◽  
Daniela Fignani ◽  
Caterina Formichi ◽  
...  
Keyword(s):  
Diabetes Mellitus ◽  
Metabolic Disorders ◽  
Molecular Mechanisms ◽  
Β Cell ◽  
Physiological Mechanisms ◽  
Effective Strategies ◽  
Chronic Hyperglycaemia ◽  
Shed Light

Diabetes mellitus is a group of heterogeneous metabolic disorders characterized by chronic hyperglycaemia mainly due to pancreatic β cell death and/or dysfunction, caused by several types of stress such as glucotoxicity, lipotoxicity and inflammation. Different patho-physiological mechanisms driving β cell response to these stresses are tightly regulated by microRNAs (miRNAs), a class of negative regulators of gene expression, involved in pathogenic mechanisms occurring in diabetes and in its complications. In this review, we aim to shed light on the most important miRNAs regulating the maintenance and the robustness of β cell identity, as well as on those miRNAs involved in the pathogenesis of the two main forms of diabetes mellitus, i.e., type 1 and type 2 diabetes. Additionally, we acknowledge that the understanding of miRNAs-regulated molecular mechanisms is fundamental in order to develop specific and effective strategies based on miRNAs as therapeutic targets, employing innovative molecules.

scholarly journals Amynthas corticis genome reveals molecular mechanisms behind global distribution

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Xing Wang ◽  
Yi Zhang ◽  
Yufeng Zhang ◽  
Mingming Kang ◽  
Yuanbo Li ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Molecular Mechanisms ◽  
Gene Families ◽  
The Body ◽  
Gene Family Evolution ◽  
Complex Environments ◽  
Protein Coding ◽  
Itraq Analysis ◽  
Rdna Sequencing ◽  
Long Read

AbstractEarthworms (Annelida: Crassiclitellata) are widely distributed around the world due to their ancient origination as well as adaptation and invasion after introduction into new habitats over the past few centuries. Herein, we report a 1.2 Gb complete genome assembly of the earthworm Amynthas corticis based on a strategy combining third-generation long-read sequencing and Hi-C mapping. A total of 29,256 protein-coding genes are annotated in this genome. Analysis of resequencing data indicates that this earthworm is a triploid species. Furthermore, gene family evolution analysis shows that comprehensive expansion of gene families in the Amynthas corticis genome has produced more defensive functions compared with other species in Annelida. Quantitative proteomic iTRAQ analysis shows that expression of 147 proteins changed in the body of Amynthas corticis and 16 S rDNA sequencing shows that abundance of 28 microorganisms changed in the gut of Amynthas corticis when the earthworm was incubated with pathogenic Escherichia coli O157:H7. Our genome assembly provides abundant and valuable resources for the earthworm research community, serving as a first step toward uncovering the mysteries of this species, and may provide molecular level indicators of its powerful defensive functions, adaptation to complex environments and invasion ability.

scholarly journals Non-Coding RNA Signatures of B-Cell Acute Lymphoblastic Leukemia

2021 ◽  
Vol 22 (5) ◽  
pp. 2683
Author(s):  
Princess D. Rodriguez ◽  
Hana Paculova ◽  
Sophie Kogut ◽  
Jessica Heath ◽  
Hilde Schjerven ◽  
...  
Keyword(s):  
Acute Lymphoblastic Leukemia ◽  
B Cell ◽  
Molecular Mechanisms ◽  
Lymphoblastic Leukemia ◽  
Transcriptome Profiling ◽  
Rna Seq ◽  
Protein Coding ◽  
Non Coding Rna ◽  
Technological Developments ◽  
Cell Acute Lymphoblastic Leukemia

Non-coding RNAs (ncRNAs) comprise a diverse class of non-protein coding transcripts that regulate critical cellular processes associated with cancer. Advances in RNA-sequencing (RNA-Seq) have led to the characterization of non-coding RNA expression across different types of human cancers. Through comprehensive RNA-Seq profiling, a growing number of studies demonstrate that ncRNAs, including long non-coding RNA (lncRNAs) and microRNAs (miRNA), play central roles in progenitor B-cell acute lymphoblastic leukemia (B-ALL) pathogenesis. Furthermore, due to their central roles in cellular homeostasis and their potential as biomarkers, the study of ncRNAs continues to provide new insight into the molecular mechanisms of B-ALL. This article reviews the ncRNA signatures reported for all B-ALL subtypes, focusing on technological developments in transcriptome profiling and recently discovered examples of ncRNAs with biologic and therapeutic relevance in B-ALL.

scholarly journals Evolutionary Patterns of Sex-Biased Genes in Three Species of Haplodiploid Insects

Insects ◽  
2020 ◽  
Vol 11 (6) ◽  
pp. 326
Author(s):  
Yu-Jun Wang ◽  
Hua-Ling Wang ◽  
Xiao-Wei Wang ◽  
Shu-Sheng Liu
Keyword(s):  
Gene Expression ◽  
Slow Rate ◽  
Species Complex ◽  
Evolutionary Patterns ◽  
Protein Coding ◽  
Coding Sequences ◽  
Species Comparisons ◽  
Differential Gene ◽  
Males And Females ◽  
And Behavior

Females and males often differ obviously in morphology and behavior, and the differences between sexes are the result of natural selection and/or sexual selection. To a great extent, the differences between the two sexes are the result of differential gene expression. In haplodiploid insects, this phenomenon is obvious, since males develop from unfertilized zygotes and females develop from fertilized zygotes. Whiteflies of the Bemisia tabaci species complex are typical haplodiploid insects, and some species of this complex are important pests of many crops worldwide. Here, we report the transcriptome profiles of males and females in three species of this whitefly complex. Between-species comparisons revealed that non-sex-biased genes display higher variation than male-biased or female-biased genes. Sex-biased genes evolve at a slow rate in protein coding sequences and gene expression and have a pattern of evolution that differs from those of social haplodiploid insects and diploid animals. Genes with high evolutionary rates are more related to non-sex-biased traits—such as nutrition, immune system, and detoxification—than to sex-biased traits, indicating that the evolution of protein coding sequences and gene expression has been mainly driven by non-sex-biased traits.

scholarly journals Comparative Transcriptome Analysis Reveals Regulatory Networks during the Maize Ear Shank Elongation Process

2021 ◽  
Vol 22 (13) ◽  
pp. 7029
Author(s):  
Cai-Yun Xiong ◽  
Qing-You Gong ◽  
Hu Pei ◽  
Chang-Jian Liao ◽  
Rui-Chun Yang ◽  
...  
Keyword(s):  
Regulatory Networks ◽  
Molecular Mechanisms ◽  
Developmental Stages ◽  
Rna Seq ◽  
Short Branch ◽  
Transcriptional Dynamics ◽  
New Varieties ◽  
Elongation Process ◽  
Temporal Expression Pattern ◽  
Maize Ear

In maize, the ear shank is a short branch that connects the ear to the stalk. The length of the ear shank mainly affects the transportation of photosynthetic products to the ear, and also influences the dehydration of the grain by adjusting the tightness of the husks. However, the molecular mechanisms of maize shank elongation have rarely been described. It has been reported that the maize ear shank length is a quantitative trait, but its genetic basis is still unclear. In this study, RNA-seq was performed to explore the transcriptional dynamics and determine the key genes involved in maize shank elongation at four different developmental stages. A total of 8145 differentially expressed genes (DEGs) were identified, including 729 transcription factors (TFs). Some important genes which participate in shank elongation were detected via function annotation and temporal expression pattern analyses, including genes related to signal transduction hormones (auxin, brassinosteroids, gibberellin, etc.), xyloglucan and xyloglucan xyloglucosyl transferase, and transcription factor families. The results provide insights into the genetic architecture of maize ear shanks and developing new varieties with ideal ear shank lengths, enabling adjustments for mechanized harvesting in the future.

scholarly journals Draft Genome Sequences of 10 Clinical K2-Type Klebsiella pneumoniae Strains Isolated in Russia

2018 ◽  
Vol 7 (14) ◽  
Author(s):  
Nikolay V. Volozhantsev ◽  
Angelina A. Kislichkina ◽  
Anastasia I. Lev ◽  
Ekaterina V. Solovieva ◽  
Vera P. Myakinina ◽  
...  
Keyword(s):  
Intensive Care Unit ◽  
Klebsiella Pneumoniae ◽  
Draft Genome ◽  
Capsular Type ◽  
Genome Sequences ◽  
Protein Coding ◽  
Coding Sequences ◽  
Content Type ◽  
Neurosurgical Intensive Care ◽  
Neurosurgical Intensive Care Unit

We report here the genome sequences of 10 Klebsiella pneumoniae strains of capsular type K2 isolated in Russia from patients in an infectious clinical hospital and neurosurgical intensive care unit. The draft genome sizes range from 5.34 to 5.87 Mb and include 5,448 to 6,137 protein-coding sequences.

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