1. Genetics and Genomics
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Differing isoforms of the cobalamin binding photoreceptor AerR oppositely regulate photosystem expression

  1. Haruki Yamamoto
  2. Mingxu Fang
  3. Vladimira Dragnia
  4. Carl E Bauer  Is a corresponding author
  1. Indiana University, United States
Research Article
  • Cited 4
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Cite this article as: eLife 2018;7:e39028 doi: 10.7554/eLife.39028

Abstract

Phototrophic microorganisms adjust photosystem synthesis in response to changes in light intensity and wavelength. A variety of different photoreceptors regulate this process. Purple photosynthetic bacteria synthesize a novel photoreceptor AerR that uses cobalamin (B12) as a blue-light absorbing chromophore to control photosystem synthesis. AerR directly interacts with the redox responding transcription factor CrtJ, affecting CrtJ's interaction with photosystem promoters. In this study, we show that AerR is translated as two isoforms that differ by 41 amino acids at the amino terminus. The ratio of these isoforms was affected by light and cell growth phase with the long variant predominating during photosynthetic exponential growth and the short variant predominating in dark conditions and/or stationary phase. Pigmentation and transcriptomic analyses show that the short AerR variant represses, while long variant activates, photosynthesis genes. The long form of AerR also activates many genes involved in cellular metabolism and motility.

Data availability

RNA-seq sequence read files have been deposited in Sequence Read Archive (SRA) with the accession number SRP136743 and can be accessed at the URL: https://trace.ncbi.nlm.nih.gov/Traces/sra/?study=SRP136743.

The following data sets were generated

Article and author information

Author details

  1. Haruki Yamamoto

    Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, United States
    Competing interests
    The authors declare that no competing interests exist.

  2. Mingxu Fang

    Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1595-8046

  3. Vladimira Dragnia

    Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, United States
    Competing interests
    The authors declare that no competing interests exist.

  4. Carl E Bauer

    Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, United States
    For correspondence
    bauer@indiana.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-1432-0756

Funding

National Institutes of Health (GM040941)

  • Carl E Bauer

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Gisela Storz, National Institute of Child Health and Human Development, United States

Publication history

  1. Received: June 8, 2018
  2. Accepted: October 2, 2018
  3. Accepted Manuscript published: October 3, 2018 (version 1)
  4. Version of Record published: October 23, 2018 (version 2)

Copyright

© 2018, Yamamoto et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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Further reading

    1. Evolutionary Biology
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    Evolutionary dynamics of circular RNAs in primates

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    Many primate genes produce circular RNAs (circRNAs). However, the extent of circRNA conservation between closely related species remains unclear. By comparing tissue-specific transcriptomes across over 70 million years of primate evolution, we identify that within 3 million years circRNA expression profiles diverged such that they are more related to species identity than organ type. However, our analysis also revealed a subset of circRNAs with conserved neural expression across tens of millions of years of evolution. By comparing to species-specific circRNAs, we identified that the downstream intron of the conserved circRNAs display a dramatic lengthening during evolution due to the insertion of novel retrotransposons. Our work provides comparative analyses of the mechanisms promoting circRNAs to generate increased transcriptomic complexity in primates.

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    SMA-miRs: miR-181a-5p, -324-5p, -451a are overexpressed in spinal muscular atrophy skeletal muscle and serum samples

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    Spinal muscular atrophy (SMA) is a neuromuscular disorder characterized by the degeneration of the second motor-neuron. The phenotype ranges from very severe to very mild forms. All patients have the homozygous loss of the SMN1 gene and a variable number of SMN2 (generally two-to-four copies), inversely related with the severity. The amazing results of the available treatments have made compelling the need of prognostic biomarkers to predict the progression trajectories of patients. Beside the SMN2 products, few other biomarkers have been evaluated so far, including some miRs.

    Methods:

    We performed whole miRNome analysis of muscle samples of patients and controls (14 biopsies and 9 cultures). The levels of muscle differentially expressed miRs were evaluated in serum samples (51 patients and 37 controls) and integrated with SMN2 copies, SMN2-full length transcript levels in blood and age (SMA-score).

    Results:

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    Conclusions:

    miRNome analyses suggest the primary involvement of skeletal muscle in SMA pathogenesis; the SMA-miRs are likely actively released in the blood flow, even if their function and target cells require to be elucidated. The accuracy of the SMA-score needs to be verified in replicative studies: if confirmed, its use could be crucial for the routine prognostic assessment, also in pre-symptomatic patients.

    Funding:

    Telethon Italia (grant # GGP12116).

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