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Title: Requirements and standards for organelle genome databases

Abstract

Mitochondria and plastids (collectively called organelles)descended from prokaryotes that adopted an intracellular, endosymbioticlifestyle within early eukaryotes. Comparisons of their remnant genomesaddress a wide variety of biological questions, especially when includingthe genomes of their prokaryotic relatives and the many genes transferredto the eukaryotic nucleus during the transitions from endosymbiont toorganelle. The pace of producing complete organellar genome sequences nowmakes it unfeasible to do broad comparisons using the primary literatureand, even if it were feasible, it is now becoming uncommon for journalsto accept detailed descriptions of genome-level features. Unfortunatelyno database is currently useful for this task, since they have littlestandardization and are riddled with error. Here I outline what iscurrently wrong and what must be done to make this data useful to thescientific community.

Authors:
Publication Date:
Research Org.:
Ernest Orlando Lawrence Berkeley NationalLaboratory, Berkeley, CA (US)
Sponsoring Org.:
USDOE Director, Office of Science. Office of Biological andEnvironmental Research; National Science Foundation (NSF)
OSTI Identifier:
919820
Report Number(s):
LBNL-59357
R&D Project: Y00010; BnR: 600305000; TRN: US200822%%570
DOE Contract Number:
DE-AC02-05CH11231; NSF:EAR-0342392
Resource Type:
Journal Article
Resource Relation:
Journal Name: Journal of Integrative Biology; Journal Volume: 10; Journal Issue: 2; Related Information: Journal Publication Date: 06/2006
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; CELL CONSTITUENTS; GENES; MITOCHONDRIA; STANDARDIZATION; DATA BASE MANAGEMENT; database organelle plastid chloroplast mitochondria prokaryoteeukaroyte evolution endosymbiont

Citation Formats

Boore, Jeffrey L. Requirements and standards for organelle genome databases. United States: N. p., 2006. Web. doi:10.1089/omi.2006.10.119.
Boore, Jeffrey L. Requirements and standards for organelle genome databases. United States. doi:10.1089/omi.2006.10.119.
Boore, Jeffrey L. Mon . "Requirements and standards for organelle genome databases". United States. doi:10.1089/omi.2006.10.119. https://www.osti.gov/servlets/purl/919820.
@article{osti_919820,
title = {Requirements and standards for organelle genome databases},
author = {Boore, Jeffrey L.},
abstractNote = {Mitochondria and plastids (collectively called organelles)descended from prokaryotes that adopted an intracellular, endosymbioticlifestyle within early eukaryotes. Comparisons of their remnant genomesaddress a wide variety of biological questions, especially when includingthe genomes of their prokaryotic relatives and the many genes transferredto the eukaryotic nucleus during the transitions from endosymbiont toorganelle. The pace of producing complete organellar genome sequences nowmakes it unfeasible to do broad comparisons using the primary literatureand, even if it were feasible, it is now becoming uncommon for journalsto accept detailed descriptions of genome-level features. Unfortunatelyno database is currently useful for this task, since they have littlestandardization and are riddled with error. Here I outline what iscurrently wrong and what must be done to make this data useful to thescientific community.},
doi = {10.1089/omi.2006.10.119},
journal = {Journal of Integrative Biology},
number = 2,
volume = 10,
place = {United States},
year = {Mon Jan 09 00:00:00 EST 2006},
month = {Mon Jan 09 00:00:00 EST 2006}
}
  • DNA double-strand breaks are highly detrimental to all organisms and need to be quickly and accurately repaired. Although several proteins are known to maintain plastid and mitochondrial genome stability in plants, little is known about the mechanisms of DNA repair in these organelles and the roles of specific proteins. Here, using ciprofloxacin as a DNA damaging agent specific to the organelles, we show that plastids and mitochondria can repair DNA double-strand breaks through an error-prone pathway similar to the microhomology-mediated break-induced replication observed in humans, yeast, and bacteria. This pathway is negatively regulated by the single-stranded DNA (ssDNA) binding proteinsmore » from the Whirly family, thus indicating that these proteins could contribute to the accurate repair of plant organelle genomes. To understand the role of Whirly proteins in this process, we solved the crystal structures of several Whirly-DNA complexes. These reveal a nonsequence-specific ssDNA binding mechanism in which DNA is stabilized between domains of adjacent subunits and rendered unavailable for duplex formation and/or protein interactions. Our results suggest a model in which the binding of Whirly proteins to ssDNA would favor accurate repair of DNA double-strand breaks over an error-prone microhomology-mediated break-induced replication repair pathway.« less
  • A group of 2000 DNA sequences representing human genes was published in October 1992 by Genethon. Since then, more than half (possibly up to 85%) of the sequences appear to be from yeast and unidentified bacteria. This represents the problem of researchers submitting sequences directly to databases without peer review or serious error checking. While database managers rely on scientists to submit correct data, the managers can take steps to detect obvious errors. Further cases of gross contamination will require more stringent quality control, even at the expense of some delay.
  • No abstract prepared.
  • No abstract prepared.