Difference between revisions of "Microbial Mythology"

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== Nuclear membrane: Do bacteria have one? ==
 
== Nuclear membrane: Do bacteria have one? ==
  
Introductory texts often give the impression that bacterial DNA lacks organization, basically distributed in the cytoplasm.  In fact, however, bacterial DNA is tightly organized in looped domains of the nucleoid.  See for example "The bacterial nucleoid: a highly organized and dynamic structure," [http://www.ncbi.nlm.nih.gov/pubmed/15988757?ordinalpos=30&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Thanbichler et al 2005.]  Furthermore, some bacteria actually contain their DNA within a membrane very much like a "nuclear membrane."  Such bacteria include the Planctomycetes, studied by [http://florey.biosci.uq.edu.au/mypa/academic/fuerst/fuerst.htm John Fuerst] and colleagues.  Planctomycetes are commonly found in soil and water, where they have important ecological functions such as association with invertebrates, and the conduct of anaerobic ammonia oxidation (anammox metabolism).  Some archaea associated with sponges also appear to possess something like "nuclear" membranes.<br>
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Introductory texts often give the impression that [[bacteria]]l DNA lacks organization, basically distributed in the [[cytoplasm]].  In fact, however, bacterial DNA is tightly organized in looped domains of the [[nucleoid]].  See for example "The bacterial nucleoid: a highly organized and dynamic structure," [http://www.ncbi.nlm.nih.gov/pubmed/15988757 Thanbichler et al 2005.]  Furthermore, some bacteria actually contain their DNA within a membrane very much like a "nuclear membrane."  Such bacteria include the [[Planctomycetes]], studied by [http://florey.biosci.uq.edu.au/mypa/academic/fuerst/fuerst.htm John Fuerst] and colleagues.  Planctomycetes are commonly found in soil and water, where they have important ecological functions such as association with invertebrates, and the conduct of [[anaerobic]] ammonia oxidation (anammox metabolism).  Some [[archaea]] associated with sponges also appear to possess something like "nuclear" membranes.
 
 
  
 
== TCA cycle: Does succinyl-CoA synthetase use ATP or GTP? ==
 
== TCA cycle: Does succinyl-CoA synthetase use ATP or GTP? ==

Revision as of 15:48, 25 February 2008

Textbooks and web sites propagate various misconceptions and simple errors about microbiology. Here we provide a place for microbiology educators to set the record straight.
Authors: Please provide primary references, in open-access sources whenever possible.

Nuclear membrane: Do bacteria have one?

Introductory texts often give the impression that bacterial DNA lacks organization, basically distributed in the cytoplasm. In fact, however, bacterial DNA is tightly organized in looped domains of the nucleoid. See for example "The bacterial nucleoid: a highly organized and dynamic structure," Thanbichler et al 2005. Furthermore, some bacteria actually contain their DNA within a membrane very much like a "nuclear membrane." Such bacteria include the Planctomycetes, studied by John Fuerst and colleagues. Planctomycetes are commonly found in soil and water, where they have important ecological functions such as association with invertebrates, and the conduct of anaerobic ammonia oxidation (anammox metabolism). Some archaea associated with sponges also appear to possess something like "nuclear" membranes.

TCA cycle: Does succinyl-CoA synthetase use ATP or GTP?

Succinyl-CoA synthetase, also known as succinate thiokinase, is the enzyme of the TCA cycle that interconverts succinyl-CoA with succinate, coupled to formation of a nucleotide triphosphate. Many textbooks and web sites state that succinyl-CoA synthetase phosphorylates only GDP to GTP. See example.

According to the primary literature, however, ADP phosphorylation predominates in E. coli (Margaret Birney et al, 1996) whereas in Pseudomonas sp., various nucleotide diphosphates are phosphorylated (Vinayak Kapatral et al, 2000). Human mitochondria have two forms of the enzyme, which phosphorylate ATP and GTP respectively (David Lambeth et al, 2004).


Conjugation in bacteria: Do pili mediate DNA transfer?

During bacterial conjugation, the donor and recipient cells are brought together by protein filaments called pili. Since the pili are composed of hollow tubes of protein subunits, like a turret, it was thought for a while that DNA might travel down the hollow tube. The hollow tube theory is still taught; see example.

Actually, DNA is transferred across the bacterial envelope by a protein complex embedded in the membranes. For review of classic experiments, see Brigette Dreiseikelmann, 1994. For a more current review, see Inês Chen et al, 2005.

Fossil record: Do microbes have any?

Admittedly the fossil records of micro-organisms are sparse, and often taxonomically ambiguous. But they're there. In fact, considering that microorganisms were the first organisms to develop on the planet, it should be no surprise that the oldest fossil organisms are actually microbes. The earliest convincing microfossils are of colonial cyanobacteria dated to 2 Gya (two billion years ago). More recent fossils known as stromatolites are also the products of microbes affecting the deposition of sediment clasts and the precipitation of chemical sediments. For a good general discussion of microbial fossils, see Life on a Young Planet: The First Three Billion Years of Evolution on Earth by Andrew H. Knoll.